diff --git a/devtools/conda-envs/proteinbenchmark.yaml b/devtools/conda-envs/proteinbenchmark.yaml
index a419716..c80a1db 100644
--- a/devtools/conda-envs/proteinbenchmark.yaml
+++ b/devtools/conda-envs/proteinbenchmark.yaml
@@ -18,11 +18,11 @@ dependencies:
# MM calculations
- ambertools
- cudatoolkit
- - openeye-toolkits
+ - openeye-toolkits=2022.1.1
- openff-forcefields
- openff-toolkit>=0.13.0
- openff-units
- - openmm>=8.0.0
+ - openmm>=8.1.1
- openmmforcefields>=0.12.0
- openmmtools
diff --git a/proteinbenchmark/analysis.py b/proteinbenchmark/analysis.py
index f93cbb0..9cff0f7 100644
--- a/proteinbenchmark/analysis.py
+++ b/proteinbenchmark/analysis.py
@@ -1,4 +1,6 @@
from pathlib import Path
+import shutil
+import subprocess
from typing import List
import loos
@@ -256,7 +258,7 @@ def measure_dihedrals(
# Write dihedrals to file every 10 000 frames to avoid pandas
# out-of-memory
- if frame_index % 10000 == 0 and frame_index > 0:
+ if frame_index % 10000 == 9999 and frame_index > 0:
list_of_dicts_to_csv(dihedrals, f"{output_path}-{fragment_index}")
fragment_index += 1
dihedrals = list()
@@ -505,6 +507,7 @@ def measure_h_bond_geometries(
fragment_index = 0
h_bond_geometries = list()
+ # Load one frame into memory at a time
for frame in trajectory:
frame_time += frame_length
@@ -513,7 +516,7 @@ def measure_h_bond_geometries(
# Write hydrogen bond geomtries to file every 10 000 frames to avoid
# pandas out-of-memory
- if frame_index % 10000 == 0 and frame_index > 0:
+ if frame_index % 10000 == 9999 and frame_index > 0:
list_of_dicts_to_csv(h_bond_geometries, f"{output_path}-{fragment_index}")
fragment_index += 1
h_bond_geometries = list()
@@ -563,6 +566,337 @@ def measure_h_bond_geometries(
return fragment_index
+def compute_chemical_shifts_shiftx2(
+ topology_path: str,
+ trajectory_path: str,
+ frame_length: unit.Quantity,
+ output_path: str,
+ ph: float,
+ temperature: unit.Quantity,
+ shiftx2_output_dir: str = None,
+ shiftx2_install_dir: str = None,
+ python2_path: str = None,
+):
+ """
+ Compute the chemical shifts of protein atoms using ShiftX2.
+
+ Parameters
+ ---------
+ topology_path
+ The path to the system topology, e.g. a PDB file.
+ trajectory_path
+ The path to the trajectory.
+ frame_length
+ The amount of simulation time between frames in the trajectory.
+ output_path
+ The path to write the computed chemical shifts.
+ ph
+ The pH of the benchmark target.
+ temperature
+ The temperature of the benchmark target.
+ shiftx2_output_dir
+ The directory to write output from ShiftX2.
+ shiftx2_install_dir
+ The root directory for the installation of ShiftX2.
+ python2_path
+ The path to the python2 executable to pass to subprocess.
+ """
+
+ # ShiftX2 v1.13 has a few quirks that make it unwieldy for analyzing MD
+ # trajectories. The ShiftX2 estimate is a combination of the sequence-based
+ # ShiftY+ estimator and the structure-based ShiftX+ estimator. ShiftX2 has
+ # an NMR mode that will extract models from a PDB file into single-model PDB
+ # files, run ShiftX+ on each model PDB, average them, then run ShiftY+ once
+ # and combine it with the average ShiftX+ prediction. We want the combined
+ # ShiftX+ and ShiftY+ estimates for each frame. Additionally, the main
+ # ShiftX2 script calls the shell `python` through `os.system()` but expects
+ # python2, making it fail in environments that default to python3. To solve
+ # this, we are going to call ShiftY+ once on the topology, extract frames to
+ # temporary PDBs, call ShiftX+ on each frame PDB in batch mode, then combine
+ # the ShiftX+ and ShiftY+ estimates for each frame. We will use `python2`
+ # explicitly in calls to `subprocess.run()`.
+
+ # Get python2 executable
+ if python2_path is None:
+ python2_path = shutil.which("python2")
+
+ # Get ShiftX2 installation directory
+ if shiftx2_install_dir is None:
+ shiftx2_install_dir = Path(shutil.which("shiftx2.py")).parent
+
+ # Set up directory to store shiftx2 output
+ if shiftx2_output_dir is None:
+ shiftx2_output_dir = Path(Path(output_path).parent, "shiftx2")
+ else:
+ shiftx2_output_dir = Path(shiftx2_output_dir)
+
+ shiftx2_output_dir.mkdir(parents=True, exist_ok=True)
+
+ # Load topology
+ topology = loos.createSystem(topology_path)
+
+ resname_by_resid = {
+ residue[0].resid(): residue[0].resname()
+ for residue in topology.splitByResidue()
+ }
+
+ # Set up trajectory
+ trajectory = Trajectory(trajectory_path, topology)
+
+ # Write each frame to temporary PDB
+ tmp_pdb_prefix = Path(shiftx2_output_dir, Path(trajectory_path).stem)
+ for frame_index, frame in enumerate(trajectory):
+ frame_pdb_path = f"{tmp_pdb_prefix}-{frame_index}.pdb"
+ with open(frame_pdb_path, "w") as pdb_file:
+ pdb_file.write(str(loos.PDB.fromAtomicGroup(frame)))
+
+ # Compute sequence-based estimate of chemical shifts by runnnig ShiftY+ on
+ # the topology PDB
+ shifty_output_path = Path(
+ shiftx2_output_dir,
+ f"{Path(topology_path).stem}.shifty",
+ )
+ shifty_sequence_similarity_cutoff = "40"
+ shifty_return_value = subprocess.run(
+ [
+ python2_path,
+ "shifty3.py",
+ "-i",
+ Path(topology_path).resolve(),
+ "-o",
+ shifty_output_path.resolve(),
+ "-c",
+ shifty_sequence_similarity_cutoff,
+ "-t",
+ shiftx2_output_dir.resolve(),
+ ],
+ cwd=Path(shiftx2_install_dir, "shifty3"),
+ )
+
+ # Compute structure-based estimate of chemical shifts by running ShiftX+
+ # on the temporary frame PDBs
+ shiftxp_output_path = f"{str(frame_pdb_path)}.sxp"
+ shiftxp_bin_dir = Path(shiftx2_install_dir, "bin")
+ shiftxp_lib_jar = Path(shiftx2_install_dir, "lib", "weka.jar")
+ shiftxp_return_value = subprocess.run(
+ [
+ "java",
+ "-Xmx1900m",
+ "-cp",
+ f"{shiftxp_bin_dir}:{shiftxp_lib_jar}",
+ "ShiftXp",
+ "-b",
+ f"{tmp_pdb_prefix}-*.pdb",
+ "-atoms",
+ "ALL",
+ "-ph",
+ str(ph),
+ "-temp",
+ str(temperature.m_as(unit.kelvin)),
+ "-dir",
+ shiftx2_install_dir,
+ ]
+ )
+
+ # Set up ShiftX2 combine options
+ shiftx2_combine_path = Path(shiftx2_install_dir, "script", "combine_cs.py")
+ shiftx2_combine_csv_format = "1"
+ shiftx2_combine_all_atoms = "1"
+
+ # Set up list of dicts to store chemical shifts
+ frame_time = 0.0 * unit.picosecond
+ fragment_index = 0
+ chemical_shifts = list()
+
+ N_frames = frame_index + 1
+ for frame_index in range(N_frames):
+ frame_time += frame_length
+ frame_time_ns = frame_time.m_as(unit.nanosecond)
+
+ # Write chemical shifts to file every 10 000 frames to avoid pandas
+ # out-of-memory
+ if frame_index % 10000 == 9999 and frame_index > 0:
+ list_of_dicts_to_csv(
+ chemical_shifts,
+ f"{output_path}-{fragment_index}",
+ )
+ fragment_index += 1
+ chemical_shifts = list()
+
+ # Compute the ShiftX2 estimate of chemical shifts by combining the
+ # SHIFTX+ and SHIFTY+ estimates
+ shiftxp_output_path = f"{tmp_pdb_prefix}-{frame_index}.pdb.sxp"
+ shiftx2_combine_output_path = f"{tmp_pdb_prefix}-{frame_index}.cs"
+ shiftx2_combine_return_value = subprocess.run(
+ [
+ python2_path,
+ shiftx2_combine_path,
+ shiftxp_output_path,
+ shifty_output_path,
+ shiftx2_combine_output_path,
+ shiftx2_combine_csv_format,
+ shiftx2_combine_all_atoms,
+ ]
+ )
+
+ # Read ShiftX2 estimate
+ for index, row in pandas.read_csv(shiftx2_combine_output_path).iterrows():
+ resid = row["NUM"]
+ chemical_shifts.append(
+ {
+ "Frame": frame_index,
+ "Time (ns)": frame_time_ns,
+ "Resid": resid,
+ "Resname": resname_by_resid[resid],
+ "Atom": row["ATOMNAME"],
+ "Chemical Shift": row["SHIFT"],
+ }
+ )
+
+ if fragment_index == 0:
+ list_of_dicts_to_csv(chemical_shifts, output_path)
+
+ else:
+ list_of_dicts_to_csv(chemical_shifts, f"{output_path}-{fragment_index}")
+
+ # Remove temporary files
+ shutil.rmtree(shiftx2_output_dir)
+
+ return fragment_index
+
+
+def compute_chemical_shifts_sparta_plus(
+ topology_path: str,
+ trajectory_path: str,
+ frame_length: unit.Quantity,
+ output_path: str,
+ spartap_output_dir: str = None,
+):
+ """
+ Compute the chemical shifts of protein atoms using SPARTA+.
+
+ Parameters
+ ---------
+ topology_path
+ The path to the system topology, e.g. a PDB file.
+ trajectory_path
+ The path to the trajectory.
+ frame_length
+ The amount of simulation time between frames in the trajectory.
+ output_path
+ The path to write the computed chemical shifts.
+ shiftx2_output_dir
+ The directory to write output from SPARTA+.
+ """
+
+ # Set up directory to store SPARTA+ output
+ if spartap_output_dir is None:
+ spartap_output_dir = Path(Path(output_path).parent, "spartap")
+ else:
+ spartap_output_dir = Path(spartap_output_dir)
+
+ spartap_output_dir.mkdir(parents=True, exist_ok=True)
+
+ # Load topology
+ topology = loos.createSystem(topology_path)
+
+ resname_by_resid = {
+ residue[0].resid(): residue[0].resname()
+ for residue in topology.splitByResidue()
+ }
+
+ # Set up trajectory
+ trajectory = Trajectory(trajectory_path, topology)
+
+ # Write each frame to temporary PDB
+ pdb_filename_prefix = Path(trajectory_path).stem
+ tmp_pdb_prefix = Path(spartap_output_dir, pdb_filename_prefix)
+ for frame_index, frame in enumerate(trajectory):
+ pass
+ frame_pdb_path = f"{tmp_pdb_prefix}-{frame_index}.pdb"
+ with open(frame_pdb_path, "w") as pdb_file:
+ pdb_file.write(str(loos.PDB.fromAtomicGroup(frame)))
+
+ # Estimate chemical shifts by running SPARTA+ on the temporary frame
+ # PDBs every 2000 frames to avoid shell error "argument list too long"
+ if frame_index % 2000 == 1999 and frame_index > 0:
+ spartap_return_value = subprocess.run(
+ [
+ "sparta+",
+ "-in",
+ f"{pdb_filename_prefix}-*.pdb",
+ ],
+ cwd=spartap_output_dir,
+ )
+ for tmp_file in Path(spartap_output_dir).glob(f"{pdb_filename_prefix}-*.pdb"):
+ tmp_file.unlink()
+
+ spartap_return_value = subprocess.run(
+ [
+ "sparta+",
+ "-in",
+ f"{pdb_filename_prefix}-*.pdb",
+ ],
+ cwd=spartap_output_dir,
+ )
+
+ # Set up list of dicts to store chemical shifts
+ frame_time = 0.0 * unit.picosecond
+ fragment_index = 0
+ chemical_shifts = list()
+
+ N_frames = frame_index + 1
+ for frame_index in range(N_frames):
+ frame_time += frame_length
+ frame_time_ns = frame_time.m_as(unit.nanosecond)
+
+ # Write chemical shifts to file every 10 000 frames to avoid pandas
+ # out-of-memory
+ if frame_index % 10000 == 9999 and frame_index > 0:
+ list_of_dicts_to_csv(
+ chemical_shifts,
+ f"{output_path}-{fragment_index}",
+ )
+ fragment_index += 1
+ chemical_shifts = list()
+
+ # Read SPARTA+ estimate
+ first_data_line = numpy.infty
+ with open(f"{tmp_pdb_prefix}-{frame_index}_pred.tab", "r") as spartap_file:
+ for line_index, line in enumerate(spartap_file):
+ fields = line.split()
+ if line_index >= first_data_line and fields[4] != "9999.000":
+ resid = int(fields[0])
+ chemical_shifts.append(
+ {
+ "Frame": frame_index,
+ "Time (ns)": frame_time_ns,
+ "Resid": resid,
+ "Resname": resname_by_resid[resid],
+ "Atom": fields[2],
+ "Chemical Shift": float(fields[4]),
+ "Secondary Shift": float(fields[3]),
+ "Random Coil Shift": float(fields[5]),
+ "Ring Current Shift": float(fields[6]),
+ "Electric Field Shift": float(fields[7]),
+ "Shift Uncertainty": float(fields[8]),
+ }
+ )
+ elif fields and fields[0] == "FORMAT":
+ first_data_line = line_index + 2
+
+ if fragment_index == 0:
+ list_of_dicts_to_csv(chemical_shifts, output_path)
+
+ else:
+ list_of_dicts_to_csv(chemical_shifts, f"{output_path}-{fragment_index}")
+
+ # Remove temporary files
+ shutil.rmtree(spartap_output_dir)
+
+ return fragment_index
+
+
def assign_dihedral_clusters(
dihedrals_path: str,
output_path: str,
@@ -1075,6 +1409,7 @@ def compute_fraction_helix(
observable_path: str,
dihedral_clusters_path: str,
h_bond_geometries_path: str,
+ chemical_shifts_path: str,
output_path: str,
h_bond_distance_cutoff: unit.Quantity = 3.5 * unit.angstrom,
h_bond_angle_cutoff: float = 30,
@@ -1090,6 +1425,8 @@ def compute_fraction_helix(
The path to the time series of dihedral cluster assignments.
h_bond_geometries_path
The path to the time series of hydrogen bond geometries.
+ chemical_shifts_path
+ The path to the time series of chemical shifts.
output_path
The path to write the computed helical fractions.
h_bond_distance_cutoff
@@ -1108,14 +1445,41 @@ def compute_fraction_helix(
observable_path,
sep="\s+",
skiprows=1,
- names=["Resid", "Resname", "Experiment"],
+ names=[
+ "Resid", "Resname", "Experiment", "Shift Coil", "Delta Shift",
+ "Delta Shift Residue", "SPARTA+ Alpha", "SPARTA+ PII",
+ "ShiftX2 Alpha", "ShiftX2 PII",
+ ],
)
+ chunk_size = 1E6
+
# Read time series of dihedral cluster assignments
dihedral_df = pandas.read_csv(dihedral_clusters_path, index_col=0)
- # Read time series of hydrogen bond geometries
- h_bond_df = pandas.read_csv(h_bond_geometries_path, index_col=0)
+ # Read time series of hydrogen bond geometries for backbone amide H bonds
+ h_bond_df = pandas.concat(
+ [
+ chunk[
+ (chunk["Donor Name"] == "N")
+ & (chunk["Hydrogen Name"] == "H")
+ & (chunk["Acceptor Name"] == "O")
+ ]
+ for chunk in pandas.read_csv(
+ h_bond_geometries_path, index_col=0, chunksize=chunk_size,
+ )
+ ]
+ )
+
+ # Read time series of chemical shifts for backbone carbonyl carbons
+ chemical_shift_df = pandas.concat(
+ [
+ chunk[chunk["Atom"] == "C"]
+ for chunk in pandas.read_csv(
+ chemical_shifts_path, index_col=0, chunksize=chunk_size,
+ )
+ ]
+ )
# Compute observables
computed_observables = list()
@@ -1123,9 +1487,10 @@ def compute_fraction_helix(
for index, row in observable_df.iterrows():
observable_resid = row["Resid"]
- # Dihedral clusters resid is offset by 1 due to aaqaa3 initial structure
- dihedral_resid = observable_resid + 1
- residue_dihedral_df = dihedral_df[dihedral_df["Resid"] == dihedral_resid]
+ # observable_resid is 0-based, but some measured properties use 1-based
+ # residue indices due to the capped initial structure
+ capped_resid = observable_resid + 1
+ residue_dihedral_df = dihedral_df[dihedral_df["Resid"] == capped_resid]
# Get frames where (phi, psi) is closer than 30 deg to ideal alpha helix
# at (-63, -43)
@@ -1134,43 +1499,72 @@ def compute_fraction_helix(
+ (residue_dihedral_df["psi (deg)"] + 43) ** 2
) < 900
- computed_dihedral_fraction_helix = helical_dihedrals.mean()
+ computed_dihedral_fraction_helix = numpy.mean(helical_dihedrals)
helical_dihedral_frames = residue_dihedral_df[helical_dihedrals]["Frame"]
# Get hydrogen bonds to i-4 and i+4 residues
residue_h_bond_df = h_bond_df[
(
- (
- (h_bond_df["Donor Resid"] == observable_resid)
- & (h_bond_df["Acceptor Resid"] == observable_resid - 4)
- )
- | (
- (h_bond_df["Donor Resid"] == observable_resid + 4)
- & (h_bond_df["Acceptor Resid"] == observable_resid)
- )
+ (h_bond_df["Donor Resid"] == observable_resid)
+ & (h_bond_df["Acceptor Resid"] == observable_resid - 4)
+ )
+ | (
+ (h_bond_df["Donor Resid"] == observable_resid + 4)
+ & (h_bond_df["Acceptor Resid"] == observable_resid)
)
- & (h_bond_df["Donor Name"] == "N")
- & (h_bond_df["Hydrogen Name"] == "H")
- & (h_bond_df["Acceptor Name"] == "O")
]
if len(residue_h_bond_df) > 0:
- computed_h_bond_fraction_helix = (
+ computed_h_bond_fraction_helix = numpy.mean(
(
residue_h_bond_df["DA Distance (Angstrom)"]
< h_bond_distance_threshold
)
& (residue_h_bond_df["DHA Angle (deg)"] > h_bond_angle_threshold)
& (residue_h_bond_df["Frame"].isin(helical_dihedral_frames))
- ).mean()
+ )
else:
computed_h_bond_fraction_helix = 0.0
+ # Get mean chemical shift of backbone carbonyl carbon
+ residue_chemical_shift_df = chemical_shift_df[
+ chemical_shift_df["Resid"] == capped_resid
+ ]
+ carbonyl_chemical_shift = numpy.mean(
+ residue_chemical_shift_df["Chemical Shift"]
+ )
+
+ # Compute fraction helix from carbonyl chemical shift using experimental
+ # reference values for helix and coil
+ coil_chemical_shift = row["Shift Coil"]
+ delta_helix_coil_shift = row["Delta Shift Residue"]
+ computed_chemical_shift_fraction_helix = (
+ carbonyl_chemical_shift - coil_chemical_shift
+ ) / delta_helix_coil_shift
+ computed_chemical_shift_fraction_helix = numpy.clip(
+ computed_chemical_shift_fraction_helix, 0.0, 1.0,
+ )
+
+ # Compute fraction helix from carbonyl chemical shift using ShiftX2
+ # reference values for helix and coil
+ #coil_chemical_shift = row["ShiftX2 PII"]
+ #delta_helix_coil_shift = row["ShiftX2 Alpha"] - row["ShiftX2 PII"]
+ coil_chemical_shift = row["SPARTA+ PII"]
+ delta_helix_coil_shift = row["SPARTA+ Alpha"] - row["SPARTA+ PII"]
+ computed_spartap_fraction_helix = (
+ carbonyl_chemical_shift - coil_chemical_shift
+ ) / delta_helix_coil_shift
+ computed_spartap_fraction_helix = numpy.clip(
+ computed_spartap_fraction_helix, 0.0, 1.0,
+ )
+
computed_observables.append(
{
"Computed Dihedrals": computed_dihedral_fraction_helix,
"Computed H Bonds": computed_h_bond_fraction_helix,
+ "Computed Chemical Shifts": computed_chemical_shift_fraction_helix,
+ "Computed SPARTA+": computed_spartap_fraction_helix,
}
)
diff --git a/proteinbenchmark/benchmark_targets.py b/proteinbenchmark/benchmark_targets.py
index 2bcbcf4..4ec6f61 100644
--- a/proteinbenchmark/benchmark_targets.py
+++ b/proteinbenchmark/benchmark_targets.py
@@ -47,7 +47,7 @@
},
"aaqaa3-helix": {
"target_type": "disordered",
- "build_method": "helical",
+ "build_method": "alpha",
"aa_sequence": "AAQAAAAQAAAAQAA",
"nterm_cap": "ace",
"cterm_cap": "nh2",
diff --git a/proteinbenchmark/data/force-fields/Protein-Null-0.0.2-Ala5-OPC3.offxml b/proteinbenchmark/data/force-fields/Protein-Null-0.0.2-Ala5-OPC3.offxml
new file mode 100644
index 0000000..5cae064
--- /dev/null
+++ b/proteinbenchmark/data/force-fields/Protein-Null-0.0.2-Ala5-OPC3.offxml
@@ -0,0 +1,529 @@
+
+
+ The Open Force Field Initiative
+ 2021-08-16
+
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\ No newline at end of file
diff --git a/proteinbenchmark/data/force-fields/Protein-Null-0.0.2-Ala5-TIP3P-FB.offxml b/proteinbenchmark/data/force-fields/Protein-Null-0.0.2-Ala5-TIP3P-FB.offxml
new file mode 100644
index 0000000..abce62c
--- /dev/null
+++ b/proteinbenchmark/data/force-fields/Protein-Null-0.0.2-Ala5-TIP3P-FB.offxml
@@ -0,0 +1,529 @@
+
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+ The Open Force Field Initiative
+ 2021-08-16
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\ No newline at end of file
diff --git a/proteinbenchmark/data/force-fields/Protein-Null-0.0.2-OPC3-2.offxml b/proteinbenchmark/data/force-fields/Protein-Null-0.0.2-OPC3-2.offxml
new file mode 100644
index 0000000..707ccb1
--- /dev/null
+++ b/proteinbenchmark/data/force-fields/Protein-Null-0.0.2-OPC3-2.offxml
@@ -0,0 +1,529 @@
+
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+ The Open Force Field Initiative
+ 2021-08-16
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\ No newline at end of file
diff --git a/proteinbenchmark/data/force-fields/Protein-Null-0.0.2-TIP3P-FB-2.offxml b/proteinbenchmark/data/force-fields/Protein-Null-0.0.2-TIP3P-FB-2.offxml
new file mode 100644
index 0000000..1429d67
--- /dev/null
+++ b/proteinbenchmark/data/force-fields/Protein-Null-0.0.2-TIP3P-FB-2.offxml
@@ -0,0 +1,529 @@
+
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+ The Open Force Field Initiative
+ 2021-08-16
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\ No newline at end of file
diff --git a/proteinbenchmark/data/force-fields/Protein-Null-0.0.3-NBAmber.offxml b/proteinbenchmark/data/force-fields/Protein-Null-0.0.3-NBAmber.offxml
new file mode 100644
index 0000000..7eefcb1
--- /dev/null
+++ b/proteinbenchmark/data/force-fields/Protein-Null-0.0.3-NBAmber.offxml
@@ -0,0 +1,1708 @@
+
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+ The Open Force Field Initiative
+ 2023-05-02
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diff --git a/proteinbenchmark/data/force-fields/Protein-Null-0.0.3-QAmber.offxml b/proteinbenchmark/data/force-fields/Protein-Null-0.0.3-QAmber.offxml
new file mode 100644
index 0000000..6e46630
--- /dev/null
+++ b/proteinbenchmark/data/force-fields/Protein-Null-0.0.3-QAmber.offxml
@@ -0,0 +1,467 @@
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\ No newline at end of file
diff --git a/proteinbenchmark/data/force-fields/Protein-Null-0.0.3-abinitio-default-weights.offxml b/proteinbenchmark/data/force-fields/Protein-Null-0.0.3-abinitio-default-weights.offxml
new file mode 100644
index 0000000..2e2f564
--- /dev/null
+++ b/proteinbenchmark/data/force-fields/Protein-Null-0.0.3-abinitio-default-weights.offxml
@@ -0,0 +1,525 @@
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\ No newline at end of file
diff --git a/proteinbenchmark/data/force-fields/Protein-Null-0.0.3-abinitio.offxml b/proteinbenchmark/data/force-fields/Protein-Null-0.0.3-abinitio.offxml
new file mode 100644
index 0000000..f8a9836
--- /dev/null
+++ b/proteinbenchmark/data/force-fields/Protein-Null-0.0.3-abinitio.offxml
@@ -0,0 +1,525 @@
+
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+ The Open Force Field Initiative
+ 2023-05-02
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\ No newline at end of file
diff --git a/proteinbenchmark/data/force-fields/Protein-Null-0.0.3-default-weights.offxml b/proteinbenchmark/data/force-fields/Protein-Null-0.0.3-default-weights.offxml
new file mode 100644
index 0000000..5732228
--- /dev/null
+++ b/proteinbenchmark/data/force-fields/Protein-Null-0.0.3-default-weights.offxml
@@ -0,0 +1,525 @@
+
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+ 2023-05-02
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\ No newline at end of file
diff --git a/proteinbenchmark/data/force-fields/Protein-Null-0.0.3.offxml b/proteinbenchmark/data/force-fields/Protein-Null-0.0.3.offxml
new file mode 100644
index 0000000..a60008a
--- /dev/null
+++ b/proteinbenchmark/data/force-fields/Protein-Null-0.0.3.offxml
@@ -0,0 +1,525 @@
+
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+ The Open Force Field Initiative
+ 2023-05-02
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\ No newline at end of file
diff --git a/proteinbenchmark/data/force-fields/Protein-Specific-0.0.2-Ala5-OPC3.offxml b/proteinbenchmark/data/force-fields/Protein-Specific-0.0.2-Ala5-OPC3.offxml
new file mode 100644
index 0000000..3450017
--- /dev/null
+++ b/proteinbenchmark/data/force-fields/Protein-Specific-0.0.2-Ala5-OPC3.offxml
@@ -0,0 +1,556 @@
+
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+ The Open Force Field Initiative
+ 2021-08-16
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\ No newline at end of file
diff --git a/proteinbenchmark/data/force-fields/Protein-Specific-0.0.2-Ala5-TIP3P-FB.offxml b/proteinbenchmark/data/force-fields/Protein-Specific-0.0.2-Ala5-TIP3P-FB.offxml
new file mode 100644
index 0000000..a8bab32
--- /dev/null
+++ b/proteinbenchmark/data/force-fields/Protein-Specific-0.0.2-Ala5-TIP3P-FB.offxml
@@ -0,0 +1,556 @@
+
+
+ The Open Force Field Initiative
+ 2021-08-16
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\ No newline at end of file
diff --git a/proteinbenchmark/data/force-fields/Protein-Specific-0.0.2-OPC3-2.offxml b/proteinbenchmark/data/force-fields/Protein-Specific-0.0.2-OPC3-2.offxml
new file mode 100644
index 0000000..42bbd4f
--- /dev/null
+++ b/proteinbenchmark/data/force-fields/Protein-Specific-0.0.2-OPC3-2.offxml
@@ -0,0 +1,556 @@
+
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+ The Open Force Field Initiative
+ 2021-08-16
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diff --git a/proteinbenchmark/data/force-fields/Protein-Specific-0.0.2-TIP3P-FB-2.offxml b/proteinbenchmark/data/force-fields/Protein-Specific-0.0.2-TIP3P-FB-2.offxml
new file mode 100644
index 0000000..0daa3fc
--- /dev/null
+++ b/proteinbenchmark/data/force-fields/Protein-Specific-0.0.2-TIP3P-FB-2.offxml
@@ -0,0 +1,556 @@
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+ 2021-08-16
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diff --git a/proteinbenchmark/data/force-fields/Protein-Specific-0.0.3-abinitio.offxml b/proteinbenchmark/data/force-fields/Protein-Specific-0.0.3-abinitio.offxml
new file mode 100644
index 0000000..1bc34c5
--- /dev/null
+++ b/proteinbenchmark/data/force-fields/Protein-Specific-0.0.3-abinitio.offxml
@@ -0,0 +1,558 @@
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+ The Open Force Field Initiative
+ 2023-05-02
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diff --git a/proteinbenchmark/data/force-fields/Protein-Specific-0.0.3-default-weights.offxml b/proteinbenchmark/data/force-fields/Protein-Specific-0.0.3-default-weights.offxml
new file mode 100644
index 0000000..fc36e7e
--- /dev/null
+++ b/proteinbenchmark/data/force-fields/Protein-Specific-0.0.3-default-weights.offxml
@@ -0,0 +1,558 @@
+
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+ The Open Force Field Initiative
+ 2023-05-02
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\ No newline at end of file
diff --git a/proteinbenchmark/data/force-fields/Protein-Specific-0.0.3.offxml b/proteinbenchmark/data/force-fields/Protein-Specific-0.0.3.offxml
new file mode 100644
index 0000000..7c44a19
--- /dev/null
+++ b/proteinbenchmark/data/force-fields/Protein-Specific-0.0.3.offxml
@@ -0,0 +1,558 @@
+
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+ The Open Force Field Initiative
+ 2023-05-02
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\ No newline at end of file
diff --git a/proteinbenchmark/data/force-fields/nerenberg_ff14sbonlysc_c0ala_c0gly_c0val.xml b/proteinbenchmark/data/force-fields/nerenberg_ff14sbonlysc_c0ala_c0gly_c0val.xml
new file mode 100644
index 0000000..3dd7226
--- /dev/null
+++ b/proteinbenchmark/data/force-fields/nerenberg_ff14sbonlysc_c0ala_c0gly_c0val.xml
@@ -0,0 +1,94 @@
+
+
+ 2022-12-13
+ Chapin Cavender
+ Nerenberg, P.S. and Head-Gordon, T. (2011). Optimizing Protein-Solvent Force Fields to Reproduce Intrinsic Conformational Preferences of Model Peptides. J. Chem. Theory Comput. 7, 4, 1220-1230.
