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Merge pull request #34 from molssi-seamm/dev
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Improved handling of SDF files.
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@seamm
seamm authored Sep 27, 2022
2 parents 3e4f924 + a01a670 commit 8a19838
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Showing 7 changed files with 274 additions and 177 deletions.
2 changes: 1 addition & 1 deletion Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -51,7 +51,7 @@ clean-test: ## remove test and coverage artifacts

lint: ## check style with black and flake8
black --extend-exclude '_version.py' --check --diff $(MODULE) tests
flake8 $(MODULE) tests
flake8 --color never $(MODULE) tests

format: ## reformat with with black
black --extend-exclude '_version.py' $(MODULE) tests
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253 changes: 137 additions & 116 deletions read_structure_step/formats/sdf/sdf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@
Implementation of the reader for SDF files using OpenBabel
"""

import gzip
from pathlib import Path
import shutil
import string
Expand Down Expand Up @@ -132,13 +133,15 @@ def load_sdf(
path.expanduser().resolve()

# Get the information for progress output, if requested.
compress = path.suffix == ".gz"
if printer is not None:
n_structures = 0
with path.open() as fd:
with gzip.open(path, mode="rt") if compress else open(path, "r") as fd:
for line in fd:
if line[0:4] == "$$$$":
n_structures += 1
printer(f"The SDF file contains {n_structures} structures.")
printer("")
printer(f" The SDF file contains {n_structures} structures.")
last_percent = 0
t0 = time.time()
last_t = t0
Expand All @@ -148,79 +151,98 @@ def load_sdf(

configurations = []
structure_no = 1
while True:
if structure_no == 1:
obMol = openbabel.OBMol()
not_done = obConversion.ReadFile(obMol, str(path))
else:
obMol = openbabel.OBMol()
not_done = obConversion.Read(obMol)

if not not_done:
break

if add_hydrogens:
obMol.AddHydrogens()

if structure_no > 1:
if subsequent_as_configurations:
configuration = system.create_configuration()
else:
system = system_db.create_system()
configuration = system.create_configuration()

configuration.from_OBMol(obMol)
configurations.append(configuration)

# Set the system name
if system_name is not None and system_name != "":
lower_name = system_name.lower()
if "from file" in lower_name:
system.name = obMol.GetTitle()
elif "canonical smiles" in lower_name:
system.name = configuration.canonical_smiles
elif "smiles" in lower_name:
system.name = configuration.smiles
else:
system.name = system_name

# And the configuration name
if configuration_name is not None and configuration_name != "":
lower_name = configuration_name.lower()
if "from file" in lower_name:
configuration.name = obMol.GetTitle()
elif "canonical smiles" in lower_name:
configuration.name = configuration.canonical_smiles
elif "smiles" in lower_name:
configuration.name = configuration.smiles
elif lower_name == "sequential":
configuration.name = str(structure_no)
else:
configuration.name = configuration_name

structure_no += 1
if printer:
percent = int(100 * structure_no / n_structures)
if percent > last_percent:
t1 = time.time()
if t1 - last_t >= 60:
t = int(t1 - t0)
rate = structure_no / (t1 - t0)
t_left = int((n_structures - structure_no) / rate)
printer(
f"\t{structure_no:6} ({percent}%) structures read in {t} "
f"seconds. About {t_left} seconds remaining."
)
last_t = t1
last_percent = percent
n_errors = 0
obMol = openbabel.OBMol()
text = ""
with gzip.open(path, mode="rt") if compress else open(path, "r") as fd:
for line in fd:
text += line

if line[0:4] != "$$$$":
continue

obConversion.ReadString(obMol, text)

if add_hydrogens:
obMol.AddHydrogens()

if structure_no > 1:
if subsequent_as_configurations:
configuration = system.create_configuration()
else:
system = system_db.create_system()
configuration = system.create_configuration()

structure_no += 1
try:
configuration.from_OBMol(obMol)
except Exception as e:
n_errors += 1
printer("")
printer(f" Error handling entry {structure_no} in the SDF file:")
printer(" " + str(e))
printer(" Text of the entry is")
printer(" " + 60 * "-")
for line in text.splitlines():
printer(" " + line)
printer(" " + 60 * "-")
printer("")
text = ""
continue

configurations.append(configuration)
text = ""

# Set the system name
if system_name is not None and system_name != "":
lower_name = system_name.lower()
if "from file" in lower_name:
system.name = obMol.GetTitle()
elif "canonical smiles" in lower_name:
system.name = configuration.canonical_smiles
elif "smiles" in lower_name:
system.name = configuration.smiles
else:
system.name = system_name

# And the configuration name
if configuration_name is not None and configuration_name != "":
lower_name = configuration_name.lower()
if "from file" in lower_name:
configuration.name = obMol.GetTitle()
elif "canonical smiles" in lower_name:
configuration.name = configuration.canonical_smiles
elif "smiles" in lower_name:
configuration.name = configuration.smiles
elif lower_name == "sequential":
configuration.name = str(structure_no)
else:
configuration.name = configuration_name

if printer:
percent = int(100 * structure_no / n_structures)
if percent > last_percent:
t1 = time.time()
if t1 - last_t >= 60:
t = int(t1 - t0)
rate = structure_no / (t1 - t0)
t_left = int((n_structures - structure_no) / rate)
printer(
f"\t{structure_no:6} ({percent}%) structures read in {t} "
f"seconds. About {t_left} seconds remaining."
)
last_t = t1
last_percent = percent

if printer:
t1 = time.time()
rate = structure_no / (t1 - t0)
printer(
f"Read {structure_no} structures in {t1 - t0:.1f} seconds = {rate:.2f} "
"per second"
f" Read {structure_no - n_errors - 1} structures in {t1 - t0:.1f} "
f"seconds = {rate:.2f} per second"
)
if n_errors > 0:
printer(f" {n_errors} structures could not be read due to errors.")

