ValueError: invalid literal for int() with base 10: ''

[h-aitken-uq]

Hi there,

I saw someone using PyLipID at the Biophysical Society Conference 2023 and wanted to give it a try but unfortunately I'm getting the following error at the first stage of li.collect_residue_contacts() (see below). I've tried depreciating numpy to no avail, as that seems to have been the fix for other packages lately. I'm using the sample trajectories.

Many thanks!

---

ValueError Traceback (most recent call last)
Cell In[1], line 69
58 # i.e. None, the functions will use up all the cpus available. This can use up all the memory in
59 # some cases.
60
(...)
64
65 #### calculate lipid interactions
66 li = LipidInteraction(trajfile_list, topfile_list=topfile_list, cutoffs=cutoffs, lipid=lipid,
67 lipid_atoms=lipid_atoms, nprot=1, resi_offset=resi_offset,
68 timeunit=timeunit, save_dir=save_dir, stride=stride, dt_traj=dt_traj)
---> 69 li.collect_residue_contacts()
70 li.compute_residue_duration(residue_id=None)
71 li.compute_residue_occupancy(residue_id=None)

File ~/anaconda3/envs/membrane/lib/python3.11/site-packages/pylipid/api/api.py:333, in LipidInteraction.collect_residue_contacts(self)
330 # calculate interactions from trajectories
331 for traj_idx in trange(len(self._trajfile_list), desc="COLLECT INTERACTIONS FROM TRAJECTORIES",
332 total=len(self._trajfile_list)):
--> 333 traj = md.load(self._trajfile_list[traj_idx], top=self._topfile_list[traj_idx], stride=self._stride)
334 traj_info, self._protein_ref, self._lipid_ref = get_traj_info(traj, lipid=self._lipid,
335 lipid_atoms=self._lipid_atoms,
336 resi_offset=self._resi_offset,
337 nprot=self._nprot,
338 protein_ref=self._protein_ref,
339 lipid_ref=self._lipid_ref)
340 if self._dt_traj is None:

File ~/anaconda3/envs/membrane/lib/python3.11/site-packages/mdtraj/core/trajectory.py:396, in load(filename_or_filenames, discard_overlapping_frames, **kwargs)
394 topkwargs.pop("stride", None)
395 topkwargs.pop("start", None)
--> 396 kwargs["top"] = _parse_topology(kwargs.get("top", filename_or_filenames[0]), **topkwargs)
398 #get the right loader
399 try:
400 #loader = _LoaderRegistry[extension][0]

File ~/anaconda3/envs/membrane/lib/python3.11/site-packages/mdtraj/core/trajectory.py:183, in _parse_topology(top, **kwargs)
181 topology = load_mol2(top, **kwargs).topology
182 elif isinstance(top, (string_types, os.PathLike)) and (ext in ['.gro']):
--> 183 topology = load_gro(top, **kwargs).topology
184 elif isinstance(top, (string_types, os.PathLike)) and (ext in ['.arc']):
185 topology = load_arc(top, **kwargs).topology

File ~/anaconda3/envs/membrane/lib/python3.11/site-packages/mdtraj/formats/gro.py:94, in load_gro(filename, stride, atom_indices, frame, top)
73 """Load a GROMACS GRO file.
74
75 Parameters
(...)
90 it saves time if you have to parse a big number of files
91 """
92 from mdtraj.core.trajectory import _parse_topology, Trajectory
---> 94 with GroTrajectoryFile(filename, 'r', top=top) as f:
95 topology = f.topology
96 if frame is not None:

File ~/anaconda3/envs/membrane/lib/python3.11/site-packages/mdtraj/formats/gro.py:148, in GroTrajectoryFile.init(self, filename, mode, force_overwrite, top)
146 try:
147 if self.topology is None:
--> 148 self.n_atoms, self.topology = self._read_topology()
149 else:
150 self.n_atoms = self.topology.n_atoms

File ~/anaconda3/envs/membrane/lib/python3.11/site-packages/mdtraj/formats/gro.py:315, in GroTrajectoryFile._read_topology(self)
313 for ln, line in enumerate(self._file):
314 if ln == 1:
--> 315 n_atoms = int(line.strip())
316 elif ln > 1 and ln < n_atoms + 2:
317 (thisresnum, thisresname, thisatomname, thisatomnum) =
318 [line[i5:i5+5].strip() for i in range(4)]

ValueError: invalid literal for int() with base 10: ''