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diff --git a/proteinbenchmark/data/observables/aaqaa3/aaqaa3-PII-initial.pdb b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-PII-initial.pdb
new file mode 100644
index 0000000..6a6e458
--- /dev/null
+++ b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-PII-initial.pdb
@@ -0,0 +1,181 @@
+TITLE < Chain: id = nres = 17 natoms = 180 >
+ATOM 1 HH33 ACE 0 -6.144 -4.743 7.145 1.00 0.00
+ATOM 2 CH3 ACE 0 -5.435 -4.265 6.627 1.00 0.00
+ATOM 3 HH31 ACE 0 -5.193 -4.824 5.719 1.00 0.00
+ATOM 4 HH32 ACE 0 -5.785 -3.276 6.332 1.00 0.00
+ATOM 5 C ACE 0 -4.171 -4.171 7.487 1.00 0.00
+ATOM 6 O ACE 0 -4.257 -3.840 8.671 1.00 0.00
+ATOM 7 N ALA 1 -2.983 -4.446 6.956 1.00 0.00
+ATOM 8 H ALA 1 -2.914 -4.717 5.987 1.00 0.00
+ATOM 9 CA ALA 1 -1.682 -4.415 7.599 1.00 0.00
+ATOM 10 HA ALA 1 -1.755 -3.777 8.482 1.00 0.00
+ATOM 11 CB ALA 1 -1.331 -5.849 8.014 1.00 0.00
+ATOM 12 HB1 ALA 1 -0.379 -5.890 8.545 1.00 0.00
+ATOM 13 HB2 ALA 1 -2.088 -6.265 8.678 1.00 0.00
+ATOM 14 HB3 ALA 1 -1.251 -6.503 7.144 1.00 0.00
+ATOM 15 C ALA 1 -0.613 -3.805 6.676 1.00 0.00
+ATOM 16 O ALA 1 -0.653 -3.993 5.459 1.00 0.00
+ATOM 17 N ALA 2 0.366 -3.066 7.191 1.00 0.00
+ATOM 18 H ALA 2 0.407 -2.908 8.177 1.00 0.00
+ATOM 19 CA ALA 2 1.375 -2.490 6.320 1.00 0.00
+ATOM 20 HA ALA 2 0.864 -1.935 5.531 1.00 0.00
+ATOM 21 CB ALA 2 2.231 -1.537 7.163 1.00 0.00
+ATOM 22 HB1 ALA 2 2.986 -1.035 6.556 1.00 0.00
+ATOM 23 HB2 ALA 2 1.621 -0.762 7.625 1.00 0.00
+ATOM 24 HB3 ALA 2 2.752 -2.074 7.958 1.00 0.00
+ATOM 25 C ALA 2 2.223 -3.581 5.644 1.00 0.00
+ATOM 26 O ALA 2 2.500 -4.621 6.242 1.00 0.00
+ATOM 27 N GLN 3 2.664 -3.405 4.401 1.00 0.00
+ATOM 28 H GLN 3 2.444 -2.564 3.907 1.00 0.00
+ATOM 29 CA GLN 3 3.469 -4.441 3.758 1.00 0.00
+ATOM 30 HA GLN 3 2.931 -5.386 3.865 1.00 0.00
+ATOM 31 CB GLN 3 3.677 -4.128 2.253 1.00 0.00
+ATOM 32 HB1 GLN 3 2.704 -3.983 1.786 1.00 0.00
+ATOM 33 HB2 GLN 3 4.205 -3.177 2.166 1.00 0.00
+ATOM 34 CG GLN 3 4.425 -5.215 1.441 1.00 0.00
+ATOM 35 HG1 GLN 3 5.434 -5.363 1.821 1.00 0.00
+ATOM 36 HG2 GLN 3 3.909 -6.171 1.538 1.00 0.00
+ATOM 37 CD GLN 3 4.577 -4.912 -0.050 1.00 0.00
+ATOM 38 OE1 GLN 3 5.168 -5.700 -0.776 1.00 0.00
+ATOM 39 NE2 GLN 3 4.072 -3.785 -0.538 1.00 0.00
+ATOM 40 HE21 GLN 3 3.568 -3.148 0.057 1.00 0.00
+ATOM 41 HE22 GLN 3 4.197 -3.598 -1.521 1.00 0.00
+ATOM 42 C GLN 3 4.791 -4.549 4.541 1.00 0.00
+ATOM 43 O GLN 3 5.305 -3.544 5.032 1.00 0.00
+ATOM 44 N ALA 4 5.382 -5.732 4.688 1.00 0.00
+ATOM 45 H ALA 4 4.968 -6.551 4.290 1.00 0.00
+ATOM 46 CA ALA 4 6.628 -5.834 5.425 1.00 0.00
+ATOM 47 HA ALA 4 6.484 -5.366 6.401 1.00 0.00
+ATOM 48 CB ALA 4 6.947 -7.324 5.600 1.00 0.00
+ATOM 49 HB1 ALA 4 7.855 -7.473 6.187 1.00 0.00
+ATOM 50 HB2 ALA 4 6.141 -7.843 6.116 1.00 0.00
+ATOM 51 HB3 ALA 4 7.097 -7.811 4.635 1.00 0.00
+ATOM 52 C ALA 4 7.765 -5.081 4.715 1.00 0.00
+ATOM 53 O ALA 4 7.822 -5.046 3.484 1.00 0.00
+ATOM 54 N ALA 5 8.700 -4.460 5.429 1.00 0.00
+ATOM 55 H ALA 5 8.663 -4.483 6.428 1.00 0.00
+ATOM 56 CA ALA 5 9.773 -3.750 4.759 1.00 0.00
+ATOM 57 HA ALA 5 9.326 -3.055 4.045 1.00 0.00
+ATOM 58 CB ALA 5 10.559 -2.976 5.824 1.00 0.00
+ATOM 59 HB1 ALA 5 11.359 -2.382 5.379 1.00 0.00
+ATOM 60 HB2 ALA 5 9.914 -2.289 6.370 1.00 0.00
+ATOM 61 HB3 ALA 5 11.017 -3.654 6.547 1.00 0.00
+ATOM 62 C ALA 5 10.674 -4.711 3.964 1.00 0.00
+ATOM 63 O ALA 5 10.905 -5.846 4.384 1.00 0.00
+ATOM 64 N ALA 6 11.211 -4.319 2.812 1.00 0.00
+ATOM 65 H ALA 6 11.030 -3.400 2.463 1.00 0.00
+ATOM 66 CA ALA 6 12.061 -5.226 2.062 1.00 0.00
+ATOM 67 HA ALA 6 11.517 -6.162 1.921 1.00 0.00
+ATOM 68 CB ALA 6 12.354 -4.577 0.704 1.00 0.00
+ATOM 69 HB1 ALA 6 12.956 -5.230 0.070 1.00 0.00
+ATOM 70 HB2 ALA 6 11.433 -4.363 0.162 1.00 0.00
+ATOM 71 HB3 ALA 6 12.900 -3.641 0.823 1.00 0.00
+ATOM 72 C ALA 6 13.351 -5.555 2.833 1.00 0.00
+ATOM 73 O ALA 6 13.894 -4.704 3.540 1.00 0.00
+ATOM 74 N ALA 7 13.891 -6.767 2.740 1.00 0.00
+ATOM 75 H ALA 7 13.458 -7.464 2.169 1.00 0.00
+ATOM 76 CA ALA 7 15.108 -7.077 3.467 1.00 0.00
+ATOM 77 HA ALA 7 14.952 -6.818 4.516 1.00 0.00
+ATOM 78 CB ALA 7 15.364 -8.583 3.331 1.00 0.00
+ATOM 79 HB1 ALA 7 16.246 -8.892 3.894 1.00 0.00
+ATOM 80 HB2 ALA 7 14.522 -9.163 3.707 1.00 0.00
+ATOM 81 HB3 ALA 7 15.525 -8.863 2.288 1.00 0.00
+ATOM 82 C ALA 7 16.295 -6.243 2.958 1.00 0.00
+ATOM 83 O ALA 7 16.392 -5.952 1.764 1.00 0.00
+ATOM 84 N GLN 8 17.230 -5.828 3.808 1.00 0.00
+ATOM 85 H GLN 8 17.161 -6.058 4.779 1.00 0.00
+ATOM 86 CA GLN 8 18.358 -5.035 3.324 1.00 0.00
+ATOM 87 HA GLN 8 17.949 -4.207 2.740 1.00 0.00
+ATOM 88 CB GLN 8 19.192 -4.474 4.508 1.00 0.00
+ATOM 89 HB1 GLN 8 18.529 -3.924 5.175 1.00 0.00
+ATOM 90 HB2 GLN 8 19.582 -5.314 5.085 1.00 0.00
+ATOM 91 CG GLN 8 20.352 -3.526 4.118 1.00 0.00
+ATOM 92 HG1 GLN 8 21.086 -4.037 3.498 1.00 0.00
+ATOM 93 HG2 GLN 8 19.967 -2.693 3.527 1.00 0.00
+ATOM 94 CD GLN 8 21.130 -2.944 5.299 1.00 0.00
+ATOM 95 OE1 GLN 8 22.077 -2.196 5.097 1.00 0.00
+ATOM 96 NE2 GLN 8 20.772 -3.270 6.536 1.00 0.00
+ATOM 97 HE21 GLN 8 19.979 -3.869 6.700 1.00 0.00
+ATOM 98 HE22 GLN 8 21.308 -2.887 7.298 1.00 0.00
+ATOM 99 C GLN 8 19.180 -5.931 2.378 1.00 0.00
+ATOM 100 O GLN 8 19.287 -7.137 2.605 1.00 0.00
+ATOM 101 N ALA 9 19.776 -5.403 1.313 1.00 0.00
+ATOM 102 H ALA 9 19.691 -4.424 1.126 1.00 0.00
+ATOM 103 CA ALA 9 20.550 -6.247 0.421 1.00 0.00
+ATOM 104 HA ALA 9 19.922 -7.087 0.119 1.00 0.00
+ATOM 105 CB ALA 9 20.931 -5.408 -0.804 1.00 0.00
+ATOM 106 HB1 ALA 9 21.481 -5.998 -1.539 1.00 0.00
+ATOM 107 HB2 ALA 9 20.046 -5.014 -1.304 1.00 0.00
+ATOM 108 HB3 ALA 9 21.562 -4.563 -0.523 1.00 0.00
+ATOM 109 C ALA 9 21.786 -6.827 1.129 1.00 0.00
+ATOM 110 O ALA 9 22.394 -6.167 1.974 1.00 0.00
+ATOM 111 N ALA 10 22.209 -8.052 0.831 1.00 0.00
+ATOM 112 H ALA 10 21.724 -8.596 0.147 1.00 0.00
+ATOM 113 CA ALA 10 23.376 -8.600 1.498 1.00 0.00
+ATOM 114 HA ALA 10 23.224 -8.509 2.576 1.00 0.00
+ATOM 115 CB ALA 10 23.490 -10.078 1.105 1.00 0.00
+ATOM 116 HB1 ALA 10 24.326 -10.563 1.610 1.00 0.00
+ATOM 117 HB2 ALA 10 22.589 -10.628 1.374 1.00 0.00
+ATOM 118 HB3 ALA 10 23.645 -10.190 0.031 1.00 0.00
+ATOM 119 C ALA 10 24.648 -7.811 1.144 1.00 0.00
+ATOM 120 O ALA 10 24.797 -7.331 0.019 1.00 0.00
+ATOM 121 N ALA 11 25.601 -7.641 2.057 1.00 0.00
+ATOM 122 H ALA 11 25.490 -8.026 2.973 1.00 0.00
+ATOM 123 CA ALA 11 26.801 -6.896 1.723 1.00 0.00
+ATOM 124 HA ALA 11 26.499 -5.930 1.315 1.00 0.00
+ATOM 125 CB ALA 11 27.602 -6.694 3.016 1.00 0.00
+ATOM 126 HB1 ALA 11 28.500 -6.100 2.841 1.00 0.00
+ATOM 127 HB2 ALA 11 27.011 -6.172 3.768 1.00 0.00
+ATOM 128 HB3 ALA 11 27.916 -7.650 3.439 1.00 0.00
+ATOM 129 C ALA 11 27.626 -7.615 0.642 1.00 0.00
+ATOM 130 O ALA 11 27.680 -8.846 0.608 1.00 0.00
+ATOM 131 N ALA 12 28.290 -6.908 -0.268 1.00 0.00
+ATOM 132 H ALA 12 28.253 -5.908 -0.249 1.00 0.00
+ATOM 133 CA ALA 12 29.069 -7.586 -1.288 1.00 0.00
+ATOM 134 HA ALA 12 28.421 -8.314 -1.781 1.00 0.00
+ATOM 135 CB ALA 12 29.538 -6.531 -2.298 1.00 0.00
+ATOM 136 HB1 ALA 12 30.096 -6.983 -3.119 1.00 0.00
+ATOM 137 HB2 ALA 12 28.693 -6.000 -2.735 1.00 0.00
+ATOM 138 HB3 ALA 12 30.190 -5.794 -1.824 1.00 0.00
+ATOM 139 C ALA 12 30.248 -8.360 -0.674 1.00 0.00
+ATOM 140 O ALA 12 30.843 -7.919 0.311 1.00 0.00
+ATOM 141 N GLN 13 30.634 -9.516 -1.206 1.00 0.00
+ATOM 142 H GLN 13 30.157 -9.882 -2.006 1.00 0.00
+ATOM 143 CA GLN 13 31.754 -10.251 -0.623 1.00 0.00
+ATOM 144 HA GLN 13 31.560 -10.345 0.449 1.00 0.00
+ATOM 145 CB GLN 13 31.881 -11.663 -1.254 1.00 0.00
+ATOM 146 HB1 GLN 13 30.926 -12.179 -1.158 1.00 0.00
+ATOM 147 HB2 GLN 13 32.063 -11.549 -2.324 1.00 0.00
+ATOM 148 CG GLN 13 32.967 -12.576 -0.636 1.00 0.00
+ATOM 149 HG1 GLN 13 33.959 -12.144 -0.757 1.00 0.00
+ATOM 150 HG2 GLN 13 32.798 -12.680 0.437 1.00 0.00
+ATOM 151 CD GLN 13 33.045 -13.980 -1.237 1.00 0.00
+ATOM 152 OE1 GLN 13 33.882 -14.775 -0.830 1.00 0.00
+ATOM 153 NE2 GLN 13 32.204 -14.317 -2.209 1.00 0.00
+ATOM 154 HE21 GLN 13 31.502 -13.669 -2.528 1.00 0.00
+ATOM 155 HE22 GLN 13 32.282 -15.243 -2.601 1.00 0.00
+ATOM 156 C GLN 13 33.018 -9.390 -0.809 1.00 0.00
+ATOM 157 O GLN 13 33.154 -8.700 -1.820 1.00 0.00
+ATOM 158 N ALA 14 33.966 -9.391 0.124 1.00 0.00
+ATOM 159 H ALA 14 33.858 -9.950 0.946 1.00 0.00
+ATOM 160 CA ALA 14 35.157 -8.580 -0.051 1.00 0.00
+ATOM 161 HA ALA 14 34.842 -7.556 -0.263 1.00 0.00
+ATOM 162 CB ALA 14 35.951 -8.626 1.260 1.00 0.00
+ATOM 163 HB1 ALA 14 36.842 -7.998 1.210 1.00 0.00
+ATOM 164 HB2 ALA 14 35.352 -8.269 2.097 1.00 0.00
+ATOM 165 HB3 ALA 14 36.278 -9.642 1.488 1.00 0.00
+ATOM 166 C ALA 14 35.994 -9.061 -1.249 1.00 0.00
+ATOM 167 O ALA 14 36.064 -10.260 -1.524 1.00 0.00
+ATOM 168 N ALA 15 36.650 -8.180 -1.998 1.00 0.00
+ATOM 169 H ALA 15 36.600 -7.205 -1.784 1.00 0.00
+ATOM 170 CA ALA 15 37.440 -8.634 -3.128 1.00 0.00
+ATOM 171 HA ALA 15 36.804 -9.259 -3.758 1.00 0.00
+ATOM 172 CB ALA 15 37.897 -7.395 -3.908 1.00 0.00
+ATOM 173 HB1 ALA 15 38.463 -7.669 -4.800 1.00 0.00
+ATOM 174 HB2 ALA 15 37.046 -6.799 -4.237 1.00 0.00
+ATOM 175 HB3 ALA 15 38.538 -6.758 -3.296 1.00 0.00
+ATOM 176 C ALA 15 38.628 -9.498 -2.673 1.00 0.00
+ATOM 177 O ALA 15 39.329 -9.150 -1.721 1.00 0.00
+ATOM 178 N NH2 16 38.907 -10.633 -3.308 1.00 0.00
+ATOM 179 HN1 NH2 16 38.344 -10.925 -4.081 1.00 0.00
+ATOM 180 HN2 NH2 16 39.679 -11.195 -3.012 1.00 0.00
diff --git a/proteinbenchmark/data/observables/aaqaa3/aaqaa3-PII-protonated.pdb b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-PII-protonated.pdb
new file mode 100644
index 0000000..25006fb
--- /dev/null
+++ b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-PII-protonated.pdb
@@ -0,0 +1,182 @@
+ATOM 1 HH33 ACE A 0 -6.144 -4.743 7.145 1.00 0.00
+ATOM 2 CH3 ACE A 0 -5.435 -4.265 6.627 1.00 0.00
+ATOM 3 HH31 ACE A 0 -5.193 -4.824 5.719 1.00 0.00
+ATOM 4 HH32 ACE A 0 -5.785 -3.276 6.332 1.00 0.00
+ATOM 5 C ACE A 0 -4.171 -4.171 7.487 1.00 0.00
+ATOM 6 O ACE A 0 -4.257 -3.840 8.671 1.00 0.00
+ATOM 7 N ALA A 1 -2.983 -4.446 6.956 1.00 0.00
+ATOM 8 CA ALA A 1 -1.682 -4.415 7.599 1.00 0.00
+ATOM 9 CB ALA A 1 -1.331 -5.849 8.014 1.00 0.00
+ATOM 10 C ALA A 1 -0.613 -3.805 6.676 1.00 0.00
+ATOM 11 O ALA A 1 -0.653 -3.993 5.459 1.00 0.00
+ATOM 12 H ALA A 1 -3.162 -4.109 6.020 1.00 0.00 H
+ATOM 13 HA ALA A 1 -1.737 -3.848 8.431 1.00 0.00 H
+ATOM 14 HB1 ALA A 1 -0.778 -6.272 7.299 1.00 0.00 H
+ATOM 15 HB2 ALA A 1 -0.817 -5.827 8.869 1.00 0.00 H
+ATOM 16 HB3 ALA A 1 -2.173 -6.370 8.140 1.00 0.00 H
+ATOM 17 N ALA A 2 0.366 -3.066 7.191 1.00 0.00
+ATOM 18 CA ALA A 2 1.375 -2.490 6.320 1.00 0.00
+ATOM 19 CB ALA A 2 2.231 -1.537 7.163 1.00 0.00
+ATOM 20 C ALA A 2 2.223 -3.581 5.644 1.00 0.00
+ATOM 21 O ALA A 2 2.500 -4.621 6.242 1.00 0.00
+ATOM 22 H ALA A 2 0.342 -2.947 8.211 1.00 0.00 H
+ATOM 23 HA ALA A 2 0.921 -1.954 5.597 1.00 0.00 H
+ATOM 24 HB1 ALA A 2 1.862 -0.613 7.091 1.00 0.00 H
+ATOM 25 HB2 ALA A 2 2.212 -1.834 8.115 1.00 0.00 H
+ATOM 26 HB3 ALA A 2 3.169 -1.552 6.824 1.00 0.00 H
+ATOM 27 N GLN A 3 2.664 -3.405 4.401 1.00 0.00
+ATOM 28 CA GLN A 3 3.469 -4.441 3.758 1.00 0.00
+ATOM 29 CB GLN A 3 3.677 -4.128 2.253 1.00 0.00
+ATOM 30 CG GLN A 3 4.425 -5.215 1.441 1.00 0.00
+ATOM 31 CD GLN A 3 4.577 -4.912 -0.050 1.00 0.00
+ATOM 32 C GLN A 3 4.791 -4.549 4.541 1.00 0.00
+ATOM 33 O GLN A 3 5.305 -3.544 5.032 1.00 0.00
+ATOM 34 H GLN A 3 2.401 -2.519 3.956 1.00 0.00 H
+ATOM 35 HA GLN A 3 2.996 -5.307 3.850 1.00 0.00 H
+ATOM 36 HB2 GLN A 3 2.778 -3.996 1.828 1.00 0.00 H
+ATOM 37 HB3 GLN A 3 4.202 -3.275 2.174 1.00 0.00 H
+ATOM 38 HG2 GLN A 3 5.341 -5.325 1.840 1.00 0.00 H
+ATOM 39 HG3 GLN A 3 3.923 -6.079 1.543 1.00 0.00 H
+ATOM 40 OE1 GLN A 3 5.168 -5.700 -0.776 1.00 0.00 O
+ATOM 41 NE2 GLN A 3 4.072 -3.785 -0.538 1.00 0.00 N
+ATOM 42 HE21 GLN A 3 4.156 -3.535 -1.495 1.00 0.00 H
+ATOM 43 HE22 GLN A 3 3.577 -3.160 0.117 1.00 0.00 H
+ATOM 44 N ALA A 4 5.382 -5.732 4.688 1.00 0.00
+ATOM 45 CA ALA A 4 6.628 -5.834 5.425 1.00 0.00
+ATOM 46 CB ALA A 4 6.947 -7.324 5.600 1.00 0.00
+ATOM 47 C ALA A 4 7.765 -5.081 4.715 1.00 0.00
+ATOM 48 O ALA A 4 7.822 -5.046 3.484 1.00 0.00
+ATOM 49 H ALA A 4 4.897 -6.526 4.252 1.00 0.00 H
+ATOM 50 HA ALA A 4 6.506 -5.426 6.340 1.00 0.00 H
+ATOM 51 HB1 ALA A 4 6.316 -7.862 5.045 1.00 0.00 H
+ATOM 52 HB2 ALA A 4 7.885 -7.496 5.306 1.00 0.00 H
+ATOM 53 HB3 ALA A 4 6.845 -7.571 6.561 1.00 0.00 H
+ATOM 54 N ALA A 5 8.700 -4.460 5.429 1.00 0.00
+ATOM 55 CA ALA A 5 9.773 -3.750 4.759 1.00 0.00
+ATOM 56 CB ALA A 5 10.559 -2.976 5.824 1.00 0.00
+ATOM 57 C ALA A 5 10.674 -4.711 3.964 1.00 0.00
+ATOM 58 O ALA A 5 10.905 -5.846 4.384 1.00 0.00
+ATOM 59 H ALA A 5 8.595 -4.528 6.450 1.00 0.00 H
+ATOM 60 HA ALA A 5 9.377 -3.085 4.111 1.00 0.00 H
+ATOM 61 HB1 ALA A 5 10.312 -3.319 6.728 1.00 0.00 H
+ATOM 62 HB2 ALA A 5 11.536 -3.106 5.670 1.00 0.00 H
+ATOM 63 HB3 ALA A 5 10.334 -2.006 5.759 1.00 0.00 H
+ATOM 64 N ALA A 6 11.211 -4.319 2.812 1.00 0.00
+ATOM 65 CA ALA A 6 12.061 -5.226 2.062 1.00 0.00
+ATOM 66 CB ALA A 6 12.354 -4.577 0.704 1.00 0.00
+ATOM 67 C ALA A 6 13.351 -5.555 2.833 1.00 0.00
+ATOM 68 O ALA A 6 13.894 -4.704 3.540 1.00 0.00
+ATOM 69 H ALA A 6 10.979 -3.362 2.518 1.00 0.00 H
+ATOM 70 HA ALA A 6 11.564 -6.089 1.901 1.00 0.00 H
+ATOM 71 HB1 ALA A 6 12.643 -5.281 0.059 1.00 0.00 H
+ATOM 72 HB2 ALA A 6 11.527 -4.131 0.368 1.00 0.00 H
+ATOM 73 HB3 ALA A 6 13.080 -3.901 0.813 1.00 0.00 H
+ATOM 74 N ALA A 7 13.891 -6.767 2.740 1.00 0.00
+ATOM 75 CA ALA A 7 15.108 -7.077 3.467 1.00 0.00
+ATOM 76 CB ALA A 7 15.364 -8.583 3.331 1.00 0.00
+ATOM 77 C ALA A 7 16.295 -6.243 2.958 1.00 0.00
+ATOM 78 O ALA A 7 16.392 -5.952 1.764 1.00 0.00
+ATOM 79 H ALA A 7 13.390 -7.430 2.135 1.00 0.00 H
+ATOM 80 HA ALA A 7 14.973 -6.866 4.444 1.00 0.00 H
+ATOM 81 HB1 ALA A 7 16.147 -8.730 2.730 1.00 0.00 H
+ATOM 82 HB2 ALA A 7 15.554 -8.966 4.232 1.00 0.00 H
+ATOM 83 HB3 ALA A 7 14.555 -9.020 2.943 1.00 0.00 H
+ATOM 84 N GLN A 8 17.230 -5.828 3.808 1.00 0.00
+ATOM 85 CA GLN A 8 18.358 -5.035 3.324 1.00 0.00
+ATOM 86 CB GLN A 8 19.192 -4.474 4.508 1.00 0.00
+ATOM 87 CG GLN A 8 20.352 -3.526 4.118 1.00 0.00
+ATOM 88 CD GLN A 8 21.130 -2.944 5.299 1.00 0.00
+ATOM 89 C GLN A 8 19.180 -5.931 2.378 1.00 0.00
+ATOM 90 O GLN A 8 19.287 -7.137 2.605 1.00 0.00
+ATOM 91 H GLN A 8 17.095 -6.101 4.788 1.00 0.00 H
+ATOM 92 HA GLN A 8 18.003 -4.281 2.787 1.00 0.00 H
+ATOM 93 HB2 GLN A 8 18.577 -3.968 5.118 1.00 0.00 H
+ATOM 94 HB3 GLN A 8 19.587 -5.247 5.013 1.00 0.00 H
+ATOM 95 HG2 GLN A 8 20.991 -4.039 3.537 1.00 0.00 H
+ATOM 96 HG3 GLN A 8 19.967 -2.767 3.583 1.00 0.00 H
+ATOM 97 OE1 GLN A 8 22.077 -2.196 5.097 1.00 0.00 O
+ATOM 98 NE2 GLN A 8 20.772 -3.270 6.536 1.00 0.00 N
+ATOM 99 HE21 GLN A 8 21.252 -2.931 7.335 1.00 0.00 H
+ATOM 100 HE22 GLN A 8 19.962 -3.899 6.649 1.00 0.00 H
+ATOM 101 N ALA A 9 19.776 -5.403 1.313 1.00 0.00
+ATOM 102 CA ALA A 9 20.550 -6.247 0.421 1.00 0.00
+ATOM 103 CB ALA A 9 20.931 -5.408 -0.804 1.00 0.00
+ATOM 104 C ALA A 9 21.786 -6.827 1.129 1.00 0.00
+ATOM 105 O ALA A 9 22.394 -6.167 1.974 1.00 0.00
+ATOM 106 H ALA A 9 19.644 -4.391 1.187 1.00 0.00 H
+ATOM 107 HA ALA A 9 19.976 -7.017 0.113 1.00 0.00 H
+ATOM 108 HB1 ALA A 9 21.907 -5.203 -0.771 1.00 0.00 H
+ATOM 109 HB2 ALA A 9 20.723 -5.923 -1.633 1.00 0.00 H
+ATOM 110 HB3 ALA A 9 20.408 -4.558 -0.796 1.00 0.00 H
+ATOM 111 N ALA A 10 22.209 -8.052 0.831 1.00 0.00
+ATOM 112 CA ALA A 10 23.376 -8.600 1.498 1.00 0.00
+ATOM 113 CB ALA A 10 23.490 -10.078 1.105 1.00 0.00
+ATOM 114 C ALA A 10 24.648 -7.811 1.144 1.00 0.00
+ATOM 115 O ALA A 10 24.797 -7.331 0.019 1.00 0.00
+ATOM 116 H ALA A 10 21.659 -8.550 0.119 1.00 0.00 H
+ATOM 117 HA ALA A 10 23.242 -8.547 2.496 1.00 0.00 H
+ATOM 118 HB1 ALA A 10 22.725 -10.583 1.500 1.00 0.00 H
+ATOM 119 HB2 ALA A 10 23.468 -10.156 0.111 1.00 0.00 H
+ATOM 120 HB3 ALA A 10 24.350 -10.445 1.452 1.00 0.00 H
+ATOM 121 N ALA A 11 25.601 -7.641 2.057 1.00 0.00
+ATOM 122 CA ALA A 11 26.801 -6.896 1.723 1.00 0.00
+ATOM 123 CB ALA A 11 27.602 -6.694 3.016 1.00 0.00
+ATOM 124 C ALA A 11 27.626 -7.615 0.642 1.00 0.00
+ATOM 125 O ALA A 11 27.680 -8.846 0.608 1.00 0.00
+ATOM 126 H ALA A 11 25.416 -8.066 2.974 1.00 0.00 H
+ATOM 127 HA ALA A 11 26.540 -5.990 1.366 1.00 0.00 H
+ATOM 128 HB1 ALA A 11 28.405 -7.286 3.000 1.00 0.00 H
+ATOM 129 HB2 ALA A 11 27.888 -5.740 3.079 1.00 0.00 H
+ATOM 130 HB3 ALA A 11 27.027 -6.926 3.798 1.00 0.00 H
+ATOM 131 N ALA A 12 28.290 -6.908 -0.268 1.00 0.00
+ATOM 132 CA ALA A 12 29.069 -7.586 -1.288 1.00 0.00
+ATOM 133 CB ALA A 12 29.538 -6.531 -2.298 1.00 0.00
+ATOM 134 C ALA A 12 30.248 -8.360 -0.674 1.00 0.00
+ATOM 135 O ALA A 12 30.843 -7.919 0.311 1.00 0.00
+ATOM 136 H ALA A 12 28.204 -5.887 -0.185 1.00 0.00 H
+ATOM 137 HA ALA A 12 28.479 -8.246 -1.771 1.00 0.00 H
+ATOM 138 HB1 ALA A 12 30.507 -6.344 -2.151 1.00 0.00 H
+ATOM 139 HB2 ALA A 12 29.398 -6.877 -3.223 1.00 0.00 H
+ATOM 140 HB3 ALA A 12 29.010 -5.694 -2.168 1.00 0.00 H
+ATOM 141 N GLN A 13 30.634 -9.516 -1.206 1.00 0.00
+ATOM 142 CA GLN A 13 31.754 -10.251 -0.623 1.00 0.00
+ATOM 143 CB GLN A 13 31.881 -11.663 -1.254 1.00 0.00
+ATOM 144 CG GLN A 13 32.967 -12.576 -0.636 1.00 0.00
+ATOM 145 CD GLN A 13 33.045 -13.980 -1.237 1.00 0.00
+ATOM 146 C GLN A 13 33.018 -9.390 -0.809 1.00 0.00
+ATOM 147 O GLN A 13 33.154 -8.700 -1.820 1.00 0.00
+ATOM 148 H GLN A 13 30.100 -9.831 -2.024 1.00 0.00 H
+ATOM 149 HA GLN A 13 31.596 -10.342 0.351 1.00 0.00 H
+ATOM 150 HB2 GLN A 13 30.999 -12.133 -1.162 1.00 0.00 H
+ATOM 151 HB3 GLN A 13 32.092 -11.557 -2.230 1.00 0.00 H
+ATOM 152 HG2 GLN A 13 33.858 -12.127 -0.758 1.00 0.00 H
+ATOM 153 HG3 GLN A 13 32.781 -12.659 0.348 1.00 0.00 H
+ATOM 154 OE1 GLN A 13 33.882 -14.775 -0.830 1.00 0.00 O
+ATOM 155 NE2 GLN A 13 32.204 -14.317 -2.209 1.00 0.00 N
+ATOM 156 HE21 GLN A 13 32.222 -15.210 -2.642 1.00 0.00 H
+ATOM 157 HE22 GLN A 13 31.514 -13.611 -2.510 1.00 0.00 H
+ATOM 158 N ALA A 14 33.966 -9.391 0.124 1.00 0.00
+ATOM 159 CA ALA A 14 35.157 -8.580 -0.051 1.00 0.00
+ATOM 160 CB ALA A 14 35.951 -8.626 1.260 1.00 0.00
+ATOM 161 C ALA A 14 35.994 -9.061 -1.249 1.00 0.00
+ATOM 162 O ALA A 14 36.064 -10.260 -1.524 1.00 0.00
+ATOM 163 H ALA A 14 33.785 -9.990 0.939 1.00 0.00 H
+ATOM 164 HA ALA A 14 34.885 -7.624 -0.224 1.00 0.00 H
+ATOM 165 HB1 ALA A 14 35.640 -9.401 1.806 1.00 0.00 H
+ATOM 166 HB2 ALA A 14 36.922 -8.728 1.053 1.00 0.00 H
+ATOM 167 HB3 ALA A 14 35.802 -7.778 1.764 1.00 0.00 H
+ATOM 168 N ALA A 15 36.650 -8.180 -1.998 1.00 0.00
+ATOM 169 CA ALA A 15 37.440 -8.634 -3.128 1.00 0.00
+ATOM 170 CB ALA A 15 37.897 -7.395 -3.908 1.00 0.00
+ATOM 171 C ALA A 15 38.628 -9.498 -2.673 1.00 0.00
+ATOM 172 O ALA A 15 39.329 -9.150 -1.721 1.00 0.00
+ATOM 173 H ALA A 15 36.550 -7.197 -1.716 1.00 0.00 H
+ATOM 174 HA ALA A 15 36.860 -9.194 -3.734 1.00 0.00 H
+ATOM 175 HB1 ALA A 15 37.752 -6.582 -3.348 1.00 0.00 H
+ATOM 176 HB2 ALA A 15 38.866 -7.484 -4.127 1.00 0.00 H
+ATOM 177 HB3 ALA A 15 37.366 -7.323 -4.750 1.00 0.00 H
+ATOM 178 N NH2 A 16 38.907 -10.633 -3.308 1.00 0.00
+ATOM 179 HN1 NH2 A 16 38.344 -10.925 -4.081 1.00 0.00
+ATOM 180 HN2 NH2 A 16 39.679 -11.195 -3.012 1.00 0.00
+TER
+END
\ No newline at end of file
diff --git a/proteinbenchmark/data/observables/aaqaa3/aaqaa3-PII-protonated.pdb.cs b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-PII-protonated.pdb.cs
new file mode 100644
index 0000000..b4e5c4a
--- /dev/null
+++ b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-PII-protonated.pdb.cs
@@ -0,0 +1,151 @@
+NUM,RES,ATOMNAME,SHIFT
+1,A,C,175.0654
+1,A,CA,52.0195
+1,A,CB,19.5000
+1,A,H,8.2598
+1,A,HA,4.2948
+1,A,HB,1.4323
+1,A,HB2,1.5736
+1,A,HB3,1.4934
+1,A,N,124.8779
+2,A,C,177.2514
+2,A,CA,52.1551
+2,A,CB,19.1918
+2,A,H,8.2466
+2,A,HA,4.2479
+2,A,HB,1.4011
+2,A,HB2,1.5837
+2,A,HB3,1.4948
+2,A,N,124.6586
+3,Q,C,175.7348
+3,Q,CA,56.1117
+3,Q,CB,29.5038
+3,Q,CD,179.8192
+3,Q,CG,34.1290
+3,Q,H,8.2580
+3,Q,HA,4.1730
+3,Q,HB2,2.0489
+3,Q,HB3,1.9489
+3,Q,HE21,7.5076
+3,Q,HE22,6.9040
+3,Q,HG2,2.3413
+3,Q,HG3,2.3748
+3,Q,N,120.9513
+4,A,C,176.7229
+4,A,CA,52.0678
+4,A,CB,19.1234
+4,A,H,8.2980
+4,A,HA,4.2681
+4,A,HB,1.4339
+4,A,HB2,1.6095
+4,A,HB3,1.5174
+4,A,N,127.3261
+5,A,C,177.2289
+5,A,CA,52.0397
+5,A,CB,18.9835
+5,A,H,8.1915
+5,A,HA,4.1599
+5,A,HB,1.3964
+5,A,HB2,1.5724
+5,A,HB3,1.5761
+5,A,N,123.8717
+6,A,C,177.0653
+6,A,CA,52.0695
+6,A,CB,19.2212
+6,A,H,8.1302
+6,A,HA,4.1978
+6,A,HB,1.4019
+6,A,HB2,1.5673
+6,A,HB3,1.4532
+6,A,N,124.1902
+7,A,C,176.9004
+7,A,CA,51.9903
+7,A,CB,18.9353
+7,A,H,8.2640
+7,A,HA,4.2093
+7,A,HB,1.3604
+7,A,HB2,1.5768
+7,A,HB3,1.4721
+7,A,N,124.5144
+8,Q,C,175.5587
+8,Q,CA,56.1801
+8,Q,CB,29.7106
+8,Q,CD,179.7621
+8,Q,CG,34.1542
+8,Q,H,8.3208
+8,Q,HA,4.1127
+8,Q,HB2,1.8994
+8,Q,HB3,1.9840
+8,Q,HE21,7.5105
+8,Q,HE22,6.8730
+8,Q,HG2,2.3531
+8,Q,HG3,2.4433
+8,Q,N,120.9008
+9,A,C,176.9001
+9,A,CA,51.8990
+9,A,CB,19.3025
+9,A,H,8.3199
+9,A,HA,4.2647
+9,A,HB,1.4024
+9,A,HB2,1.6178
+9,A,HB3,1.4977
+9,A,N,127.5980
+10,A,C,177.2649
+10,A,CA,51.9997
+10,A,CB,18.8398
+10,A,H,8.2567
+10,A,HA,4.2526
+10,A,HB,1.4126
+10,A,HB2,1.6070
+10,A,HB3,1.5315
+10,A,N,124.2351
+11,A,C,177.2738
+11,A,CA,52.1148
+11,A,CB,19.3249
+11,A,H,8.3650
+11,A,HA,4.2127
+11,A,HB,1.4291
+11,A,HB2,1.5818
+11,A,HB3,1.5004
+11,A,N,124.3207
+12,A,C,176.9196
+12,A,CA,52.0626
+12,A,CB,19.0414
+12,A,H,8.3677
+12,A,HA,4.2469
+12,A,HB,1.4170
+12,A,HB2,1.6085
+12,A,HB3,1.5302
+12,A,N,124.5875
+13,Q,C,175.4033
+13,Q,CA,56.0968
+13,Q,CB,29.3585
+13,Q,CD,179.8377
+13,Q,CG,34.0522
+13,Q,H,8.3045
+13,Q,HA,4.1273
+13,Q,HB2,1.9757
+13,Q,HB3,1.9548
+13,Q,HE21,7.4560
+13,Q,HE22,6.8533
+13,Q,HG2,2.3481
+13,Q,HG3,2.4155
+13,Q,N,120.7096
+14,A,C,177.0125
+14,A,CA,52.1056
+14,A,CB,18.9565
+14,A,H,8.1559
+14,A,HA,4.1932
+14,A,HB,1.4002
+14,A,HB2,1.4482
+14,A,HB3,1.5941
+14,A,N,127.4300
+15,A,C,179.3703
+15,A,CA,53.1890
+15,A,CB,19.0769
+15,A,H,8.0788
+15,A,HA,4.0893
+15,A,HB,1.3779
+15,A,HB2,1.5064
+15,A,HB3,1.5935
+15,A,N,126.1606
diff --git a/proteinbenchmark/data/observables/aaqaa3/aaqaa3-PII-protonated.pdb.shifty b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-PII-protonated.pdb.shifty
new file mode 100644
index 0000000..e69de29
diff --git a/proteinbenchmark/data/observables/aaqaa3/aaqaa3-PII-protonated.pdb.sxp b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-PII-protonated.pdb.sxp
new file mode 100644
index 0000000..a192e7f
--- /dev/null
+++ b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-PII-protonated.pdb.sxp
@@ -0,0 +1,151 @@
+NUM,RES,IUPAC,ATOM,PRED_CS
+1,ALA,A,H,8.2598
+1,ALA,A,HA,4.2948
+1,ALA,A,C,175.0654
+1,ALA,A,CA,52.0195
+1,ALA,A,CB,19.5000
+1,ALA,A,N,124.8779
+1,ALA,A,HB,1.4323
+1,ALA,A,HB2,1.5736
+1,ALA,A,HB3,1.4934
+2,ALA,A,H,8.2466
+2,ALA,A,HA,4.2479
+2,ALA,A,C,177.2514
+2,ALA,A,CA,52.1551
+2,ALA,A,CB,19.1918
+2,ALA,A,N,124.6586
+2,ALA,A,HB,1.4011
+2,ALA,A,HB2,1.5837
+2,ALA,A,HB3,1.4948
+3,GLN,Q,H,8.2580
+3,GLN,Q,HA,4.1730
+3,GLN,Q,C,175.7348
+3,GLN,Q,CA,56.1117
+3,GLN,Q,CB,29.5038
+3,GLN,Q,N,120.9513
+3,GLN,Q,CD,179.8192
+3,GLN,Q,CG,34.1290
+3,GLN,Q,HB2,2.0489
+3,GLN,Q,HB3,1.9489
+3,GLN,Q,HE21,7.5076
+3,GLN,Q,HE22,6.9040
+3,GLN,Q,HG2,2.3413
+3,GLN,Q,HG3,2.3748
+4,ALA,A,H,8.2980
+4,ALA,A,HA,4.2681
+4,ALA,A,C,176.7229
+4,ALA,A,CA,52.0678
+4,ALA,A,CB,19.1234
+4,ALA,A,N,127.3261
+4,ALA,A,HB,1.4339
+4,ALA,A,HB2,1.6095
+4,ALA,A,HB3,1.5174
+5,ALA,A,H,8.1915
+5,ALA,A,HA,4.1599
+5,ALA,A,C,177.2289
+5,ALA,A,CA,52.0397
+5,ALA,A,CB,18.9835
+5,ALA,A,N,123.8717
+5,ALA,A,HB,1.3964
+5,ALA,A,HB2,1.5724
+5,ALA,A,HB3,1.5761
+6,ALA,A,H,8.1302
+6,ALA,A,HA,4.1978
+6,ALA,A,C,177.0653
+6,ALA,A,CA,52.0695
+6,ALA,A,CB,19.2212
+6,ALA,A,N,124.1902
+6,ALA,A,HB,1.4019
+6,ALA,A,HB2,1.5673
+6,ALA,A,HB3,1.4532
+7,ALA,A,H,8.2640
+7,ALA,A,HA,4.2093
+7,ALA,A,C,176.9004
+7,ALA,A,CA,51.9903
+7,ALA,A,CB,18.9353
+7,ALA,A,N,124.5144
+7,ALA,A,HB,1.3604
+7,ALA,A,HB2,1.5768
+7,ALA,A,HB3,1.4721
+8,GLN,Q,H,8.3208
+8,GLN,Q,HA,4.1127
+8,GLN,Q,C,175.5587
+8,GLN,Q,CA,56.1801
+8,GLN,Q,CB,29.7106
+8,GLN,Q,N,120.9008
+8,GLN,Q,CD,179.7621
+8,GLN,Q,CG,34.1542
+8,GLN,Q,HB2,1.8994
+8,GLN,Q,HB3,1.9840
+8,GLN,Q,HE21,7.5105
+8,GLN,Q,HE22,6.8730
+8,GLN,Q,HG2,2.3531
+8,GLN,Q,HG3,2.4433
+9,ALA,A,H,8.3199
+9,ALA,A,HA,4.2647
+9,ALA,A,C,176.9001
+9,ALA,A,CA,51.8990
+9,ALA,A,CB,19.3025
+9,ALA,A,N,127.5980
+9,ALA,A,HB,1.4024
+9,ALA,A,HB2,1.6178
+9,ALA,A,HB3,1.4977
+10,ALA,A,H,8.2567
+10,ALA,A,HA,4.2526
+10,ALA,A,C,177.2649
+10,ALA,A,CA,51.9997
+10,ALA,A,CB,18.8398
+10,ALA,A,N,124.2351
+10,ALA,A,HB,1.4126
+10,ALA,A,HB2,1.6070
+10,ALA,A,HB3,1.5315
+11,ALA,A,H,8.3650
+11,ALA,A,HA,4.2127
+11,ALA,A,C,177.2738
+11,ALA,A,CA,52.1148
+11,ALA,A,CB,19.3249
+11,ALA,A,N,124.3207
+11,ALA,A,HB,1.4291
+11,ALA,A,HB2,1.5818
+11,ALA,A,HB3,1.5004
+12,ALA,A,H,8.3677
+12,ALA,A,HA,4.2469
+12,ALA,A,C,176.9196
+12,ALA,A,CA,52.0626
+12,ALA,A,CB,19.0414
+12,ALA,A,N,124.5875
+12,ALA,A,HB,1.4170
+12,ALA,A,HB2,1.6085
+12,ALA,A,HB3,1.5302
+13,GLN,Q,H,8.3045
+13,GLN,Q,HA,4.1273
+13,GLN,Q,C,175.4033
+13,GLN,Q,CA,56.0968
+13,GLN,Q,CB,29.3585
+13,GLN,Q,N,120.7096
+13,GLN,Q,CD,179.8377
+13,GLN,Q,CG,34.0522
+13,GLN,Q,HB2,1.9757
+13,GLN,Q,HB3,1.9548
+13,GLN,Q,HE21,7.4560
+13,GLN,Q,HE22,6.8533
+13,GLN,Q,HG2,2.3481
+13,GLN,Q,HG3,2.4155
+14,ALA,A,H,8.1559
+14,ALA,A,HA,4.1932
+14,ALA,A,C,177.0125
+14,ALA,A,CA,52.1056
+14,ALA,A,CB,18.9565
+14,ALA,A,N,127.4300
+14,ALA,A,HB,1.4002
+14,ALA,A,HB2,1.4482
+14,ALA,A,HB3,1.5941
+15,ALA,A,H,8.0788
+15,ALA,A,HA,4.0893
+15,ALA,A,C,179.3703
+15,ALA,A,CA,53.1890
+15,ALA,A,CB,19.0769
+15,ALA,A,N,126.1606
+15,ALA,A,HB,1.3779
+15,ALA,A,HB2,1.5064
+15,ALA,A,HB3,1.5935
diff --git a/proteinbenchmark/data/observables/aaqaa3/aaqaa3-PII-protonated.spartap b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-PII-protonated.spartap
new file mode 100644
index 0000000..1a132dc
--- /dev/null
+++ b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-PII-protonated.spartap
@@ -0,0 +1,114 @@
+REMARK SPARTA+ Protein Chemical Shift Prediction Table
+REMARK
+REMARK All chemical shifts are reported in ppm:
+REMARK
+REMARK SHIFT is the predicted chemical shift.
+REMARK SS_SHIFT is the predicted secondary chemical shift.
+REMARK RC_SHIFT is the random coil chemical shift.
+REMARK HM_SHIFT is the ring current shift; a correction
+REMARK of 0.6 times this value is applied.
+REMARK EF_SHIFT is the adjustment for electric field effect,
+REMARK applied to proton shifts only.
+REMARK SIGMA is the estimated prediction error.
+REMARK
+REMARK Reference:
+REMARK Y. Shen and A. Bax: SPARTA+: a modest improvement in empirical NMR
+REMARK chemical shift prediction by means of an artificial neural network.
+REMARK J. Biomol. NMR 48, 13-22 (2010).
+
+DATA SOURCE aaqaa3-PII-protonated.pdb
+
+DATA FIRST_RESID 0
+
+DATA SEQUENCE ?AAQAAAAQA AAAQAA?
+
+VARS RESID RESNAME ATOMNAME SS_SHIFT SHIFT RC_SHIFT HM_SHIFT EF_SHIFT SIGMA
+FORMAT %4d %4s %4s %9.3f %9.3f %9.3f %9.3f %9.3f %9.3f
+
+ 0 ? HA 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 0 ? C 0.000 9999.000 9999.000 -0.000 0.000 0.000
+ 0 ? CA 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 0 ? CB 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 2 A N 0.817 123.637 122.820 -0.000 0.000 2.483
+ 2 A HA 0.099 4.419 4.320 -0.000 0.000 0.238
+ 2 A C -0.030 177.554 177.584 -0.000 0.000 1.070
+ 2 A CA -0.043 51.994 52.037 -0.000 0.000 0.770
+ 2 A CB 0.419 19.419 19.000 -0.000 0.000 1.008
+ 2 A HN 0.033 8.183 8.150 -0.000 0.000 0.497
+ 3 Q N 1.777 121.577 119.800 -0.000 0.000 2.392
+ 3 Q HA -0.132 4.208 4.340 -0.000 0.000 0.262
+ 3 Q C -0.085 175.915 176.000 -0.000 0.000 1.003
+ 3 Q CA -0.419 55.384 55.803 -0.000 0.000 0.888
+ 3 Q CB 0.863 29.601 28.738 -0.000 0.000 1.260
+ 3 Q HN 0.052 8.322 8.270 -0.000 0.000 0.435
+ 4 A N 2.616 125.436 122.820 -0.000 0.000 2.483
+ 4 A HA -0.042 4.278 4.320 -0.000 0.000 0.238
+ 4 A C -0.402 177.182 177.584 -0.000 0.000 1.070
+ 4 A CA -0.143 51.894 52.037 -0.000 0.000 0.770
+ 4 A CB 0.271 19.271 19.000 -0.000 0.000 1.008
+ 4 A HN 0.238 8.388 8.150 -0.000 0.000 0.497
+ 5 A N 1.718 124.538 122.820 -0.000 0.000 2.498
+ 5 A HA -0.106 4.214 4.320 -0.000 0.000 0.239
+ 5 A C 0.154 177.738 177.584 -0.000 0.000 1.068
+ 5 A CA -0.262 51.775 52.037 -0.000 0.000 0.766
+ 5 A CB 0.409 19.409 19.000 -0.000 0.000 1.003
+ 5 A HN 0.012 8.162 8.150 -0.000 0.000 0.497
+ 6 A N 1.896 124.716 122.820 -0.000 0.000 2.483
+ 6 A HA -0.101 4.219 4.320 -0.000 0.000 0.238
+ 6 A C 0.156 177.740 177.584 -0.000 0.000 1.070
+ 6 A CA -0.279 51.758 52.037 -0.000 0.000 0.770
+ 6 A CB 0.397 19.397 19.000 -0.000 0.000 1.008
+ 6 A HN 0.019 8.169 8.150 -0.000 0.000 0.497
+ 7 A N 1.624 124.444 122.820 -0.000 0.000 2.483
+ 7 A HA -0.030 4.290 4.320 -0.000 0.000 0.238
+ 7 A C 0.090 177.674 177.584 -0.000 0.000 1.070
+ 7 A CA -0.227 51.810 52.037 -0.000 0.000 0.770
+ 7 A CB 0.430 19.430 19.000 -0.000 0.000 1.008
+ 7 A HN -0.003 8.147 8.150 -0.000 0.000 0.497
+ 8 Q N 1.901 121.701 119.800 -0.000 0.000 2.392
+ 8 Q HA -0.140 4.200 4.340 -0.000 0.000 0.262
+ 8 Q C -0.047 175.953 176.000 -0.000 0.000 1.003
+ 8 Q CA -0.411 55.392 55.803 -0.000 0.000 0.888
+ 8 Q CB 0.820 29.558 28.738 -0.000 0.000 1.260
+ 8 Q HN 0.051 8.321 8.270 -0.000 0.000 0.435
+ 9 A N 2.639 125.459 122.820 -0.000 0.000 2.498
+ 9 A HA -0.042 4.278 4.320 -0.000 0.000 0.239
+ 9 A C -0.401 177.183 177.584 -0.000 0.000 1.068
+ 9 A CA -0.139 51.898 52.037 -0.000 0.000 0.766
+ 9 A CB 0.269 19.269 19.000 -0.000 0.000 1.003
+ 9 A HN 0.239 8.389 8.150 -0.000 0.000 0.497
+ 10 A N 1.720 124.540 122.820 -0.000 0.000 2.498
+ 10 A HA -0.106 4.214 4.320 -0.000 0.000 0.239
+ 10 A C 0.153 177.737 177.584 -0.000 0.000 1.068
+ 10 A CA -0.262 51.775 52.037 -0.000 0.000 0.766
+ 10 A CB 0.409 19.409 19.000 -0.000 0.000 1.003
+ 10 A HN 0.012 8.162 8.150 -0.000 0.000 0.497
+ 11 A N 1.893 124.713 122.820 -0.000 0.000 2.445
+ 11 A HA -0.101 4.219 4.320 -0.000 0.000 0.242
+ 11 A C 0.155 177.739 177.584 -0.000 0.000 1.075
+ 11 A CA -0.280 51.757 52.037 -0.000 0.000 0.777
+ 11 A CB 0.398 19.398 19.000 -0.000 0.000 1.013
+ 11 A HN 0.019 8.169 8.150 -0.000 0.000 0.493
+ 12 A N 1.622 124.442 122.820 -0.000 0.000 2.498
+ 12 A HA -0.030 4.290 4.320 -0.000 0.000 0.239
+ 12 A C 0.091 177.675 177.584 -0.000 0.000 1.068
+ 12 A CA -0.227 51.810 52.037 -0.000 0.000 0.766
+ 12 A CB 0.430 19.430 19.000 -0.000 0.000 1.003
+ 12 A HN -0.003 8.147 8.150 -0.000 0.000 0.497
+ 13 Q N 1.901 121.701 119.800 -0.000 0.000 2.361
+ 13 Q HA -0.140 4.200 4.340 -0.000 0.000 0.276
+ 13 Q C -0.041 175.959 176.000 -0.000 0.000 1.022
+ 13 Q CA -0.411 55.392 55.803 -0.000 0.000 0.898
+ 13 Q CB 0.819 29.557 28.738 -0.000 0.000 1.246
+ 13 Q HN 0.050 8.320 8.270 -0.000 0.000 0.410
+ 14 A N 3.173 125.993 122.820 -0.000 0.000 2.498
+ 14 A HA -0.045 4.275 4.320 -0.000 0.000 0.239
+ 14 A C -0.117 177.467 177.584 -0.000 0.000 1.068
+ 14 A CA -0.176 51.861 52.037 -0.000 0.000 0.766
+ 14 A CB 0.218 19.218 19.000 -0.000 0.000 1.003
+ 14 A HN 0.268 8.418 8.150 -0.000 0.000 0.497
+ 16 ? N 0.000 9999.000 9999.000 -0.000 0.000 0.000
+ 16 ? HA 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 16 ? CA 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 16 ? CB 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 16 ? HN 0.000 9999.000 9999.000 0.000 0.000 0.000
diff --git a/proteinbenchmark/data/observables/aaqaa3/aaqaa3-PII-protonated_pred.tab b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-PII-protonated_pred.tab
new file mode 100644
index 0000000..bf3aa09
--- /dev/null
+++ b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-PII-protonated_pred.tab
@@ -0,0 +1,114 @@
+REMARK SPARTA+ Protein Chemical Shift Prediction Table
+REMARK
+REMARK All chemical shifts are reported in ppm:
+REMARK
+REMARK SHIFT is the predicted chemical shift.
+REMARK SS_SHIFT is the predicted secondary chemical shift.
+REMARK RC_SHIFT is the random coil chemical shift.
+REMARK HM_SHIFT is the ring current shift; a correction
+REMARK of 0.6 times this value is applied.