if references:
# Add the citations for Open Babel
Expand Down Expand Up @@ -330,57 +352,56 @@ def write_sdf(

path.expanduser().resolve()

# Get the information for progress output, if requested.
if printer is not None:
n_structures = 0
with path.open() as fd:
for line in fd:
if line[0:4] == "$$$$":
n_structures += 1
printer(f"The SDF file contains {n_structures} structures.")
last_percent = 0
t0 = time.time()
last_t = t0

obConversion = openbabel.OBConversion()
obConversion.SetInAndOutFormats("smi", "sdf")

n_structures = len(configurations)
last_percent = 0
last_t = t0 = time.time()
structure_no = 1
for configuration in configurations:
obMol = configuration.to_OBMol()

system = configuration.system
title = f"{system.name}/{configuration.name}"
obMol.SetTitle(title)

if remove_hydrogens == "nonpolar":
obMol.DeleteNonPolarHydrogens()
elif remove_hydrogens == "all":
obMol.DeleteHydrogens()

if structure_no == 1:
ok = obConversion.WriteFile(obMol, str(path))
else:
ok = obConversion.Write(obMol)

if not ok:
raise RuntimeError("Error writing file")

structure_no += 1
if printer:
percent = int(100 * structure_no / n_structures)
if percent > last_percent:
t1 = time.time()
if t1 - last_t >= 60:
t = int(t1 - t0)
rate = structure_no / (t1 - t0)
t_left = int((n_structures - structure_no) / rate)
printer(
f"\t{structure_no:6} ({percent}%) structures wrote in {t} "
f"seconds. About {t_left} seconds remaining."
)
last_t = t1
last_percent = percent
compress = path.suffix == ".gz"
with gzip.open(path, mode="wb") if compress else open(path, "w") as fd:
for configuration in configurations:
obMol = configuration.to_OBMol(properties="all")

system = configuration.system
title = f"{system.name}/{configuration.name}"
obMol.SetTitle(title)

if remove_hydrogens == "nonpolar":
obMol.DeleteNonPolarHydrogens()
elif remove_hydrogens == "all":
obMol.DeleteHydrogens()

if structure_no == 1:
text = obConversion.WriteString(obMol)
else:
text = obConversion.WriteString(obMol)

# if not ok
if text is None or text == "":
raise RuntimeError("Error writing file")

if compress:
fd.write(bytes(text, "utf-8"))
else:
fd.write(text)

structure_no += 1
if printer:
percent = int(100 * structure_no / n_structures)
if percent > last_percent:
t1 = time.time()
if t1 - last_t >= 60:
t = int(t1 - t0)
rate = structure_no / (t1 - t0)
t_left = int((n_structures - structure_no) / rate)
printer(
f"\t{structure_no:6} ({percent}%) structures wrote in {t} "
f"seconds. About {t_left} seconds remaining."
)
last_t = t1
last_percent = percent

if printer:
t1 = time.time()
Expand Down
53 changes: 27 additions & 26 deletions read_structure_step/read_structure.py
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Original file line number Diff line number Diff line change
Expand Up @@ -159,7 +159,7 @@ def description_text(self, P=None):
path = PurePath(filename)
extension = path.suffix
if extension == ".gz":
extension = path.stem.suffix
extension = path.with_suffix("").suffix

# Get the metadata for the format
metadata = get_format_metadata(extension)
Expand Down Expand Up @@ -200,7 +200,7 @@ def run(self):
else:
extension = path.suffix
if extension == ".gz":
extension = path.stem.suffix
extension = path.with_suffix("").suffix

if extension == "":
extension = guess_extension(filename, use_file_name=False)
Expand All @@ -215,7 +215,7 @@ def run(self):
P, structure_handling=True
)

read(
configurations = read(
filename,
configuration,
extension=extension,
Expand All @@ -237,31 +237,32 @@ def run(self):
system, configuration = self.get_system_configuration(
P, structure_handling=False
)
if configuration.periodicity == 3:
space_group = configuration.symmetry.group
if space_group == "":
symmetry_info = ""
else:
symmetry_info = f" The space group is {space_group}."
printer.important(
__(
"\n Created a periodic structure with "
f"{configuration.n_atoms} atoms. {symmetry_info}"
f"\n System name = {system.name}"
f"\n Configuration name = {configuration.name}",
indent=4 * " ",
if len(configurations) == 1:
if configuration.periodicity == 3:
space_group = configuration.symmetry.group
if space_group == "":
symmetry_info = ""
else:
symmetry_info = f" The space group is {space_group}."
printer.important(
__(
"\n Created a periodic structure with "
f"{configuration.n_atoms} atoms. {symmetry_info}"
f"\n System name = {system.name}"
f"\n Configuration name = {configuration.name}",
indent=4 * " ",
)
)
)
else:
printer.important(
__(
"\n Created a molecular structure with "
f"{configuration.n_atoms} atoms."
f"\n System name = {system.name}"
f"\n Configuration name = {configuration.name}",
indent=4 * " ",
else:
printer.important(
__(
"\n Created a molecular structure with "
f"{configuration.n_atoms} atoms."
f"\n System name = {system.name}"
f"\n Configuration name = {configuration.name}",
indent=4 * " ",
)
)
)

printer.important("")

Expand Down
2 changes: 1 addition & 1 deletion read_structure_step/tk_read_structure.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -120,7 +120,7 @@ def reset_dialog(self, widget=None):
path = PurePath(filename)
extension = path.suffix
if extension == ".gz":
extension = path.stem.suffix
extension = path.with_suffix("").suffix

# Get the metadata for the format
metadata = get_format_metadata(extension)
Expand Down
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