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Acellera / htmd

HTMD: Programming Environment for Molecular Discovery
https://software.acellera.com/docs/latest/htmd/index.html
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ValueError: all the input array dimensions except for the concatenation axis must match exactly #128

Closed giadefa closed 7 years ago

giadefa commented 8 years ago

I am getting this error on a trajectory that seemed to work last week. Any recent change?

Traj id = 2017 parent = None input = [] trajectory = ['/workspace1/D3R/D3R-467/batches/5/filtered/1-7/e5s87_e1s336p2f175/e5s87_e1s336p2f175-NOELIA_c36x467x5-0-4-RND1667_9.filtered.xtc', '/workspace1/D3R/D3R-467/batches/5/filtered/1-7/e5s87_e1s336p2f175/e5s87_e1s336p2f175-NOELIA_c36x467x5-1-4-RND1667_9.filtered.xtc', '/workspace1/D3R/D3R-467/batches/5/filtered/1-7/e5s87_e1s336p2f175/e5s87_e1s336p2f175-NOELIA_c36x467x5-2-4-RND1667_9.filtered.xtc', '/workspace1/D3R/D3R-467/batches/5/filtered/1-7/e5s87_e1s336p2f175/e5s87_e1s336p2f175-NOELIA_c36x467x5-3-4-RND1667_9.filtered.xtc'] molfile = /workspace1/D3R/D3R-467/batches/4/filtered/filtered.pdb

ValueError Traceback (most recent call last)

in () ----> 1 m = Molecule(sims[2017]) /shared/gianni/Code/acellera/htmd/htmd/molecule/molecule.py in **init**(self, filename, name) 157 158 if filename: --> 159 self.read(filename) 160 if isinstance(filename, str): 161 self.topoloc = os.path.abspath(filename) /shared/gianni/Code/acellera/htmd/htmd/molecule/molecule.py in read(self, filename, type, skip, frames, append, overwrite) 669 if isinstance(filename, Sim): 670 self.read(filename.molfile) --> 671 self.read(filename.trajectory) 672 return 673 /shared/gianni/Code/acellera/htmd/htmd/molecule/molecule.py in read(self, filename, type, skip, frames, append, overwrite) 687 self._readPDB(filename, mode='pdbqt', overwrite=overwrite) 688 elif type == "xtc" or ext == "xtc": --> 689 self._readTraj(filename, skip=skip, frames=frames, append=append) 690 elif type == "coor" or ext == "coor": 691 if append: /shared/gianni/Code/acellera/htmd/htmd/molecule/molecule.py in _readTraj(self, filename, skip, frames, append, mdtraj) 857 self.coords = np.append(self.coords, coords, 2) 858 self.box = np.append(self.box, box, 1) --> 859 self.boxangles = np.append(self.boxangles, boxangles, 0) 860 861 if skip is not None: /shared/gianni/miniconda3/lib/python3.5/site-packages/numpy/lib/function_base.py in append(arr, values, axis) 4584 values = ravel(values) 4585 axis = arr.ndim-1 -> 4586 return concatenate((arr, values), axis=axis) 4587 ValueError: all the input array dimensions except for the concatenation axis must match exactly
stefdoerr commented 8 years ago

Yeah, the addition of box angles which don't seem to append nicely. Will fix tomorrow

giadefa commented 8 years ago

it does happen only to few traj

stefdoerr commented 7 years ago

Fixed in https://github.com/Acellera/htmd/commit/bba92efa4ebb1b8fb085b547e47e9225de3a814d

stefdoerr commented 7 years ago

Added test case to catch similar problems in future: https://github.com/Acellera/htmd/commit/38e32ec16467798f6f3c54bd5ab1f49aae233427