+REMARK EF_SHIFT is the adjustment for electric field effect,
+REMARK applied to proton shifts only.
+REMARK SIGMA is the estimated prediction error.
+REMARK
+REMARK Reference:
+REMARK Y. Shen and A. Bax: SPARTA+: a modest improvement in empirical NMR
+REMARK chemical shift prediction by means of an artificial neural network.
+REMARK J. Biomol. NMR 48, 13-22 (2010).
+
+DATA SOURCE aaqaa3-PII-protonated
+
+DATA FIRST_RESID 0
+
+DATA SEQUENCE ?AAQAAAAQA AAAQAA?
+
+VARS RESID RESNAME ATOMNAME SS_SHIFT SHIFT RC_SHIFT HM_SHIFT EF_SHIFT SIGMA
+FORMAT %4d %4s %4s %9.3f %9.3f %9.3f %9.3f %9.3f %9.3f
+
+ 0 ? HA 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 0 ? C 0.000 9999.000 9999.000 -0.000 0.000 0.000
+ 0 ? CA 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 0 ? CB 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 2 A N 0.817 123.637 122.820 -0.000 0.000 2.483
+ 2 A HA 0.099 4.419 4.320 -0.000 0.000 0.238
+ 2 A C -0.030 177.554 177.584 -0.000 0.000 1.070
+ 2 A CA -0.043 51.994 52.037 -0.000 0.000 0.770
+ 2 A CB 0.419 19.419 19.000 -0.000 0.000 1.008
+ 2 A HN 0.033 8.183 8.150 -0.000 0.000 0.497
+ 3 Q N 1.777 121.577 119.800 -0.000 0.000 2.392
+ 3 Q HA -0.132 4.208 4.340 -0.000 0.000 0.262
+ 3 Q C -0.085 175.915 176.000 -0.000 0.000 1.003
+ 3 Q CA -0.419 55.384 55.803 -0.000 0.000 0.888
+ 3 Q CB 0.863 29.601 28.738 -0.000 0.000 1.260
+ 3 Q HN 0.052 8.322 8.270 -0.000 0.000 0.435
+ 4 A N 2.616 125.436 122.820 -0.000 0.000 2.483
+ 4 A HA -0.042 4.278 4.320 -0.000 0.000 0.238
+ 4 A C -0.402 177.182 177.584 -0.000 0.000 1.070
+ 4 A CA -0.143 51.894 52.037 -0.000 0.000 0.770
+ 4 A CB 0.271 19.271 19.000 -0.000 0.000 1.008
+ 4 A HN 0.238 8.388 8.150 -0.000 0.000 0.497
+ 5 A N 1.718 124.538 122.820 -0.000 0.000 2.498
+ 5 A HA -0.106 4.214 4.320 -0.000 0.000 0.239
+ 5 A C 0.154 177.738 177.584 -0.000 0.000 1.068
+ 5 A CA -0.262 51.775 52.037 -0.000 0.000 0.766
+ 5 A CB 0.409 19.409 19.000 -0.000 0.000 1.003
+ 5 A HN 0.012 8.162 8.150 -0.000 0.000 0.497
+ 6 A N 1.896 124.716 122.820 -0.000 0.000 2.483
+ 6 A HA -0.101 4.219 4.320 -0.000 0.000 0.238
+ 6 A C 0.156 177.740 177.584 -0.000 0.000 1.070
+ 6 A CA -0.279 51.758 52.037 -0.000 0.000 0.770
+ 6 A CB 0.397 19.397 19.000 -0.000 0.000 1.008
+ 6 A HN 0.019 8.169 8.150 -0.000 0.000 0.497
+ 7 A N 1.624 124.444 122.820 -0.000 0.000 2.483
+ 7 A HA -0.030 4.290 4.320 -0.000 0.000 0.238
+ 7 A C 0.090 177.674 177.584 -0.000 0.000 1.070
+ 7 A CA -0.227 51.810 52.037 -0.000 0.000 0.770
+ 7 A CB 0.430 19.430 19.000 -0.000 0.000 1.008
+ 7 A HN -0.003 8.147 8.150 -0.000 0.000 0.497
+ 8 Q N 1.901 121.701 119.800 -0.000 0.000 2.392
+ 8 Q HA -0.140 4.200 4.340 -0.000 0.000 0.262
+ 8 Q C -0.047 175.953 176.000 -0.000 0.000 1.003
+ 8 Q CA -0.411 55.392 55.803 -0.000 0.000 0.888
+ 8 Q CB 0.820 29.558 28.738 -0.000 0.000 1.260
+ 8 Q HN 0.051 8.321 8.270 -0.000 0.000 0.435
+ 9 A N 2.639 125.459 122.820 -0.000 0.000 2.498
+ 9 A HA -0.042 4.278 4.320 -0.000 0.000 0.239
+ 9 A C -0.401 177.183 177.584 -0.000 0.000 1.068
+ 9 A CA -0.139 51.898 52.037 -0.000 0.000 0.766
+ 9 A CB 0.269 19.269 19.000 -0.000 0.000 1.003
+ 9 A HN 0.239 8.389 8.150 -0.000 0.000 0.497
+ 10 A N 1.720 124.540 122.820 -0.000 0.000 2.498
+ 10 A HA -0.106 4.214 4.320 -0.000 0.000 0.239
+ 10 A C 0.153 177.737 177.584 -0.000 0.000 1.068
+ 10 A CA -0.262 51.775 52.037 -0.000 0.000 0.766
+ 10 A CB 0.409 19.409 19.000 -0.000 0.000 1.003
+ 10 A HN 0.012 8.162 8.150 -0.000 0.000 0.497
+ 11 A N 1.893 124.713 122.820 -0.000 0.000 2.445
+ 11 A HA -0.101 4.219 4.320 -0.000 0.000 0.242
+ 11 A C 0.155 177.739 177.584 -0.000 0.000 1.075
+ 11 A CA -0.280 51.757 52.037 -0.000 0.000 0.777
+ 11 A CB 0.398 19.398 19.000 -0.000 0.000 1.013
+ 11 A HN 0.019 8.169 8.150 -0.000 0.000 0.493
+ 12 A N 1.622 124.442 122.820 -0.000 0.000 2.498
+ 12 A HA -0.030 4.290 4.320 -0.000 0.000 0.239
+ 12 A C 0.091 177.675 177.584 -0.000 0.000 1.068
+ 12 A CA -0.227 51.810 52.037 -0.000 0.000 0.766
+ 12 A CB 0.430 19.430 19.000 -0.000 0.000 1.003
+ 12 A HN -0.003 8.147 8.150 -0.000 0.000 0.497
+ 13 Q N 1.901 121.701 119.800 -0.000 0.000 2.361
+ 13 Q HA -0.140 4.200 4.340 -0.000 0.000 0.276
+ 13 Q C -0.041 175.959 176.000 -0.000 0.000 1.022
+ 13 Q CA -0.411 55.392 55.803 -0.000 0.000 0.898
+ 13 Q CB 0.819 29.557 28.738 -0.000 0.000 1.246
+ 13 Q HN 0.050 8.320 8.270 -0.000 0.000 0.410
+ 14 A N 3.173 125.993 122.820 -0.000 0.000 2.498
+ 14 A HA -0.045 4.275 4.320 -0.000 0.000 0.239
+ 14 A C -0.117 177.467 177.584 -0.000 0.000 1.068
+ 14 A CA -0.176 51.861 52.037 -0.000 0.000 0.766
+ 14 A CB 0.218 19.218 19.000 -0.000 0.000 1.003
+ 14 A HN 0.268 8.418 8.150 -0.000 0.000 0.497
+ 16 ? N 0.000 9999.000 9999.000 -0.000 0.000 0.000
+ 16 ? HA 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 16 ? CA 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 16 ? CB 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 16 ? HN 0.000 9999.000 9999.000 0.000 0.000 0.000
diff --git a/proteinbenchmark/data/observables/aaqaa3/aaqaa3-PII-protonated_struct.tab b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-PII-protonated_struct.tab
new file mode 100644
index 0000000..97e4d49
--- /dev/null
+++ b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-PII-protonated_struct.tab
@@ -0,0 +1,140 @@
+REMARK SPARTA+ Structural Parameters Table derived from input PDB cooridnates
+REMARK
+REMARK PHI_R1 PSI_R1 CHI1_R1 and CHI2_R1 are the backbone and sidechain
+REMARK torsion angles of the first residue in a triplet.
+REMARK
+REMARK PHI_R2 PSI_R2 CHI1_R2 and CHI2_R2 are the backbone and sidechain
+REMARK torsion angles of the second (central) residue in a triplet.
+REMARK
+REMARK PHI_R3 PSI_R3 CHI1_R3 and CHI2_R3 are the backbone and sidechain
+REMARK torsion angles of the third residue in a triplet.
+REMARK
+REMARK H-Bond Distances are given in Angstroms:
+REMARK
+REMARK HN_HB_DIST_R2 H-bond distance for the HN atom in the central residue.
+REMARK HA_HB_DIST_R2 H-bond distance for the HA atom in the central residue.
+REMARK CO_HB_DIST_R2 H-bond distance for the CO atom in the central residue.
+REMARK
+REMARK HN_S2_R2 is the Bruschweiler structure-based HN order parameter of
+REMARK the central residue. Reference: Zhang FL, Bruschweiler R
+REMARK JACS 124, 12654-12655 (2002)
+REMARK
+REMARK Reference:
+REMARK Y. Shen and A. Bax: SPARTA+: a modest improvement in empirical NMR
+REMARK chemical shift prediction by means of an artificial neural network.
+REMARK J. Biomol. NMR 48, 13-22 (2010).
+REMARK SPARTA+ Structural Parameters Table derived from input PDB cooridnates
+REMARK
+REMARK PHI_R1 PSI_R1 CHI1_R1 and CHI2_R1 are the backbone and sidechain
+REMARK torsion angles of the first residue in a triplet.
+REMARK
+REMARK PHI_R2 PSI_R2 CHI1_R2 and CHI2_R2 are the backbone and sidechain
+REMARK torsion angles of the second (central) residue in a triplet.
+REMARK
+REMARK PHI_R3 PSI_R3 CHI1_R3 and CHI2_R3 are the backbone and sidechain
+REMARK torsion angles of the third residue in a triplet.
+REMARK
+REMARK H-Bond Distances are given in Angstroms:
+REMARK
+REMARK HN_HB_DIST_R2 H-bond distance for the HN atom in the central residue.
+REMARK HA_HB_DIST_R2 H-bond distance for the HA atom in the central residue.
+REMARK CO_HB_DIST_R2 H-bond distance for the CO atom in the central residue.
+REMARK
+REMARK HN_S2_R2 is the Bruschweiler structure-based HN order parameter of
+REMARK the central residue. Reference: Zhang FL, Bruschweiler R
+REMARK JACS 124, 12654-12655 (2002)
+REMARK
+REMARK Reference:
+REMARK Y. Shen and A. Bax: SPARTA+: a modest improvement in empirical NMR
+REMARK chemical shift prediction by means of an artificial neural network.
+REMARK J. Biomol. NMR 48, 13-22 (2010).
+REMARK SPARTA+ Structural Parameters Table derived from input PDB cooridnates
+REMARK
+REMARK PHI_R1 PSI_R1 CHI1_R1 and CHI2_R1 are the backbone and sidechain
+REMARK torsion angles of the first residue in a triplet.
+REMARK
+REMARK PHI_R2 PSI_R2 CHI1_R2 and CHI2_R2 are the backbone and sidechain
+REMARK torsion angles of the second (central) residue in a triplet.
+REMARK
+REMARK PHI_R3 PSI_R3 CHI1_R3 and CHI2_R3 are the backbone and sidechain
+REMARK torsion angles of the third residue in a triplet.
+REMARK
+REMARK H-Bond Distances are given in Angstroms:
+REMARK
+REMARK HN_HB_DIST_R2 H-bond distance for the HN atom in the central residue.
+REMARK HA_HB_DIST_R2 H-bond distance for the HA atom in the central residue.
+REMARK CO_HB_DIST_R2 H-bond distance for the CO atom in the central residue.
+REMARK
+REMARK HN_S2_R2 is the Bruschweiler structure-based HN order parameter of
+REMARK the central residue. Reference: Zhang FL, Bruschweiler R
+REMARK JACS 124, 12654-12655 (2002)
+REMARK
+REMARK Reference:
+REMARK Y. Shen and A. Bax: SPARTA+: a modest improvement in empirical NMR
+REMARK chemical shift prediction by means of an artificial neural network.
+REMARK J. Biomol. NMR 48, 13-22 (2010).
+REMARK SPARTA+ Structural Parameters Table derived from input PDB cooridnates
+REMARK
+REMARK PHI_R1 PSI_R1 CHI1_R1 and CHI2_R1 are the backbone and sidechain
+REMARK torsion angles of the first residue in a triplet.
+REMARK
+REMARK PHI_R2 PSI_R2 CHI1_R2 and CHI2_R2 are the backbone and sidechain
+REMARK torsion angles of the second (central) residue in a triplet.
+REMARK
+REMARK PHI_R3 PSI_R3 CHI1_R3 and CHI2_R3 are the backbone and sidechain
+REMARK torsion angles of the third residue in a triplet.
+REMARK
+REMARK H-Bond Distances are given in Angstroms:
+REMARK
+REMARK HN_HB_DIST_R2 H-bond distance for the HN atom in the central residue.
+REMARK HA_HB_DIST_R2 H-bond distance for the HA atom in the central residue.
+REMARK CO_HB_DIST_R2 H-bond distance for the CO atom in the central residue.
+REMARK
+REMARK HN_S2_R2 is the Bruschweiler structure-based HN order parameter of
+REMARK the central residue. Reference: Zhang FL, Bruschweiler R
+REMARK JACS 124, 12654-12655 (2002)
+REMARK
+REMARK Reference:
+REMARK Y. Shen and A. Bax: SPARTA+: a modest improvement in empirical NMR
+REMARK chemical shift prediction by means of an artificial neural network.
+REMARK J. Biomol. NMR 48, 13-22 (2010).
+
+DATA SOURCE aaqaa3-alpha-protonated
+
+DATA FIRST_RESID 0
+
+DATA SEQUENCE ?AAQAAAAQA AAAQAA?
+DATA SOURCE aaqaa3-beta-protonated
+
+DATA FIRST_RESID 0
+
+DATA SEQUENCE ?AAQAAAAQA AAAQAA?
+DATA SOURCE aaqaa3-extended-protonated
+
+DATA FIRST_RESID 0
+
+DATA SEQUENCE ?AAQAAAAQA AAAQAA?
+DATA SOURCE aaqaa3-PII-protonated
+
+DATA FIRST_RESID 0
+
+DATA SEQUENCE ?AAQAAAAQA AAAQAA?
+
+VARS RESID_R1 RESNAME_R1 PHI_R1 PSI_R1 CHI1_R1 CHI2_R1 RESID_R2 RESNAME_R2 PHI_R2 PSI_R2 CHI1_R2 CHI2_R2 RESID_R3 RESNAME_R3 PHI_R3 PSI_R3 CHI1_R3 CHI2_R3 HN_HB_DIST_R2 HA_HB_DIST_R2 CO_HB_DIST_R2 HN_S2_R2
+FORMAT %4d %s %8.3f %8.3f %8.3f %8.3f %4d %s %8.3f %8.3f %8.3f %8.3f %4d %s %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f
+
+ 0 ? 9999.000 9999.000 9999.000 9999.000 1 A -139.036 144.976 9999.000 9999.000 2 A -64.993 145.004 9999.000 9999.000 0.000 0.000 4.199 0.025
+ 1 A -139.036 144.976 9999.000 9999.000 2 A -64.993 145.004 9999.000 9999.000 3 Q -65.013 145.008 -175.456 177.924 0.000 0.000 4.087 0.198
+ 2 A -64.993 145.004 9999.000 9999.000 3 Q -65.013 145.008 -175.456 177.924 4 A -64.972 145.010 9999.000 9999.000 0.000 4.199 4.200 0.427
+ 3 Q -65.013 145.008 -175.456 177.924 4 A -64.972 145.010 9999.000 9999.000 5 A -64.997 144.962 9999.000 9999.000 0.000 4.087 4.195 0.454
+ 4 A -64.972 145.010 9999.000 9999.000 5 A -64.997 144.962 9999.000 9999.000 6 A -64.958 145.001 9999.000 9999.000 0.000 4.200 4.194 0.502
+ 5 A -64.997 144.962 9999.000 9999.000 6 A -64.958 145.001 9999.000 9999.000 7 A -64.999 145.001 9999.000 9999.000 0.000 4.195 4.199 0.439
+ 6 A -64.958 145.001 9999.000 9999.000 7 A -64.999 145.001 9999.000 9999.000 8 Q -65.031 145.009 -175.474 177.899 0.000 4.194 4.087 0.438
+ 7 A -64.999 145.001 9999.000 9999.000 8 Q -65.031 145.009 -175.474 177.899 9 A -64.993 144.998 9999.000 9999.000 0.000 4.199 4.200 0.441
+ 8 Q -65.031 145.009 -175.474 177.899 9 A -64.993 144.998 9999.000 9999.000 10 A -64.980 144.969 9999.000 9999.000 0.000 4.087 4.194 0.455
+ 9 A -64.993 144.998 9999.000 9999.000 10 A -64.980 144.969 9999.000 9999.000 11 A -65.034 145.011 9999.000 9999.000 0.000 4.200 4.195 0.502
+ 10 A -64.980 144.969 9999.000 9999.000 11 A -65.034 145.011 9999.000 9999.000 12 A -64.959 144.977 9999.000 9999.000 0.000 4.194 4.200 0.439
+ 11 A -65.034 145.011 9999.000 9999.000 12 A -64.959 144.977 9999.000 9999.000 13 Q -64.992 144.997 -175.441 177.952 0.000 4.195 4.088 0.438
+ 12 A -64.959 144.977 9999.000 9999.000 13 Q -64.992 144.997 -175.441 177.952 14 A -64.981 144.995 9999.000 9999.000 0.000 4.200 4.200 0.440
+ 13 Q -64.992 144.997 -175.441 177.952 14 A -64.981 144.995 9999.000 9999.000 15 A -64.999 134.982 9999.000 9999.000 0.000 4.088 0.000 0.451
+ 14 A -64.981 144.995 9999.000 9999.000 15 A -64.999 134.982 9999.000 9999.000 16 ? 9999.000 9999.000 9999.000 9999.000 0.000 4.200 0.000 0.450
diff --git a/proteinbenchmark/data/observables/aaqaa3/aaqaa3-alpha-initial.pdb b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-alpha-initial.pdb
new file mode 100644
index 0000000..e2ba352
--- /dev/null
+++ b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-alpha-initial.pdb
@@ -0,0 +1,181 @@
+TITLE < Chain: id = nres = 17 natoms = 180 >
+ATOM 1 HH33 ACE 0 -6.139 -4.798 7.137 1.00 0.00
+ATOM 2 CH3 ACE 0 -5.438 -4.293 6.634 1.00 0.00
+ATOM 3 HH31 ACE 0 -5.188 -4.819 5.709 1.00 0.00
+ATOM 4 HH32 ACE 0 -5.804 -3.301 6.370 1.00 0.00
+ATOM 5 C ACE 0 -4.174 -4.206 7.496 1.00 0.00
+ATOM 6 O ACE 0 -4.265 -3.913 8.690 1.00 0.00
+ATOM 7 N ALA 1 -2.983 -4.446 6.956 1.00 0.00
+ATOM 8 H ALA 1 -2.911 -4.685 5.979 1.00 0.00
+ATOM 9 CA ALA 1 -1.682 -4.415 7.599 1.00 0.00
+ATOM 10 HA ALA 1 -1.764 -3.806 8.502 1.00 0.00
+ATOM 11 CB ALA 1 -1.308 -5.856 7.969 1.00 0.00
+ATOM 12 HB1 ALA 1 -0.355 -5.899 8.498 1.00 0.00
+ATOM 13 HB2 ALA 1 -2.058 -6.304 8.620 1.00 0.00
+ATOM 14 HB3 ALA 1 -1.219 -6.481 7.079 1.00 0.00
+ATOM 15 C ALA 1 -0.624 -3.760 6.695 1.00 0.00
+ATOM 16 O ALA 1 0.189 -2.958 7.160 1.00 0.00
+ATOM 17 N ALA 2 -0.580 -4.056 5.400 1.00 0.00
+ATOM 18 H ALA 2 -1.235 -4.705 5.013 1.00 0.00
+ATOM 19 CA ALA 2 0.419 -3.438 4.547 1.00 0.00
+ATOM 20 HA ALA 2 1.402 -3.630 4.981 1.00 0.00
+ATOM 21 CB ALA 2 0.319 -4.089 3.162 1.00 0.00
+ATOM 22 HB1 ALA 2 1.076 -3.697 2.481 1.00 0.00
+ATOM 23 HB2 ALA 2 0.465 -5.167 3.221 1.00 0.00
+ATOM 24 HB3 ALA 2 -0.657 -3.905 2.709 1.00 0.00
+ATOM 25 C ALA 2 0.235 -1.912 4.481 1.00 0.00
+ATOM 26 O ALA 2 1.208 -1.159 4.547 1.00 0.00
+ATOM 27 N GLN 3 -0.983 -1.394 4.351 1.00 0.00
+ATOM 28 H GLN 3 -1.779 -1.997 4.296 1.00 0.00
+ATOM 29 CA GLN 3 -1.158 0.055 4.288 1.00 0.00
+ATOM 30 HA GLN 3 -0.502 0.429 3.498 1.00 0.00
+ATOM 31 CB GLN 3 -2.629 0.424 3.959 1.00 0.00
+ATOM 32 HB1 GLN 3 -2.924 -0.089 3.044 1.00 0.00
+ATOM 33 HB2 GLN 3 -3.270 0.033 4.751 1.00 0.00
+ATOM 34 CG GLN 3 -2.912 1.932 3.757 1.00 0.00
+ATOM 35 HG1 GLN 3 -2.696 2.497 4.663 1.00 0.00
+ATOM 36 HG2 GLN 3 -2.262 2.330 2.977 1.00 0.00
+ATOM 37 CD GLN 3 -4.356 2.272 3.385 1.00 0.00
+ATOM 38 OE1 GLN 3 -4.687 3.439 3.221 1.00 0.00
+ATOM 39 NE2 GLN 3 -5.241 1.289 3.256 1.00 0.00
+ATOM 40 HE21 GLN 3 -4.961 0.329 3.372 1.00 0.00
+ATOM 41 HE22 GLN 3 -6.190 1.537 3.025 1.00 0.00
+ATOM 42 C GLN 3 -0.675 0.637 5.630 1.00 0.00
+ATOM 43 O GLN 3 0.014 1.657 5.650 1.00 0.00
+ATOM 44 N ALA 4 -1.003 0.038 6.771 1.00 0.00
+ATOM 45 H ALA 4 -1.563 -0.791 6.757 1.00 0.00
+ATOM 46 CA ALA 4 -0.549 0.586 8.035 1.00 0.00
+ATOM 47 HA ALA 4 -0.866 1.629 8.087 1.00 0.00
+ATOM 48 CB ALA 4 -1.209 -0.221 9.160 1.00 0.00
+ATOM 49 HB1 ALA 4 -0.942 0.170 10.143 1.00 0.00
+ATOM 50 HB2 ALA 4 -2.296 -0.187 9.084 1.00 0.00
+ATOM 51 HB3 ALA 4 -0.902 -1.268 9.127 1.00 0.00
+ATOM 52 C ALA 4 0.986 0.566 8.137 1.00 0.00
+ATOM 53 O ALA 4 1.598 1.536 8.589 1.00 0.00
+ATOM 54 N ALA 5 1.665 -0.505 7.737 1.00 0.00
+ATOM 55 H ALA 5 1.178 -1.297 7.369 1.00 0.00
+ATOM 56 CA ALA 5 3.113 -0.524 7.833 1.00 0.00
+ATOM 57 HA ALA 5 3.388 -0.305 8.867 1.00 0.00
+ATOM 58 CB ALA 5 3.590 -1.931 7.449 1.00 0.00
+ATOM 59 HB1 ALA 5 4.672 -2.026 7.543 1.00 0.00
+ATOM 60 HB2 ALA 5 3.143 -2.688 8.092 1.00 0.00
+ATOM 61 HB3 ALA 5 3.327 -2.168 6.417 1.00 0.00
+ATOM 62 C ALA 5 3.750 0.561 6.948 1.00 0.00
+ATOM 63 O ALA 5 4.685 1.245 7.368 1.00 0.00
+ATOM 64 N ALA 6 3.293 0.768 5.716 1.00 0.00
+ATOM 65 H ALA 6 2.535 0.217 5.366 1.00 0.00
+ATOM 66 CA ALA 6 3.894 1.791 4.881 1.00 0.00
+ATOM 67 HA ALA 6 4.966 1.597 4.825 1.00 0.00
+ATOM 68 CB ALA 6 3.266 1.684 3.485 1.00 0.00
+ATOM 69 HB1 ALA 6 3.708 2.402 2.792 1.00 0.00
+ATOM 70 HB2 ALA 6 3.416 0.692 3.061 1.00 0.00
+ATOM 71 HB3 ALA 6 2.193 1.877 3.519 1.00 0.00
+ATOM 72 C ALA 6 3.709 3.192 5.489 1.00 0.00
+ATOM 73 O ALA 6 4.639 4.001 5.495 1.00 0.00
+ATOM 74 N ALA 7 2.538 3.541 6.013 1.00 0.00
+ATOM 75 H ALA 7 1.777 2.892 6.013 1.00 0.00
+ATOM 76 CA ALA 7 2.364 4.863 6.587 1.00 0.00
+ATOM 77 HA ALA 7 2.639 5.600 5.830 1.00 0.00
+ATOM 78 CB ALA 7 0.885 5.020 6.961 1.00 0.00
+ATOM 79 HB1 ALA 7 0.676 6.014 7.360 1.00 0.00
+ATOM 80 HB2 ALA 7 0.241 4.880 6.093 1.00 0.00
+ATOM 81 HB3 ALA 7 0.590 4.293 7.719 1.00 0.00
+ATOM 82 C ALA 7 3.290 5.077 7.796 1.00 0.00
+ATOM 83 O ALA 7 3.898 6.139 7.941 1.00 0.00
+ATOM 84 N GLN 8 3.439 4.112 8.699 1.00 0.00
+ATOM 85 H GLN 8 2.950 3.246 8.591 1.00 0.00
+ATOM 86 CA GLN 8 4.318 4.316 9.848 1.00 0.00
+ATOM 87 HA GLN 8 4.009 5.244 10.335 1.00 0.00
+ATOM 88 CB GLN 8 4.202 3.138 10.852 1.00 0.00
+ATOM 89 HB1 GLN 8 3.155 3.009 11.124 1.00 0.00
+ATOM 90 HB2 GLN 8 4.504 2.220 10.346 1.00 0.00
+ATOM 91 CG GLN 8 5.007 3.297 12.165 1.00 0.00
+ATOM 92 HG1 GLN 8 6.075 3.367 11.965 1.00 0.00
+ATOM 93 HG2 GLN 8 4.720 4.222 12.667 1.00 0.00
+ATOM 94 CD GLN 8 4.842 2.150 13.163 1.00 0.00
+ATOM 95 OE1 GLN 8 5.450 2.171 14.225 1.00 0.00
+ATOM 96 NE2 GLN 8 4.044 1.133 12.856 1.00 0.00
+ATOM 97 HE21 GLN 8 3.529 1.128 11.991 1.00 0.00
+ATOM 98 HE22 GLN 8 3.960 0.381 13.522 1.00 0.00
+ATOM 99 C GLN 8 5.747 4.509 9.307 1.00 0.00
+ATOM 100 O GLN 8 6.474 5.386 9.776 1.00 0.00
+ATOM 101 N ALA 9 6.201 3.728 8.331 1.00 0.00
+ATOM 102 H ALA 9 5.613 3.015 7.947 1.00 0.00
+ATOM 103 CA ALA 9 7.547 3.911 7.821 1.00 0.00
+ATOM 104 HA ALA 9 8.240 3.852 8.663 1.00 0.00
+ATOM 105 CB ALA 9 7.829 2.777 6.827 1.00 0.00
+ATOM 106 HB1 ALA 9 8.847 2.831 6.437 1.00 0.00
+ATOM 107 HB2 ALA 9 7.716 1.802 7.299 1.00 0.00
+ATOM 108 HB3 ALA 9 7.148 2.820 5.976 1.00 0.00
+ATOM 109 C ALA 9 7.722 5.297 7.177 1.00 0.00
+ATOM 110 O ALA 9 8.736 5.964 7.388 1.00 0.00
+ATOM 111 N ALA 10 6.773 5.787 6.385 1.00 0.00
+ATOM 112 H ALA 10 5.945 5.254 6.207 1.00 0.00
+ATOM 113 CA ALA 10 6.937 7.095 5.777 1.00 0.00
+ATOM 114 HA ALA 10 7.882 7.098 5.231 1.00 0.00
+ATOM 115 CB ALA 10 5.768 7.311 4.808 1.00 0.00
+ATOM 116 HB1 ALA 10 5.855 8.263 4.282 1.00 0.00
+ATOM 117 HB2 ALA 10 5.733 6.528 4.052 1.00 0.00
+ATOM 118 HB3 ALA 10 4.813 7.313 5.336 1.00 0.00
+ATOM 119 C ALA 10 7.015 8.203 6.841 1.00 0.00
+ATOM 120 O ALA 10 7.845 9.109 6.744 1.00 0.00
+ATOM 121 N ALA 11 6.183 8.189 7.878 1.00 0.00
+ATOM 122 H ALA 11 5.506 7.458 7.966 1.00 0.00
+ATOM 123 CA ALA 11 6.256 9.235 8.882 1.00 0.00
+ATOM 124 HA ALA 11 6.165 10.198 8.376 1.00 0.00
+ATOM 125 CB ALA 11 5.083 9.037 9.851 1.00 0.00
+ATOM 126 HB1 ALA 11 5.055 9.820 10.610 1.00 0.00
+ATOM 127 HB2 ALA 11 4.129 9.062 9.326 1.00 0.00
+ATOM 128 HB3 ALA 11 5.157 8.079 10.369 1.00 0.00
+ATOM 129 C ALA 11 7.612 9.222 9.609 1.00 0.00
+ATOM 130 O ALA 11 8.208 10.275 9.844 1.00 0.00
+ATOM 131 N ALA 12 8.151 8.068 9.990 1.00 0.00
+ATOM 132 H ALA 12 7.676 7.208 9.804 1.00 0.00
+ATOM 133 CA ALA 12 9.430 8.056 10.676 1.00 0.00
+ATOM 134 HA ALA 12 9.354 8.708 11.548 1.00 0.00
+ATOM 135 CB ALA 12 9.710 6.614 11.120 1.00 0.00
+ATOM 136 HB1 ALA 12 10.641 6.543 11.683 1.00 0.00
+ATOM 137 HB2 ALA 12 8.915 6.239 11.763 1.00 0.00
+ATOM 138 HB3 ALA 12 9.792 5.946 10.262 1.00 0.00
+ATOM 139 C ALA 12 10.553 8.610 9.782 1.00 0.00
+ATOM 140 O ALA 12 11.394 9.385 10.239 1.00 0.00
+ATOM 141 N GLN 13 10.622 8.253 8.503 1.00 0.00
+ATOM 142 H GLN 13 9.944 7.625 8.122 1.00 0.00
+ATOM 143 CA GLN 13 11.688 8.780 7.654 1.00 0.00
+ATOM 144 HA GLN 13 12.637 8.574 8.156 1.00 0.00
+ATOM 145 CB GLN 13 11.677 8.097 6.260 1.00 0.00
+ATOM 146 HB1 GLN 13 11.725 7.017 6.397 1.00 0.00
+ATOM 147 HB2 GLN 13 10.720 8.304 5.780 1.00 0.00
+ATOM 148 CG GLN 13 12.833 8.497 5.311 1.00 0.00
+ATOM 149 HG1 GLN 13 12.804 9.560 5.082 1.00 0.00
+ATOM 150 HG2 GLN 13 13.793 8.305 5.794 1.00 0.00
+ATOM 151 CD GLN 13 12.835 7.777 3.961 1.00 0.00
+ATOM 152 OE1 GLN 13 13.698 8.034 3.132 1.00 0.00
+ATOM 153 NE2 GLN 13 11.886 6.884 3.702 1.00 0.00
+ATOM 154 HE21 GLN 13 11.190 6.659 4.393 1.00 0.00
+ATOM 155 HE22 GLN 13 11.898 6.432 2.801 1.00 0.00
+ATOM 156 C GLN 13 11.506 10.308 7.579 1.00 0.00
+ATOM 157 O GLN 13 12.482 11.053 7.669 1.00 0.00
+ATOM 158 N ALA 14 10.292 10.826 7.415 1.00 0.00
+ATOM 159 H ALA 14 9.497 10.223 7.341 1.00 0.00
+ATOM 160 CA ALA 14 10.121 12.265 7.345 1.00 0.00
+ATOM 161 HA ALA 14 10.770 12.646 6.554 1.00 0.00
+ATOM 162 CB ALA 14 8.653 12.545 6.999 1.00 0.00
+ATOM 163 HB1 ALA 14 8.465 13.614 6.888 1.00 0.00
+ATOM 164 HB2 ALA 14 8.370 12.069 6.062 1.00 0.00
+ATOM 165 HB3 ALA 14 7.986 12.174 7.780 1.00 0.00
+ATOM 166 C ALA 14 10.544 12.947 8.657 1.00 0.00
+ATOM 167 O ALA 14 11.209 13.985 8.639 1.00 0.00
+ATOM 168 N ALA 15 10.192 12.417 9.825 1.00 0.00
+ATOM 169 H ALA 15 9.653 11.576 9.850 1.00 0.00
+ATOM 170 CA ALA 15 10.591 13.061 11.063 1.00 0.00
+ATOM 171 HA ALA 15 10.248 14.096 11.034 1.00 0.00
+ATOM 172 CB ALA 15 9.913 12.314 12.218 1.00 0.00
+ATOM 173 HB1 ALA 15 10.138 12.776 13.181 1.00 0.00
+ATOM 174 HB2 ALA 15 8.829 12.314 12.106 1.00 0.00
+ATOM 175 HB3 ALA 15 10.246 11.276 12.267 1.00 0.00
+ATOM 176 C ALA 15 12.122 13.087 11.215 1.00 0.00
+ATOM 177 O ALA 15 12.794 12.084 10.971 1.00 0.00
+ATOM 178 N NH2 16 12.731 14.200 11.614 1.00 0.00
+ATOM 179 HN1 NH2 16 12.195 15.020 11.815 1.00 0.00
+ATOM 180 HN2 NH2 16 13.726 14.217 11.713 1.00 0.00
diff --git a/proteinbenchmark/data/observables/aaqaa3/aaqaa3-alpha-protonated.pdb b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-alpha-protonated.pdb
new file mode 100644
index 0000000..0e9b95f
--- /dev/null
+++ b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-alpha-protonated.pdb
@@ -0,0 +1,182 @@
+ATOM 1 HH33 ACE A 0 -6.139 -4.798 7.137 1.00 0.00
+ATOM 2 CH3 ACE A 0 -5.438 -4.293 6.634 1.00 0.00
+ATOM 3 HH31 ACE A 0 -5.188 -4.819 5.709 1.00 0.00
+ATOM 4 HH32 ACE A 0 -5.804 -3.301 6.370 1.00 0.00
+ATOM 5 C ACE A 0 -4.174 -4.206 7.496 1.00 0.00
+ATOM 6 O ACE A 0 -4.265 -3.913 8.690 1.00 0.00
+ATOM 7 N ALA A 1 -2.983 -4.446 6.956 1.00 0.00
+ATOM 8 CA ALA A 1 -1.682 -4.415 7.599 1.00 0.00
+ATOM 9 CB ALA A 1 -1.308 -5.856 7.969 1.00 0.00
+ATOM 10 C ALA A 1 -0.624 -3.760 6.695 1.00 0.00
+ATOM 11 O ALA A 1 0.189 -2.958 7.160 1.00 0.00
+ATOM 12 H ALA A 1 -3.168 -4.083 6.031 1.00 0.00 H
+ATOM 13 HA ALA A 1 -1.745 -3.875 8.449 1.00 0.00 H
+ATOM 14 HB1 ALA A 1 -0.669 -6.214 7.291 1.00 0.00 H
+ATOM 15 HB2 ALA A 1 -0.882 -5.863 8.871 1.00 0.00 H
+ATOM 16 HB3 ALA A 1 -2.133 -6.416 7.982 1.00 0.00 H
+ATOM 17 N ALA A 2 -0.580 -4.056 5.400 1.00 0.00
+ATOM 18 CA ALA A 2 0.419 -3.438 4.547 1.00 0.00
+ATOM 19 CB ALA A 2 0.319 -4.089 3.162 1.00 0.00
+ATOM 20 C ALA A 2 0.235 -1.912 4.481 1.00 0.00
+ATOM 21 O ALA A 2 1.208 -1.159 4.547 1.00 0.00
+ATOM 22 H ALA A 2 -1.285 -4.730 5.075 1.00 0.00 H
+ATOM 23 HA ALA A 2 1.336 -3.627 4.921 1.00 0.00 H
+ATOM 24 HB1 ALA A 2 0.944 -3.627 2.536 1.00 0.00 H
+ATOM 25 HB2 ALA A 2 0.565 -5.053 3.234 1.00 0.00 H
+ATOM 26 HB3 ALA A 2 -0.617 -4.005 2.826 1.00 0.00 H
+ATOM 27 N GLN A 3 -0.983 -1.394 4.351 1.00 0.00
+ATOM 28 CA GLN A 3 -1.158 0.055 4.288 1.00 0.00
+ATOM 29 CB GLN A 3 -2.629 0.424 3.959 1.00 0.00
+ATOM 30 CG GLN A 3 -2.912 1.932 3.757 1.00 0.00
+ATOM 31 CD GLN A 3 -4.356 2.272 3.385 1.00 0.00
+ATOM 32 C GLN A 3 -0.675 0.637 5.630 1.00 0.00
+ATOM 33 O GLN A 3 0.014 1.657 5.650 1.00 0.00
+ATOM 34 H GLN A 3 -1.753 -2.071 4.301 1.00 0.00 H
+ATOM 35 HA GLN A 3 -0.566 0.411 3.577 1.00 0.00 H
+ATOM 36 HB2 GLN A 3 -2.895 -0.051 3.116 1.00 0.00 H
+ATOM 37 HB3 GLN A 3 -3.213 0.103 4.710 1.00 0.00 H
+ATOM 38 HG2 GLN A 3 -2.682 2.409 4.611 1.00 0.00 H
+ATOM 39 HG3 GLN A 3 -2.306 2.268 3.028 1.00 0.00 H
+ATOM 40 OE1 GLN A 3 -4.687 3.439 3.221 1.00 0.00 O
+ATOM 41 NE2 GLN A 3 -5.241 1.289 3.256 1.00 0.00 N
+ATOM 42 HE21 GLN A 3 -6.193 1.457 3.030 1.00 0.00 H
+ATOM 43 HE22 GLN A 3 -4.907 0.324 3.399 1.00 0.00 H
+ATOM 44 N ALA A 4 -1.003 0.038 6.771 1.00 0.00
+ATOM 45 CA ALA A 4 -0.549 0.586 8.035 1.00 0.00
+ATOM 46 CB ALA A 4 -1.209 -0.221 9.160 1.00 0.00
+ATOM 47 C ALA A 4 0.986 0.566 8.137 1.00 0.00
+ATOM 48 O ALA A 4 1.598 1.536 8.589 1.00 0.00
+ATOM 49 H ALA A 4 -1.580 -0.808 6.677 1.00 0.00 H
+ATOM 50 HA ALA A 4 -0.855 1.544 8.110 1.00 0.00 H
+ATOM 51 HB1 ALA A 4 -1.568 -1.073 8.786 1.00 0.00 H
+ATOM 52 HB2 ALA A 4 -0.529 -0.422 9.862 1.00 0.00 H
+ATOM 53 HB3 ALA A 4 -1.953 0.314 9.555 1.00 0.00 H
+ATOM 54 N ALA A 5 1.665 -0.505 7.737 1.00 0.00
+ATOM 55 CA ALA A 5 3.113 -0.524 7.833 1.00 0.00
+ATOM 56 CB ALA A 5 3.590 -1.931 7.449 1.00 0.00
+ATOM 57 C ALA A 5 3.750 0.561 6.948 1.00 0.00
+ATOM 58 O ALA A 5 4.685 1.245 7.368 1.00 0.00
+ATOM 59 H ALA A 5 1.096 -1.279 7.372 1.00 0.00 H
+ATOM 60 HA ALA A 5 3.384 -0.347 8.789 1.00 0.00 H
+ATOM 61 HB1 ALA A 5 3.938 -1.916 6.514 1.00 0.00 H
+ATOM 62 HB2 ALA A 5 4.314 -2.214 8.074 1.00 0.00 H
+ATOM 63 HB3 ALA A 5 2.823 -2.566 7.513 1.00 0.00 H
+ATOM 64 N ALA A 6 3.293 0.768 5.716 1.00 0.00
+ATOM 65 CA ALA A 6 3.894 1.791 4.881 1.00 0.00
+ATOM 66 CB ALA A 6 3.266 1.684 3.485 1.00 0.00
+ATOM 67 C ALA A 6 3.709 3.192 5.489 1.00 0.00
+ATOM 68 O ALA A 6 4.639 4.001 5.495 1.00 0.00
+ATOM 69 H ALA A 6 2.513 0.164 5.426 1.00 0.00 H
+ATOM 70 HA ALA A 6 4.884 1.614 4.800 1.00 0.00 H
+ATOM 71 HB1 ALA A 6 3.760 2.281 2.857 1.00 0.00 H
+ATOM 72 HB2 ALA A 6 3.326 0.739 3.170 1.00 0.00 H
+ATOM 73 HB3 ALA A 6 2.309 1.963 3.533 1.00 0.00 H
+ATOM 74 N ALA A 7 2.538 3.541 6.013 1.00 0.00
+ATOM 75 CA ALA A 7 2.364 4.863 6.587 1.00 0.00
+ATOM 76 CB ALA A 7 0.885 5.020 6.961 1.00 0.00
+ATOM 77 C ALA A 7 3.290 5.077 7.796 1.00 0.00
+ATOM 78 O ALA A 7 3.898 6.139 7.941 1.00 0.00
+ATOM 79 H ALA A 7 1.804 2.822 5.975 1.00 0.00 H
+ATOM 80 HA ALA A 7 2.591 5.558 5.892 1.00 0.00 H
+ATOM 81 HB1 ALA A 7 0.335 5.031 6.129 1.00 0.00 H
+ATOM 82 HB2 ALA A 7 0.609 4.253 7.537 1.00 0.00 H
+ATOM 83 HB3 ALA A 7 0.761 5.876 7.458 1.00 0.00 H
+ATOM 84 N GLN A 8 3.439 4.112 8.699 1.00 0.00
+ATOM 85 CA GLN A 8 4.318 4.316 9.848 1.00 0.00
+ATOM 86 CB GLN A 8 4.202 3.138 10.852 1.00 0.00
+ATOM 87 CG GLN A 8 5.007 3.297 12.165 1.00 0.00
+ATOM 88 CD GLN A 8 4.842 2.150 13.163 1.00 0.00
+ATOM 89 C GLN A 8 5.747 4.509 9.307 1.00 0.00
+ATOM 90 O GLN A 8 6.474 5.386 9.776 1.00 0.00
+ATOM 91 H GLN A 8 2.907 3.252 8.525 1.00 0.00 H
+ATOM 92 HA GLN A 8 4.053 5.158 10.299 1.00 0.00 H
+ATOM 93 HB2 GLN A 8 3.236 3.025 11.099 1.00 0.00 H
+ATOM 94 HB3 GLN A 8 4.522 2.301 10.399 1.00 0.00 H
+ATOM 95 HG2 GLN A 8 5.980 3.375 11.926 1.00 0.00 H
+ATOM 96 HG3 GLN A 8 4.715 4.151 12.607 1.00 0.00 H
+ATOM 97 OE1 GLN A 8 5.450 2.171 14.225 1.00 0.00 O
+ATOM 98 NE2 GLN A 8 4.044 1.133 12.856 1.00 0.00 N
+ATOM 99 HE21 GLN A 8 3.913 0.358 13.462 1.00 0.00 H
+ATOM 100 HE22 GLN A 8 3.551 1.169 11.951 1.00 0.00 H
+ATOM 101 N ALA A 9 6.201 3.728 8.331 1.00 0.00
+ATOM 102 CA ALA A 9 7.547 3.911 7.821 1.00 0.00
+ATOM 103 CB ALA A 9 7.829 2.777 6.827 1.00 0.00
+ATOM 104 C ALA A 9 7.722 5.297 7.177 1.00 0.00
+ATOM 105 O ALA A 9 8.736 5.964 7.388 1.00 0.00
+ATOM 106 H ALA A 9 5.541 3.018 7.989 1.00 0.00 H
+ATOM 107 HA ALA A 9 8.203 3.835 8.583 1.00 0.00 H
+ATOM 108 HB1 ALA A 9 8.223 3.161 5.995 1.00 0.00 H
+ATOM 109 HB2 ALA A 9 8.470 2.132 7.238 1.00 0.00 H
+ATOM 110 HB3 ALA A 9 6.974 2.310 6.611 1.00 0.00 H
+ATOM 111 N ALA A 10 6.773 5.787 6.385 1.00 0.00
+ATOM 112 CA ALA A 10 6.937 7.095 5.777 1.00 0.00
+ATOM 113 CB ALA A 10 5.768 7.311 4.808 1.00 0.00
+ATOM 114 C ALA A 10 7.015 8.203 6.841 1.00 0.00
+ATOM 115 O ALA A 10 7.845 9.109 6.744 1.00 0.00
+ATOM 116 H ALA A 10 5.952 5.182 6.250 1.00 0.00 H
+ATOM 117 HA ALA A 10 7.795 7.109 5.247 1.00 0.00 H
+ATOM 118 HB1 ALA A 10 5.689 8.284 4.600 1.00 0.00 H
+ATOM 119 HB2 ALA A 10 5.939 6.800 3.968 1.00 0.00 H
+ATOM 120 HB3 ALA A 10 4.925 6.988 5.233 1.00 0.00 H
+ATOM 121 N ALA A 11 6.183 8.189 7.878 1.00 0.00
+ATOM 122 CA ALA A 11 6.256 9.235 8.882 1.00 0.00
+ATOM 123 CB ALA A 11 5.083 9.037 9.851 1.00 0.00
+ATOM 124 C ALA A 11 7.612 9.222 9.609 1.00 0.00
+ATOM 125 O ALA A 11 8.208 10.275 9.844 1.00 0.00
+ATOM 126 H ALA A 11 5.516 7.407 7.901 1.00 0.00 H
+ATOM 127 HA ALA A 11 6.150 10.132 8.434 1.00 0.00 H
+ATOM 128 HB1 ALA A 11 4.319 9.609 9.562 1.00 0.00 H
+ATOM 129 HB2 ALA A 11 4.808 8.078 9.842 1.00 0.00 H
+ATOM 130 HB3 ALA A 11 5.370 9.297 10.771 1.00 0.00 H
+ATOM 131 N ALA A 12 8.151 8.068 9.990 1.00 0.00
+ATOM 132 CA ALA A 12 9.430 8.056 10.676 1.00 0.00
+ATOM 133 CB ALA A 12 9.710 6.614 11.120 1.00 0.00
+ATOM 134 C ALA A 12 10.553 8.610 9.782 1.00 0.00
+ATOM 135 O ALA A 12 11.394 9.385 10.239 1.00 0.00
+ATOM 136 H ALA A 12 7.604 7.227 9.764 1.00 0.00 H
+ATOM 137 HA ALA A 12 9.370 8.637 11.499 1.00 0.00 H
+ATOM 138 HB1 ALA A 12 9.094 6.376 11.868 1.00 0.00 H
+ATOM 139 HB2 ALA A 12 9.559 5.998 10.350 1.00 0.00 H
+ATOM 140 HB3 ALA A 12 10.656 6.543 11.427 1.00 0.00 H
+ATOM 141 N GLN A 13 10.622 8.253 8.503 1.00 0.00
+ATOM 142 CA GLN A 13 11.688 8.780 7.654 1.00 0.00
+ATOM 143 CB GLN A 13 11.677 8.097 6.260 1.00 0.00
+ATOM 144 CG GLN A 13 12.833 8.497 5.311 1.00 0.00
+ATOM 145 CD GLN A 13 12.835 7.777 3.961 1.00 0.00
+ATOM 146 C GLN A 13 11.506 10.308 7.579 1.00 0.00
+ATOM 147 O GLN A 13 12.482 11.053 7.669 1.00 0.00
+ATOM 148 H GLN A 13 9.894 7.605 8.181 1.00 0.00 H
+ATOM 149 HA GLN A 13 12.557 8.604 8.097 1.00 0.00 H
+ATOM 150 HB2 GLN A 13 11.722 7.104 6.392 1.00 0.00 H
+ATOM 151 HB3 GLN A 13 10.814 8.325 5.801 1.00 0.00 H
+ATOM 152 HG2 GLN A 13 12.771 9.486 5.145 1.00 0.00 H
+ATOM 153 HG3 GLN A 13 13.701 8.302 5.779 1.00 0.00 H
+ATOM 154 OE1 GLN A 13 13.698 8.034 3.132 1.00 0.00 O
+ATOM 155 NE2 GLN A 13 11.886 6.884 3.702 1.00 0.00 N
+ATOM 156 HE21 GLN A 13 11.834 6.400 2.837 1.00 0.00 H
+ATOM 157 HE22 GLN A 13 11.188 6.701 4.439 1.00 0.00 H
+ATOM 158 N ALA A 14 10.292 10.826 7.415 1.00 0.00
+ATOM 159 CA ALA A 14 10.121 12.265 7.345 1.00 0.00
+ATOM 160 CB ALA A 14 8.653 12.545 6.999 1.00 0.00
+ATOM 161 C ALA A 14 10.544 12.947 8.657 1.00 0.00
+ATOM 162 O ALA A 14 11.209 13.985 8.639 1.00 0.00
+ATOM 163 H ALA A 14 9.525 10.145 7.346 1.00 0.00 H
+ATOM 164 HA ALA A 14 10.697 12.631 6.602 1.00 0.00 H
+ATOM 165 HB1 ALA A 14 8.259 13.139 7.697 1.00 0.00 H
+ATOM 166 HB2 ALA A 14 8.605 12.993 6.109 1.00 0.00 H
+ATOM 167 HB3 ALA A 14 8.153 11.682 6.969 1.00 0.00 H
+ATOM 168 N ALA A 15 10.192 12.417 9.825 1.00 0.00
+ATOM 169 CA ALA A 15 10.591 13.061 11.063 1.00 0.00
+ATOM 170 CB ALA A 15 9.913 12.314 12.218 1.00 0.00
+ATOM 171 C ALA A 15 12.122 13.087 11.215 1.00 0.00
+ATOM 172 O ALA A 15 12.794 12.084 10.971 1.00 0.00
+ATOM 173 H ALA A 15 9.639 11.552 9.771 1.00 0.00 H
+ATOM 174 HA ALA A 15 10.261 14.014 11.062 1.00 0.00 H
+ATOM 175 HB1 ALA A 15 10.611 11.880 12.784 1.00 0.00 H
+ATOM 176 HB2 ALA A 15 9.390 12.963 12.767 1.00 0.00 H
+ATOM 177 HB3 ALA A 15 9.302 11.619 11.846 1.00 0.00 H
+ATOM 178 N NH2 A 16 12.731 14.200 11.614 1.00 0.00
+ATOM 179 HN1 NH2 A 16 12.195 15.020 11.815 1.00 0.00
+ATOM 180 HN2 NH2 A 16 13.726 14.217 11.713 1.00 0.00
+TER
+END
\ No newline at end of file
diff --git a/proteinbenchmark/data/observables/aaqaa3/aaqaa3-alpha-protonated.pdb.cs b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-alpha-protonated.pdb.cs
new file mode 100644
index 0000000..53d8531
--- /dev/null
+++ b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-alpha-protonated.pdb.cs
@@ -0,0 +1,151 @@
+NUM,RES,ATOMNAME,SHIFT
+1,A,C,178.2764
+1,A,CA,54.6150
+1,A,CB,19.0302
+1,A,H,8.3240
+1,A,HA,4.2415
+1,A,HB,1.4136
+1,A,HB2,1.7327
+1,A,HB3,1.5492
+1,A,N,124.0719
+2,A,C,179.5608
+2,A,CA,54.6817
+2,A,CB,18.6426
+2,A,H,8.3157
+2,A,HA,4.1061
+2,A,HB,1.4431
+2,A,HB2,1.7247
+2,A,HB3,1.5513
+2,A,N,121.4007
+3,Q,C,178.0077
+3,Q,CA,58.9437
+3,Q,CB,28.5291
+3,Q,CD,179.7902
+3,Q,CG,34.2645
+3,Q,H,7.7366
+3,Q,HA,4.0338
+3,Q,HB2,1.9661
+3,Q,HB3,2.1315
+3,Q,HE21,7.4683
+3,Q,HE22,6.9817
+3,Q,HG2,2.4187
+3,Q,HG3,2.3743
+3,Q,N,117.7885
+4,A,C,179.8554
+4,A,CA,55.0145
+4,A,CB,18.2228
+4,A,H,7.6522
+4,A,HA,4.0912
+4,A,HB,1.4413
+4,A,HB2,1.7780
+4,A,HB3,1.5272
+4,A,N,121.4464
+5,A,C,179.6231
+5,A,CA,54.6295
+5,A,CB,18.1907
+5,A,H,8.1558
+5,A,HA,4.1479
+5,A,HB,1.4600
+5,A,HB2,1.7494
+5,A,HB3,1.5965
+5,A,N,120.6378
+6,A,C,179.9898
+6,A,CA,55.1863
+6,A,CB,18.3743
+6,A,H,8.0033
+6,A,HA,4.0955
+6,A,HB,1.4412
+6,A,HB2,1.7030
+6,A,HB3,1.4201
+6,A,N,120.9539
+7,A,C,179.9331
+7,A,CA,55.0228
+7,A,CB,18.1836
+7,A,H,7.6498
+7,A,HA,4.1029
+7,A,HB,1.4993
+7,A,HB2,1.8029
+7,A,HB3,1.5949
+7,A,N,120.9109
+8,Q,C,178.1360
+8,Q,CA,58.9707
+8,Q,CB,28.4561
+8,Q,CD,179.7411
+8,Q,CG,34.1724
+8,Q,H,7.8249
+8,Q,HA,4.0409
+8,Q,HB2,1.9867
+8,Q,HB3,2.1296
+8,Q,HE21,7.4553
+8,Q,HE22,6.9988
+8,Q,HG2,2.4060
+8,Q,HG3,2.3931
+8,Q,N,117.7643
+9,A,C,179.4932
+9,A,CA,55.1230
+9,A,CB,18.1578
+9,A,H,7.9991
+9,A,HA,4.0716
+9,A,HB,1.4565
+9,A,HB2,1.8276
+9,A,HB3,1.5254
+9,A,N,121.3254
+10,A,C,179.6180
+10,A,CA,55.2088
+10,A,CB,18.1200
+10,A,H,8.1312
+10,A,HA,4.0736
+10,A,HB,1.4566
+10,A,HB2,1.7282
+10,A,HB3,1.4371
+10,A,N,120.5697
+11,A,C,180.0429
+11,A,CA,55.0777
+11,A,CB,18.3117
+11,A,H,8.0171
+11,A,HA,4.1490
+11,A,HB,1.4678
+11,A,HB2,1.7145
+11,A,HB3,1.4883
+11,A,N,120.8786
+12,A,C,180.0147
+12,A,CA,54.7364
+12,A,CB,18.1542
+12,A,H,7.6810
+12,A,HA,4.1266
+12,A,HB,1.4539
+12,A,HB2,1.7667
+12,A,HB3,1.6911
+12,A,N,120.6034
+13,Q,C,178.2669
+13,Q,CA,58.6474
+13,Q,CB,28.4963
+13,Q,CD,179.8184
+13,Q,CG,34.0365
+13,Q,H,7.6907
+13,Q,HA,4.0266
+13,Q,HB2,2.0857
+13,Q,HB3,2.0420
+13,Q,HE21,7.3064
+13,Q,HE22,6.9052
+13,Q,HG2,2.3783
+13,Q,HG3,2.3765
+13,Q,N,117.7800
+14,A,C,178.7382
+14,A,CA,54.3606
+14,A,CB,18.6205
+14,A,H,7.8747
+14,A,HA,4.1403
+14,A,HB,1.4634
+14,A,HB2,1.6744
+14,A,HB3,1.6343
+14,A,N,121.4970
+15,A,C,178.6609
+15,A,CA,53.7688
+15,A,CB,18.9988
+15,A,H,7.9746
+15,A,HA,4.1637
+15,A,HB,1.4219
+15,A,HB2,1.7189
+15,A,HB3,1.6463
+15,A,N,122.7496
diff --git a/proteinbenchmark/data/observables/aaqaa3/aaqaa3-alpha-protonated.pdb.shifty b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-alpha-protonated.pdb.shifty
new file mode 100644
index 0000000..e69de29
diff --git a/proteinbenchmark/data/observables/aaqaa3/aaqaa3-alpha-protonated.pdb.sxp b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-alpha-protonated.pdb.sxp
new file mode 100644
index 0000000..bb903bc
--- /dev/null
+++ b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-alpha-protonated.pdb.sxp
@@ -0,0 +1,151 @@
+NUM,RES,IUPAC,ATOM,PRED_CS
+1,ALA,A,H,8.3240
+1,ALA,A,HA,4.2415
+1,ALA,A,C,178.2764
+1,ALA,A,CA,54.6150
+1,ALA,A,CB,19.0302
+1,ALA,A,N,124.0719
+1,ALA,A,HB,1.4136
+1,ALA,A,HB2,1.7327
+1,ALA,A,HB3,1.5492
+2,ALA,A,H,8.3157
+2,ALA,A,HA,4.1061
+2,ALA,A,C,179.5608
+2,ALA,A,CA,54.6817
+2,ALA,A,CB,18.6426
+2,ALA,A,N,121.4007
+2,ALA,A,HB,1.4431
+2,ALA,A,HB2,1.7247
+2,ALA,A,HB3,1.5513
+3,GLN,Q,H,7.7366
+3,GLN,Q,HA,4.0338
+3,GLN,Q,C,178.0077
+3,GLN,Q,CA,58.9437
+3,GLN,Q,CB,28.5291
+3,GLN,Q,N,117.7885
+3,GLN,Q,CD,179.7902
+3,GLN,Q,CG,34.2645
+3,GLN,Q,HB2,1.9661
+3,GLN,Q,HB3,2.1315
+3,GLN,Q,HE21,7.4683
+3,GLN,Q,HE22,6.9817
+3,GLN,Q,HG2,2.4187
+3,GLN,Q,HG3,2.3743
+4,ALA,A,H,7.6522
+4,ALA,A,HA,4.0912
+4,ALA,A,C,179.8554
+4,ALA,A,CA,55.0145
+4,ALA,A,CB,18.2228
+4,ALA,A,N,121.4464
+4,ALA,A,HB,1.4413
+4,ALA,A,HB2,1.7780
+4,ALA,A,HB3,1.5272
+5,ALA,A,H,8.1558
+5,ALA,A,HA,4.1479
+5,ALA,A,C,179.6231
+5,ALA,A,CA,54.6295
+5,ALA,A,CB,18.1907
+5,ALA,A,N,120.6378
+5,ALA,A,HB,1.4600
+5,ALA,A,HB2,1.7494
+5,ALA,A,HB3,1.5965
+6,ALA,A,H,8.0033
+6,ALA,A,HA,4.0955
+6,ALA,A,C,179.9898
+6,ALA,A,CA,55.1863
+6,ALA,A,CB,18.3743
+6,ALA,A,N,120.9539
+6,ALA,A,HB,1.4412
+6,ALA,A,HB2,1.7030
+6,ALA,A,HB3,1.4201
+7,ALA,A,H,7.6498
+7,ALA,A,HA,4.1029
+7,ALA,A,C,179.9331
+7,ALA,A,CA,55.0228
+7,ALA,A,CB,18.1836
+7,ALA,A,N,120.9109
+7,ALA,A,HB,1.4993
+7,ALA,A,HB2,1.8029
+7,ALA,A,HB3,1.5949
+8,GLN,Q,H,7.8249
+8,GLN,Q,HA,4.0409
+8,GLN,Q,C,178.1360
+8,GLN,Q,CA,58.9707
+8,GLN,Q,CB,28.4561
+8,GLN,Q,N,117.7643
+8,GLN,Q,CD,179.7411
+8,GLN,Q,CG,34.1724
+8,GLN,Q,HB2,1.9867
+8,GLN,Q,HB3,2.1296
+8,GLN,Q,HE21,7.4553
+8,GLN,Q,HE22,6.9988
+8,GLN,Q,HG2,2.4060
+8,GLN,Q,HG3,2.3931
+9,ALA,A,H,7.9991
+9,ALA,A,HA,4.0716
+9,ALA,A,C,179.4932
+9,ALA,A,CA,55.1230
+9,ALA,A,CB,18.1578
+9,ALA,A,N,121.3254
+9,ALA,A,HB,1.4565
+9,ALA,A,HB2,1.8276
+9,ALA,A,HB3,1.5254
+10,ALA,A,H,8.1312
+10,ALA,A,HA,4.0736
+10,ALA,A,C,179.6180
+10,ALA,A,CA,55.2088
+10,ALA,A,CB,18.1200
+10,ALA,A,N,120.5697
+10,ALA,A,HB,1.4566
+10,ALA,A,HB2,1.7282
+10,ALA,A,HB3,1.4371
+11,ALA,A,H,8.0171
+11,ALA,A,HA,4.1490
+11,ALA,A,C,180.0429
+11,ALA,A,CA,55.0777
+11,ALA,A,CB,18.3117
+11,ALA,A,N,120.8786
+11,ALA,A,HB,1.4678
+11,ALA,A,HB2,1.7145
+11,ALA,A,HB3,1.4883
+12,ALA,A,H,7.6810
+12,ALA,A,HA,4.1266
+12,ALA,A,C,180.0147
+12,ALA,A,CA,54.7364
+12,ALA,A,CB,18.1542
+12,ALA,A,N,120.6034
+12,ALA,A,HB,1.4539
+12,ALA,A,HB2,1.7667
+12,ALA,A,HB3,1.6911
+13,GLN,Q,H,7.6907
+13,GLN,Q,HA,4.0266
+13,GLN,Q,C,178.2669
+13,GLN,Q,CA,58.6474
+13,GLN,Q,CB,28.4963
+13,GLN,Q,N,117.7800
+13,GLN,Q,CD,179.8184
+13,GLN,Q,CG,34.0365
+13,GLN,Q,HB2,2.0857
+13,GLN,Q,HB3,2.0420
+13,GLN,Q,HE21,7.3064
+13,GLN,Q,HE22,6.9052
+13,GLN,Q,HG2,2.3783
+13,GLN,Q,HG3,2.3765
+14,ALA,A,H,7.8747
+14,ALA,A,HA,4.1403
+14,ALA,A,C,178.7382
+14,ALA,A,CA,54.3606
+14,ALA,A,CB,18.6205
+14,ALA,A,N,121.4970
+14,ALA,A,HB,1.4634
+14,ALA,A,HB2,1.6744
+14,ALA,A,HB3,1.6343
+15,ALA,A,H,7.9746
+15,ALA,A,HA,4.1637
+15,ALA,A,C,178.6609
+15,ALA,A,CA,53.7688
+15,ALA,A,CB,18.9988
+15,ALA,A,N,122.7496
+15,ALA,A,HB,1.4219
+15,ALA,A,HB2,1.7189
+15,ALA,A,HB3,1.6463
diff --git a/proteinbenchmark/data/observables/aaqaa3/aaqaa3-alpha-protonated.spartap b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-alpha-protonated.spartap
new file mode 100644
index 0000000..08b132c
--- /dev/null
+++ b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-alpha-protonated.spartap
@@ -0,0 +1,114 @@
+REMARK SPARTA+ Protein Chemical Shift Prediction Table
+REMARK
+REMARK All chemical shifts are reported in ppm:
+REMARK
+REMARK SHIFT is the predicted chemical shift.
+REMARK SS_SHIFT is the predicted secondary chemical shift.
+REMARK RC_SHIFT is the random coil chemical shift.
+REMARK HM_SHIFT is the ring current shift; a correction
+REMARK of 0.6 times this value is applied.
+REMARK EF_SHIFT is the adjustment for electric field effect,
+REMARK applied to proton shifts only.
+REMARK SIGMA is the estimated prediction error.
+REMARK
+REMARK Reference:
+REMARK Y. Shen and A. Bax: SPARTA+: a modest improvement in empirical NMR
+REMARK chemical shift prediction by means of an artificial neural network.
+REMARK J. Biomol. NMR 48, 13-22 (2010).
+
+DATA SOURCE aaqaa3-alpha-protonated.pdb
+
+DATA FIRST_RESID 0
+
+DATA SEQUENCE ?AAQAAAAQA AAAQAA?
+
+VARS RESID RESNAME ATOMNAME SS_SHIFT SHIFT RC_SHIFT HM_SHIFT EF_SHIFT SIGMA
+FORMAT %4d %4s %4s %9.3f %9.3f %9.3f %9.3f %9.3f %9.3f
+
+ 0 ? HA 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 0 ? C 0.000 9999.000 9999.000 -0.000 0.000 0.000
+ 0 ? CA 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 0 ? CB 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 2 A N 0.268 123.088 122.820 -0.000 0.000 1.902
+ 2 A HA -0.215 4.105 4.320 -0.000 0.000 0.217
+ 2 A C 1.641 179.225 177.584 -0.000 0.000 1.181
+ 2 A CA 2.458 54.495 52.037 -0.000 0.000 0.623
+ 2 A CB -0.412 18.588 19.000 -0.000 0.000 0.818
+ 2 A HN 0.365 8.515 8.150 -0.000 0.000 0.443
+ 3 Q N -0.681 119.119 119.800 -0.000 0.000 2.084
+ 3 Q HA -0.229 4.111 4.340 -0.000 0.000 0.202
+ 3 Q C 1.973 177.973 176.000 -0.000 0.000 0.978
+ 3 Q CA 2.755 58.558 55.803 -0.000 0.000 0.844
+ 3 Q CB -0.404 28.334 28.738 -0.000 0.000 0.898
+ 3 Q HN 0.482 8.752 8.270 -0.000 0.000 0.426
+ 4 A N -1.337 121.483 122.820 -0.000 0.000 1.902
+ 4 A HA -0.218 4.102 4.320 -0.000 0.000 0.217
+ 4 A C 1.818 179.402 177.584 -0.000 0.000 1.181
+ 4 A CA 2.482 54.519 52.037 -0.000 0.000 0.623
+ 4 A CB -1.021 17.980 19.000 -0.000 0.000 0.818
+ 4 A HN 0.148 8.298 8.150 -0.000 0.000 0.443
+ 5 A N -2.082 120.738 122.820 -0.000 0.000 1.902
+ 5 A HA -0.315 4.005 4.320 -0.000 0.000 0.217
+ 5 A C 1.847 179.431 177.584 -0.000 0.000 1.181
+ 5 A CA 2.825 54.862 52.037 -0.000 0.000 0.623
+ 5 A CB -0.645 18.355 19.000 -0.000 0.000 0.818
+ 5 A HN 0.176 8.326 8.150 -0.000 0.000 0.443
+ 6 A N -2.101 120.719 122.820 -0.000 0.000 1.902
+ 6 A HA -0.321 3.999 4.320 -0.000 0.000 0.217
+ 6 A C 1.812 179.396 177.584 -0.000 0.000 1.181
+ 6 A CA 2.871 54.908 52.037 -0.000 0.000 0.623
+ 6 A CB -0.689 18.311 19.000 -0.000 0.000 0.818
+ 6 A HN -0.059 8.091 8.150 -0.000 0.000 0.443
+ 7 A N -1.773 121.047 122.820 -0.000 0.000 1.902
+ 7 A HA -0.381 3.939 4.320 -0.000 0.000 0.217
+ 7 A C 1.946 179.530 177.584 -0.000 0.000 1.181
+ 7 A CA 3.061 55.098 52.037 -0.000 0.000 0.623
+ 7 A CB -0.958 18.042 19.000 -0.000 0.000 0.818
+ 7 A HN -0.201 7.949 8.150 -0.000 0.000 0.443
+ 8 Q N -0.629 119.171 119.800 -0.000 0.000 2.084
+ 8 Q HA -0.352 3.988 4.340 -0.000 0.000 0.202
+ 8 Q C 2.068 178.068 176.000 -0.000 0.000 0.978
+ 8 Q CA 3.009 58.812 55.803 -0.000 0.000 0.844
+ 8 Q CB -0.055 28.683 28.738 -0.000 0.000 0.898
+ 8 Q HN -0.295 7.975 8.270 -0.000 0.000 0.426
+ 9 A N -1.089 121.731 122.820 -0.000 0.000 1.902
+ 9 A HA -0.301 4.019 4.320 -0.000 0.000 0.217
+ 9 A C 1.821 179.405 177.584 -0.000 0.000 1.181
+ 9 A CA 2.850 54.888 52.037 -0.000 0.000 0.623
+ 9 A CB -0.899 18.101 19.000 -0.000 0.000 0.818
+ 9 A HN -0.126 8.024 8.150 -0.000 0.000 0.443
+ 10 A N -2.115 120.705 122.820 -0.000 0.000 1.902
+ 10 A HA -0.314 4.006 4.320 -0.000 0.000 0.217
+ 10 A C 1.852 179.436 177.584 -0.000 0.000 1.181
+ 10 A CA 2.853 54.890 52.037 -0.000 0.000 0.623
+ 10 A CB -0.661 18.339 19.000 -0.000 0.000 0.818
+ 10 A HN 0.179 8.329 8.150 -0.000 0.000 0.443
+ 11 A N -2.100 120.720 122.820 -0.000 0.000 1.902
+ 11 A HA -0.321 3.999 4.320 -0.000 0.000 0.217
+ 11 A C 1.813 179.397 177.584 -0.000 0.000 1.181
+ 11 A CA 2.874 54.911 52.037 -0.000 0.000 0.623
+ 11 A CB -0.690 18.310 19.000 -0.000 0.000 0.818
+ 11 A HN -0.058 8.092 8.150 -0.000 0.000 0.443
+ 12 A N -1.593 121.227 122.820 -0.000 0.000 1.902
+ 12 A HA -0.312 4.008 4.320 -0.000 0.000 0.217
+ 12 A C 1.956 179.540 177.584 -0.000 0.000 1.181
+ 12 A CA 2.519 54.556 52.037 -0.000 0.000 0.623
+ 12 A CB -0.698 18.302 19.000 -0.000 0.000 0.818
+ 12 A HN -0.277 7.873 8.150 -0.000 0.000 0.443
+ 13 Q N -1.297 118.503 119.800 -0.000 0.000 2.084
+ 13 Q HA -0.305 4.035 4.340 -0.000 0.000 0.202
+ 13 Q C 2.265 178.265 176.000 -0.000 0.000 0.978
+ 13 Q CA 2.300 58.103 55.803 -0.000 0.000 0.844
+ 13 Q CB 0.154 28.892 28.738 -0.000 0.000 0.898
+ 13 Q HN -0.364 7.906 8.270 -0.000 0.000 0.426
+ 14 A N -0.565 122.255 122.820 -0.000 0.000 1.902
+ 14 A HA -0.160 4.160 4.320 -0.000 0.000 0.217
+ 14 A C 0.121 177.705 177.584 -0.000 0.000 1.181
+ 14 A CA 0.709 52.746 52.037 -0.000 0.000 0.623
+ 14 A CB 0.138 19.138 19.000 -0.000 0.000 0.818
+ 14 A HN -0.403 7.747 8.150 -0.000 0.000 0.443
+ 16 ? N 0.000 9999.000 9999.000 -0.000 0.000 0.000
+ 16 ? HA 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 16 ? CA 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 16 ? CB 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 16 ? HN 0.000 9999.000 9999.000 0.000 0.000 0.000
diff --git a/proteinbenchmark/data/observables/aaqaa3/aaqaa3-alpha-protonated_pred.tab b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-alpha-protonated_pred.tab
new file mode 100644
index 0000000..7def66b
--- /dev/null
+++ b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-alpha-protonated_pred.tab
@@ -0,0 +1,114 @@
+REMARK SPARTA+ Protein Chemical Shift Prediction Table
+REMARK
+REMARK All chemical shifts are reported in ppm:
+REMARK
+REMARK SHIFT is the predicted chemical shift.
+REMARK SS_SHIFT is the predicted secondary chemical shift.
+REMARK RC_SHIFT is the random coil chemical shift.
+REMARK HM_SHIFT is the ring current shift; a correction
+REMARK of 0.6 times this value is applied.
+REMARK EF_SHIFT is the adjustment for electric field effect,
+REMARK applied to proton shifts only.
+REMARK SIGMA is the estimated prediction error.
+REMARK
+REMARK Reference:
+REMARK Y. Shen and A. Bax: SPARTA+: a modest improvement in empirical NMR
+REMARK chemical shift prediction by means of an artificial neural network.
+REMARK J. Biomol. NMR 48, 13-22 (2010).
+
+DATA SOURCE aaqaa3-alpha-protonated
+
+DATA FIRST_RESID 0
+
+DATA SEQUENCE ?AAQAAAAQA AAAQAA?
+
+VARS RESID RESNAME ATOMNAME SS_SHIFT SHIFT RC_SHIFT HM_SHIFT EF_SHIFT SIGMA
+FORMAT %4d %4s %4s %9.3f %9.3f %9.3f %9.3f %9.3f %9.3f
+
+ 0 ? HA 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 0 ? C 0.000 9999.000 9999.000 -0.000 0.000 0.000
+ 0 ? CA 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 0 ? CB 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 2 A N 0.268 123.088 122.820 -0.000 0.000 1.902
+ 2 A HA -0.215 4.105 4.320 -0.000 0.000 0.217
+ 2 A C 1.641 179.225 177.584 -0.000 0.000 1.181
+ 2 A CA 2.458 54.495 52.037 -0.000 0.000 0.623
+ 2 A CB -0.412 18.588 19.000 -0.000 0.000 0.818
+ 2 A HN 0.365 8.515 8.150 -0.000 0.000 0.443
+ 3 Q N -0.681 119.119 119.800 -0.000 0.000 2.084
+ 3 Q HA -0.229 4.111 4.340 -0.000 0.000 0.202
+ 3 Q C 1.973 177.973 176.000 -0.000 0.000 0.978
+ 3 Q CA 2.755 58.558 55.803 -0.000 0.000 0.844
+ 3 Q CB -0.404 28.334 28.738 -0.000 0.000 0.898
+ 3 Q HN 0.482 8.752 8.270 -0.000 0.000 0.426
+ 4 A N -1.337 121.483 122.820 -0.000 0.000 1.902
+ 4 A HA -0.218 4.102 4.320 -0.000 0.000 0.217
+ 4 A C 1.818 179.402 177.584 -0.000 0.000 1.181
+ 4 A CA 2.482 54.519 52.037 -0.000 0.000 0.623
+ 4 A CB -1.021 17.980 19.000 -0.000 0.000 0.818
+ 4 A HN 0.148 8.298 8.150 -0.000 0.000 0.443
+ 5 A N -2.082 120.738 122.820 -0.000 0.000 1.902
+ 5 A HA -0.315 4.005 4.320 -0.000 0.000 0.217
+ 5 A C 1.847 179.431 177.584 -0.000 0.000 1.181
+ 5 A CA 2.825 54.862 52.037 -0.000 0.000 0.623
+ 5 A CB -0.645 18.355 19.000 -0.000 0.000 0.818
+ 5 A HN 0.176 8.326 8.150 -0.000 0.000 0.443
+ 6 A N -2.101 120.719 122.820 -0.000 0.000 1.902
+ 6 A HA -0.321 3.999 4.320 -0.000 0.000 0.217
+ 6 A C 1.812 179.396 177.584 -0.000 0.000 1.181
+ 6 A CA 2.871 54.908 52.037 -0.000 0.000 0.623
+ 6 A CB -0.689 18.311 19.000 -0.000 0.000 0.818
+ 6 A HN -0.059 8.091 8.150 -0.000 0.000 0.443
+ 7 A N -1.773 121.047 122.820 -0.000 0.000 1.902
+ 7 A HA -0.381 3.939 4.320 -0.000 0.000 0.217
+ 7 A C 1.946 179.530 177.584 -0.000 0.000 1.181
+ 7 A CA 3.061 55.098 52.037 -0.000 0.000 0.623
+ 7 A CB -0.958 18.042 19.000 -0.000 0.000 0.818
+ 7 A HN -0.201 7.949 8.150 -0.000 0.000 0.443
+ 8 Q N -0.629 119.171 119.800 -0.000 0.000 2.084
+ 8 Q HA -0.352 3.988 4.340 -0.000 0.000 0.202
+ 8 Q C 2.068 178.068 176.000 -0.000 0.000 0.978
+ 8 Q CA 3.009 58.812 55.803 -0.000 0.000 0.844
+ 8 Q CB -0.055 28.683 28.738 -0.000 0.000 0.898
+ 8 Q HN -0.295 7.975 8.270 -0.000 0.000 0.426
+ 9 A N -1.089 121.731 122.820 -0.000 0.000 1.902
+ 9 A HA -0.301 4.019 4.320 -0.000 0.000 0.217
+ 9 A C 1.821 179.405 177.584 -0.000 0.000 1.181
+ 9 A CA 2.850 54.888 52.037 -0.000 0.000 0.623
+ 9 A CB -0.899 18.101 19.000 -0.000 0.000 0.818
+ 9 A HN -0.126 8.024 8.150 -0.000 0.000 0.443
+ 10 A N -2.115 120.705 122.820 -0.000 0.000 1.902
+ 10 A HA -0.314 4.006 4.320 -0.000 0.000 0.217
+ 10 A C 1.852 179.436 177.584 -0.000 0.000 1.181
+ 10 A CA 2.853 54.890 52.037 -0.000 0.000 0.623
+ 10 A CB -0.661 18.339 19.000 -0.000 0.000 0.818
+ 10 A HN 0.179 8.329 8.150 -0.000 0.000 0.443
+ 11 A N -2.100 120.720 122.820 -0.000 0.000 1.902
+ 11 A HA -0.321 3.999 4.320 -0.000 0.000 0.217
+ 11 A C 1.813 179.397 177.584 -0.000 0.000 1.181
+ 11 A CA 2.874 54.911 52.037 -0.000 0.000 0.623
+ 11 A CB -0.690 18.310 19.000 -0.000 0.000 0.818
+ 11 A HN -0.058 8.092 8.150 -0.000 0.000 0.443
+ 12 A N -1.593 121.227 122.820 -0.000 0.000 1.902
+ 12 A HA -0.312 4.008 4.320 -0.000 0.000 0.217
+ 12 A C 1.956 179.540 177.584 -0.000 0.000 1.181
+ 12 A CA 2.519 54.556 52.037 -0.000 0.000 0.623
+ 12 A CB -0.698 18.302 19.000 -0.000 0.000 0.818
+ 12 A HN -0.277 7.873 8.150 -0.000 0.000 0.443
+ 13 Q N -1.297 118.503 119.800 -0.000 0.000 2.084
+ 13 Q HA -0.305 4.035 4.340 -0.000 0.000 0.202
+ 13 Q C 2.265 178.265 176.000 -0.000 0.000 0.978
+ 13 Q CA 2.300 58.103 55.803 -0.000 0.000 0.844
+ 13 Q CB 0.154 28.892 28.738 -0.000 0.000 0.898
+ 13 Q HN -0.364 7.906 8.270 -0.000 0.000 0.426
+ 14 A N -0.565 122.255 122.820 -0.000 0.000 1.902
+ 14 A HA -0.160 4.160 4.320 -0.000 0.000 0.217
+ 14 A C 0.121 177.705 177.584 -0.000 0.000 1.181
+ 14 A CA 0.709 52.746 52.037 -0.000 0.000 0.623
+ 14 A CB 0.138 19.138 19.000 -0.000 0.000 0.818
+ 14 A HN -0.403 7.747 8.150 -0.000 0.000 0.443
+ 16 ? N 0.000 9999.000 9999.000 -0.000 0.000 0.000
+ 16 ? HA 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 16 ? CA 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 16 ? CB 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 16 ? HN 0.000 9999.000 9999.000 0.000 0.000 0.000
diff --git a/proteinbenchmark/data/observables/aaqaa3/aaqaa3-alpha-protonated_struct.tab b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-alpha-protonated_struct.tab
new file mode 100644
index 0000000..57a91fa
--- /dev/null
+++ b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-alpha-protonated_struct.tab
@@ -0,0 +1,50 @@
+REMARK SPARTA+ Structural Parameters Table derived from input PDB cooridnates
+REMARK
+REMARK PHI_R1 PSI_R1 CHI1_R1 and CHI2_R1 are the backbone and sidechain
+REMARK torsion angles of the first residue in a triplet.
+REMARK
+REMARK PHI_R2 PSI_R2 CHI1_R2 and CHI2_R2 are the backbone and sidechain
+REMARK torsion angles of the second (central) residue in a triplet.
+REMARK
+REMARK PHI_R3 PSI_R3 CHI1_R3 and CHI2_R3 are the backbone and sidechain
+REMARK torsion angles of the third residue in a triplet.
+REMARK
+REMARK H-Bond Distances are given in Angstroms:
+REMARK
+REMARK HN_HB_DIST_R2 H-bond distance for the HN atom in the central residue.
+REMARK HA_HB_DIST_R2 H-bond distance for the HA atom in the central residue.
+REMARK CO_HB_DIST_R2 H-bond distance for the CO atom in the central residue.
+REMARK
+REMARK HN_S2_R2 is the Bruschweiler structure-based HN order parameter of
+REMARK the central residue. Reference: Zhang FL, Bruschweiler R
+REMARK JACS 124, 12654-12655 (2002)
+REMARK
+REMARK Reference:
+REMARK Y. Shen and A. Bax: SPARTA+: a modest improvement in empirical NMR
+REMARK chemical shift prediction by means of an artificial neural network.
+REMARK J. Biomol. NMR 48, 13-22 (2010).
+
+DATA SOURCE aaqaa3-alpha-protonated
+
+DATA FIRST_RESID 0
+
+DATA SEQUENCE ?AAQAAAAQA AAAQAA?
+
+VARS RESID_R1 RESNAME_R1 PHI_R1 PSI_R1 CHI1_R1 CHI2_R1 RESID_R2 RESNAME_R2 PHI_R2 PSI_R2 CHI1_R2 CHI2_R2 RESID_R3 RESNAME_R3 PHI_R3 PSI_R3 CHI1_R3 CHI2_R3 HN_HB_DIST_R2 HA_HB_DIST_R2 CO_HB_DIST_R2 HN_S2_R2
+FORMAT %4d %s %8.3f %8.3f %8.3f %8.3f %4d %s %8.3f %8.3f %8.3f %8.3f %4d %s %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f
+
+ 0 ? 9999.000 9999.000 9999.000 9999.000 1 A -139.022 -42.983 9999.000 9999.000 2 A -63.008 -43.003 9999.000 9999.000 0.000 0.000 1.920 0.362
+ 1 A -139.022 -42.983 9999.000 9999.000 2 A -63.008 -43.003 9999.000 9999.000 3 Q -63.001 -43.024 -175.411 177.936 0.000 0.000 2.056 0.711
+ 2 A -63.008 -43.003 9999.000 9999.000 3 Q -63.001 -43.024 -175.411 177.936 4 A -62.993 -43.050 9999.000 9999.000 0.000 0.000 2.160 0.788
+ 3 Q -63.001 -43.024 -175.411 177.936 4 A -62.993 -43.050 9999.000 9999.000 5 A -62.944 -43.020 9999.000 9999.000 0.000 0.000 2.159 0.841
+ 4 A -62.993 -43.050 9999.000 9999.000 5 A -62.944 -43.020 9999.000 9999.000 6 A -63.029 -43.014 9999.000 9999.000 1.920 0.000 2.064 0.878
+ 5 A -62.944 -43.020 9999.000 9999.000 6 A -63.029 -43.014 9999.000 9999.000 7 A -62.923 -43.099 9999.000 9999.000 2.056 0.000 1.921 0.876
+ 6 A -63.029 -43.014 9999.000 9999.000 7 A -62.923 -43.099 9999.000 9999.000 8 Q -62.990 -43.011 -175.432 177.946 2.160 0.000 2.056 0.878
+ 7 A -62.923 -43.099 9999.000 9999.000 8 Q -62.990 -43.011 -175.432 177.946 9 A -62.943 -42.977 9999.000 9999.000 2.159 0.000 2.160 0.874
+ 8 Q -62.990 -43.011 -175.432 177.946 9 A -62.943 -42.977 9999.000 9999.000 10 A -63.016 -43.014 9999.000 9999.000 2.064 0.000 2.159 0.876
+ 9 A -62.943 -42.977 9999.000 9999.000 10 A -63.016 -43.014 9999.000 9999.000 11 A -63.036 -43.029 9999.000 9999.000 1.921 0.000 2.064 0.880
+ 10 A -63.016 -43.014 9999.000 9999.000 11 A -63.036 -43.029 9999.000 9999.000 12 A -63.005 -42.998 9999.000 9999.000 2.056 0.000 1.919 0.876
+ 11 A -63.036 -43.029 9999.000 9999.000 12 A -63.005 -42.998 9999.000 9999.000 13 Q -62.970 -43.046 -175.424 177.901 2.160 0.000 0.000 0.877
+ 12 A -63.005 -42.998 9999.000 9999.000 13 Q -62.970 -43.046 -175.424 177.901 14 A -62.945 -43.010 9999.000 9999.000 2.159 4.520 0.000 0.862
+ 13 Q -62.970 -43.046 -175.424 177.901 14 A -62.945 -43.010 9999.000 9999.000 15 A -63.030 135.039 9999.000 9999.000 2.064 0.000 0.000 0.838
+ 14 A -62.945 -43.010 9999.000 9999.000 15 A -63.030 135.039 9999.000 9999.000 16 ? 9999.000 9999.000 9999.000 9999.000 1.919 0.000 4.520 0.806
diff --git a/proteinbenchmark/data/observables/aaqaa3/aaqaa3-beta-initial.pdb b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-beta-initial.pdb
new file mode 100644
index 0000000..fa9a2e0
--- /dev/null
+++ b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-beta-initial.pdb
@@ -0,0 +1,181 @@
+TITLE < Chain: id = nres = 17 natoms = 180 >
+ATOM 1 HH33 ACE 0 -5.960 -3.356 6.707 1.00 0.00
+ATOM 2 CH3 ACE 0 -5.212 -3.715 6.149 1.00 0.00
+ATOM 3 HH31 ACE 0 -5.336 -4.792 6.006 1.00 0.00
+ATOM 4 HH32 ACE 0 -5.211 -3.242 5.168 1.00 0.00
+ATOM 5 C ACE 0 -3.889 -3.475 6.882 1.00 0.00
+ATOM 6 O ACE 0 -3.665 -2.380 7.403 1.00 0.00
+ATOM 7 N ALA 1 -2.983 -4.446 6.956 1.00 0.00
+ATOM 8 H ALA 1 -3.168 -5.341 6.529 1.00 0.00
+ATOM 9 CA ALA 1 -1.682 -4.415 7.599 1.00 0.00
+ATOM 10 HA ALA 1 -1.378 -3.371 7.700 1.00 0.00
+ATOM 11 CB ALA 1 -1.830 -5.056 8.985 1.00 0.00
+ATOM 12 HB1 ALA 1 -0.892 -5.026 9.541 1.00 0.00
+ATOM 13 HB2 ALA 1 -2.577 -4.536 9.583 1.00 0.00
+ATOM 14 HB3 ALA 1 -2.131 -6.102 8.905 1.00 0.00
+ATOM 15 C ALA 1 -0.616 -5.125 6.747 1.00 0.00
+ATOM 16 O ALA 1 -0.821 -6.255 6.300 1.00 0.00
+ATOM 17 N ALA 2 0.538 -4.519 6.485 1.00 0.00
+ATOM 18 H ALA 2 0.714 -3.602 6.843 1.00 0.00
+ATOM 19 CA ALA 2 1.544 -5.189 5.681 1.00 0.00
+ATOM 20 HA ALA 2 1.169 -6.183 5.429 1.00 0.00
+ATOM 21 CB ALA 2 1.748 -4.364 4.404 1.00 0.00
+ATOM 22 HB1 ALA 2 2.464 -4.838 3.732 1.00 0.00
+ATOM 23 HB2 ALA 2 0.814 -4.251 3.854 1.00 0.00
+ATOM 24 HB3 ALA 2 2.125 -3.366 4.636 1.00 0.00
+ATOM 25 C ALA 2 2.856 -5.375 6.462 1.00 0.00
+ATOM 26 O ALA 2 3.376 -4.426 7.052 1.00 0.00
+ATOM 27 N GLN 3 3.441 -6.569 6.505 1.00 0.00
+ATOM 28 H GLN 3 3.027 -7.346 6.029 1.00 0.00
+ATOM 29 CA GLN 3 4.687 -6.746 7.246 1.00 0.00
+ATOM 30 HA GLN 3 4.986 -5.763 7.621 1.00 0.00
+ATOM 31 CB GLN 3 4.491 -7.720 8.439 1.00 0.00
+ATOM 32 HB1 GLN 3 3.667 -7.360 9.054 1.00 0.00
+ATOM 33 HB2 GLN 3 4.182 -8.690 8.047 1.00 0.00
+ATOM 34 CG GLN 3 5.719 -7.899 9.365 1.00 0.00
+ATOM 35 HG1 GLN 3 6.563 -8.317 8.820 1.00 0.00
+ATOM 36 HG2 GLN 3 6.040 -6.929 9.747 1.00 0.00
+ATOM 37 CD GLN 3 5.491 -8.823 10.562 1.00 0.00
+ATOM 38 OE1 GLN 3 6.405 -9.045 11.346 1.00 0.00
+ATOM 39 NE2 GLN 3 4.300 -9.386 10.730 1.00 0.00
+ATOM 40 HE21 GLN 3 3.543 -9.186 10.096 1.00 0.00
+ATOM 41 HE22 GLN 3 4.176 -10.003 11.517 1.00 0.00
+ATOM 42 C GLN 3 5.756 -7.225 6.246 1.00 0.00
+ATOM 43 O GLN 3 5.521 -8.172 5.495 1.00 0.00
+ATOM 44 N ALA 4 6.936 -6.615 6.191 1.00 0.00
+ATOM 45 H ALA 4 7.130 -5.845 6.800 1.00 0.00
+ATOM 46 CA ALA 4 7.943 -7.066 5.248 1.00 0.00
+ATOM 47 HA ALA 4 7.545 -7.931 4.714 1.00 0.00
+ATOM 48 CB ALA 4 8.211 -5.919 4.265 1.00 0.00
+ATOM 49 HB1 ALA 4 8.931 -6.209 3.499 1.00 0.00
+ATOM 50 HB2 ALA 4 7.298 -5.618 3.752 1.00 0.00
+ATOM 51 HB3 ALA 4 8.612 -5.044 4.780 1.00 0.00
+ATOM 52 C ALA 4 9.225 -7.518 5.968 1.00 0.00
+ATOM 53 O ALA 4 9.757 -6.798 6.815 1.00 0.00
+ATOM 54 N ALA 5 9.770 -8.696 5.678 1.00 0.00
+ATOM 55 H ALA 5 9.346 -9.288 4.993 1.00 0.00
+ATOM 56 CA ALA 5 10.980 -9.123 6.358 1.00 0.00
+ATOM 57 HA ALA 5 11.293 -8.321 7.029 1.00 0.00
+ATOM 58 CB ALA 5 10.644 -10.384 7.164 1.00 0.00
+ATOM 59 HB1 ALA 5 11.504 -10.734 7.736 1.00 0.00
+ATOM 60 HB2 ALA 5 9.839 -10.196 7.874 1.00 0.00
+ATOM 61 HB3 ALA 5 10.331 -11.199 6.509 1.00 0.00
+ATOM 62 C ALA 5 12.128 -9.365 5.363 1.00 0.00
+ATOM 63 O ALA 5 11.956 -10.066 4.364 1.00 0.00
+ATOM 64 N ALA 6 13.320 -8.816 5.577 1.00 0.00
+ATOM 65 H ALA 6 13.470 -8.245 6.384 1.00 0.00
+ATOM 66 CA ALA 6 14.403 -9.044 4.638 1.00 0.00
+ATOM 67 HA ALA 6 14.041 -9.717 3.859 1.00 0.00
+ATOM 68 CB ALA 6 14.786 -7.690 4.027 1.00 0.00
+ATOM 69 HB1 ALA 6 15.570 -7.798 3.276 1.00 0.00
+ATOM 70 HB2 ALA 6 13.932 -7.223 3.537 1.00 0.00
+ATOM 71 HB3 ALA 6 15.154 -7.002 4.790 1.00 0.00
+ATOM 72 C ALA 6 15.602 -9.728 5.317 1.00 0.00
+ATOM 73 O ALA 6 16.064 -9.283 6.369 1.00 0.00
+ATOM 74 N ALA 7 16.148 -10.810 4.770 1.00 0.00
+ATOM 75 H ALA 7 15.780 -11.178 3.916 1.00 0.00
+ATOM 76 CA ALA 7 17.279 -11.455 5.411 1.00 0.00
+ATOM 77 HA ALA 7 17.542 -10.876 6.299 1.00 0.00
+ATOM 78 CB ALA 7 16.843 -12.869 5.817 1.00 0.00
+ATOM 79 HB1 ALA 7 17.638 -13.396 6.346 1.00 0.00
+ATOM 80 HB2 ALA 7 15.979 -12.841 6.479 1.00 0.00
+ATOM 81 HB3 ALA 7 16.578 -13.466 4.942 1.00 0.00
+ATOM 82 C ALA 7 18.512 -11.475 4.491 1.00 0.00
+ATOM 83 O ALA 7 18.422 -11.876 3.330 1.00 0.00
+ATOM 84 N GLN 8 19.689 -11.056 4.947 1.00 0.00
+ATOM 85 H GLN 8 19.772 -10.728 5.888 1.00 0.00
+ATOM 86 CA GLN 8 20.860 -11.074 4.073 1.00 0.00
+ATOM 87 HA GLN 8 20.554 -11.529 3.127 1.00 0.00
+ATOM 88 CB GLN 8 21.382 -9.636 3.814 1.00 0.00
+ATOM 89 HB1 GLN 8 20.563 -9.028 3.430 1.00 0.00
+ATOM 90 HB2 GLN 8 21.671 -9.194 4.769 1.00 0.00
+ATOM 91 CG GLN 8 22.555 -9.522 2.810 1.00 0.00
+ATOM 92 HG1 GLN 8 23.432 -10.059 3.168 1.00 0.00
+ATOM 93 HG2 GLN 8 22.276 -9.976 1.859 1.00 0.00
+ATOM 94 CD GLN 8 23.024 -8.093 2.529 1.00 0.00
+ATOM 95 OE1 GLN 8 23.958 -7.896 1.763 1.00 0.00
+ATOM 96 NE2 GLN 8 22.414 -7.080 3.134 1.00 0.00
+ATOM 97 HE21 GLN 8 21.633 -7.243 3.747 1.00 0.00
+ATOM 98 HE22 GLN 8 22.748 -6.148 2.945 1.00 0.00
+ATOM 99 C GLN 8 21.911 -11.989 4.729 1.00 0.00
+ATOM 100 O GLN 8 22.214 -11.835 5.913 1.00 0.00
+ATOM 101 N ALA 9 22.494 -12.949 4.017 1.00 0.00
+ATOM 102 H ALA 9 22.251 -13.076 3.056 1.00 0.00
+ATOM 103 CA ALA 9 23.485 -13.811 4.635 1.00 0.00
+ATOM 104 HA ALA 9 23.628 -13.479 5.665 1.00 0.00
+ATOM 105 CB ALA 9 22.937 -15.243 4.615 1.00 0.00
+ATOM 106 HB1 ALA 9 23.618 -15.939 5.107 1.00 0.00
+ATOM 107 HB2 ALA 9 21.981 -15.307 5.134 1.00 0.00
+ATOM 108 HB3 ALA 9 22.789 -15.595 3.593 1.00 0.00
+ATOM 109 C ALA 9 24.845 -13.705 3.924 1.00 0.00
+ATOM 110 O ALA 9 24.922 -13.812 2.699 1.00 0.00
+ATOM 111 N ALA 10 25.951 -13.496 4.632 1.00 0.00
+ATOM 112 H ALA 10 25.899 -13.407 5.626 1.00 0.00
+ATOM 113 CA ALA 10 27.234 -13.396 3.960 1.00 0.00
+ATOM 114 HA ALA 10 27.072 -13.558 2.893 1.00 0.00
+ATOM 115 CB ALA 10 27.779 -11.982 4.201 1.00 0.00
+ATOM 116 HB1 ALA 10 28.727 -11.826 3.683 1.00 0.00
+ATOM 117 HB2 ALA 10 27.086 -11.225 3.838 1.00 0.00
+ATOM 118 HB3 ALA 10 27.951 -11.801 5.263 1.00 0.00
+ATOM 119 C ALA 10 28.210 -14.480 4.449 1.00 0.00
+ATOM 120 O ALA 10 28.396 -14.660 5.653 1.00 0.00
+ATOM 121 N ALA 11 28.863 -15.233 3.568 1.00 0.00
+ATOM 122 H ALA 11 28.718 -15.095 2.588 1.00 0.00
+ATOM 123 CA ALA 11 29.784 -16.256 4.029 1.00 0.00
+ATOM 124 HA ALA 11 29.820 -16.213 5.119 1.00 0.00
+ATOM 125 CB ALA 11 29.238 -17.616 3.574 1.00 0.00
+ATOM 126 HB1 ALA 11 29.864 -18.436 3.927 1.00 0.00
+ATOM 127 HB2 ALA 11 28.234 -17.787 3.960 1.00 0.00
+ATOM 128 HB3 ALA 11 29.196 -17.679 2.485 1.00 0.00
+ATOM 129 C ALA 11 31.209 -16.004 3.509 1.00 0.00
+ATOM 130 O ALA 11 31.412 -15.786 2.313 1.00 0.00
+ATOM 131 N ALA 12 32.237 -16.022 4.352 1.00 0.00
+ATOM 132 H ALA 12 32.083 -16.198 5.325 1.00 0.00
+ATOM 133 CA ALA 12 33.583 -15.784 3.862 1.00 0.00
+ATOM 134 HA ALA 12 33.531 -15.653 2.779 1.00 0.00
+ATOM 135 CB ALA 12 34.102 -14.501 4.522 1.00 0.00
+ATOM 136 HB1 ALA 12 35.098 -14.240 4.162 1.00 0.00
+ATOM 137 HB2 ALA 12 33.450 -13.655 4.308 1.00 0.00
+ATOM 138 HB3 ALA 12 34.163 -14.612 5.606 1.00 0.00
+ATOM 139 C ALA 12 34.502 -16.986 4.138 1.00 0.00
+ATOM 140 O ALA 12 34.563 -17.484 5.263 1.00 0.00
+ATOM 141 N GLN 13 35.240 -17.498 3.157 1.00 0.00
+ATOM 142 H GLN 13 35.198 -17.101 2.240 1.00 0.00
+ATOM 143 CA GLN 13 36.114 -18.639 3.419 1.00 0.00
+ATOM 144 HA GLN 13 36.052 -18.859 4.488 1.00 0.00
+ATOM 145 CB GLN 13 35.662 -19.882 2.607 1.00 0.00
+ATOM 146 HB1 GLN 13 34.612 -20.080 2.822 1.00 0.00
+ATOM 147 HB2 GLN 13 35.719 -19.642 1.544 1.00 0.00
+ATOM 148 CG GLN 13 36.448 -21.186 2.888 1.00 0.00
+ATOM 149 HG1 GLN 13 37.500 -21.074 2.632 1.00 0.00
+ATOM 150 HG2 GLN 13 36.406 -21.423 3.952 1.00 0.00
+ATOM 151 CD GLN 13 35.957 -22.412 2.115 1.00 0.00
+ATOM 152 OE1 GLN 13 36.522 -23.488 2.254 1.00 0.00
+ATOM 153 NE2 GLN 13 34.923 -22.287 1.290 1.00 0.00
+ATOM 154 HE21 GLN 13 34.447 -21.405 1.194 1.00 0.00
+ATOM 155 HE22 GLN 13 34.625 -23.104 0.781 1.00 0.00
+ATOM 156 C GLN 13 37.555 -18.201 3.100 1.00 0.00
+ATOM 157 O GLN 13 37.813 -17.652 2.028 1.00 0.00
+ATOM 158 N ALA 14 38.526 -18.414 3.983 1.00 0.00
+ATOM 159 H ALA 14 38.321 -18.860 4.854 1.00 0.00
+ATOM 160 CA ALA 14 39.885 -18.001 3.682 1.00 0.00
+ATOM 161 HA ALA 14 39.895 -17.576 2.676 1.00 0.00
+ATOM 162 CB ALA 14 40.287 -16.934 4.708 1.00 0.00
+ATOM 163 HB1 ALA 14 41.288 -16.547 4.511 1.00 0.00
+ATOM 164 HB2 ALA 14 39.604 -16.086 4.684 1.00 0.00
+ATOM 165 HB3 ALA 14 40.285 -17.340 5.721 1.00 0.00
+ATOM 166 C ALA 14 40.851 -19.198 3.688 1.00 0.00
+ATOM 167 O ALA 14 40.868 -19.987 4.634 1.00 0.00
+ATOM 168 N ALA 15 41.679 -19.389 2.664 1.00 0.00
+ATOM 169 H ALA 15 41.673 -18.755 1.891 1.00 0.00
+ATOM 170 CA ALA 15 42.590 -20.519 2.669 1.00 0.00
+ATOM 171 HA ALA 15 42.461 -21.055 3.611 1.00 0.00
+ATOM 172 CB ALA 15 42.216 -21.427 1.492 1.00 0.00
+ATOM 173 HB1 ALA 15 42.839 -22.323 1.464 1.00 0.00
+ATOM 174 HB2 ALA 15 41.180 -21.758 1.562 1.00 0.00
+ATOM 175 HB3 ALA 15 42.340 -20.910 0.539 1.00 0.00
+ATOM 176 C ALA 15 44.056 -20.058 2.598 1.00 0.00
+ATOM 177 O ALA 15 44.401 -19.182 1.803 1.00 0.00
+ATOM 178 N NH2 16 44.965 -20.607 3.398 1.00 0.00
+ATOM 179 HN1 NH2 16 44.696 -21.319 4.046 1.00 0.00
+ATOM 180 HN2 NH2 16 45.918 -20.308 3.351 1.00 0.00
diff --git a/proteinbenchmark/data/observables/aaqaa3/aaqaa3-beta-protonated.pdb b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-beta-protonated.pdb
new file mode 100644
index 0000000..2572412
--- /dev/null
+++ b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-beta-protonated.pdb
@@ -0,0 +1,182 @@
+ATOM 1 HH33 ACE A 0 -5.960 -3.356 6.707 1.00 0.00
+ATOM 2 CH3 ACE A 0 -5.212 -3.715 6.149 1.00 0.00
+ATOM 3 HH31 ACE A 0 -5.336 -4.792 6.006 1.00 0.00
+ATOM 4 HH32 ACE A 0 -5.211 -3.242 5.168 1.00 0.00
+ATOM 5 C ACE A 0 -3.889 -3.475 6.882 1.00 0.00
+ATOM 6 O ACE A 0 -3.665 -2.380 7.403 1.00 0.00
+ATOM 7 N ALA A 1 -2.983 -4.446 6.956 1.00 0.00
+ATOM 8 CA ALA A 1 -1.682 -4.415 7.599 1.00 0.00
+ATOM 9 CB ALA A 1 -1.830 -5.056 8.985 1.00 0.00
+ATOM 10 C ALA A 1 -0.616 -5.125 6.747 1.00 0.00
+ATOM 11 O ALA A 1 -0.821 -6.255 6.300 1.00 0.00
+ATOM 12 H ALA A 1 -3.163 -4.880 6.061 1.00 0.00 H
+ATOM 13 HA ALA A 1 -1.396 -3.455 7.722 1.00 0.00 H
+ATOM 14 HB1 ALA A 1 -1.024 -5.611 9.177 1.00 0.00 H
+ATOM 15 HB2 ALA A 1 -1.916 -4.337 9.671 1.00 0.00 H
+ATOM 16 HB3 ALA A 1 -2.645 -5.631 8.995 1.00 0.00 H
+ATOM 17 N ALA A 2 0.538 -4.519 6.485 1.00 0.00
+ATOM 18 CA ALA A 2 1.544 -5.189 5.681 1.00 0.00
+ATOM 19 CB ALA A 2 1.748 -4.364 4.404 1.00 0.00
+ATOM 20 C ALA A 2 2.856 -5.375 6.462 1.00 0.00
+ATOM 21 O ALA A 2 3.376 -4.426 7.052 1.00 0.00
+ATOM 22 H ALA A 2 0.645 -3.578 6.885 1.00 0.00 H
+ATOM 23 HA ALA A 2 1.204 -6.102 5.418 1.00 0.00 H
+ATOM 24 HB1 ALA A 2 2.128 -4.950 3.692 1.00 0.00 H
+ATOM 25 HB2 ALA A 2 0.869 -3.998 4.106 1.00 0.00 H
+ATOM 26 HB3 ALA A 2 2.378 -3.614 4.595 1.00 0.00 H
+ATOM 27 N GLN A 3 3.441 -6.569 6.505 1.00 0.00
+ATOM 28 CA GLN A 3 4.687 -6.746 7.246 1.00 0.00
+ATOM 29 CB GLN A 3 4.491 -7.720 8.439 1.00 0.00
+ATOM 30 CG GLN A 3 5.719 -7.899 9.365 1.00 0.00
+ATOM 31 CD GLN A 3 5.491 -8.823 10.562 1.00 0.00
+ATOM 32 C GLN A 3 5.756 -7.225 6.246 1.00 0.00
+ATOM 33 O GLN A 3 5.521 -8.172 5.495 1.00 0.00
+ATOM 34 H GLN A 3 2.961 -7.319 5.995 1.00 0.00 H
+ATOM 35 HA GLN A 3 4.975 -5.862 7.590 1.00 0.00 H
+ATOM 36 HB2 GLN A 3 3.732 -7.384 9.002 1.00 0.00 H
+ATOM 37 HB3 GLN A 3 4.250 -8.624 8.075 1.00 0.00 H
+ATOM 38 HG2 GLN A 3 6.473 -8.271 8.814 1.00 0.00 H
+ATOM 39 HG3 GLN A 3 5.986 -6.992 9.707 1.00 0.00 H
+ATOM 40 OE1 GLN A 3 6.405 -9.045 11.346 1.00 0.00 O
+ATOM 41 NE2 GLN A 3 4.300 -9.386 10.730 1.00 0.00 N
+ATOM 42 HE21 GLN A 3 4.105 -10.004 11.482 1.00 0.00 H
+ATOM 43 HE22 GLN A 3 3.563 -9.160 10.043 1.00 0.00 H
+ATOM 44 N ALA A 4 6.936 -6.615 6.191 1.00 0.00
+ATOM 45 CA ALA A 4 7.943 -7.066 5.248 1.00 0.00
+ATOM 46 CB ALA A 4 8.211 -5.919 4.265 1.00 0.00
+ATOM 47 C ALA A 4 9.225 -7.518 5.968 1.00 0.00
+ATOM 48 O ALA A 4 9.757 -6.798 6.815 1.00 0.00
+ATOM 49 H ALA A 4 7.062 -5.833 6.846 1.00 0.00 H
+ATOM 50 HA ALA A 4 7.582 -7.852 4.729 1.00 0.00 H
+ATOM 51 HB1 ALA A 4 7.375 -5.718 3.760 1.00 0.00 H
+ATOM 52 HB2 ALA A 4 8.500 -5.111 4.774 1.00 0.00 H
+ATOM 53 HB3 ALA A 4 8.931 -6.192 3.630 1.00 0.00 H
+ATOM 54 N ALA A 5 9.770 -8.696 5.678 1.00 0.00
+ATOM 55 CA ALA A 5 10.980 -9.123 6.358 1.00 0.00
+ATOM 56 CB ALA A 5 10.644 -10.384 7.164 1.00 0.00
+ATOM 57 C ALA A 5 12.128 -9.365 5.363 1.00 0.00
+ATOM 58 O ALA A 5 11.956 -10.066 4.364 1.00 0.00
+ATOM 59 H ALA A 5 9.279 -9.248 4.963 1.00 0.00 H
+ATOM 60 HA ALA A 5 11.270 -8.402 7.001 1.00 0.00 H
+ATOM 61 HB1 ALA A 5 11.482 -10.899 7.331 1.00 0.00 H
+ATOM 62 HB2 ALA A 5 10.233 -10.118 8.033 1.00 0.00 H
+ATOM 63 HB3 ALA A 5 10.002 -10.944 6.645 1.00 0.00 H
+ATOM 64 N ALA A 6 13.320 -8.816 5.577 1.00 0.00
+ATOM 65 CA ALA A 6 14.403 -9.044 4.638 1.00 0.00
+ATOM 66 CB ALA A 6 14.786 -7.690 4.027 1.00 0.00
+ATOM 67 C ALA A 6 15.602 -9.728 5.317 1.00 0.00
+ATOM 68 O ALA A 6 16.064 -9.283 6.369 1.00 0.00
+ATOM 69 H ALA A 6 13.398 -8.244 6.427 1.00 0.00 H
+ATOM 70 HA ALA A 6 14.078 -9.646 3.897 1.00 0.00 H
+ATOM 71 HB1 ALA A 6 14.557 -6.963 4.671 1.00 0.00 H
+ATOM 72 HB2 ALA A 6 15.766 -7.679 3.842 1.00 0.00 H
+ATOM 73 HB3 ALA A 6 14.281 -7.559 3.177 1.00 0.00 H
+ATOM 74 N ALA A 7 16.148 -10.810 4.770 1.00 0.00
+ATOM 75 CA ALA A 7 17.279 -11.455 5.411 1.00 0.00
+ATOM 76 CB ALA A 7 16.843 -12.869 5.817 1.00 0.00
+ATOM 77 C ALA A 7 18.512 -11.475 4.491 1.00 0.00
+ATOM 78 O ALA A 7 18.422 -11.876 3.330 1.00 0.00
+ATOM 79 H ALA A 7 15.715 -11.130 3.894 1.00 0.00 H
+ATOM 80 HA ALA A 7 17.521 -10.945 6.247 1.00 0.00 H
+ATOM 81 HB1 ALA A 7 16.628 -13.394 4.997 1.00 0.00 H
+ATOM 82 HB2 ALA A 7 17.586 -13.311 6.315 1.00 0.00 H
+ATOM 83 HB3 ALA A 7 16.036 -12.809 6.400 1.00 0.00 H
+ATOM 84 N GLN A 8 19.689 -11.056 4.947 1.00 0.00
+ATOM 85 CA GLN A 8 20.860 -11.074 4.073 1.00 0.00
+ATOM 86 CB GLN A 8 21.382 -9.636 3.814 1.00 0.00
+ATOM 87 CG GLN A 8 22.555 -9.522 2.810 1.00 0.00
+ATOM 88 CD GLN A 8 23.024 -8.093 2.529 1.00 0.00
+ATOM 89 C GLN A 8 21.911 -11.989 4.729 1.00 0.00
+ATOM 90 O GLN A 8 22.214 -11.835 5.913 1.00 0.00
+ATOM 91 H GLN A 8 19.701 -10.734 5.921 1.00 0.00 H
+ATOM 92 HA GLN A 8 20.600 -11.488 3.210 1.00 0.00 H
+ATOM 93 HB2 GLN A 8 20.624 -9.081 3.461 1.00 0.00 H
+ATOM 94 HB3 GLN A 8 21.690 -9.247 4.687 1.00 0.00 H
+ATOM 95 HG2 GLN A 8 23.330 -10.046 3.176 1.00 0.00 H
+ATOM 96 HG3 GLN A 8 22.265 -9.940 1.943 1.00 0.00 H
+ATOM 97 OE1 GLN A 8 23.958 -7.896 1.763 1.00 0.00 O
+ATOM 98 NE2 GLN A 8 22.414 -7.080 3.134 1.00 0.00 N
+ATOM 99 HE21 GLN A 8 22.689 -6.136 2.997 1.00 0.00 H
+ATOM 100 HE22 GLN A 8 21.628 -7.303 3.765 1.00 0.00 H
+ATOM 101 N ALA A 9 22.494 -12.949 4.017 1.00 0.00
+ATOM 102 CA ALA A 9 23.485 -13.811 4.635 1.00 0.00
+ATOM 103 CB ALA A 9 22.937 -15.243 4.615 1.00 0.00
+ATOM 104 C ALA A 9 24.845 -13.705 3.924 1.00 0.00
+ATOM 105 O ALA A 9 24.922 -13.812 2.699 1.00 0.00
+ATOM 106 H ALA A 9 22.192 -13.019 3.037 1.00 0.00 H
+ATOM 107 HA ALA A 9 23.612 -13.533 5.596 1.00 0.00 H
+ATOM 108 HB1 ALA A 9 22.907 -15.570 3.673 1.00 0.00 H
+ATOM 109 HB2 ALA A 9 23.534 -15.831 5.157 1.00 0.00 H
+ATOM 110 HB3 ALA A 9 22.018 -15.248 5.003 1.00 0.00 H
+ATOM 111 N ALA A 10 25.951 -13.496 4.632 1.00 0.00
+ATOM 112 CA ALA A 10 27.234 -13.396 3.960 1.00 0.00
+ATOM 113 CB ALA A 10 27.779 -11.982 4.201 1.00 0.00
+ATOM 114 C ALA A 10 28.210 -14.480 4.449 1.00 0.00
+ATOM 115 O ALA A 10 28.396 -14.660 5.653 1.00 0.00
+ATOM 116 H ALA A 10 25.819 -13.416 5.648 1.00 0.00 H
+ATOM 117 HA ALA A 10 27.099 -13.521 2.968 1.00 0.00 H
+ATOM 118 HB1 ALA A 10 27.068 -11.316 3.986 1.00 0.00 H
+ATOM 119 HB2 ALA A 10 28.047 -11.892 5.158 1.00 0.00 H
+ATOM 120 HB3 ALA A 10 28.571 -11.831 3.614 1.00 0.00 H
+ATOM 121 N ALA A 11 28.863 -15.233 3.568 1.00 0.00
+ATOM 122 CA ALA A 11 29.784 -16.256 4.029 1.00 0.00
+ATOM 123 CB ALA A 11 29.238 -17.616 3.574 1.00 0.00
+ATOM 124 C ALA A 11 31.209 -16.004 3.509 1.00 0.00
+ATOM 125 O ALA A 11 31.412 -15.786 2.313 1.00 0.00
+ATOM 126 H ALA A 11 28.664 -15.032 2.580 1.00 0.00 H
+ATOM 127 HA ALA A 11 29.812 -16.246 5.037 1.00 0.00 H
+ATOM 128 HB1 ALA A 11 29.413 -17.730 2.598 1.00 0.00 H
+ATOM 129 HB2 ALA A 11 29.695 -18.341 4.085 1.00 0.00 H
+ATOM 130 HB3 ALA A 11 28.256 -17.650 3.747 1.00 0.00 H
+ATOM 131 N ALA A 12 32.237 -16.022 4.352 1.00 0.00
+ATOM 132 CA ALA A 12 33.583 -15.784 3.862 1.00 0.00
+ATOM 133 CB ALA A 12 34.102 -14.501 4.522 1.00 0.00
+ATOM 134 C ALA A 12 34.502 -16.986 4.138 1.00 0.00
+ATOM 135 O ALA A 12 34.563 -17.484 5.263 1.00 0.00
+ATOM 136 H ALA A 12 32.001 -16.211 5.335 1.00 0.00 H
+ATOM 137 HA ALA A 12 33.551 -15.637 2.865 1.00 0.00 H
+ATOM 138 HB1 ALA A 12 33.336 -13.882 4.685 1.00 0.00 H
+ATOM 139 HB2 ALA A 12 34.539 -14.731 5.389 1.00 0.00 H
+ATOM 140 HB3 ALA A 12 34.764 -14.065 3.916 1.00 0.00 H
+ATOM 141 N GLN A 13 35.240 -17.498 3.157 1.00 0.00
+ATOM 142 CA GLN A 13 36.114 -18.639 3.419 1.00 0.00
+ATOM 143 CB GLN A 13 35.662 -19.882 2.607 1.00 0.00
+ATOM 144 CG GLN A 13 36.448 -21.186 2.888 1.00 0.00
+ATOM 145 CD GLN A 13 35.957 -22.412 2.115 1.00 0.00
+ATOM 146 C GLN A 13 37.555 -18.201 3.100 1.00 0.00
+ATOM 147 O GLN A 13 37.813 -17.652 2.028 1.00 0.00
+ATOM 148 H GLN A 13 35.145 -17.041 2.243 1.00 0.00 H
+ATOM 149 HA GLN A 13 36.073 -18.849 4.387 1.00 0.00 H
+ATOM 150 HB2 GLN A 13 34.695 -20.060 2.809 1.00 0.00 H
+ATOM 151 HB3 GLN A 13 35.756 -19.675 1.629 1.00 0.00 H
+ATOM 152 HG2 GLN A 13 37.412 -21.026 2.653 1.00 0.00 H
+ATOM 153 HG3 GLN A 13 36.385 -21.382 3.872 1.00 0.00 H
+ATOM 154 OE1 GLN A 13 36.522 -23.488 2.254 1.00 0.00 O
+ATOM 155 NE2 GLN A 13 34.923 -22.287 1.290 1.00 0.00 N
+ATOM 156 HE21 GLN A 13 34.575 -23.047 0.756 1.00 0.00 H
+ATOM 157 HE22 GLN A 13 34.480 -21.358 1.217 1.00 0.00 H
+ATOM 158 N ALA A 14 38.526 -18.414 3.983 1.00 0.00
+ATOM 159 CA ALA A 14 39.885 -18.001 3.682 1.00 0.00
+ATOM 160 CB ALA A 14 40.287 -16.934 4.708 1.00 0.00
+ATOM 161 C ALA A 14 40.851 -19.198 3.688 1.00 0.00
+ATOM 162 O ALA A 14 40.868 -19.987 4.634 1.00 0.00
+ATOM 163 H ALA A 14 38.238 -18.876 4.855 1.00 0.00 H
+ATOM 164 HA ALA A 14 39.909 -17.584 2.764 1.00 0.00 H
+ATOM 165 HB1 ALA A 14 39.803 -16.085 4.506 1.00 0.00 H
+ATOM 166 HB2 ALA A 14 40.045 -17.250 5.623 1.00 0.00 H
+ATOM 167 HB3 ALA A 14 41.271 -16.781 4.654 1.00 0.00 H
+ATOM 168 N ALA A 15 41.679 -19.389 2.664 1.00 0.00
+ATOM 169 CA ALA A 15 42.590 -20.519 2.669 1.00 0.00
+ATOM 170 CB ALA A 15 42.216 -21.427 1.492 1.00 0.00
+ATOM 171 C ALA A 15 44.056 -20.058 2.598 1.00 0.00
+ATOM 172 O ALA A 15 44.401 -19.182 1.803 1.00 0.00
+ATOM 173 H ALA A 15 41.615 -18.696 1.908 1.00 0.00 H
+ATOM 174 HA ALA A 15 42.467 -21.040 3.524 1.00 0.00 H
+ATOM 175 HB1 ALA A 15 42.622 -22.328 1.630 1.00 0.00 H
+ATOM 176 HB2 ALA A 15 41.223 -21.510 1.443 1.00 0.00 H
+ATOM 177 HB3 ALA A 15 42.562 -21.028 0.646 1.00 0.00 H
+ATOM 178 N NH2 A 16 44.965 -20.607 3.398 1.00 0.00
+ATOM 179 HN1 NH2 A 16 44.696 -21.319 4.046 1.00 0.00
+ATOM 180 HN2 NH2 A 16 45.918 -20.308 3.351 1.00 0.00
+TER
+END
\ No newline at end of file
diff --git a/proteinbenchmark/data/observables/aaqaa3/aaqaa3-beta-protonated.pdb.cs b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-beta-protonated.pdb.cs
new file mode 100644
index 0000000..a028723
--- /dev/null
+++ b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-beta-protonated.pdb.cs
@@ -0,0 +1,151 @@
+NUM,RES,ATOMNAME,SHIFT
+1,A,C,176.1590
+1,A,CA,52.2475
+1,A,CB,19.6067
+1,A,H,8.3129
+1,A,HA,4.3652
+1,A,HB,1.4195
+1,A,HB2,1.5965
+1,A,HB3,1.4662
+1,A,N,126.4881
+2,A,C,176.3547
+2,A,CA,51.7401
+2,A,CB,21.0854
+2,A,H,8.4077
+2,A,HA,4.4974
+2,A,HB,1.2983
+2,A,HB2,1.5485
+2,A,HB3,1.4106
+2,A,N,125.4199
+3,Q,C,174.6153
+3,Q,CA,54.9044
+3,Q,CB,31.1575
+3,Q,CD,179.7136
+3,Q,CG,34.0103
+3,Q,H,8.5192
+3,Q,HA,4.4817
+3,Q,HB2,1.8072
+3,Q,HB3,1.7884
+3,Q,HE21,7.3305
+3,Q,HE22,6.8118
+3,Q,HG2,2.1778
+3,Q,HG3,2.2376
+3,Q,N,122.5336
+4,A,C,175.7593
+4,A,CA,51.4154
+4,A,CB,21.2060
+4,A,H,8.5774
+4,A,HA,4.4916
+4,A,HB,1.2951
+4,A,HB2,1.6668
+4,A,HB3,1.3740
+4,A,N,129.6472
+5,A,C,176.1992
+5,A,CA,51.6237
+5,A,CB,21.1208
+5,A,H,8.4601
+5,A,HA,4.4752
+5,A,HB,1.3672
+5,A,HB2,1.5729
+5,A,HB3,1.3611
+5,A,N,125.2517
+6,A,C,176.5251
+6,A,CA,51.2451
+6,A,CB,21.0890
+6,A,H,8.4615
+6,A,HA,4.4166
+6,A,HB,1.3270
+6,A,HB2,1.5588
+6,A,HB3,1.4212
+6,A,N,125.3266
+7,A,C,176.4972
+7,A,CA,51.5592
+7,A,CB,21.2824
+7,A,H,8.5058
+7,A,HA,4.5432
+7,A,HB,1.2907
+7,A,HB2,1.5865
+7,A,HB3,1.4535
+7,A,N,125.3602
+8,Q,C,174.5090
+8,Q,CA,54.4517
+8,Q,CB,31.2830
+8,Q,CD,179.7094
+8,Q,CG,34.0243
+8,Q,H,8.5204
+8,Q,HA,4.4607
+8,Q,HB2,1.9740
+8,Q,HB3,1.7628
+8,Q,HE21,7.3628
+8,Q,HE22,6.8360
+8,Q,HG2,2.1711
+8,Q,HG3,2.1760
+8,Q,N,122.5543
+9,A,C,175.9841
+9,A,CA,51.5696
+9,A,CB,20.9836
+9,A,H,8.4998
+9,A,HA,4.4990
+9,A,HB,1.2940
+9,A,HB2,1.6281
+9,A,HB3,1.4420
+9,A,N,129.1969
+10,A,C,176.1223
+10,A,CA,51.2455
+10,A,CB,21.1468
+10,A,H,8.5092
+10,A,HA,4.5304
+10,A,HB,1.3184
+10,A,HB2,1.5798
+10,A,HB3,1.3253
+10,A,N,125.4462
+11,A,C,176.6412
+11,A,CA,51.1775
+11,A,CB,21.2107
+11,A,H,8.5688
+11,A,HA,4.5435
+11,A,HB,1.2926
+11,A,HB2,1.5597
+11,A,HB3,1.4692
+11,A,N,125.3556
+12,A,C,176.5419
+12,A,CA,51.2117
+12,A,CB,21.4180
+12,A,H,8.6768
+12,A,HA,4.5113
+12,A,HB,1.2681
+12,A,HB2,1.5680
+12,A,HB3,1.4587
+12,A,N,125.6466
+13,Q,C,174.5757
+13,Q,CA,54.4678
+13,Q,CB,31.2236
+13,Q,CD,179.7542
+13,Q,CG,33.9507
+13,Q,H,8.5331
+13,Q,HA,4.4826
+13,Q,HB2,1.9371
+13,Q,HB3,1.7609
+13,Q,HE21,7.3233
+13,Q,HE22,6.7971
+13,Q,HG2,2.1479
+13,Q,HG3,2.2069
+13,Q,N,122.7265
+14,A,C,176.0113
+14,A,CA,51.8992
+14,A,CB,21.0349
+14,A,H,8.4020
+14,A,HA,4.3997
+14,A,HB,1.3178
+14,A,HB2,1.4726
+14,A,HB3,1.4908
+14,A,N,129.4663
+15,A,C,177.6320
+15,A,CA,52.7883
+15,A,CB,21.6193
+15,A,H,8.2814
+15,A,HA,4.2404
+15,A,HB,1.3288
+15,A,HB2,1.5186
+15,A,HB3,1.4800
+15,A,N,127.0994
diff --git a/proteinbenchmark/data/observables/aaqaa3/aaqaa3-beta-protonated.pdb.shifty b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-beta-protonated.pdb.shifty
new file mode 100644
index 0000000..e69de29
diff --git a/proteinbenchmark/data/observables/aaqaa3/aaqaa3-beta-protonated.pdb.sxp b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-beta-protonated.pdb.sxp
new file mode 100644
index 0000000..1d3e266
--- /dev/null
+++ b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-beta-protonated.pdb.sxp
@@ -0,0 +1,151 @@
+NUM,RES,IUPAC,ATOM,PRED_CS
+1,ALA,A,H,8.3129
+1,ALA,A,HA,4.3652
+1,ALA,A,C,176.1590
+1,ALA,A,CA,52.2475
+1,ALA,A,CB,19.6067
+1,ALA,A,N,126.4881
+1,ALA,A,HB,1.4195
+1,ALA,A,HB2,1.5965
+1,ALA,A,HB3,1.4662
+2,ALA,A,H,8.4077
+2,ALA,A,HA,4.4974
+2,ALA,A,C,176.3547
+2,ALA,A,CA,51.7401
+2,ALA,A,CB,21.0854
+2,ALA,A,N,125.4199
+2,ALA,A,HB,1.2983
+2,ALA,A,HB2,1.5485
+2,ALA,A,HB3,1.4106
+3,GLN,Q,H,8.5192
+3,GLN,Q,HA,4.4817
+3,GLN,Q,C,174.6153
+3,GLN,Q,CA,54.9044
+3,GLN,Q,CB,31.1575
+3,GLN,Q,N,122.5336
+3,GLN,Q,CD,179.7136
+3,GLN,Q,CG,34.0103
+3,GLN,Q,HB2,1.8072
+3,GLN,Q,HB3,1.7884
+3,GLN,Q,HE21,7.3305
+3,GLN,Q,HE22,6.8118
+3,GLN,Q,HG2,2.1778
+3,GLN,Q,HG3,2.2376
+4,ALA,A,H,8.5774
+4,ALA,A,HA,4.4916
+4,ALA,A,C,175.7593
+4,ALA,A,CA,51.4154
+4,ALA,A,CB,21.2060
+4,ALA,A,N,129.6472
+4,ALA,A,HB,1.2951
+4,ALA,A,HB2,1.6668
+4,ALA,A,HB3,1.3740
+5,ALA,A,H,8.4601
+5,ALA,A,HA,4.4752
+5,ALA,A,C,176.1992
+5,ALA,A,CA,51.6237
+5,ALA,A,CB,21.1208
+5,ALA,A,N,125.2517
+5,ALA,A,HB,1.3672
+5,ALA,A,HB2,1.5729
+5,ALA,A,HB3,1.3611
+6,ALA,A,H,8.4615
+6,ALA,A,HA,4.4166
+6,ALA,A,C,176.5251
+6,ALA,A,CA,51.2451
+6,ALA,A,CB,21.0890
+6,ALA,A,N,125.3266
+6,ALA,A,HB,1.3270
+6,ALA,A,HB2,1.5588
+6,ALA,A,HB3,1.4212
+7,ALA,A,H,8.5058
+7,ALA,A,HA,4.5432
+7,ALA,A,C,176.4972
+7,ALA,A,CA,51.5592
+7,ALA,A,CB,21.2824
+7,ALA,A,N,125.3602
+7,ALA,A,HB,1.2907
+7,ALA,A,HB2,1.5865
+7,ALA,A,HB3,1.4535
+8,GLN,Q,H,8.5204
+8,GLN,Q,HA,4.4607
+8,GLN,Q,C,174.5090
+8,GLN,Q,CA,54.4517
+8,GLN,Q,CB,31.2830
+8,GLN,Q,N,122.5543
+8,GLN,Q,CD,179.7094
+8,GLN,Q,CG,34.0243
+8,GLN,Q,HB2,1.9740
+8,GLN,Q,HB3,1.7628
+8,GLN,Q,HE21,7.3628
+8,GLN,Q,HE22,6.8360
+8,GLN,Q,HG2,2.1711
+8,GLN,Q,HG3,2.1760
+9,ALA,A,H,8.4998
+9,ALA,A,HA,4.4990
+9,ALA,A,C,175.9841
+9,ALA,A,CA,51.5696
+9,ALA,A,CB,20.9836
+9,ALA,A,N,129.1969
+9,ALA,A,HB,1.2940
+9,ALA,A,HB2,1.6281
+9,ALA,A,HB3,1.4420
+10,ALA,A,H,8.5092
+10,ALA,A,HA,4.5304
+10,ALA,A,C,176.1223
+10,ALA,A,CA,51.2455
+10,ALA,A,CB,21.1468
+10,ALA,A,N,125.4462
+10,ALA,A,HB,1.3184
+10,ALA,A,HB2,1.5798
+10,ALA,A,HB3,1.3253
+11,ALA,A,H,8.5688
+11,ALA,A,HA,4.5435
+11,ALA,A,C,176.6412
+11,ALA,A,CA,51.1775
+11,ALA,A,CB,21.2107
+11,ALA,A,N,125.3556
+11,ALA,A,HB,1.2926
+11,ALA,A,HB2,1.5597
+11,ALA,A,HB3,1.4692
+12,ALA,A,H,8.6768
+12,ALA,A,HA,4.5113
+12,ALA,A,C,176.5419
+12,ALA,A,CA,51.2117
+12,ALA,A,CB,21.4180
+12,ALA,A,N,125.6466
+12,ALA,A,HB,1.2681
+12,ALA,A,HB2,1.5680
+12,ALA,A,HB3,1.4587
+13,GLN,Q,H,8.5331
+13,GLN,Q,HA,4.4826
+13,GLN,Q,C,174.5757
+13,GLN,Q,CA,54.4678
+13,GLN,Q,CB,31.2236
+13,GLN,Q,N,122.7265
+13,GLN,Q,CD,179.7542
+13,GLN,Q,CG,33.9507
+13,GLN,Q,HB2,1.9371
+13,GLN,Q,HB3,1.7609
+13,GLN,Q,HE21,7.3233
+13,GLN,Q,HE22,6.7971
+13,GLN,Q,HG2,2.1479
+13,GLN,Q,HG3,2.2069
+14,ALA,A,H,8.4020
+14,ALA,A,HA,4.3997
+14,ALA,A,C,176.0113
+14,ALA,A,CA,51.8992
+14,ALA,A,CB,21.0349
+14,ALA,A,N,129.4663
+14,ALA,A,HB,1.3178
+14,ALA,A,HB2,1.4726
+14,ALA,A,HB3,1.4908
+15,ALA,A,H,8.2814
+15,ALA,A,HA,4.2404
+15,ALA,A,C,177.6320
+15,ALA,A,CA,52.7883
+15,ALA,A,CB,21.6193
+15,ALA,A,N,127.0994
+15,ALA,A,HB,1.3288
+15,ALA,A,HB2,1.5186
+15,ALA,A,HB3,1.4800
diff --git a/proteinbenchmark/data/observables/aaqaa3/aaqaa3-beta-protonated.spartap b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-beta-protonated.spartap
new file mode 100644
index 0000000..ab3905b
--- /dev/null
+++ b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-beta-protonated.spartap
@@ -0,0 +1,114 @@
+REMARK SPARTA+ Protein Chemical Shift Prediction Table
+REMARK
+REMARK All chemical shifts are reported in ppm:
+REMARK
+REMARK SHIFT is the predicted chemical shift.
+REMARK SS_SHIFT is the predicted secondary chemical shift.
+REMARK RC_SHIFT is the random coil chemical shift.
+REMARK HM_SHIFT is the ring current shift; a correction
+REMARK of 0.6 times this value is applied.
+REMARK EF_SHIFT is the adjustment for electric field effect,
+REMARK applied to proton shifts only.
+REMARK SIGMA is the estimated prediction error.
+REMARK
+REMARK Reference:
+REMARK Y. Shen and A. Bax: SPARTA+: a modest improvement in empirical NMR
+REMARK chemical shift prediction by means of an artificial neural network.
+REMARK J. Biomol. NMR 48, 13-22 (2010).
+
+DATA SOURCE aaqaa3-beta-protonated.pdb
+
+DATA FIRST_RESID 0
+
+DATA SEQUENCE ?AAQAAAAQA AAAQAA?
+
+VARS RESID RESNAME ATOMNAME SS_SHIFT SHIFT RC_SHIFT HM_SHIFT EF_SHIFT SIGMA
+FORMAT %4d %4s %4s %9.3f %9.3f %9.3f %9.3f %9.3f %9.3f
+
+ 0 ? HA 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 0 ? C 0.000 9999.000 9999.000 -0.000 0.000 0.000
+ 0 ? CA 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 0 ? CB 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 2 A N 1.771 124.591 122.820 -0.000 0.000 2.331
+ 2 A HA 0.316 4.636 4.320 -0.000 0.000 0.320
+ 2 A C -0.798 176.786 177.584 -0.000 0.000 1.138
+ 2 A CA -0.232 51.805 52.037 -0.000 0.000 0.790
+ 2 A CB 0.753 19.753 19.000 -0.000 0.000 1.206
+ 2 A HN 0.118 8.268 8.150 -0.000 0.000 0.470
+ 3 Q N 2.862 122.662 119.800 -0.000 0.000 2.330
+ 3 Q HA 0.222 4.562 4.340 -0.000 0.000 0.269
+ 3 Q C -1.131 174.869 176.000 -0.000 0.000 1.022
+ 3 Q CA -0.257 55.546 55.803 -0.000 0.000 0.796
+ 3 Q CB 1.390 30.128 28.738 -0.000 0.000 1.271
+ 3 Q HN 0.305 8.575 8.270 -0.000 0.000 0.450
+ 4 A N 3.851 126.671 122.820 -0.000 0.000 2.331
+ 4 A HA 0.363 4.683 4.320 -0.000 0.000 0.320
+ 4 A C -1.517 176.067 177.584 -0.000 0.000 1.138
+ 4 A CA -0.341 51.696 52.037 -0.000 0.000 0.790
+ 4 A CB 1.068 20.068 19.000 -0.000 0.000 1.206
+ 4 A HN 0.364 8.514 8.150 -0.000 0.000 0.470
+ 5 A N 2.189 125.009 122.820 -0.000 0.000 2.343
+ 5 A HA 0.352 4.672 4.320 -0.000 0.000 0.316
+ 5 A C -1.049 176.535 177.584 -0.000 0.000 1.104
+ 5 A CA -0.224 51.813 52.037 -0.000 0.000 0.768
+ 5 A CB 1.025 20.025 19.000 -0.000 0.000 1.213
+ 5 A HN 0.269 8.419 8.150 -0.000 0.000 0.456
+ 6 A N 2.315 125.135 122.820 -0.000 0.000 2.330
+ 6 A HA 0.360 4.680 4.320 -0.000 0.000 0.313
+ 6 A C -1.066 176.518 177.584 -0.000 0.000 1.124
+ 6 A CA -0.227 51.810 52.037 -0.000 0.000 0.774
+ 6 A CB 1.026 20.026 19.000 -0.000 0.000 1.198
+ 6 A HN 0.272 8.422 8.150 -0.000 0.000 0.465
+ 7 A N 1.943 124.763 122.820 -0.000 0.000 2.331
+ 7 A HA 0.321 4.641 4.320 -0.000 0.000 0.320
+ 7 A C -0.966 176.618 177.584 -0.000 0.000 1.138
+ 7 A CA -0.196 51.841 52.037 -0.000 0.000 0.790
+ 7 A CB 0.895 19.895 19.000 -0.000 0.000 1.206
+ 7 A HN 0.198 8.348 8.150 -0.000 0.000 0.470
+ 8 Q N 3.003 122.803 119.800 -0.000 0.000 2.331
+ 8 Q HA 0.223 4.563 4.340 -0.000 0.000 0.267
+ 8 Q C -1.145 174.855 176.000 -0.000 0.000 1.006
+ 8 Q CA -0.274 55.529 55.803 -0.000 0.000 0.818
+ 8 Q CB 1.404 30.142 28.738 -0.000 0.000 1.276
+ 8 Q HN 0.307 8.577 8.270 -0.000 0.000 0.450
+ 9 A N 3.862 126.682 122.820 -0.000 0.000 2.331
+ 9 A HA 0.363 4.683 4.320 -0.000 0.000 0.320
+ 9 A C -1.517 176.067 177.584 -0.000 0.000 1.138
+ 9 A CA -0.343 51.694 52.037 -0.000 0.000 0.790
+ 9 A CB 1.068 20.067 19.000 -0.000 0.000 1.206
+ 9 A HN 0.364 8.514 8.150 -0.000 0.000 0.470
+ 10 A N 2.189 125.009 122.820 -0.000 0.000 2.343
+ 10 A HA 0.352 4.672 4.320 -0.000 0.000 0.316
+ 10 A C -1.050 176.534 177.584 -0.000 0.000 1.104
+ 10 A CA -0.224 51.813 52.037 -0.000 0.000 0.768
+ 10 A CB 1.026 20.026 19.000 -0.000 0.000 1.213
+ 10 A HN 0.268 8.418 8.150 -0.000 0.000 0.456
+ 11 A N 2.308 125.128 122.820 -0.000 0.000 2.343
+ 11 A HA 0.360 4.680 4.320 -0.000 0.000 0.316
+ 11 A C -1.068 176.516 177.584 -0.000 0.000 1.104
+ 11 A CA -0.228 51.809 52.037 -0.000 0.000 0.768
+ 11 A CB 1.028 20.028 19.000 -0.000 0.000 1.213
+ 11 A HN 0.272 8.422 8.150 -0.000 0.000 0.456
+ 12 A N 1.939 124.759 122.820 -0.000 0.000 2.330
+ 12 A HA 0.321 4.641 4.320 -0.000 0.000 0.313
+ 12 A C -0.966 176.618 177.584 -0.000 0.000 1.124
+ 12 A CA -0.195 51.842 52.037 -0.000 0.000 0.774
+ 12 A CB 0.894 19.894 19.000 -0.000 0.000 1.198
+ 12 A HN 0.198 8.348 8.150 -0.000 0.000 0.465
+ 13 Q N 3.007 122.807 119.800 -0.000 0.000 2.331
+ 13 Q HA 0.223 4.563 4.340 -0.000 0.000 0.267
+ 13 Q C -1.141 174.859 176.000 -0.000 0.000 1.006
+ 13 Q CA -0.273 55.529 55.803 -0.000 0.000 0.818
+ 13 Q CB 1.403 30.141 28.738 -0.000 0.000 1.276
+ 13 Q HN 0.307 8.577 8.270 -0.000 0.000 0.450
+ 14 A N 2.886 125.706 122.820 -0.000 0.000 2.331
+ 14 A HA 0.437 4.757 4.320 -0.000 0.000 0.320
+ 14 A C -1.249 176.335 177.584 -0.000 0.000 1.138
+ 14 A CA 0.031 52.068 52.037 -0.000 0.000 0.790
+ 14 A CB 1.009 20.009 19.000 -0.000 0.000 1.206
+ 14 A HN 0.428 8.578 8.150 -0.000 0.000 0.470
+ 16 ? N 0.000 9999.000 9999.000 -0.000 0.000 0.000
+ 16 ? HA 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 16 ? CA 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 16 ? CB 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 16 ? HN 0.000 9999.000 9999.000 0.000 0.000 0.000
diff --git a/proteinbenchmark/data/observables/aaqaa3/aaqaa3-beta-protonated_pred.tab b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-beta-protonated_pred.tab
new file mode 100644
index 0000000..efeef3d
--- /dev/null
+++ b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-beta-protonated_pred.tab
@@ -0,0 +1,114 @@
+REMARK SPARTA+ Protein Chemical Shift Prediction Table
+REMARK
+REMARK All chemical shifts are reported in ppm:
+REMARK
+REMARK SHIFT is the predicted chemical shift.
+REMARK SS_SHIFT is the predicted secondary chemical shift.
+REMARK RC_SHIFT is the random coil chemical shift.
+REMARK HM_SHIFT is the ring current shift; a correction
+REMARK of 0.6 times this value is applied.
+REMARK EF_SHIFT is the adjustment for electric field effect,
+REMARK applied to proton shifts only.
+REMARK SIGMA is the estimated prediction error.
+REMARK
+REMARK Reference:
+REMARK Y. Shen and A. Bax: SPARTA+: a modest improvement in empirical NMR
+REMARK chemical shift prediction by means of an artificial neural network.
+REMARK J. Biomol. NMR 48, 13-22 (2010).
+
+DATA SOURCE aaqaa3-beta-protonated
+
+DATA FIRST_RESID 0
+
+DATA SEQUENCE ?AAQAAAAQA AAAQAA?
+
+VARS RESID RESNAME ATOMNAME SS_SHIFT SHIFT RC_SHIFT HM_SHIFT EF_SHIFT SIGMA
+FORMAT %4d %4s %4s %9.3f %9.3f %9.3f %9.3f %9.3f %9.3f
+
+ 0 ? HA 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 0 ? C 0.000 9999.000 9999.000 -0.000 0.000 0.000
+ 0 ? CA 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 0 ? CB 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 2 A N 1.771 124.591 122.820 -0.000 0.000 2.331
+ 2 A HA 0.316 4.636 4.320 -0.000 0.000 0.320
+ 2 A C -0.798 176.786 177.584 -0.000 0.000 1.138
+ 2 A CA -0.232 51.805 52.037 -0.000 0.000 0.790
+ 2 A CB 0.753 19.753 19.000 -0.000 0.000 1.206
+ 2 A HN 0.118 8.268 8.150 -0.000 0.000 0.470
+ 3 Q N 2.862 122.662 119.800 -0.000 0.000 2.330
+ 3 Q HA 0.222 4.562 4.340 -0.000 0.000 0.269
+ 3 Q C -1.131 174.869 176.000 -0.000 0.000 1.022
+ 3 Q CA -0.257 55.546 55.803 -0.000 0.000 0.796
+ 3 Q CB 1.390 30.128 28.738 -0.000 0.000 1.271
+ 3 Q HN 0.305 8.575 8.270 -0.000 0.000 0.450
+ 4 A N 3.851 126.671 122.820 -0.000 0.000 2.331
+ 4 A HA 0.363 4.683 4.320 -0.000 0.000 0.320
+ 4 A C -1.517 176.067 177.584 -0.000 0.000 1.138
+ 4 A CA -0.341 51.696 52.037 -0.000 0.000 0.790
+ 4 A CB 1.068 20.068 19.000 -0.000 0.000 1.206
+ 4 A HN 0.364 8.514 8.150 -0.000 0.000 0.470
+ 5 A N 2.189 125.009 122.820 -0.000 0.000 2.343
+ 5 A HA 0.352 4.672 4.320 -0.000 0.000 0.316
+ 5 A C -1.049 176.535 177.584 -0.000 0.000 1.104
+ 5 A CA -0.224 51.813 52.037 -0.000 0.000 0.768
+ 5 A CB 1.025 20.025 19.000 -0.000 0.000 1.213
+ 5 A HN 0.269 8.419 8.150 -0.000 0.000 0.456
+ 6 A N 2.315 125.135 122.820 -0.000 0.000 2.330
+ 6 A HA 0.360 4.680 4.320 -0.000 0.000 0.313
+ 6 A C -1.066 176.518 177.584 -0.000 0.000 1.124
+ 6 A CA -0.227 51.810 52.037 -0.000 0.000 0.774
+ 6 A CB 1.026 20.026 19.000 -0.000 0.000 1.198
+ 6 A HN 0.272 8.422 8.150 -0.000 0.000 0.465
+ 7 A N 1.943 124.763 122.820 -0.000 0.000 2.331
+ 7 A HA 0.321 4.641 4.320 -0.000 0.000 0.320
+ 7 A C -0.966 176.618 177.584 -0.000 0.000 1.138
+ 7 A CA -0.196 51.841 52.037 -0.000 0.000 0.790
+ 7 A CB 0.895 19.895 19.000 -0.000 0.000 1.206
+ 7 A HN 0.198 8.348 8.150 -0.000 0.000 0.470
+ 8 Q N 3.003 122.803 119.800 -0.000 0.000 2.331
+ 8 Q HA 0.223 4.563 4.340 -0.000 0.000 0.267
+ 8 Q C -1.145 174.855 176.000 -0.000 0.000 1.006
+ 8 Q CA -0.274 55.529 55.803 -0.000 0.000 0.818
+ 8 Q CB 1.404 30.142 28.738 -0.000 0.000 1.276
+ 8 Q HN 0.307 8.577 8.270 -0.000 0.000 0.450
+ 9 A N 3.862 126.682 122.820 -0.000 0.000 2.331
+ 9 A HA 0.363 4.683 4.320 -0.000 0.000 0.320
+ 9 A C -1.517 176.067 177.584 -0.000 0.000 1.138
+ 9 A CA -0.343 51.694 52.037 -0.000 0.000 0.790
+ 9 A CB 1.068 20.067 19.000 -0.000 0.000 1.206
+ 9 A HN 0.364 8.514 8.150 -0.000 0.000 0.470
+ 10 A N 2.189 125.009 122.820 -0.000 0.000 2.343
+ 10 A HA 0.352 4.672 4.320 -0.000 0.000 0.316
+ 10 A C -1.050 176.534 177.584 -0.000 0.000 1.104
+ 10 A CA -0.224 51.813 52.037 -0.000 0.000 0.768
+ 10 A CB 1.026 20.026 19.000 -0.000 0.000 1.213
+ 10 A HN 0.268 8.418 8.150 -0.000 0.000 0.456
+ 11 A N 2.308 125.128 122.820 -0.000 0.000 2.343
+ 11 A HA 0.360 4.680 4.320 -0.000 0.000 0.316
+ 11 A C -1.068 176.516 177.584 -0.000 0.000 1.104
+ 11 A CA -0.228 51.809 52.037 -0.000 0.000 0.768
+ 11 A CB 1.028 20.028 19.000 -0.000 0.000 1.213
+ 11 A HN 0.272 8.422 8.150 -0.000 0.000 0.456
+ 12 A N 1.939 124.759 122.820 -0.000 0.000 2.330
+ 12 A HA 0.321 4.641 4.320 -0.000 0.000 0.313
+ 12 A C -0.966 176.618 177.584 -0.000 0.000 1.124
+ 12 A CA -0.195 51.842 52.037 -0.000 0.000 0.774
+ 12 A CB 0.894 19.894 19.000 -0.000 0.000 1.198
+ 12 A HN 0.198 8.348 8.150 -0.000 0.000 0.465
+ 13 Q N 3.007 122.807 119.800 -0.000 0.000 2.331
+ 13 Q HA 0.223 4.563 4.340 -0.000 0.000 0.267
+ 13 Q C -1.141 174.859 176.000 -0.000 0.000 1.006
+ 13 Q CA -0.273 55.529 55.803 -0.000 0.000 0.818
+ 13 Q CB 1.403 30.141 28.738 -0.000 0.000 1.276
+ 13 Q HN 0.307 8.577 8.270 -0.000 0.000 0.450
+ 14 A N 2.886 125.706 122.820 -0.000 0.000 2.331
+ 14 A HA 0.437 4.757 4.320 -0.000 0.000 0.320
+ 14 A C -1.249 176.335 177.584 -0.000 0.000 1.138
+ 14 A CA 0.031 52.068 52.037 -0.000 0.000 0.790
+ 14 A CB 1.009 20.009 19.000 -0.000 0.000 1.206
+ 14 A HN 0.428 8.578 8.150 -0.000 0.000 0.470
+ 16 ? N 0.000 9999.000 9999.000 -0.000 0.000 0.000
+ 16 ? HA 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 16 ? CA 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 16 ? CB 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 16 ? HN 0.000 9999.000 9999.000 0.000 0.000 0.000
diff --git a/proteinbenchmark/data/observables/aaqaa3/aaqaa3-beta-protonated_struct.tab b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-beta-protonated_struct.tab
new file mode 100644
index 0000000..983f6ff
--- /dev/null
+++ b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-beta-protonated_struct.tab
@@ -0,0 +1,80 @@
+REMARK SPARTA+ Structural Parameters Table derived from input PDB cooridnates
+REMARK
+REMARK PHI_R1 PSI_R1 CHI1_R1 and CHI2_R1 are the backbone and sidechain
+REMARK torsion angles of the first residue in a triplet.
+REMARK
+REMARK PHI_R2 PSI_R2 CHI1_R2 and CHI2_R2 are the backbone and sidechain
+REMARK torsion angles of the second (central) residue in a triplet.
+REMARK
+REMARK PHI_R3 PSI_R3 CHI1_R3 and CHI2_R3 are the backbone and sidechain
+REMARK torsion angles of the third residue in a triplet.
+REMARK
+REMARK H-Bond Distances are given in Angstroms:
+REMARK
+REMARK HN_HB_DIST_R2 H-bond distance for the HN atom in the central residue.
+REMARK HA_HB_DIST_R2 H-bond distance for the HA atom in the central residue.
+REMARK CO_HB_DIST_R2 H-bond distance for the CO atom in the central residue.
+REMARK
+REMARK HN_S2_R2 is the Bruschweiler structure-based HN order parameter of
+REMARK the central residue. Reference: Zhang FL, Bruschweiler R
+REMARK JACS 124, 12654-12655 (2002)
+REMARK
+REMARK Reference:
+REMARK Y. Shen and A. Bax: SPARTA+: a modest improvement in empirical NMR
+REMARK chemical shift prediction by means of an artificial neural network.
+REMARK J. Biomol. NMR 48, 13-22 (2010).
+REMARK SPARTA+ Structural Parameters Table derived from input PDB cooridnates
+REMARK
+REMARK PHI_R1 PSI_R1 CHI1_R1 and CHI2_R1 are the backbone and sidechain
+REMARK torsion angles of the first residue in a triplet.
+REMARK
+REMARK PHI_R2 PSI_R2 CHI1_R2 and CHI2_R2 are the backbone and sidechain
+REMARK torsion angles of the second (central) residue in a triplet.
+REMARK
+REMARK PHI_R3 PSI_R3 CHI1_R3 and CHI2_R3 are the backbone and sidechain
+REMARK torsion angles of the third residue in a triplet.
+REMARK
+REMARK H-Bond Distances are given in Angstroms:
+REMARK
+REMARK HN_HB_DIST_R2 H-bond distance for the HN atom in the central residue.
+REMARK HA_HB_DIST_R2 H-bond distance for the HA atom in the central residue.
+REMARK CO_HB_DIST_R2 H-bond distance for the CO atom in the central residue.
+REMARK
+REMARK HN_S2_R2 is the Bruschweiler structure-based HN order parameter of
+REMARK the central residue. Reference: Zhang FL, Bruschweiler R
+REMARK JACS 124, 12654-12655 (2002)
+REMARK
+REMARK Reference:
+REMARK Y. Shen and A. Bax: SPARTA+: a modest improvement in empirical NMR
+REMARK chemical shift prediction by means of an artificial neural network.
+REMARK J. Biomol. NMR 48, 13-22 (2010).
+
+DATA SOURCE aaqaa3-alpha-protonated
+
+DATA FIRST_RESID 0
+
+DATA SEQUENCE ?AAQAAAAQA AAAQAA?
+DATA SOURCE aaqaa3-beta-protonated
+
+DATA FIRST_RESID 0
+
+DATA SEQUENCE ?AAQAAAAQA AAAQAA?
+
+VARS RESID_R1 RESNAME_R1 PHI_R1 PSI_R1 CHI1_R1 CHI2_R1 RESID_R2 RESNAME_R2 PHI_R2 PSI_R2 CHI1_R2 CHI2_R2 RESID_R3 RESNAME_R3 PHI_R3 PSI_R3 CHI1_R3 CHI2_R3 HN_HB_DIST_R2 HA_HB_DIST_R2 CO_HB_DIST_R2 HN_S2_R2
+FORMAT %4d %s %8.3f %8.3f %8.3f %8.3f %4d %s %8.3f %8.3f %8.3f %8.3f %4d %s %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f
+
+ 0 ? 9999.000 9999.000 9999.000 9999.000 1 A -139.015 129.942 9999.000 9999.000 2 A -119.942 130.012 9999.000 9999.000 0.000 0.000 3.941 0.028
+ 1 A -139.015 129.942 9999.000 9999.000 2 A -119.942 130.012 9999.000 9999.000 3 Q -120.011 129.953 -175.404 177.919 4.503 0.000 3.951 0.135
+ 2 A -119.942 130.012 9999.000 9999.000 3 Q -120.011 129.953 -175.404 177.919 4 A -119.978 130.029 9999.000 9999.000 3.941 0.000 3.945 0.213
+ 3 Q -120.011 129.953 -175.404 177.919 4 A -119.978 130.029 9999.000 9999.000 5 A -120.041 130.009 9999.000 9999.000 3.951 0.000 3.937 0.220
+ 4 A -119.978 130.029 9999.000 9999.000 5 A -120.041 130.009 9999.000 9999.000 6 A -120.020 129.940 9999.000 9999.000 3.945 0.000 3.935 0.253
+ 5 A -120.041 130.009 9999.000 9999.000 6 A -120.020 129.940 9999.000 9999.000 7 A -119.968 130.001 9999.000 9999.000 3.937 0.000 3.941 0.215
+ 6 A -120.020 129.940 9999.000 9999.000 7 A -119.968 130.001 9999.000 9999.000 8 Q -119.993 129.963 -175.387 177.928 3.935 0.000 3.950 0.219
+ 7 A -119.968 130.001 9999.000 9999.000 8 Q -119.993 129.963 -175.387 177.928 9 A -119.949 130.016 9999.000 9999.000 3.941 0.000 3.945 0.217
+ 8 Q -119.993 129.963 -175.387 177.928 9 A -119.949 130.016 9999.000 9999.000 10 A -120.048 130.058 9999.000 9999.000 3.950 0.000 3.938 0.221
+ 9 A -119.949 130.016 9999.000 9999.000 10 A -120.048 130.058 9999.000 9999.000 11 A -120.036 130.061 9999.000 9999.000 3.945 0.000 3.937 0.253
+ 10 A -120.048 130.058 9999.000 9999.000 11 A -120.036 130.061 9999.000 9999.000 12 A -120.048 129.934 9999.000 9999.000 3.938 0.000 3.939 0.215
+ 11 A -120.036 130.061 9999.000 9999.000 12 A -120.048 129.934 9999.000 9999.000 13 Q -119.949 129.989 -175.403 177.957 3.937 0.000 3.951 0.219
+ 12 A -120.048 129.934 9999.000 9999.000 13 Q -119.949 129.989 -175.403 177.957 14 A -120.000 130.018 9999.000 9999.000 3.939 0.000 3.945 0.217
+ 13 Q -119.949 129.989 -175.403 177.957 14 A -120.000 130.018 9999.000 9999.000 15 A -119.998 135.011 9999.000 9999.000 3.951 0.000 0.000 0.219
+ 14 A -120.000 130.018 9999.000 9999.000 15 A -119.998 135.011 9999.000 9999.000 16 ? 9999.000 9999.000 9999.000 9999.000 3.945 0.000 0.000 0.203
diff --git a/proteinbenchmark/data/observables/aaqaa3/aaqaa3-extended-initial.pdb b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-extended-initial.pdb
new file mode 100644
index 0000000..6196b1f
--- /dev/null
+++ b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-extended-initial.pdb
@@ -0,0 +1,181 @@
+TITLE < Chain: id = nres = 17 natoms = 180 >
+ATOM 1 HH33 ACE 0 -5.284 -2.981 5.320 1.00 0.00
+ATOM 2 CH3 ACE 0 -4.851 -3.877 5.426 1.00 0.00
+ATOM 3 HH31 ACE 0 -5.412 -4.481 6.144 1.00 0.00
+ATOM 4 HH32 ACE 0 -4.840 -4.406 4.474 1.00 0.00
+ATOM 5 C ACE 0 -3.431 -3.679 5.966 1.00 0.00
+ATOM 6 O ACE 0 -2.705 -2.809 5.481 1.00 0.00
+ATOM 7 N ALA 1 -2.983 -4.446 6.956 1.00 0.00
+ATOM 8 H ALA 1 -3.578 -5.158 7.351 1.00 0.00
+ATOM 9 CA ALA 1 -1.682 -4.415 7.599 1.00 0.00
+ATOM 10 HA ALA 1 -0.980 -3.928 6.920 1.00 0.00
+ATOM 11 CB ALA 1 -1.818 -3.599 8.890 1.00 0.00
+ATOM 12 HB1 ALA 1 -0.860 -3.499 9.403 1.00 0.00
+ATOM 13 HB2 ALA 1 -2.179 -2.592 8.685 1.00 0.00
+ATOM 14 HB3 ALA 1 -2.515 -4.071 9.584 1.00 0.00
+ATOM 15 C ALA 1 -1.154 -5.834 7.868 1.00 0.00
+ATOM 16 O ALA 1 -1.816 -6.822 7.546 1.00 0.00
+ATOM 17 N ALA 2 0.028 -6.004 8.453 1.00 0.00
+ATOM 18 H ALA 2 0.574 -5.209 8.719 1.00 0.00
+ATOM 19 CA ALA 2 0.527 -7.343 8.707 1.00 0.00
+ATOM 20 HA ALA 2 -0.165 -7.839 9.392 1.00 0.00
+ATOM 21 CB ALA 2 0.566 -8.090 7.368 1.00 0.00
+ATOM 22 HB1 ALA 2 0.893 -9.123 7.495 1.00 0.00
+ATOM 23 HB2 ALA 2 -0.419 -8.118 6.903 1.00 0.00
+ATOM 24 HB3 ALA 2 1.255 -7.611 6.670 1.00 0.00
+ATOM 25 C ALA 2 1.905 -7.311 9.389 1.00 0.00
+ATOM 26 O ALA 2 2.450 -6.237 9.652 1.00 0.00
+ATOM 27 N GLN 3 2.521 -8.448 9.700 1.00 0.00
+ATOM 28 H GLN 3 2.087 -9.324 9.490 1.00 0.00
+ATOM 29 CA GLN 3 3.831 -8.417 10.347 1.00 0.00
+ATOM 30 HA GLN 3 4.530 -7.954 9.646 1.00 0.00
+ATOM 31 CB GLN 3 3.783 -7.587 11.657 1.00 0.00
+ATOM 32 HB1 GLN 3 3.386 -6.597 11.433 1.00 0.00
+ATOM 33 HB2 GLN 3 3.072 -8.056 12.339 1.00 0.00
+ATOM 34 CG GLN 3 5.141 -7.391 12.375 1.00 0.00
+ATOM 35 HG1 GLN 3 5.563 -8.346 12.683 1.00 0.00
+ATOM 36 HG2 GLN 3 5.859 -6.936 11.691 1.00 0.00
+ATOM 37 CD GLN 3 5.083 -6.530 13.637 1.00 0.00
+ATOM 38 OE1 GLN 3 6.100 -6.328 14.287 1.00 0.00
+ATOM 39 NE2 GLN 3 3.919 -6.017 14.020 1.00 0.00
+ATOM 40 HE21 GLN 3 3.087 -6.167 13.472 1.00 0.00
+ATOM 41 HE22 GLN 3 3.901 -5.465 14.862 1.00 0.00
+ATOM 42 C GLN 3 4.269 -9.876 10.572 1.00 0.00
+ATOM 43 O GLN 3 3.541 -10.803 10.217 1.00 0.00
+ATOM 44 N ALA 4 5.438 -10.137 11.151 1.00 0.00
+ATOM 45 H ALA 4 6.031 -9.387 11.440 1.00 0.00
+ATOM 46 CA ALA 4 5.851 -11.513 11.363 1.00 0.00
+ATOM 47 HA ALA 4 5.129 -11.985 12.032 1.00 0.00
+ATOM 48 CB ALA 4 5.845 -12.218 10.001 1.00 0.00
+ATOM 49 HB1 ALA 4 6.106 -13.273 10.096 1.00 0.00
+ATOM 50 HB2 ALA 4 4.861 -12.170 9.536 1.00 0.00
+ATOM 51 HB3 ALA 4 6.563 -11.762 9.318 1.00 0.00
+ATOM 52 C ALA 4 7.228 -11.587 12.044 1.00 0.00
+ATOM 53 O ALA 4 7.838 -10.559 12.340 1.00 0.00
+ATOM 54 N ALA 5 7.771 -12.770 12.319 1.00 0.00
+ATOM 55 H ALA 5 7.283 -13.611 12.083 1.00 0.00
+ATOM 56 CA ALA 5 9.070 -12.840 12.962 1.00 0.00
+ATOM 57 HA ALA 5 9.803 -12.377 12.298 1.00 0.00
+ATOM 58 CB ALA 5 8.984 -12.057 14.278 1.00 0.00
+ATOM 59 HB1 ALA 5 9.945 -12.034 14.793 1.00 0.00
+ATOM 60 HB2 ALA 5 8.687 -11.024 14.104 1.00 0.00
+ATOM 61 HB3 ALA 5 8.258 -12.507 14.958 1.00 0.00
+ATOM 62 C ALA 5 9.508 -14.298 13.187 1.00 0.00
+ATOM 63 O ALA 5 8.785 -15.232 12.835 1.00 0.00
+ATOM 64 N ALA 6 10.676 -14.559 13.766 1.00 0.00
+ATOM 65 H ALA 6 11.270 -13.808 14.055 1.00 0.00
+ATOM 66 CA ALA 6 11.090 -15.934 13.978 1.00 0.00
+ATOM 67 HA ALA 6 10.368 -16.406 14.647 1.00 0.00
+ATOM 68 CB ALA 6 11.084 -16.640 12.616 1.00 0.00
+ATOM 69 HB1 ALA 6 11.345 -17.695 12.711 1.00 0.00
+ATOM 70 HB2 ALA 6 10.100 -16.592 12.151 1.00 0.00
+ATOM 71 HB3 ALA 6 11.802 -16.184 11.933 1.00 0.00
+ATOM 72 C ALA 6 12.467 -16.009 14.659 1.00 0.00
+ATOM 73 O ALA 6 13.077 -14.980 14.955 1.00 0.00
+ATOM 74 N ALA 7 13.009 -17.192 14.934 1.00 0.00
+ATOM 75 H ALA 7 12.522 -18.032 14.698 1.00 0.00
+ATOM 76 CA ALA 7 14.309 -17.262 15.577 1.00 0.00
+ATOM 77 HA ALA 7 15.042 -16.799 14.913 1.00 0.00
+ATOM 78 CB ALA 7 14.223 -16.479 16.893 1.00 0.00
+ATOM 79 HB1 ALA 7 15.184 -16.456 17.408 1.00 0.00
+ATOM 80 HB2 ALA 7 13.926 -15.446 16.719 1.00 0.00
+ATOM 81 HB3 ALA 7 13.497 -16.928 17.573 1.00 0.00
+ATOM 82 C ALA 7 14.747 -18.719 15.802 1.00 0.00
+ATOM 83 O ALA 7 14.024 -19.653 15.450 1.00 0.00
+ATOM 84 N GLN 8 15.915 -18.981 16.381 1.00 0.00
+ATOM 85 H GLN 8 16.509 -18.230 16.670 1.00 0.00
+ATOM 86 CA GLN 8 16.331 -20.365 16.594 1.00 0.00
+ATOM 87 HA GLN 8 15.618 -20.817 17.289 1.00 0.00
+ATOM 88 CB GLN 8 16.331 -21.158 15.260 1.00 0.00
+ATOM 89 HB1 GLN 8 15.349 -21.066 14.797 1.00 0.00
+ATOM 90 HB2 GLN 8 17.039 -20.686 14.577 1.00 0.00
+ATOM 91 CG GLN 8 16.650 -22.668 15.379 1.00 0.00
+ATOM 92 HG1 GLN 8 17.649 -22.828 15.780 1.00 0.00
+ATOM 93 HG2 GLN 8 15.953 -23.140 16.074 1.00 0.00
+ATOM 94 CD GLN 8 16.596 -23.442 14.061 1.00 0.00
+ATOM 95 OE1 GLN 8 16.849 -24.639 14.045 1.00 0.00
+ATOM 96 NE2 GLN 8 16.285 -22.797 12.942 1.00 0.00
+ATOM 97 HE21 GLN 8 16.057 -21.816 12.962 1.00 0.00
+ATOM 98 HE22 GLN 8 16.269 -23.324 12.083 1.00 0.00
+ATOM 99 C GLN 8 17.712 -20.332 17.277 1.00 0.00
+ATOM 100 O GLN 8 18.249 -19.255 17.536 1.00 0.00
+ATOM 101 N ALA 9 18.327 -21.470 17.587 1.00 0.00
+ATOM 102 H ALA 9 17.894 -22.346 17.378 1.00 0.00
+ATOM 103 CA ALA 9 19.628 -21.439 18.230 1.00 0.00
+ATOM 104 HA ALA 9 20.331 -20.951 17.552 1.00 0.00
+ATOM 105 CB ALA 9 19.493 -20.622 19.522 1.00 0.00
+ATOM 106 HB1 ALA 9 20.451 -20.523 20.035 1.00 0.00
+ATOM 107 HB2 ALA 9 19.131 -19.615 19.316 1.00 0.00
+ATOM 108 HB3 ALA 9 18.796 -21.095 20.216 1.00 0.00
+ATOM 109 C ALA 9 20.157 -22.858 18.500 1.00 0.00
+ATOM 110 O ALA 9 19.494 -23.846 18.178 1.00 0.00
+ATOM 111 N ALA 10 21.339 -23.028 19.085 1.00 0.00
+ATOM 112 H ALA 10 21.884 -22.233 19.350 1.00 0.00
+ATOM 113 CA ALA 10 21.837 -24.367 19.339 1.00 0.00
+ATOM 114 HA ALA 10 21.146 -24.862 20.023 1.00 0.00
+ATOM 115 CB ALA 10 21.877 -25.113 17.999 1.00 0.00
+ATOM 116 HB1 ALA 10 22.203 -26.147 18.127 1.00 0.00
+ATOM 117 HB2 ALA 10 20.892 -25.142 17.534 1.00 0.00
+ATOM 118 HB3 ALA 10 22.565 -24.635 17.301 1.00 0.00
+ATOM 119 C ALA 10 23.216 -24.334 20.020 1.00 0.00
+ATOM 120 O ALA 10 23.760 -23.261 20.283 1.00 0.00
+ATOM 121 N ALA 11 23.831 -25.472 20.331 1.00 0.00
+ATOM 122 H ALA 11 23.398 -26.348 20.122 1.00 0.00
+ATOM 123 CA ALA 11 25.132 -25.441 20.974 1.00 0.00
+ATOM 124 HA ALA 11 25.835 -24.953 20.295 1.00 0.00
+ATOM 125 CB ALA 11 24.997 -24.624 22.265 1.00 0.00
+ATOM 126 HB1 ALA 11 25.954 -24.525 22.778 1.00 0.00
+ATOM 127 HB2 ALA 11 24.635 -23.617 22.060 1.00 0.00
+ATOM 128 HB3 ALA 11 24.299 -25.097 22.959 1.00 0.00
+ATOM 129 C ALA 11 25.660 -26.860 21.243 1.00 0.00
+ATOM 130 O ALA 11 24.998 -27.848 20.921 1.00 0.00
+ATOM 131 N ALA 12 26.843 -27.030 21.828 1.00 0.00
+ATOM 132 H ALA 12 27.388 -26.235 22.094 1.00 0.00
+ATOM 133 CA ALA 12 27.341 -28.369 22.082 1.00 0.00
+ATOM 134 HA ALA 12 26.650 -28.864 22.767 1.00 0.00
+ATOM 135 CB ALA 12 27.380 -29.115 20.743 1.00 0.00
+ATOM 136 HB1 ALA 12 27.707 -30.149 20.870 1.00 0.00
+ATOM 137 HB2 ALA 12 26.396 -29.144 20.278 1.00 0.00
+ATOM 138 HB3 ALA 12 28.069 -28.637 20.045 1.00 0.00
+ATOM 139 C ALA 12 28.720 -28.336 22.764 1.00 0.00
+ATOM 140 O ALA 12 29.264 -27.263 23.027 1.00 0.00
+ATOM 141 N GLN 13 29.335 -29.474 23.074 1.00 0.00
+ATOM 142 H GLN 13 28.902 -30.350 22.865 1.00 0.00
+ATOM 143 CA GLN 13 30.645 -29.442 23.722 1.00 0.00
+ATOM 144 HA GLN 13 31.345 -28.980 23.021 1.00 0.00
+ATOM 145 CB GLN 13 30.597 -28.612 25.032 1.00 0.00
+ATOM 146 HB1 GLN 13 30.200 -27.623 24.808 1.00 0.00
+ATOM 147 HB2 GLN 13 29.887 -29.082 25.714 1.00 0.00
+ATOM 148 CG GLN 13 31.955 -28.417 25.749 1.00 0.00
+ATOM 149 HG1 GLN 13 32.378 -29.371 26.058 1.00 0.00
+ATOM 150 HG2 GLN 13 32.674 -27.962 25.066 1.00 0.00
+ATOM 151 CD GLN 13 31.898 -27.555 27.012 1.00 0.00
+ATOM 152 OE1 GLN 13 32.915 -27.354 27.662 1.00 0.00
+ATOM 153 NE2 GLN 13 30.733 -27.043 27.395 1.00 0.00
+ATOM 154 HE21 GLN 13 29.901 -27.193 26.847 1.00 0.00
+ATOM 155 HE22 GLN 13 30.715 -26.490 28.237 1.00 0.00
+ATOM 156 C GLN 13 31.083 -30.902 23.947 1.00 0.00
+ATOM 157 O GLN 13 30.355 -31.829 23.592 1.00 0.00
+ATOM 158 N ALA 14 32.252 -31.163 24.526 1.00 0.00
+ATOM 159 H ALA 14 32.846 -30.412 24.815 1.00 0.00
+ATOM 160 CA ALA 14 32.665 -32.538 24.738 1.00 0.00
+ATOM 161 HA ALA 14 31.943 -33.010 25.407 1.00 0.00
+ATOM 162 CB ALA 14 32.659 -33.244 23.376 1.00 0.00
+ATOM 163 HB1 ALA 14 32.920 -34.299 23.471 1.00 0.00
+ATOM 164 HB2 ALA 14 31.676 -33.196 22.911 1.00 0.00
+ATOM 165 HB3 ALA 14 33.378 -32.788 22.693 1.00 0.00
+ATOM 166 C ALA 14 34.042 -32.613 25.419 1.00 0.00
+ATOM 167 O ALA 14 34.653 -31.584 25.715 1.00 0.00
+ATOM 168 N ALA 15 34.585 -33.796 25.694 1.00 0.00
+ATOM 169 H ALA 15 34.098 -34.636 25.458 1.00 0.00
+ATOM 170 CA ALA 15 35.884 -33.866 26.337 1.00 0.00
+ATOM 171 HA ALA 15 36.617 -33.403 25.673 1.00 0.00
+ATOM 172 CB ALA 15 35.798 -33.083 27.653 1.00 0.00
+ATOM 173 HB1 ALA 15 36.760 -33.060 28.168 1.00 0.00
+ATOM 174 HB2 ALA 15 35.501 -32.050 27.479 1.00 0.00
+ATOM 175 HB3 ALA 15 35.072 -33.532 28.333 1.00 0.00
+ATOM 176 C ALA 15 36.322 -35.323 26.562 1.00 0.00
+ATOM 177 O ALA 15 35.531 -36.154 27.012 1.00 0.00
+ATOM 178 N NH2 16 37.565 -35.697 26.270 1.00 0.00
+ATOM 179 HN1 NH2 16 38.214 -35.030 25.904 1.00 0.00
+ATOM 180 HN2 NH2 16 37.850 -36.644 26.416 1.00 0.00
diff --git a/proteinbenchmark/data/observables/aaqaa3/aaqaa3-extended-protonated.pdb b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-extended-protonated.pdb
new file mode 100644
index 0000000..260000e
--- /dev/null
+++ b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-extended-protonated.pdb
@@ -0,0 +1,182 @@
+ATOM 1 HH33 ACE A 0 -5.284 -2.981 5.320 1.00 0.00
+ATOM 2 CH3 ACE A 0 -4.851 -3.877 5.426 1.00 0.00
+ATOM 3 HH31 ACE A 0 -5.412 -4.481 6.144 1.00 0.00
+ATOM 4 HH32 ACE A 0 -4.840 -4.406 4.474 1.00 0.00
+ATOM 5 C ACE A 0 -3.431 -3.679 5.966 1.00 0.00
+ATOM 6 O ACE A 0 -2.705 -2.809 5.481 1.00 0.00
+ATOM 7 N ALA A 1 -2.983 -4.446 6.956 1.00 0.00
+ATOM 8 CA ALA A 1 -1.682 -4.415 7.599 1.00 0.00
+ATOM 9 CB ALA A 1 -1.818 -3.599 8.890 1.00 0.00
+ATOM 10 C ALA A 1 -1.154 -5.834 7.868 1.00 0.00
+ATOM 11 O ALA A 1 -1.816 -6.822 7.546 1.00 0.00
+ATOM 12 H ALA A 1 -3.478 -5.294 6.716 1.00 0.00 H
+ATOM 13 HA ALA A 1 -1.025 -3.946 6.994 1.00 0.00 H
+ATOM 14 HB1 ALA A 1 -2.653 -3.055 8.848 1.00 0.00 H
+ATOM 15 HB2 ALA A 1 -1.860 -4.221 9.669 1.00 0.00 H
+ATOM 16 HB3 ALA A 1 -1.028 -2.996 8.983 1.00 0.00 H
+ATOM 17 N ALA A 2 0.028 -6.004 8.453 1.00 0.00
+ATOM 18 CA ALA A 2 0.527 -7.343 8.707 1.00 0.00
+ATOM 19 CB ALA A 2 0.566 -8.090 7.368 1.00 0.00
+ATOM 20 C ALA A 2 1.905 -7.311 9.389 1.00 0.00
+ATOM 21 O ALA A 2 2.450 -6.237 9.652 1.00 0.00
+ATOM 22 H ALA A 2 0.530 -5.140 8.696 1.00 0.00 H
+ATOM 23 HA ALA A 2 -0.114 -7.825 9.319 1.00 0.00 H
+ATOM 24 HB1 ALA A 2 0.915 -9.013 7.517 1.00 0.00 H
+ATOM 25 HB2 ALA A 2 -0.356 -8.136 6.990 1.00 0.00 H
+ATOM 26 HB3 ALA A 2 1.164 -7.601 6.737 1.00 0.00 H
+ATOM 27 N GLN A 3 2.521 -8.448 9.700 1.00 0.00
+ATOM 28 CA GLN A 3 3.831 -8.417 10.347 1.00 0.00
+ATOM 29 CB GLN A 3 3.783 -7.587 11.657 1.00 0.00
+ATOM 30 CG GLN A 3 5.141 -7.391 12.375 1.00 0.00
+ATOM 31 CD GLN A 3 5.083 -6.530 13.637 1.00 0.00
+ATOM 32 C GLN A 3 4.269 -9.876 10.572 1.00 0.00
+ATOM 33 O GLN A 3 3.541 -10.803 10.217 1.00 0.00
+ATOM 34 H GLN A 3 2.018 -9.309 9.457 1.00 0.00 H
+ATOM 35 HA GLN A 3 4.479 -8.003 9.721 1.00 0.00 H
+ATOM 36 HB2 GLN A 3 3.418 -6.677 11.444 1.00 0.00 H
+ATOM 37 HB3 GLN A 3 3.162 -8.044 12.301 1.00 0.00 H
+ATOM 38 HG2 GLN A 3 5.495 -8.298 12.623 1.00 0.00 H
+ATOM 39 HG3 GLN A 3 5.778 -6.964 11.725 1.00 0.00 H
+ATOM 40 OE1 GLN A 3 6.100 -6.328 14.287 1.00 0.00 O
+ATOM 41 NE2 GLN A 3 3.919 -6.017 14.020 1.00 0.00 N
+ATOM 42 HE21 GLN A 3 3.825 -5.463 14.838 1.00 0.00 H
+ATOM 43 HE22 GLN A 3 3.094 -6.212 13.431 1.00 0.00 H
+ATOM 44 N ALA A 4 5.438 -10.137 11.151 1.00 0.00
+ATOM 45 CA ALA A 4 5.851 -11.513 11.363 1.00 0.00
+ATOM 46 CB ALA A 4 5.845 -12.218 10.001 1.00 0.00
+ATOM 47 C ALA A 4 7.228 -11.587 12.044 1.00 0.00
+ATOM 48 O ALA A 4 7.838 -10.559 12.340 1.00 0.00
+ATOM 49 H ALA A 4 5.993 -9.315 11.420 1.00 0.00 H
+ATOM 50 HA ALA A 4 5.181 -11.971 11.961 1.00 0.00 H
+ATOM 51 HB1 ALA A 4 5.086 -12.865 9.969 1.00 0.00 H
+ATOM 52 HB2 ALA A 4 5.738 -11.537 9.279 1.00 0.00 H
+ATOM 53 HB3 ALA A 4 6.707 -12.705 9.879 1.00 0.00 H
+ATOM 54 N ALA A 5 7.771 -12.770 12.319 1.00 0.00
+ATOM 55 CA ALA A 5 9.070 -12.840 12.962 1.00 0.00
+ATOM 56 CB ALA A 5 8.984 -12.057 14.278 1.00 0.00
+ATOM 57 C ALA A 5 9.508 -14.298 13.187 1.00 0.00
+ATOM 58 O ALA A 5 8.785 -15.232 12.835 1.00 0.00
+ATOM 59 H ALA A 5 7.211 -13.588 12.047 1.00 0.00 H
+ATOM 60 HA ALA A 5 9.756 -12.395 12.372 1.00 0.00 H
+ATOM 61 HB1 ALA A 5 9.781 -12.269 14.839 1.00 0.00 H
+ATOM 62 HB2 ALA A 5 8.963 -11.080 14.078 1.00 0.00 H
+ATOM 63 HB3 ALA A 5 8.152 -12.319 14.762 1.00 0.00 H
+ATOM 64 N ALA A 6 10.676 -14.559 13.766 1.00 0.00
+ATOM 65 CA ALA A 6 11.090 -15.934 13.978 1.00 0.00
+ATOM 66 CB ALA A 6 11.084 -16.640 12.616 1.00 0.00
+ATOM 67 C ALA A 6 12.467 -16.009 14.659 1.00 0.00
+ATOM 68 O ALA A 6 13.077 -14.980 14.955 1.00 0.00
+ATOM 69 H ALA A 6 11.230 -13.736 14.036 1.00 0.00 H
+ATOM 70 HA ALA A 6 10.420 -16.393 14.576 1.00 0.00 H
+ATOM 71 HB1 ALA A 6 11.507 -16.045 11.936 1.00 0.00 H
+ATOM 72 HB2 ALA A 6 11.599 -17.492 12.686 1.00 0.00 H
+ATOM 73 HB3 ALA A 6 10.142 -16.837 12.352 1.00 0.00 H
+ATOM 74 N ALA A 7 13.009 -17.192 14.934 1.00 0.00
+ATOM 75 CA ALA A 7 14.309 -17.262 15.577 1.00 0.00
+ATOM 76 CB ALA A 7 14.223 -16.479 16.893 1.00 0.00
+ATOM 77 C ALA A 7 14.747 -18.719 15.802 1.00 0.00
+ATOM 78 O ALA A 7 14.024 -19.653 15.450 1.00 0.00
+ATOM 79 H ALA A 7 12.450 -18.010 14.662 1.00 0.00 H
+ATOM 80 HA ALA A 7 14.995 -16.817 14.986 1.00 0.00 H
+ATOM 81 HB1 ALA A 7 15.019 -16.693 17.455 1.00 0.00 H
+ATOM 82 HB2 ALA A 7 14.204 -15.502 16.693 1.00 0.00 H
+ATOM 83 HB3 ALA A 7 13.390 -16.740 17.376 1.00 0.00 H
+ATOM 84 N GLN A 8 15.915 -18.981 16.381 1.00 0.00
+ATOM 85 CA GLN A 8 16.331 -20.365 16.594 1.00 0.00
+ATOM 86 CB GLN A 8 16.331 -21.158 15.260 1.00 0.00
+ATOM 87 CG GLN A 8 16.650 -22.668 15.379 1.00 0.00
+ATOM 88 CD GLN A 8 16.596 -23.442 14.061 1.00 0.00
+ATOM 89 C GLN A 8 17.712 -20.332 17.277 1.00 0.00
+ATOM 90 O GLN A 8 18.249 -19.255 17.536 1.00 0.00
+ATOM 91 H GLN A 8 16.472 -18.163 16.652 1.00 0.00 H
+ATOM 92 HA GLN A 8 15.696 -20.790 17.226 1.00 0.00 H
+ATOM 93 HB2 GLN A 8 15.425 -21.071 14.838 1.00 0.00 H
+ATOM 94 HB3 GLN A 8 17.015 -20.750 14.647 1.00 0.00 H
+ATOM 95 HG2 GLN A 8 17.573 -22.762 15.766 1.00 0.00 H
+ATOM 96 HG3 GLN A 8 15.990 -23.076 16.017 1.00 0.00 H
+ATOM 97 OE1 GLN A 8 16.849 -24.639 14.045 1.00 0.00 O
+ATOM 98 NE2 GLN A 8 16.285 -22.797 12.942 1.00 0.00 N
+ATOM 99 HE21 GLN A 8 16.250 -23.250 12.060 1.00 0.00 H
+ATOM 100 HE22 GLN A 8 16.075 -21.789 13.014 1.00 0.00 H
+ATOM 101 N ALA A 9 18.327 -21.470 17.587 1.00 0.00
+ATOM 102 CA ALA A 9 19.628 -21.439 18.230 1.00 0.00
+ATOM 103 CB ALA A 9 19.493 -20.622 19.522 1.00 0.00
+ATOM 104 C ALA A 9 20.157 -22.858 18.500 1.00 0.00
+ATOM 105 O ALA A 9 19.494 -23.846 18.178 1.00 0.00
+ATOM 106 H ALA A 9 17.820 -22.329 17.341 1.00 0.00 H
+ATOM 107 HA ALA A 9 20.285 -20.970 17.625 1.00 0.00 H
+ATOM 108 HB1 ALA A 9 18.647 -20.094 19.489 1.00 0.00 H
+ATOM 109 HB2 ALA A 9 19.473 -21.243 20.302 1.00 0.00 H
+ATOM 110 HB3 ALA A 9 20.273 -20.005 19.603 1.00 0.00 H
+ATOM 111 N ALA A 10 21.339 -23.028 19.085 1.00 0.00
+ATOM 112 CA ALA A 10 21.837 -24.367 19.339 1.00 0.00
+ATOM 113 CB ALA A 10 21.877 -25.113 17.999 1.00 0.00
+ATOM 114 C ALA A 10 23.216 -24.334 20.020 1.00 0.00
+ATOM 115 O ALA A 10 23.760 -23.261 20.283 1.00 0.00
+ATOM 116 H ALA A 10 21.841 -22.164 19.328 1.00 0.00 H
+ATOM 117 HA ALA A 10 21.197 -24.848 19.952 1.00 0.00 H
+ATOM 118 HB1 ALA A 10 21.085 -25.716 17.936 1.00 0.00 H
+ATOM 119 HB2 ALA A 10 21.856 -24.450 17.254 1.00 0.00 H
+ATOM 120 HB3 ALA A 10 22.715 -25.651 17.948 1.00 0.00 H
+ATOM 121 N ALA A 11 23.831 -25.472 20.331 1.00 0.00
+ATOM 122 CA ALA A 11 25.132 -25.441 20.974 1.00 0.00
+ATOM 123 CB ALA A 11 24.997 -24.624 22.265 1.00 0.00
+ATOM 124 C ALA A 11 25.660 -26.860 21.243 1.00 0.00
+ATOM 125 O ALA A 11 24.998 -27.848 20.921 1.00 0.00
+ATOM 126 H ALA A 11 23.324 -26.331 20.085 1.00 0.00 H
+ATOM 127 HA ALA A 11 25.789 -24.972 20.369 1.00 0.00 H
+ATOM 128 HB1 ALA A 11 24.489 -25.156 22.939 1.00 0.00 H
+ATOM 129 HB2 ALA A 11 25.907 -24.415 22.618 1.00 0.00 H
+ATOM 130 HB3 ALA A 11 24.509 -23.776 22.068 1.00 0.00 H
+ATOM 131 N ALA A 12 26.843 -27.030 21.828 1.00 0.00
+ATOM 132 CA ALA A 12 27.341 -28.369 22.082 1.00 0.00
+ATOM 133 CB ALA A 12 27.380 -29.115 20.743 1.00 0.00
+ATOM 134 C ALA A 12 28.720 -28.336 22.764 1.00 0.00
+ATOM 135 O ALA A 12 29.264 -27.263 23.027 1.00 0.00
+ATOM 136 H ALA A 12 27.345 -26.166 22.070 1.00 0.00 H
+ATOM 137 HA ALA A 12 26.701 -28.850 22.695 1.00 0.00 H
+ATOM 138 HB1 ALA A 12 26.602 -29.737 20.691 1.00 0.00 H
+ATOM 139 HB2 ALA A 12 27.333 -28.454 19.997 1.00 0.00 H
+ATOM 140 HB3 ALA A 12 28.230 -29.633 20.680 1.00 0.00 H
+ATOM 141 N GLN A 13 29.335 -29.474 23.074 1.00 0.00
+ATOM 142 CA GLN A 13 30.645 -29.442 23.722 1.00 0.00
+ATOM 143 CB GLN A 13 30.597 -28.612 25.032 1.00 0.00
+ATOM 144 CG GLN A 13 31.955 -28.417 25.749 1.00 0.00
+ATOM 145 CD GLN A 13 31.898 -27.555 27.012 1.00 0.00
+ATOM 146 C GLN A 13 31.083 -30.902 23.947 1.00 0.00
+ATOM 147 O GLN A 13 30.355 -31.829 23.592 1.00 0.00
+ATOM 148 H GLN A 13 28.833 -30.334 22.830 1.00 0.00 H
+ATOM 149 HA GLN A 13 31.293 -29.029 23.097 1.00 0.00 H
+ATOM 150 HB2 GLN A 13 30.232 -27.702 24.819 1.00 0.00 H
+ATOM 151 HB3 GLN A 13 29.976 -29.069 25.676 1.00 0.00 H
+ATOM 152 HG2 GLN A 13 32.309 -29.324 25.998 1.00 0.00 H
+ATOM 153 HG3 GLN A 13 32.592 -27.990 25.099 1.00 0.00 H
+ATOM 154 OE1 GLN A 13 32.915 -27.354 27.662 1.00 0.00 O
+ATOM 155 NE2 GLN A 13 30.733 -27.043 27.395 1.00 0.00 N
+ATOM 156 HE21 GLN A 13 30.640 -26.489 28.213 1.00 0.00 H
+ATOM 157 HE22 GLN A 13 29.909 -27.239 26.807 1.00 0.00 H
+ATOM 158 N ALA A 14 32.252 -31.163 24.526 1.00 0.00
+ATOM 159 CA ALA A 14 32.665 -32.538 24.738 1.00 0.00
+ATOM 160 CB ALA A 14 32.659 -33.244 23.376 1.00 0.00
+ATOM 161 C ALA A 14 34.042 -32.613 25.419 1.00 0.00
+ATOM 162 O ALA A 14 34.653 -31.584 25.715 1.00 0.00
+ATOM 163 H ALA A 14 32.806 -30.341 24.795 1.00 0.00 H
+ATOM 164 HA ALA A 14 31.995 -32.997 25.336 1.00 0.00 H
+ATOM 165 HB1 ALA A 14 33.373 -32.852 22.800 1.00 0.00 H
+ATOM 166 HB2 ALA A 14 32.831 -34.218 23.510 1.00 0.00 H
+ATOM 167 HB3 ALA A 14 31.769 -33.115 22.944 1.00 0.00 H
+ATOM 168 N ALA A 15 34.585 -33.796 25.694 1.00 0.00
+ATOM 169 CA ALA A 15 35.884 -33.866 26.337 1.00 0.00
+ATOM 170 CB ALA A 15 35.798 -33.083 27.653 1.00 0.00
+ATOM 171 C ALA A 15 36.322 -35.323 26.562 1.00 0.00
+ATOM 172 O ALA A 15 35.531 -36.154 27.012 1.00 0.00
+ATOM 173 H ALA A 15 34.025 -34.614 25.422 1.00 0.00 H
+ATOM 174 HA ALA A 15 36.570 -33.421 25.747 1.00 0.00 H
+ATOM 175 HB1 ALA A 15 36.589 -33.305 28.219 1.00 0.00 H
+ATOM 176 HB2 ALA A 15 35.790 -32.105 27.454 1.00 0.00 H
+ATOM 177 HB3 ALA A 15 34.960 -33.336 28.131 1.00 0.00 H
+ATOM 178 N NH2 A 16 37.565 -35.697 26.270 1.00 0.00
+ATOM 179 HN1 NH2 A 16 38.214 -35.030 25.904 1.00 0.00
+ATOM 180 HN2 NH2 A 16 37.850 -36.644 26.416 1.00 0.00
+TER
+END
\ No newline at end of file
diff --git a/proteinbenchmark/data/observables/aaqaa3/aaqaa3-extended-protonated.pdb.cs b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-extended-protonated.pdb.cs
new file mode 100644
index 0000000..6804a41
--- /dev/null
+++ b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-extended-protonated.pdb.cs
@@ -0,0 +1,151 @@
+NUM,RES,ATOMNAME,SHIFT
+1,A,C,175.4647
+1,A,CA,52.0717
+1,A,CB,20.3054
+1,A,H,8.0190
+1,A,HA,4.3700
+1,A,HB,1.3904
+1,A,HB2,1.6177
+1,A,HB3,1.6065
+1,A,N,124.6220
+2,A,C,175.5896
+2,A,CA,51.5475
+2,A,CB,21.2993
+2,A,H,7.9373
+2,A,HA,4.4308
+2,A,HB,1.3097
+2,A,HB2,1.7062
+2,A,HB3,1.2199
+2,A,N,119.1753
+3,Q,C,174.5205
+3,Q,CA,56.4489
+3,Q,CB,30.4786
+3,Q,CD,179.9008
+3,Q,CG,33.6165
+3,Q,H,8.0027
+3,Q,HA,4.3862
+3,Q,HB2,2.2655
+3,Q,HB3,1.9860
+3,Q,HE21,7.4017
+3,Q,HE22,6.8489
+3,Q,HG2,2.3998
+3,Q,HG3,2.3719
+3,Q,N,117.4928
+4,A,C,175.8268
+4,A,CA,52.5384
+4,A,CB,20.9832
+4,A,H,7.8202
+4,A,HA,4.5557
+4,A,HB,1.3514
+4,A,HB2,1.9596
+4,A,HB3,1.3559
+4,A,N,123.3477
+5,A,C,175.6529
+5,A,CA,52.5743
+5,A,CB,20.4765
+5,A,H,8.0257
+5,A,HA,4.4514
+5,A,HB,1.4266
+5,A,HB2,1.9391
+5,A,HB3,1.2087
+5,A,N,121.7814
+6,A,C,176.5102
+6,A,CA,51.8226
+6,A,CB,20.9210
+6,A,H,7.8947
+6,A,HA,4.4997
+6,A,HB,1.3507
+6,A,HB2,2.0612
+6,A,HB3,1.3823
+6,A,N,120.3285
+7,A,C,175.9885
+7,A,CA,52.3489
+7,A,CB,20.6634
+7,A,H,7.4180
+7,A,HA,4.4346
+7,A,HB,1.2766
+7,A,HB2,2.0342
+7,A,HB3,1.4809
+7,A,N,120.2946
+8,Q,C,173.7657
+8,Q,CA,54.1394
+8,Q,CB,31.3109
+8,Q,CD,179.5623
+8,Q,CG,32.9382
+8,Q,H,8.2134
+8,Q,HA,4.5636
+8,Q,HB2,2.1276
+8,Q,HB3,1.8291
+8,Q,HE21,7.3151
+8,Q,HE22,6.8800
+8,Q,HG2,2.2666
+8,Q,HG3,2.1524
+8,Q,N,116.2490
+9,A,C,175.0261
+9,A,CA,51.7460
+9,A,CB,20.2234
+9,A,H,8.1837
+9,A,HA,4.3539
+9,A,HB,1.5421
+9,A,HB2,2.0471
+9,A,HB3,1.3567
+9,A,N,121.5645
+10,A,C,175.7468
+10,A,CA,51.7924
+10,A,CB,20.8989
+10,A,H,8.1378
+10,A,HA,4.5568
+10,A,HB,1.3751
+10,A,HB2,1.8717
+10,A,HB3,1.3141
+10,A,N,120.5500
+11,A,C,175.7607
+11,A,CA,52.1613
+11,A,CB,21.3830
+11,A,H,7.5873
+11,A,HA,4.4395
+11,A,HB,1.3247
+11,A,HB2,1.7960
+11,A,HB3,1.5145
+11,A,N,120.3965
+12,A,C,175.3634
+12,A,CA,52.6466
+12,A,CB,19.8756
+12,A,H,7.6852
+12,A,HA,4.6079
+12,A,HB,1.3081
+12,A,HB2,1.9996
+12,A,HB3,1.1214
+12,A,N,120.1126
+13,Q,C,174.7503
+13,Q,CA,56.2064
+13,Q,CB,30.8413
+13,Q,CD,179.8751
+13,Q,CG,33.6761
+13,Q,H,8.0171
+13,Q,HA,4.4065
+13,Q,HB2,2.1249
+13,Q,HB3,1.8790
+13,Q,HE21,7.4703
+13,Q,HE22,6.9234
+13,Q,HG2,2.3495
+13,Q,HG3,2.3245
+13,Q,N,117.6665
+14,A,C,176.0446
+14,A,CA,51.8485
+14,A,CB,20.2733
+14,A,H,8.0579
+14,A,HA,4.4591
+14,A,HB,1.3911
+14,A,HB2,2.0739
+14,A,HB3,1.4379
+14,A,N,123.3186
+15,A,C,178.5353
+15,A,CA,53.0776
+15,A,CB,19.6182
+15,A,H,8.2124
+15,A,HA,4.2442
+15,A,HB,1.3748
+15,A,HB2,1.8515
+15,A,HB3,1.4706
+15,A,N,124.9759
diff --git a/proteinbenchmark/data/observables/aaqaa3/aaqaa3-extended-protonated.pdb.shifty b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-extended-protonated.pdb.shifty
new file mode 100644
index 0000000..e69de29
diff --git a/proteinbenchmark/data/observables/aaqaa3/aaqaa3-extended-protonated.pdb.sxp b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-extended-protonated.pdb.sxp
new file mode 100644
index 0000000..d3abf54
--- /dev/null
+++ b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-extended-protonated.pdb.sxp
@@ -0,0 +1,151 @@
+NUM,RES,IUPAC,ATOM,PRED_CS
+1,ALA,A,H,8.0190
+1,ALA,A,HA,4.3700
+1,ALA,A,C,175.4647
+1,ALA,A,CA,52.0717
+1,ALA,A,CB,20.3054
+1,ALA,A,N,124.6220
+1,ALA,A,HB,1.3904
+1,ALA,A,HB2,1.6177
+1,ALA,A,HB3,1.6065
+2,ALA,A,H,7.9373
+2,ALA,A,HA,4.4308
+2,ALA,A,C,175.5896
+2,ALA,A,CA,51.5475
+2,ALA,A,CB,21.2993
+2,ALA,A,N,119.1753
+2,ALA,A,HB,1.3097
+2,ALA,A,HB2,1.7062
+2,ALA,A,HB3,1.2199
+3,GLN,Q,H,8.0027
+3,GLN,Q,HA,4.3862
+3,GLN,Q,C,174.5205
+3,GLN,Q,CA,56.4489
+3,GLN,Q,CB,30.4786
+3,GLN,Q,N,117.4928
+3,GLN,Q,CD,179.9008
+3,GLN,Q,CG,33.6165
+3,GLN,Q,HB2,2.2655
+3,GLN,Q,HB3,1.9860
+3,GLN,Q,HE21,7.4017
+3,GLN,Q,HE22,6.8489
+3,GLN,Q,HG2,2.3998
+3,GLN,Q,HG3,2.3719
+4,ALA,A,H,7.8202
+4,ALA,A,HA,4.5557
+4,ALA,A,C,175.8268
+4,ALA,A,CA,52.5384
+4,ALA,A,CB,20.9832
+4,ALA,A,N,123.3477
+4,ALA,A,HB,1.3514
+4,ALA,A,HB2,1.9596
+4,ALA,A,HB3,1.3559
+5,ALA,A,H,8.0257
+5,ALA,A,HA,4.4514
+5,ALA,A,C,175.6529
+5,ALA,A,CA,52.5743
+5,ALA,A,CB,20.4765
+5,ALA,A,N,121.7814
+5,ALA,A,HB,1.4266
+5,ALA,A,HB2,1.9391
+5,ALA,A,HB3,1.2087
+6,ALA,A,H,7.8947
+6,ALA,A,HA,4.4997
+6,ALA,A,C,176.5102
+6,ALA,A,CA,51.8226
+6,ALA,A,CB,20.9210
+6,ALA,A,N,120.3285
+6,ALA,A,HB,1.3507
+6,ALA,A,HB2,2.0612
+6,ALA,A,HB3,1.3823
+7,ALA,A,H,7.4180
+7,ALA,A,HA,4.4346
+7,ALA,A,C,175.9885
+7,ALA,A,CA,52.3489
+7,ALA,A,CB,20.6634
+7,ALA,A,N,120.2946
+7,ALA,A,HB,1.2766
+7,ALA,A,HB2,2.0342
+7,ALA,A,HB3,1.4809
+8,GLN,Q,H,8.2134
+8,GLN,Q,HA,4.5636
+8,GLN,Q,C,173.7657
+8,GLN,Q,CA,54.1394
+8,GLN,Q,CB,31.3109
+8,GLN,Q,N,116.2490
+8,GLN,Q,CD,179.5623
+8,GLN,Q,CG,32.9382
+8,GLN,Q,HB2,2.1276
+8,GLN,Q,HB3,1.8291
+8,GLN,Q,HE21,7.3151
+8,GLN,Q,HE22,6.8800
+8,GLN,Q,HG2,2.2666
+8,GLN,Q,HG3,2.1524
+9,ALA,A,H,8.1837
+9,ALA,A,HA,4.3539
+9,ALA,A,C,175.0261
+9,ALA,A,CA,51.7460
+9,ALA,A,CB,20.2234
+9,ALA,A,N,121.5645
+9,ALA,A,HB,1.5421
+9,ALA,A,HB2,2.0471
+9,ALA,A,HB3,1.3567
+10,ALA,A,H,8.1378
+10,ALA,A,HA,4.5568
+10,ALA,A,C,175.7468
+10,ALA,A,CA,51.7924
+10,ALA,A,CB,20.8989
+10,ALA,A,N,120.5500
+10,ALA,A,HB,1.3751
+10,ALA,A,HB2,1.8717
+10,ALA,A,HB3,1.3141
+11,ALA,A,H,7.5873
+11,ALA,A,HA,4.4395
+11,ALA,A,C,175.7607
+11,ALA,A,CA,52.1613
+11,ALA,A,CB,21.3830
+11,ALA,A,N,120.3965
+11,ALA,A,HB,1.3247
+11,ALA,A,HB2,1.7960
+11,ALA,A,HB3,1.5145
+12,ALA,A,H,7.6852
+12,ALA,A,HA,4.6079
+12,ALA,A,C,175.3634
+12,ALA,A,CA,52.6466
+12,ALA,A,CB,19.8756
+12,ALA,A,N,120.1126
+12,ALA,A,HB,1.3081
+12,ALA,A,HB2,1.9996
+12,ALA,A,HB3,1.1214
+13,GLN,Q,H,8.0171
+13,GLN,Q,HA,4.4065
+13,GLN,Q,C,174.7503
+13,GLN,Q,CA,56.2064
+13,GLN,Q,CB,30.8413
+13,GLN,Q,N,117.6665
+13,GLN,Q,CD,179.8751
+13,GLN,Q,CG,33.6761
+13,GLN,Q,HB2,2.1249
+13,GLN,Q,HB3,1.8790
+13,GLN,Q,HE21,7.4703
+13,GLN,Q,HE22,6.9234
+13,GLN,Q,HG2,2.3495
+13,GLN,Q,HG3,2.3245
+14,ALA,A,H,8.0579
+14,ALA,A,HA,4.4591
+14,ALA,A,C,176.0446
+14,ALA,A,CA,51.8485
+14,ALA,A,CB,20.2733
+14,ALA,A,N,123.3186
+14,ALA,A,HB,1.3911
+14,ALA,A,HB2,2.0739
+14,ALA,A,HB3,1.4379
+15,ALA,A,H,8.2124
+15,ALA,A,HA,4.2442
+15,ALA,A,C,178.5353
+15,ALA,A,CA,53.0776
+15,ALA,A,CB,19.6182
+15,ALA,A,N,124.9759
+15,ALA,A,HB,1.3748
+15,ALA,A,HB2,1.8515
+15,ALA,A,HB3,1.4706
diff --git a/proteinbenchmark/data/observables/aaqaa3/aaqaa3-extended-protonated.spartap b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-extended-protonated.spartap
new file mode 100644
index 0000000..4392bb4
--- /dev/null
+++ b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-extended-protonated.spartap
@@ -0,0 +1,114 @@
+REMARK SPARTA+ Protein Chemical Shift Prediction Table
+REMARK
+REMARK All chemical shifts are reported in ppm:
+REMARK
+REMARK SHIFT is the predicted chemical shift.
+REMARK SS_SHIFT is the predicted secondary chemical shift.
+REMARK RC_SHIFT is the random coil chemical shift.
+REMARK HM_SHIFT is the ring current shift; a correction
+REMARK of 0.6 times this value is applied.
+REMARK EF_SHIFT is the adjustment for electric field effect,
+REMARK applied to proton shifts only.
+REMARK SIGMA is the estimated prediction error.
+REMARK
+REMARK Reference:
+REMARK Y. Shen and A. Bax: SPARTA+: a modest improvement in empirical NMR
+REMARK chemical shift prediction by means of an artificial neural network.
+REMARK J. Biomol. NMR 48, 13-22 (2010).
+
+DATA SOURCE aaqaa3-extended-protonated.pdb
+
+DATA FIRST_RESID 0
+
+DATA SEQUENCE ?AAQAAAAQA AAAQAA?
+
+VARS RESID RESNAME ATOMNAME SS_SHIFT SHIFT RC_SHIFT HM_SHIFT EF_SHIFT SIGMA
+FORMAT %4d %4s %4s %9.3f %9.3f %9.3f %9.3f %9.3f %9.3f
+
+ 0 ? HA 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 0 ? C 0.000 9999.000 9999.000 -0.000 0.000 0.000
+ 0 ? CA 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 0 ? CB 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 2 A N -1.199 121.621 122.820 -0.000 0.000 2.426
+ 2 A HA 0.738 5.058 4.320 -0.000 0.000 0.297
+ 2 A C -1.279 176.305 177.584 -0.000 0.000 1.067
+ 2 A CA 0.509 52.546 52.037 -0.000 0.000 0.616
+ 2 A CB 0.997 19.997 19.000 -0.000 0.000 1.353
+ 2 A HN 1.384 9.534 8.150 -0.000 0.000 0.484
+ 3 Q N -1.872 117.928 119.800 -0.000 0.000 0.000
+ 3 Q HA 0.606 4.946 4.340 -0.000 0.000 0.000
+ 3 Q C -1.948 174.052 176.000 -0.000 0.000 0.000
+ 3 Q CA 0.045 55.848 55.803 -0.000 0.000 0.000
+ 3 Q CB 1.578 30.316 28.738 -0.000 0.000 0.000
+ 3 Q HN 2.423 10.693 8.270 -0.000 0.000 0.000
+ 4 A N -0.451 122.369 122.820 -0.000 0.000 2.401
+ 4 A HA 0.955 5.275 4.320 -0.000 0.000 0.296
+ 4 A C -2.111 175.473 177.584 -0.000 0.000 1.047
+ 4 A CA 0.218 52.255 52.037 -0.000 0.000 0.606
+ 4 A CB 0.952 19.951 19.000 -0.000 0.000 1.376
+ 4 A HN 1.183 9.333 8.150 -0.000 0.000 0.496
+ 5 A N -1.759 121.061 122.820 -0.000 0.000 2.381
+ 5 A HA 1.107 5.427 4.320 -0.000 0.000 0.296
+ 5 A C -0.727 176.857 177.584 -0.000 0.000 1.028
+ 5 A CA 0.509 52.546 52.037 -0.000 0.000 0.595
+ 5 A CB 0.069 19.069 19.000 -0.000 0.000 1.399
+ 5 A HN 2.692 10.842 8.150 -0.000 0.000 0.509
+ 6 A N -1.688 121.132 122.820 -0.000 0.000 2.433
+ 6 A HA 1.112 5.432 4.320 -0.000 0.000 0.294
+ 6 A C -0.736 176.848 177.584 -0.000 0.000 1.037
+ 6 A CA 0.471 52.508 52.037 -0.000 0.000 0.613
+ 6 A CB 0.002 19.002 19.000 -0.000 0.000 1.359
+ 6 A HN 2.700 10.850 8.150 -0.000 0.000 0.473
+ 7 A N -0.972 121.848 122.820 -0.000 0.000 2.401
+ 7 A HA 0.834 5.154 4.320 -0.000 0.000 0.296
+ 7 A C -1.237 176.347 177.584 -0.000 0.000 1.047
+ 7 A CA 0.710 52.747 52.037 -0.000 0.000 0.606
+ 7 A CB 1.128 20.128 19.000 -0.000 0.000 1.376
+ 7 A HN 1.612 9.762 8.150 -0.000 0.000 0.496
+ 8 Q N -1.862 117.938 119.800 -0.000 0.000 3.040
+ 8 Q HA 0.607 4.947 4.340 -0.000 0.000 0.321
+ 8 Q C -1.960 174.040 176.000 -0.000 0.000 0.849
+ 8 Q CA 0.047 55.850 55.803 -0.000 0.000 0.811
+ 8 Q CB 1.586 30.324 28.738 -0.000 0.000 1.485
+ 8 Q HN 2.384 10.654 8.270 -0.000 0.000 0.469
+ 9 A N -0.451 122.369 122.820 -0.000 0.000 2.415
+ 9 A HA 0.955 5.275 4.320 -0.000 0.000 0.294
+ 9 A C -2.111 175.473 177.584 -0.000 0.000 1.019
+ 9 A CA 0.218 52.255 52.037 -0.000 0.000 0.603
+ 9 A CB 0.950 19.951 19.000 -0.000 0.000 1.382
+ 9 A HN 1.182 9.332 8.150 -0.000 0.000 0.483
+ 10 A N -1.757 121.063 122.820 -0.000 0.000 2.433
+ 10 A HA 1.107 5.427 4.320 -0.000 0.000 0.294
+ 10 A C -0.727 176.857 177.584 -0.000 0.000 1.037
+ 10 A CA 0.509 52.546 52.037 -0.000 0.000 0.613
+ 10 A CB 0.070 19.070 19.000 -0.000 0.000 1.359
+ 10 A HN 2.692 10.842 8.150 -0.000 0.000 0.473
+ 11 A N -1.687 121.133 122.820 -0.000 0.000 2.456
+ 11 A HA 1.112 5.432 4.320 -0.000 0.000 0.294
+ 11 A C -0.736 176.848 177.584 -0.000 0.000 1.057
+ 11 A CA 0.471 52.508 52.037 -0.000 0.000 0.623
+ 11 A CB 0.003 19.003 19.000 -0.000 0.000 1.338
+ 11 A HN 2.700 10.850 8.150 -0.000 0.000 0.464
+ 12 A N -0.972 121.848 122.820 -0.000 0.000 2.410
+ 12 A HA 0.834 5.154 4.320 -0.000 0.000 0.300
+ 12 A C -1.237 176.347 177.584 -0.000 0.000 1.077
+ 12 A CA 0.709 52.746 52.037 -0.000 0.000 0.610
+ 12 A CB 1.130 20.130 19.000 -0.000 0.000 1.371
+ 12 A HN 1.612 9.762 8.150 -0.000 0.000 0.510
+ 13 Q N -1.864 117.936 119.800 -0.000 0.000 3.077
+ 13 Q HA 0.607 4.947 4.340 -0.000 0.000 0.317
+ 13 Q C -1.958 174.042 176.000 -0.000 0.000 0.864
+ 13 Q CA 0.047 55.850 55.803 -0.000 0.000 0.808
+ 13 Q CB 1.584 30.322 28.738 -0.000 0.000 1.532
+ 13 Q HN 2.385 10.655 8.270 -0.000 0.000 0.474
+ 14 A N -0.265 122.555 122.820 -0.000 0.000 2.401
+ 14 A HA 0.914 5.234 4.320 -0.000 0.000 0.296
+ 14 A C -2.141 175.443 177.584 -0.000 0.000 1.047
+ 14 A CA 0.134 52.171 52.037 -0.000 0.000 0.606
+ 14 A CB 1.148 20.148 19.000 -0.000 0.000 1.376
+ 14 A HN 1.184 9.334 8.150 -0.000 0.000 0.496
+ 16 ? N 0.000 9999.000 9999.000 -0.000 0.000 0.000
+ 16 ? HA 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 16 ? CA 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 16 ? CB 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 16 ? HN 0.000 9999.000 9999.000 0.000 0.000 0.000
diff --git a/proteinbenchmark/data/observables/aaqaa3/aaqaa3-extended-protonated_pred.tab b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-extended-protonated_pred.tab
new file mode 100644
index 0000000..c2180b7
--- /dev/null
+++ b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-extended-protonated_pred.tab
@@ -0,0 +1,114 @@
+REMARK SPARTA+ Protein Chemical Shift Prediction Table
+REMARK
+REMARK All chemical shifts are reported in ppm:
+REMARK
+REMARK SHIFT is the predicted chemical shift.
+REMARK SS_SHIFT is the predicted secondary chemical shift.
+REMARK RC_SHIFT is the random coil chemical shift.
+REMARK HM_SHIFT is the ring current shift; a correction
+REMARK of 0.6 times this value is applied.
+REMARK EF_SHIFT is the adjustment for electric field effect,
+REMARK applied to proton shifts only.
+REMARK SIGMA is the estimated prediction error.
+REMARK
+REMARK Reference:
+REMARK Y. Shen and A. Bax: SPARTA+: a modest improvement in empirical NMR
+REMARK chemical shift prediction by means of an artificial neural network.
+REMARK J. Biomol. NMR 48, 13-22 (2010).
+
+DATA SOURCE aaqaa3-extended-protonated
+
+DATA FIRST_RESID 0
+
+DATA SEQUENCE ?AAQAAAAQA AAAQAA?
+
+VARS RESID RESNAME ATOMNAME SS_SHIFT SHIFT RC_SHIFT HM_SHIFT EF_SHIFT SIGMA
+FORMAT %4d %4s %4s %9.3f %9.3f %9.3f %9.3f %9.3f %9.3f
+
+ 0 ? HA 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 0 ? C 0.000 9999.000 9999.000 -0.000 0.000 0.000
+ 0 ? CA 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 0 ? CB 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 2 A N -1.199 121.621 122.820 -0.000 0.000 2.426
+ 2 A HA 0.738 5.058 4.320 -0.000 0.000 0.297
+ 2 A C -1.279 176.305 177.584 -0.000 0.000 1.067
+ 2 A CA 0.509 52.546 52.037 -0.000 0.000 0.616
+ 2 A CB 0.997 19.997 19.000 -0.000 0.000 1.353
+ 2 A HN 1.384 9.534 8.150 -0.000 0.000 0.484
+ 3 Q N -1.872 117.928 119.800 -0.000 0.000 0.000
+ 3 Q HA 0.606 4.946 4.340 -0.000 0.000 0.000
+ 3 Q C -1.948 174.052 176.000 -0.000 0.000 0.000
+ 3 Q CA 0.045 55.848 55.803 -0.000 0.000 0.000
+ 3 Q CB 1.578 30.316 28.738 -0.000 0.000 0.000
+ 3 Q HN 2.423 10.693 8.270 -0.000 0.000 0.000
+ 4 A N -0.451 122.369 122.820 -0.000 0.000 2.401
+ 4 A HA 0.955 5.275 4.320 -0.000 0.000 0.296
+ 4 A C -2.111 175.473 177.584 -0.000 0.000 1.047
+ 4 A CA 0.218 52.255 52.037 -0.000 0.000 0.606
+ 4 A CB 0.952 19.951 19.000 -0.000 0.000 1.376
+ 4 A HN 1.183 9.333 8.150 -0.000 0.000 0.496
+ 5 A N -1.759 121.061 122.820 -0.000 0.000 2.381
+ 5 A HA 1.107 5.427 4.320 -0.000 0.000 0.296
+ 5 A C -0.727 176.857 177.584 -0.000 0.000 1.028
+ 5 A CA 0.509 52.546 52.037 -0.000 0.000 0.595
+ 5 A CB 0.069 19.069 19.000 -0.000 0.000 1.399
+ 5 A HN 2.692 10.842 8.150 -0.000 0.000 0.509
+ 6 A N -1.688 121.132 122.820 -0.000 0.000 2.433
+ 6 A HA 1.112 5.432 4.320 -0.000 0.000 0.294
+ 6 A C -0.736 176.848 177.584 -0.000 0.000 1.037
+ 6 A CA 0.471 52.508 52.037 -0.000 0.000 0.613
+ 6 A CB 0.002 19.002 19.000 -0.000 0.000 1.359
+ 6 A HN 2.700 10.850 8.150 -0.000 0.000 0.473
+ 7 A N -0.972 121.848 122.820 -0.000 0.000 2.401
+ 7 A HA 0.834 5.154 4.320 -0.000 0.000 0.296
+ 7 A C -1.237 176.347 177.584 -0.000 0.000 1.047
+ 7 A CA 0.710 52.747 52.037 -0.000 0.000 0.606
+ 7 A CB 1.128 20.128 19.000 -0.000 0.000 1.376
+ 7 A HN 1.612 9.762 8.150 -0.000 0.000 0.496
+ 8 Q N -1.862 117.938 119.800 -0.000 0.000 3.040
+ 8 Q HA 0.607 4.947 4.340 -0.000 0.000 0.321
+ 8 Q C -1.960 174.040 176.000 -0.000 0.000 0.849
+ 8 Q CA 0.047 55.850 55.803 -0.000 0.000 0.811
+ 8 Q CB 1.586 30.324 28.738 -0.000 0.000 1.485
+ 8 Q HN 2.384 10.654 8.270 -0.000 0.000 0.469
+ 9 A N -0.451 122.369 122.820 -0.000 0.000 2.415
+ 9 A HA 0.955 5.275 4.320 -0.000 0.000 0.294
+ 9 A C -2.111 175.473 177.584 -0.000 0.000 1.019
+ 9 A CA 0.218 52.255 52.037 -0.000 0.000 0.603
+ 9 A CB 0.950 19.951 19.000 -0.000 0.000 1.382
+ 9 A HN 1.182 9.332 8.150 -0.000 0.000 0.483
+ 10 A N -1.757 121.063 122.820 -0.000 0.000 2.433
+ 10 A HA 1.107 5.427 4.320 -0.000 0.000 0.294
+ 10 A C -0.727 176.857 177.584 -0.000 0.000 1.037
+ 10 A CA 0.509 52.546 52.037 -0.000 0.000 0.613
+ 10 A CB 0.070 19.070 19.000 -0.000 0.000 1.359
+ 10 A HN 2.692 10.842 8.150 -0.000 0.000 0.473
+ 11 A N -1.687 121.133 122.820 -0.000 0.000 2.456
+ 11 A HA 1.112 5.432 4.320 -0.000 0.000 0.294
+ 11 A C -0.736 176.848 177.584 -0.000 0.000 1.057
+ 11 A CA 0.471 52.508 52.037 -0.000 0.000 0.623
+ 11 A CB 0.003 19.003 19.000 -0.000 0.000 1.338
+ 11 A HN 2.700 10.850 8.150 -0.000 0.000 0.464
+ 12 A N -0.972 121.848 122.820 -0.000 0.000 2.410
+ 12 A HA 0.834 5.154 4.320 -0.000 0.000 0.300
+ 12 A C -1.237 176.347 177.584 -0.000 0.000 1.077
+ 12 A CA 0.709 52.746 52.037 -0.000 0.000 0.610
+ 12 A CB 1.130 20.130 19.000 -0.000 0.000 1.371
+ 12 A HN 1.612 9.762 8.150 -0.000 0.000 0.510
+ 13 Q N -1.864 117.936 119.800 -0.000 0.000 3.077
+ 13 Q HA 0.607 4.947 4.340 -0.000 0.000 0.317
+ 13 Q C -1.958 174.042 176.000 -0.000 0.000 0.864
+ 13 Q CA 0.047 55.850 55.803 -0.000 0.000 0.808
+ 13 Q CB 1.584 30.322 28.738 -0.000 0.000 1.532
+ 13 Q HN 2.385 10.655 8.270 -0.000 0.000 0.474
+ 14 A N -0.265 122.555 122.820 -0.000 0.000 2.401
+ 14 A HA 0.914 5.234 4.320 -0.000 0.000 0.296
+ 14 A C -2.141 175.443 177.584 -0.000 0.000 1.047
+ 14 A CA 0.134 52.171 52.037 -0.000 0.000 0.606
+ 14 A CB 1.148 20.148 19.000 -0.000 0.000 1.376
+ 14 A HN 1.184 9.334 8.150 -0.000 0.000 0.496
+ 16 ? N 0.000 9999.000 9999.000 -0.000 0.000 0.000
+ 16 ? HA 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 16 ? CA 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 16 ? CB 0.000 9999.000 9999.000 0.000 0.000 0.000
+ 16 ? HN 0.000 9999.000 9999.000 0.000 0.000 0.000
diff --git a/proteinbenchmark/data/observables/aaqaa3/aaqaa3-extended-protonated_struct.tab b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-extended-protonated_struct.tab
new file mode 100644
index 0000000..deba4b3
--- /dev/null
+++ b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-extended-protonated_struct.tab
@@ -0,0 +1,110 @@
+REMARK SPARTA+ Structural Parameters Table derived from input PDB cooridnates
+REMARK
+REMARK PHI_R1 PSI_R1 CHI1_R1 and CHI2_R1 are the backbone and sidechain
+REMARK torsion angles of the first residue in a triplet.
+REMARK
+REMARK PHI_R2 PSI_R2 CHI1_R2 and CHI2_R2 are the backbone and sidechain
+REMARK torsion angles of the second (central) residue in a triplet.
+REMARK
+REMARK PHI_R3 PSI_R3 CHI1_R3 and CHI2_R3 are the backbone and sidechain
+REMARK torsion angles of the third residue in a triplet.
+REMARK
+REMARK H-Bond Distances are given in Angstroms:
+REMARK
+REMARK HN_HB_DIST_R2 H-bond distance for the HN atom in the central residue.
+REMARK HA_HB_DIST_R2 H-bond distance for the HA atom in the central residue.
+REMARK CO_HB_DIST_R2 H-bond distance for the CO atom in the central residue.
+REMARK
+REMARK HN_S2_R2 is the Bruschweiler structure-based HN order parameter of
+REMARK the central residue. Reference: Zhang FL, Bruschweiler R
+REMARK JACS 124, 12654-12655 (2002)
+REMARK
+REMARK Reference:
+REMARK Y. Shen and A. Bax: SPARTA+: a modest improvement in empirical NMR
+REMARK chemical shift prediction by means of an artificial neural network.
+REMARK J. Biomol. NMR 48, 13-22 (2010).
+REMARK SPARTA+ Structural Parameters Table derived from input PDB cooridnates
+REMARK
+REMARK PHI_R1 PSI_R1 CHI1_R1 and CHI2_R1 are the backbone and sidechain
+REMARK torsion angles of the first residue in a triplet.
+REMARK
+REMARK PHI_R2 PSI_R2 CHI1_R2 and CHI2_R2 are the backbone and sidechain
+REMARK torsion angles of the second (central) residue in a triplet.
+REMARK
+REMARK PHI_R3 PSI_R3 CHI1_R3 and CHI2_R3 are the backbone and sidechain
+REMARK torsion angles of the third residue in a triplet.
+REMARK
+REMARK H-Bond Distances are given in Angstroms:
+REMARK
+REMARK HN_HB_DIST_R2 H-bond distance for the HN atom in the central residue.
+REMARK HA_HB_DIST_R2 H-bond distance for the HA atom in the central residue.
+REMARK CO_HB_DIST_R2 H-bond distance for the CO atom in the central residue.
+REMARK
+REMARK HN_S2_R2 is the Bruschweiler structure-based HN order parameter of
+REMARK the central residue. Reference: Zhang FL, Bruschweiler R
+REMARK JACS 124, 12654-12655 (2002)
+REMARK
+REMARK Reference:
+REMARK Y. Shen and A. Bax: SPARTA+: a modest improvement in empirical NMR
+REMARK chemical shift prediction by means of an artificial neural network.
+REMARK J. Biomol. NMR 48, 13-22 (2010).
+REMARK SPARTA+ Structural Parameters Table derived from input PDB cooridnates
+REMARK
+REMARK PHI_R1 PSI_R1 CHI1_R1 and CHI2_R1 are the backbone and sidechain
+REMARK torsion angles of the first residue in a triplet.
+REMARK
+REMARK PHI_R2 PSI_R2 CHI1_R2 and CHI2_R2 are the backbone and sidechain
+REMARK torsion angles of the second (central) residue in a triplet.
+REMARK
+REMARK PHI_R3 PSI_R3 CHI1_R3 and CHI2_R3 are the backbone and sidechain
+REMARK torsion angles of the third residue in a triplet.
+REMARK
+REMARK H-Bond Distances are given in Angstroms:
+REMARK
+REMARK HN_HB_DIST_R2 H-bond distance for the HN atom in the central residue.
+REMARK HA_HB_DIST_R2 H-bond distance for the HA atom in the central residue.
+REMARK CO_HB_DIST_R2 H-bond distance for the CO atom in the central residue.
+REMARK
+REMARK HN_S2_R2 is the Bruschweiler structure-based HN order parameter of
+REMARK the central residue. Reference: Zhang FL, Bruschweiler R
+REMARK JACS 124, 12654-12655 (2002)
+REMARK
+REMARK Reference:
+REMARK Y. Shen and A. Bax: SPARTA+: a modest improvement in empirical NMR
+REMARK chemical shift prediction by means of an artificial neural network.
+REMARK J. Biomol. NMR 48, 13-22 (2010).
+
+DATA SOURCE aaqaa3-alpha-protonated
+
+DATA FIRST_RESID 0
+
+DATA SEQUENCE ?AAQAAAAQA AAAQAA?
+DATA SOURCE aaqaa3-beta-protonated
+
+DATA FIRST_RESID 0
+
+DATA SEQUENCE ?AAQAAAAQA AAAQAA?
+DATA SOURCE aaqaa3-extended-protonated
+
+DATA FIRST_RESID 0
+
+DATA SEQUENCE ?AAQAAAAQA AAAQAA?
+
+VARS RESID_R1 RESNAME_R1 PHI_R1 PSI_R1 CHI1_R1 CHI2_R1 RESID_R2 RESNAME_R2 PHI_R2 PSI_R2 CHI1_R2 CHI2_R2 RESID_R3 RESNAME_R3 PHI_R3 PSI_R3 CHI1_R3 CHI2_R3 HN_HB_DIST_R2 HA_HB_DIST_R2 CO_HB_DIST_R2 HN_S2_R2
+FORMAT %4d %s %8.3f %8.3f %8.3f %8.3f %4d %s %8.3f %8.3f %8.3f %8.3f %4d %s %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f
+
+ 0 ? 9999.000 9999.000 9999.000 9999.000 1 A -139.006 180.000 9999.000 9999.000 2 A -179.956 180.000 9999.000 9999.000 0.000 0.000 0.000 0.006
+ 1 A -139.006 180.000 9999.000 9999.000 2 A -179.956 180.000 9999.000 9999.000 3 Q 180.000 180.000 -175.446 177.952 0.000 0.000 0.000 0.121
+ 2 A -179.956 180.000 9999.000 9999.000 3 Q 180.000 180.000 -175.446 177.952 4 A -180.000 -180.000 9999.000 9999.000 0.000 0.000 0.000 0.156
+ 3 Q 180.000 180.000 -175.446 177.952 4 A -180.000 -180.000 9999.000 9999.000 5 A 179.980 180.000 9999.000 9999.000 0.000 0.000 0.000 0.160
+ 4 A -180.000 -180.000 9999.000 9999.000 5 A 179.980 180.000 9999.000 9999.000 6 A 180.000 179.966 9999.000 9999.000 0.000 0.000 0.000 0.230
+ 5 A 179.980 180.000 9999.000 9999.000 6 A 180.000 179.966 9999.000 9999.000 7 A -180.000 -180.000 9999.000 9999.000 0.000 0.000 0.000 0.152
+ 6 A 180.000 179.966 9999.000 9999.000 7 A -180.000 -180.000 9999.000 9999.000 8 Q -180.000 -180.000 -175.448 177.906 0.000 0.000 0.000 0.161
+ 7 A -180.000 -180.000 9999.000 9999.000 8 Q -180.000 -180.000 -175.448 177.906 9 A 179.960 179.980 9999.000 9999.000 0.000 0.000 0.000 0.157
+ 8 Q -180.000 -180.000 -175.448 177.906 9 A 179.960 179.980 9999.000 9999.000 10 A 180.000 179.980 9999.000 9999.000 0.000 0.000 0.000 0.160
+ 9 A 179.960 179.980 9999.000 9999.000 10 A 180.000 179.980 9999.000 9999.000 11 A -179.972 179.966 9999.000 9999.000 0.000 0.000 0.000 0.230
+ 10 A 180.000 179.980 9999.000 9999.000 11 A -179.972 179.966 9999.000 9999.000 12 A -179.948 -179.966 9999.000 9999.000 0.000 0.000 0.000 0.152
+ 11 A -179.972 179.966 9999.000 9999.000 12 A -179.948 -179.966 9999.000 9999.000 13 Q 179.966 179.960 -175.472 177.935 0.000 0.000 0.000 0.161
+ 12 A -179.948 -179.966 9999.000 9999.000 13 Q 179.966 179.960 -175.472 177.935 14 A -180.000 -180.000 9999.000 9999.000 0.000 0.000 0.000 0.157
+ 13 Q 179.966 179.960 -175.472 177.935 14 A -180.000 -180.000 9999.000 9999.000 15 A 179.980 134.988 9999.000 9999.000 0.000 0.000 0.000 0.159
+ 14 A -180.000 -180.000 9999.000 9999.000 15 A 179.980 134.988 9999.000 9999.000 16 ? 9999.000 9999.000 9999.000 9999.000 0.000 0.000 0.000 0.194
diff --git a/proteinbenchmark/data/observables/aaqaa3/aaqaa3-fraction-helix-by-residue.dat b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-fraction-helix-by-residue.dat
index fa1c1f5..b60af32 100644
--- a/proteinbenchmark/data/observables/aaqaa3/aaqaa3-fraction-helix-by-residue.dat
+++ b/proteinbenchmark/data/observables/aaqaa3/aaqaa3-fraction-helix-by-residue.dat
@@ -1,16 +1,16 @@
-Resid Resname Experiment
- 1 ALA 0.45
- 2 ALA 0.49
- 3 GLN 0.56
- 4 ALA 0.54
- 5 ALA 0.59
- 6 ALA 0.56
- 7 ALA 0.57
- 8 GLN 0.59
- 9 ALA 0.55
- 10 ALA 0.49
- 11 ALA 0.39
- 12 ALA 0.35
- 13 GLN 0.37
- 14 ALA 0.12
- 15 ALA 0.00
+Resid Resname Experiment Shift_coil Delta_shift Delta_shift_residue SpartaP_alpha SpartaP_PII ShiftX2_alpha ShiftX2_PII
+ 1 ALA 0.45 177.75 2.53 2.76 NaN NaN 178.28 175.07
+ 2 ALA 0.49 177.58 2.94 2.76 179.22 177.55 179.56 177.25
+ 3 GLN 0.56 175.11 2.93 2.95 177.97 175.92 178.01 175.73
+ 4 ALA 0.54 177.23 2.54 2.76 179.40 177.18 179.86 176.72
+ 5 ALA 0.59 177.36 2.83 2.76 179.43 177.74 179.62 177.23
+ 6 ALA 0.56 177.36 2.75 2.76 179.40 177.74 179.99 177.07
+ 7 ALA 0.57 177.60 2.71 2.76 179.53 177.67 179.93 176.90
+ 8 GLN 0.59 175.15 2.96 2.95 178.07 175.95 178.14 175.56
+ 9 ALA 0.55 177.24 2.46 2.76 179.40 177.18 179.49 176.90
+ 10 ALA 0.49 177.32 2.64 2.76 179.44 177.74 179.62 177.26
+ 11 ALA 0.39 177.29 2.48 2.76 179.40 177.74 180.04 177.27
+ 12 ALA 0.35 177.49 2.42 2.76 179.54 177.68 180.01 176.92
+ 13 GLN 0.37 175.07 2.38 2.95 178.26 175.96 178.27 175.40
+ 14 ALA 0.12 176.86 0.78 2.76 177.70 177.47 178.74 177.01
+ 15 ALA 0.00 179.98 0.00 2.76 NaN NaN 178.66 179.37
diff --git a/proteinbenchmark/data/observables/aaqaa3/get-aaqaa3-structures.py b/proteinbenchmark/data/observables/aaqaa3/get-aaqaa3-structures.py
new file mode 100644
index 0000000..051ff3f
--- /dev/null
+++ b/proteinbenchmark/data/observables/aaqaa3/get-aaqaa3-structures.py
@@ -0,0 +1,31 @@
+import click
+from proteinbenchmark.benchmark_targets import benchmark_targets
+from proteinbenchmark.system_setup import build_initial_coordinates
+
+
+@click.command()
+@click.option(
+ "-o",
+ "--output_prefix",
+ default="aaqaa3",
+ show_default=True,
+ type=click.STRING,
+ help="Prefix for path to write PDB files."
+)
+def main(output_prefix):
+
+ aaqaa3_parameters = benchmark_targets["aaqaa3"]
+ for build_method in ["alpha", "beta", "PII", "extended"]:
+ build_initial_coordinates(
+ build_method=build_method,
+ ph=aaqaa3_parameters["ph"],
+ initial_pdb=f"{output_prefix}-{build_method}-initial.pdb",
+ protonated_pdb=f"{output_prefix}-{build_method}-protonated.pdb",
+ aa_sequence=aaqaa3_parameters["aa_sequence"],
+ nterm_cap=aaqaa3_parameters["nterm_cap"],
+ cterm_cap=aaqaa3_parameters["cterm_cap"],
+ )
+
+
+if __name__ == "__main__":
+ main()
diff --git a/proteinbenchmark/force_fields.py b/proteinbenchmark/force_fields.py
index 5938510..863d6bb 100644
--- a/proteinbenchmark/force_fields.py
+++ b/proteinbenchmark/force_fields.py
@@ -1,4 +1,5 @@
"""List of force fields and water models."""
+
from pathlib import Path
from proteinbenchmark.utilities import package_data_directory
@@ -78,6 +79,36 @@
),
"water_model": "tip4p-fb",
},
+ "ff14sbonlysc-opc": {
+ "force_field_file": Path(
+ ff_directory, "nerenberg_ff14sbonlysc_c0ala_c0gly_c0val.xml"
+ ),
+ "water_model": "opc",
+ },
+ "ff14sbonlysc-opc3": {
+ "force_field_file": Path(
+ ff_directory, "nerenberg_ff14sbonlysc_c0ala_c0gly_c0val.xml"
+ ),
+ "water_model": "opc3",
+ },
+ "ff14sbonlysc-tip3p": {
+ "force_field_file": Path(
+ ff_directory, "nerenberg_ff14sbonlysc_c0ala_c0gly_c0val.xml"
+ ),
+ "water_model": "tip3p",
+ },
+ "ff14sbonlysc-tip3p-fb": {
+ "force_field_file": Path(
+ ff_directory, "nerenberg_ff14sbonlysc_c0ala_c0gly_c0val.xml"
+ ),
+ "water_model": "tip3p-fb",
+ },
+ "ff14sbonlysc-tip4p-fb": {
+ "force_field_file": Path(
+ ff_directory, "nerenberg_ff14sbonlysc_c0ala_c0gly_c0val.xml"
+ ),
+ "water_model": "tip4p-fb",
+ },
"null-0.0.1-tip3p": {
"force_field_file": Path(ff_directory, "Protein-Null-0.0.1.offxml"),
"water_model": "tip3p",
@@ -93,16 +124,38 @@
"water_model": "tip3p",
"water_model_file": None,
},
+ "null-0.0.2-nmr-ala5-opc3": {
+ "force_field_file": Path(ff_directory, "Protein-Null-0.0.2-Ala5-OPC3.offxml"),
+ "water_model": "opc3",
+ "water_model_file": Path(ff_directory, "opc3-1.0.0.offxml"),
+ },
+ "null-0.0.2-nmr-ala5-tip3p-fb": {
+ "force_field_file": Path(
+ ff_directory, "Protein-Null-0.0.2-Ala5-TIP3P-FB.offxml"
+ ),
+ "water_model": "tip3p-fb",
+ "water_model_file": Path(ff_directory, "tip3p_fb-1.1.0.offxml"),
+ },
"null-0.0.2-nmr-opc3": {
"force_field_file": Path(ff_directory, "Protein-Null-0.0.2-OPC3.offxml"),
"water_model": "opc3",
"water_model_file": Path(ff_directory, "opc3-1.0.0.offxml"),
},
+ "null-0.0.2-nmr-2-opc3": {
+ "force_field_file": Path(ff_directory, "Protein-Null-0.0.2-OPC3-2.offxml"),
+ "water_model": "opc3",
+ "water_model_file": Path(ff_directory, "opc3-1.0.0.offxml"),
+ },
"null-0.0.2-nmr-tip3p-fb": {
"force_field_file": Path(ff_directory, "Protein-Null-0.0.2-TIP3P-FB.offxml"),
"water_model": "tip3p-fb",
"water_model_file": Path(ff_directory, "tip3p_fb-1.1.0.offxml"),
},
+ "null-0.0.2-nmr-2-tip3p-fb": {
+ "force_field_file": Path(ff_directory, "Protein-Null-0.0.2-TIP3P-FB-2.offxml"),
+ "water_model": "tip3p-fb",
+ "water_model_file": Path(ff_directory, "tip3p_fb-1.1.0.offxml"),
+ },
"null-0.0.2-opc": {
"force_field_file": Path(ff_directory, "Protein-Null-0.0.2-NH2.offxml"),
"water_model": "opc",
@@ -138,6 +191,176 @@
"water_model": "tip4p-fb",
"water_model_file": Path(ff_directory, "tip4p_fb-1.0.0.offxml"),
},
+ "null-0.0.3-ai-dw-opc": {
+ "force_field_file": Path(
+ ff_directory, "Protein-Null-0.0.3-abinitio-default-weights.offxml"
+ ),
+ "water_model": "opc",
+ "water_model_file": "opc-1.0.0.offxml",
+ },
+ "null-0.0.3-ai-dw-opc3": {
+ "force_field_file": Path(
+ ff_directory, "Protein-Null-0.0.3-abinitio-default-weights.offxml"
+ ),
+ "water_model": "opc3",
+ "water_model_file": Path(ff_directory, "opc3-1.0.0.offxml"),
+ },
+ "null-0.0.3-ai-dw-tip3p": {
+ "force_field_file": Path(
+ ff_directory, "Protein-Null-0.0.3-abinitio-default-weights.offxml"
+ ),
+ "water_model": "tip3p",
+ "water_model_file": None,
+ },
+ "null-0.0.3-ai-dw-tip3p-fb": {
+ "force_field_file": Path(
+ ff_directory, "Protein-Null-0.0.3-abinitio-default-weights.offxml"
+ ),
+ "water_model": "tip3p-fb",
+ "water_model_file": Path(ff_directory, "tip3p_fb-1.1.0.offxml"),
+ },
+ "null-0.0.3-ai-dw-tip4p-fb": {
+ "force_field_file": Path(
+ ff_directory, "Protein-Null-0.0.3-abinitio-default-weights.offxml"
+ ),
+ "water_model": "tip4p-fb",
+ "water_model_file": Path(ff_directory, "tip4p_fb-1.0.0.offxml"),
+ },
+ "null-0.0.3-ai-opc": {
+ "force_field_file": Path(ff_directory, "Protein-Null-0.0.3-abinitio.offxml"),
+ "water_model": "opc",
+ "water_model_file": "opc-1.0.0.offxml",
+ },
+ "null-0.0.3-ai-opc3": {
+ "force_field_file": Path(ff_directory, "Protein-Null-0.0.3-abinitio.offxml"),
+ "water_model": "opc3",
+ "water_model_file": Path(ff_directory, "opc3-1.0.0.offxml"),
+ },
+ "null-0.0.3-ai-tip3p": {
+ "force_field_file": Path(ff_directory, "Protein-Null-0.0.3-abinitio.offxml"),
+ "water_model": "tip3p",
+ "water_model_file": None,
+ },
+ "null-0.0.3-ai-tip3p-fb": {
+ "force_field_file": Path(ff_directory, "Protein-Null-0.0.3-abinitio.offxml"),
+ "water_model": "tip3p-fb",
+ "water_model_file": Path(ff_directory, "tip3p_fb-1.1.0.offxml"),
+ },
+ "null-0.0.3-ai-tip4p-fb": {
+ "force_field_file": Path(ff_directory, "Protein-Null-0.0.3-abinitio.offxml"),
+ "water_model": "tip4p-fb",
+ "water_model_file": Path(ff_directory, "tip4p_fb-1.0.0.offxml"),
+ },
+ "null-0.0.3-dw-opc": {
+ "force_field_file": Path(
+ ff_directory, "Protein-Null-0.0.3-default-weights.offxml"
+ ),
+ "water_model": "opc",
+ "water_model_file": "opc-1.0.0.offxml",
+ },
+ "null-0.0.3-dw-opc3": {
+ "force_field_file": Path(
+ ff_directory, "Protein-Null-0.0.3-default-weights.offxml"
+ ),
+ "water_model": "opc3",
+ "water_model_file": Path(ff_directory, "opc3-1.0.0.offxml"),
+ },
+ "null-0.0.3-dw-tip3p": {
+ "force_field_file": Path(
+ ff_directory, "Protein-Null-0.0.3-default-weights.offxml"
+ ),
+ "water_model": "tip3p",
+ "water_model_file": None,
+ },
+ "null-0.0.3-dw-tip3p-fb": {
+ "force_field_file": Path(
+ ff_directory, "Protein-Null-0.0.3-default-weights.offxml"
+ ),
+ "water_model": "tip3p-fb",
+ "water_model_file": Path(ff_directory, "tip3p_fb-1.1.0.offxml"),
+ },
+ "null-0.0.3-dw-tip4p-fb": {
+ "force_field_file": Path(
+ ff_directory, "Protein-Null-0.0.3-default-weights.offxml"
+ ),
+ "water_model": "tip4p-fb",
+ "water_model_file": Path(ff_directory, "tip4p_fb-1.0.0.offxml"),
+ },
+ "null-0.0.3-nbamber-opc": {
+ "force_field_file": Path(ff_directory, "Protein-Null-0.0.3-NBAmber.offxml"),
+ "water_model": "opc",
+ "water_model_file": "opc-1.0.0.offxml",
+ },
+ "null-0.0.3-nbamber-opc3": {
+ "force_field_file": Path(ff_directory, "Protein-Null-0.0.3-NBAmber.offxml"),
+ "water_model": "opc3",
+ "water_model_file": Path(ff_directory, "opc3-1.0.0.offxml"),
+ },
+ "null-0.0.3-nbamber-tip3p": {
+ "force_field_file": Path(ff_directory, "Protein-Null-0.0.3-NBAmber.offxml"),
+ "water_model": "tip3p",
+ "water_model_file": None,
+ },
+ "null-0.0.3-nbamber-tip3p-fb": {
+ "force_field_file": Path(ff_directory, "Protein-Null-0.0.3-NBAmber.offxml"),
+ "water_model": "tip3p-fb",
+ "water_model_file": Path(ff_directory, "tip3p_fb-1.1.0.offxml"),
+ },
+ "null-0.0.3-nbamber-tip4p-fb": {
+ "force_field_file": Path(ff_directory, "Protein-Null-0.0.3-NBAmber.offxml"),
+ "water_model": "tip4p-fb",
+ "water_model_file": Path(ff_directory, "tip4p_fb-1.0.0.offxml"),
+ },
+ "null-0.0.3-opc": {
+ "force_field_file": Path(ff_directory, "Protein-Null-0.0.3.offxml"),
+ "water_model": "opc",
+ "water_model_file": "opc-1.0.0.offxml",
+ },
+ "null-0.0.3-opc3": {
+ "force_field_file": Path(ff_directory, "Protein-Null-0.0.3.offxml"),
+ "water_model": "opc3",
+ "water_model_file": Path(ff_directory, "opc3-1.0.0.offxml"),
+ },
+ "null-0.0.3-qamber-opc": {
+ "force_field_file": Path(ff_directory, "Protein-Null-0.0.3-QAmber.offxml"),
+ "water_model": "opc",
+ "water_model_file": "opc-1.0.0.offxml",
+ },
+ "null-0.0.3-qamber-opc3": {
+ "force_field_file": Path(ff_directory, "Protein-Null-0.0.3-QAmber.offxml"),
+ "water_model": "opc3",
+ "water_model_file": Path(ff_directory, "opc3-1.0.0.offxml"),
+ },
+ "null-0.0.3-qamber-tip3p": {
+ "force_field_file": Path(ff_directory, "Protein-Null-0.0.3-QAmber.offxml"),
+ "water_model": "tip3p",
+ "water_model_file": None,
+ },
+ "null-0.0.3-qamber-tip3p-fb": {
+ "force_field_file": Path(ff_directory, "Protein-Null-0.0.3-QAmber.offxml"),
+ "water_model": "tip3p-fb",
+ "water_model_file": Path(ff_directory, "tip3p_fb-1.1.0.offxml"),
+ },
+ "null-0.0.3-qamber-tip4p-fb": {
+ "force_field_file": Path(ff_directory, "Protein-Null-0.0.3-QAmber.offxml"),
+ "water_model": "tip4p-fb",
+ "water_model_file": Path(ff_directory, "tip4p_fb-1.0.0.offxml"),
+ },
+ "null-0.0.3-tip3p": {
+ "force_field_file": Path(ff_directory, "Protein-Null-0.0.3.offxml"),
+ "water_model": "tip3p",
+ "water_model_file": None,
+ },
+ "null-0.0.3-tip3p-fb": {
+ "force_field_file": Path(ff_directory, "Protein-Null-0.0.3.offxml"),
+ "water_model": "tip3p-fb",
+ "water_model_file": Path(ff_directory, "tip3p_fb-1.1.0.offxml"),
+ },
+ "null-0.0.3-tip4p-fb": {
+ "force_field_file": Path(ff_directory, "Protein-Null-0.0.3.offxml"),
+ "water_model": "tip4p-fb",
+ "water_model_file": Path(ff_directory, "tip4p_fb-1.0.0.offxml"),
+ },
"specific-0.0.1-tip3p": {
"force_field_file": Path(ff_directory, "Protein-Specific-0.0.1.offxml"),
"water_model": "tip3p",
@@ -153,11 +376,37 @@
"water_model": "tip3p",
"water_model_file": None,
},
+ "specific-0.0.2-nmr-ala5-opc3": {
+ "force_field_file": Path(
+ ff_directory, "Protein-Specific-0.0.2-Ala5-OPC3.offxml"
+ ),
+ "water_model": "opc3",
+ "water_model_file": Path(ff_directory, "opc3-1.0.0.offxml"),
+ },
+ "specific-0.0.2-nmr-ala5-tip3p-fb": {
+ "force_field_file": Path(
+ ff_directory, "Protein-Specific-0.0.2-Ala5-TIP3P-FB.offxml"
+ ),
+ "water_model": "tip3p-fb",
+ "water_model_file": Path(ff_directory, "tip3p_fb-1.1.0.offxml"),
+ },
"specific-0.0.2-nmr-opc3": {
"force_field_file": Path(ff_directory, "Protein-Specific-0.0.2-OPC3.offxml"),
"water_model": "opc3",
"water_model_file": Path(ff_directory, "opc3-1.0.0.offxml"),
},
+ "specific-0.0.2-nmr-2-opc3": {
+ "force_field_file": Path(ff_directory, "Protein-Specific-0.0.2-OPC3-2.offxml"),
+ "water_model": "opc3",
+ "water_model_file": Path(ff_directory, "opc3-1.0.0.offxml"),
+ },
+ "specific-0.0.2-nmr-2-tip3p-fb": {
+ "force_field_file": Path(
+ ff_directory, "Protein-Specific-0.0.2-TIP3P-FB-2.offxml"
+ ),
+ "water_model": "tip3p-fb",
+ "water_model_file": Path(ff_directory, "tip3p_fb-1.1.0.offxml"),
+ },
"specific-0.0.2-nmr-tip3p-fb": {
"force_field_file": Path(
ff_directory, "Protein-Specific-0.0.2-TIP3P-FB.offxml"
@@ -200,6 +449,101 @@
"water_model": "tip4p-fb",
"water_model_file": Path(ff_directory, "tip4p_fb-1.0.0.offxml"),
},
+ "specific-0.0.3-ai-opc": {
+ "force_field_file": Path(
+ ff_directory, "Protein-Specific-0.0.3-abinitio.offxml"
+ ),
+ "water_model": "opc",
+ "water_model_file": "opc-1.0.0.offxml",
+ },
+ "specific-0.0.3-ai-opc3": {
+ "force_field_file": Path(
+ ff_directory, "Protein-Specific-0.0.3-abinitio.offxml"
+ ),
+ "water_model": "opc3",
+ "water_model_file": Path(ff_directory, "opc3-1.0.0.offxml"),
+ },
+ "specific-0.0.3-ai-tip3p": {
+ "force_field_file": Path(
+ ff_directory, "Protein-Specific-0.0.3-abinitio.offxml"
+ ),
+ "water_model": "tip3p",
+ "water_model_file": None,
+ },
+ "specific-0.0.3-ai-tip3p-fb": {
+ "force_field_file": Path(
+ ff_directory, "Protein-Specific-0.0.3-abinitio.offxml"
+ ),
+ "water_model": "tip3p-fb",
+ "water_model_file": Path(ff_directory, "tip3p_fb-1.1.0.offxml"),
+ },
+ "specific-0.0.3-ai-tip4p-fb": {
+ "force_field_file": Path(
+ ff_directory, "Protein-Specific-0.0.3-abinitio.offxml"
+ ),
+ "water_model": "tip4p-fb",
+ "water_model_file": Path(ff_directory, "tip4p_fb-1.0.0.offxml"),
+ },
+ "specific-0.0.3-dw-opc": {
+ "force_field_file": Path(
+ ff_directory, "Protein-Specific-0.0.3-default-weights.offxml"
+ ),
+ "water_model": "opc",
+ "water_model_file": "opc-1.0.0.offxml",
+ },
+ "specific-0.0.3-dw-opc3": {
+ "force_field_file": Path(
+ ff_directory, "Protein-Specific-0.0.3-default-weights.offxml"
+ ),
+ "water_model": "opc3",
+ "water_model_file": Path(ff_directory, "opc3-1.0.0.offxml"),
+ },
+ "specific-0.0.3-dw-tip3p": {
+ "force_field_file": Path(
+ ff_directory, "Protein-Specific-0.0.3-default-weights.offxml"
+ ),
+ "water_model": "tip3p",
+ "water_model_file": None,
+ },
+ "specific-0.0.3-dw-tip3p-fb": {
+ "force_field_file": Path(
+ ff_directory, "Protein-Specific-0.0.3-default-weights.offxml"
+ ),
+ "water_model": "tip3p-fb",
+ "water_model_file": Path(ff_directory, "tip3p_fb-1.1.0.offxml"),
+ },
+ "specific-0.0.3-dw-tip4p-fb": {
+ "force_field_file": Path(
+ ff_directory, "Protein-Specific-0.0.3-default-weights.offxml"
+ ),
+ "water_model": "tip4p-fb",
+ "water_model_file": Path(ff_directory, "tip4p_fb-1.0.0.offxml"),
+ },
+ "specific-0.0.3-opc": {
+ "force_field_file": Path(ff_directory, "Protein-Specific-0.0.3.offxml"),
+ "water_model": "opc",
+ "water_model_file": "opc-1.0.0.offxml",
+ },
+ "specific-0.0.3-opc3": {
+ "force_field_file": Path(ff_directory, "Protein-Specific-0.0.3.offxml"),
+ "water_model": "opc3",
+ "water_model_file": Path(ff_directory, "opc3-1.0.0.offxml"),
+ },
+ "specific-0.0.3-tip3p": {
+ "force_field_file": Path(ff_directory, "Protein-Specific-0.0.3.offxml"),
+ "water_model": "tip3p",
+ "water_model_file": None,
+ },
+ "specific-0.0.3-tip3p-fb": {
+ "force_field_file": Path(ff_directory, "Protein-Specific-0.0.3.offxml"),
+ "water_model": "tip3p-fb",
+ "water_model_file": Path(ff_directory, "tip3p_fb-1.1.0.offxml"),
+ },
+ "specific-0.0.3-tip4p-fb": {
+ "force_field_file": Path(ff_directory, "Protein-Specific-0.0.3.offxml"),
+ "water_model": "tip4p-fb",
+ "water_model_file": Path(ff_directory, "tip4p_fb-1.0.0.offxml"),
+ },
}
# Add implicit water model files
diff --git a/proteinbenchmark/protein_system.py b/proteinbenchmark/protein_system.py
index 7b198fd..24c67c4 100644
--- a/proteinbenchmark/protein_system.py
+++ b/proteinbenchmark/protein_system.py
@@ -3,6 +3,7 @@
from proteinbenchmark.analysis import (
align_trajectory,
assign_dihedral_clusters,
+ compute_chemical_shifts_sparta_plus,
compute_fraction_helix,
compute_h_bond_scalar_couplings,
compute_scalar_couplings,
@@ -482,6 +483,21 @@ def analyze_observables(self, replica: int = 1, time_series_analysis: bool = Fal
reimaged_topology = f"{analysis_prefix}-reimaged.pdb"
reimaged_trajectory = f"{analysis_prefix}-reimaged.dcd"
+ if "traj_length" in self.target_parameters:
+ traj_length = self.target_parameters["traj_length"]
+ elif self.target_parameters["target_type"] == "peptide":
+ traj_length = PEPTIDE_TRAJ_LENGTH
+ elif self.target_parameters["target_type"] == "folded":
+ traj_length = FOLDED_TRAJ_LENGTH
+ elif self.target_parameters["target_type"] == "disordered":
+ traj_length = DISORDERED_TRAJ_LENGTH
+ else:
+ raise ValueError(
+ f"benchmark_targets for target {self.target_name} must "
+ f'contain "traj_length" or "target_type" must be one of '
+ '"peptide", "folded", or "disordered".'
+ )
+
if "frame_length" in self.target_parameters:
frame_length = self.target_parameters["frame_length"]
else:
@@ -531,7 +547,7 @@ def analyze_observables(self, replica: int = 1, time_series_analysis: bool = Fal
if not exists_and_not_empty(h_bond_geometries):
print(
- "Measuring hydrogen bond geometries for system " f"{self.system_name}"
+ f"Measuring hydrogen bond geometries for system {self.system_name}"
)
fragment_index = measure_h_bond_geometries(
@@ -544,6 +560,25 @@ def analyze_observables(self, replica: int = 1, time_series_analysis: bool = Fal
if fragment_index > 0:
merge_csvs(h_bond_geometries)
+ # Compute chemical shifts
+ chemical_shifts = f"{analysis_prefix}-chemical-shifts.dat"
+
+ if not exists_and_not_empty(chemical_shifts):
+ print(f"Computing chemical shifts for system {self.system_name}")
+
+ #fragment_index = compute_chemical_shifts_shiftx2(
+ fragment_index = compute_chemical_shifts_sparta_plus(
+ topology_path=reimaged_topology,
+ trajectory_path=reimaged_trajectory,
+ frame_length=frame_length,
+ output_path=chemical_shifts,
+ # ph=self.target_parameters["ph"],
+ # temperature=self.target_parameters["temperature"],
+ )
+
+ if fragment_index > 0:
+ merge_csvs(chemical_shifts)
+
# Dihedral cluster assignments
dihedral_clusters = f"{analysis_prefix}-dihedral-clusters.dat"
@@ -626,5 +661,6 @@ def analyze_observables(self, replica: int = 1, time_series_analysis: bool = Fal
observable_path=data,
dihedral_clusters_path=dihedral_clusters,
h_bond_geometries_path=h_bond_geometries,
+ chemical_shifts_path=chemical_shifts,
output_path=fraction_helix,
)
diff --git a/proteinbenchmark/system_setup.py b/proteinbenchmark/system_setup.py
index 90e8086..28a1581 100644
--- a/proteinbenchmark/system_setup.py
+++ b/proteinbenchmark/system_setup.py
@@ -63,7 +63,7 @@ def build_initial_coordinates(
f'"pdb" with initial_pdb\n {initial_pdb}'
)
- elif build_method in {"extended", "helical"}:
+ elif build_method in {"alpha", "beta", "extended", "PII"}:
if aa_sequence is None:
raise ValueError(
'aa_sequence must be set to use build_method "extended" or ' "helical"
@@ -78,12 +78,24 @@ def build_initial_coordinates(
chain = pmx.Chain().create(aa_sequence)
# Set backbone dihedrals
- if build_method == "helical":
+ if build_method == "alpha":
# Alpha helix values from
# Hollingsworth SA, Karplus PA. (2010). BioMol Concepts 1, 271-283.
build_phi = -63
build_psi = -43
+ elif build_method == "beta":
+ # Beta strand values from
+ # Hollingsworth SA, Karplus PA. (2010). BioMol Concepts 1, 271-283.
+ build_phi = -120
+ build_psi = 130
+
+ elif build_method == "PII":
+ # P_II spiral values from
+ # Hollingsworth SA, Karplus PA. (2010). BioMol Concepts 1, 271-283.
+ build_phi = -65
+ build_psi = 145
+
else:
# Extended conformation with all backbone dihedrals at -180 deg
build_phi = -180
diff --git a/proteinbenchmark/utilities.py b/proteinbenchmark/utilities.py
index 28eda00..f915e25 100644
--- a/proteinbenchmark/utilities.py
+++ b/proteinbenchmark/utilities.py
@@ -1,4 +1,5 @@
"""Utilities for file input and output."""
+
from pathlib import Path
import openmm
@@ -8,6 +9,37 @@
package_data_directory = Path(Path(__file__).parent.absolute(), "data")
+def copy_internal_coords(ra, rb, rc, rd, ta, tb, tc):
+ """
+ Given four reference atoms and three target atoms, return the coordinates of
+ a fourth target atom so that it has the same distance, angle, and dihedral
+ as the reference atoms.
+ """
+
+ distance = rd.coords().distance(rc.coords())
+ angle = numpy.deg2rad(loos.angle(rd, rc, rb))
+ dihedral = numpy.deg2rad(loos.torsion(rd, rc, rb, ra))
+ r_cb = tb.coords() - tc.coords()
+ r_cb /= r_cb.length()
+ r_ba = ta.coords() - tb.coords()
+ r_ba /= r_ba.length()
+ ba_cross_cb = r_ba.cross(r_cb)
+ ba_cross_cb /= ba_cross_cb.length()
+ z = r_cb
+ y = z.cross(ba_cross_cb)
+ y /= y.length()
+ x = y.cross(z)
+ x /= x.length()
+ dx = distance * numpy.sin(angle) * numpy.sin(dihedral)
+ dy = distance * numpy.sin(angle) * numpy.cos(dihedral)
+ dz = distance * numpy.cos(angle)
+ r_cd = numpy.dot(
+ numpy.array([[x[0], y[0], z[0]], [x[1], y[1], z[1]], [x[2], y[2], z[2]]]),
+ numpy.array([dx, dy, dz]),
+ )
+ return numpy.array([tc.coords()[0], tc.coords()[1], tc.coords()[2]]) + r_cd
+
+
def exists_and_not_empty(file_name):
"""Returns True if file_name exists and is not empty."""