I'm in version 1.0.26. I run: model.viewStates(ligand="resname MOL and noh")
. And got the following error:
What am I missing?
/nfs/grid/software/hpcc/apps/Linux-x86_64-RHEL6/acellera/current/python/lib/python3.5/site-packages/pyEMMA-2.2-py3.5-linux-x86_64.egg/pyemma/util/_ext/shimmodule.py:131: PyEMMA_DeprecationWarning: Access to a moved module 'pyemma.msm.dtraj' detected! Please use 'msmtools.dtraj' in the future.
category=PyEMMA_DeprecationWarning)
/nfs/grid/software/hpcc/apps/Linux-x86_64-RHEL6/acellera/current/python/lib/python3.5/site-packages/pyEMMA-2.2-py3.5-linux-x86_64.egg/pyemma/util/_ext/shimmodule.py:131: PyEMMA_DeprecationWarning: Access to a moved module 'pyemma.msm.analysis' detected! Please use 'msmtools.analysis' in the future.
category=PyEMMA_DeprecationWarning)
/nfs/grid/software/hpcc/apps/Linux-x86_64-RHEL6/acellera/current/python/lib/python3.5/site-packages/pyEMMA-2.2-py3.5-linux-x86_64.egg/pyemma/util/_ext/shimmodule.py:131: PyEMMA_DeprecationWarning: Access to a moved module 'pyemma.msm.generation' detected! Please use 'msmtools.generation' in the future.
category=PyEMMA_DeprecationWarning)
/nfs/grid/software/hpcc/apps/Linux-x86_64-RHEL6/acellera/current/python/lib/python3.5/site-packages/pyEMMA-2.2-py3.5-linux-x86_64.egg/pyemma/util/_ext/shimmodule.py:131: PyEMMA_DeprecationWarning: Access to a moved module 'pyemma.msm.flux' detected! Please use 'msmtools.flux' in the future.
category=PyEMMA_DeprecationWarning)
/nfs/grid/software/hpcc/apps/Linux-x86_64-RHEL6/acellera/current/python/lib/python3.5/site-packages/pyEMMA-2.2-py3.5-linux-x86_64.egg/pyemma/util/_ext/shimmodule.py:131: PyEMMA_DeprecationWarning: Access to a moved module 'pyemma.msm.estimation' detected! Please use 'msmtools.estimation' in the future.
category=PyEMMA_DeprecationWarning)
---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last)
<ipython-input-5-119f81c50177> in <module>()
2 #model.load('model-oldsimdata_25+.dat')
3 os.chdir('/hpc/grid/wip_cmg_wwmc/workspace/groups/neuro_cc/acellera/tmp/proteins/D3R/batches')
----> 4 model.viewStates(ligand="resname MOL and noh")
/path/to/htmd/model.py in viewStates(self, states, statetype, protein, ligand, viewer, mols, numsamples, wrapsel, alignsel)
395 states = [states]
396 if mols is None:
--> 397 mols = self.getStates(states, statetype, numsamples=numsamples, wrapsel=wrapsel, alignsel=alignsel)
398 colors = [0, 1, 3, 4, 5, 6, 7, 9]
399 for i, s in enumerate(states):
/path/to/htmd/model.py in getStates(self, states, statetype, wrapsel, alignsel, alignmol, samplemode, numsamples)
346 # Removed ncpus because it was giving errors on some systems.
347 mols = Parallel(n_jobs=1, verbose=11)(delayed(_loadMols)(self, i, rel, molfile, wrapsel, alignsel, refmol)
--> 348 for i, rel in enumerate(relframes))
349 return np.array(mols, dtype=object)
350
/nfs/grid/software/hpcc/apps/Linux-x86_64-RHEL6/acellera/current/python/lib/python3.5/site-packages/joblib/parallel.py in __call__(self, iterable)
798 # was dispatched. In particular this covers the edge
799 # case of Parallel used with an exhausted iterator.
--> 800 while self.dispatch_one_batch(iterator):
801 self._iterating = True
802 else:
/nfs/grid/software/hpcc/apps/Linux-x86_64-RHEL6/acellera/current/python/lib/python3.5/site-packages/joblib/parallel.py in dispatch_one_batch(self, iterator)
656 return False
657 else:
--> 658 self._dispatch(tasks)
659 return True
660
/nfs/grid/software/hpcc/apps/Linux-x86_64-RHEL6/acellera/current/python/lib/python3.5/site-packages/joblib/parallel.py in _dispatch(self, batch)
564
565 if self._pool is None:
--> 566 job = ImmediateComputeBatch(batch)
567 self._jobs.append(job)
568 self.n_dispatched_batches += 1
/nfs/grid/software/hpcc/apps/Linux-x86_64-RHEL6/acellera/current/python/lib/python3.5/site-packages/joblib/parallel.py in __init__(self, batch)
178 # Don't delay the application, to avoid keeping the input
179 # arguments in memory
--> 180 self.results = batch()
181
182 def get(self):
/nfs/grid/software/hpcc/apps/Linux-x86_64-RHEL6/acellera/current/python/lib/python3.5/site-packages/joblib/parallel.py in __call__(self)
70
71 def __call__(self):
---> 72 return [func(*args, **kwargs) for func, args, kwargs in self.items]
73
74 def __len__(self):
/nfs/grid/software/hpcc/apps/Linux-x86_64-RHEL6/acellera/current/python/lib/python3.5/site-packages/joblib/parallel.py in <listcomp>(.0)
70
71 def __call__(self):
---> 72 return [func(*args, **kwargs) for func, args, kwargs in self.items]
73
74 def __len__(self):
/path/to/htmd/model.py in _loadMols(self, i, rel, molfile, wrapsel, alignsel, refmol)
522 trajs = np.append(trajs, f.sim.trajectory[f.piece])
523 frs = np.append(frs, f.frame)
--> 524 mol.read(trajs, frames=frs)
525 if len(wrapsel) > 0:
526 mol.wrap(wrapsel)
/path/to/htmd/molecule/molecule.py in read(self, filename, type, skip, frames, append)
670 self._readPDB(filename, mode='pdbqt')
671 elif (type is None and firstfile.endswith(".xtc")) or type == "xtc":
--> 672 self._readTraj(filename, skip=skip, frames=frames, append=append)
673 elif (type is None and firstfile.endswith(".coor")) or type == "coor":
674 self._readBinCoordinates(filename)
/path/to/htmd/molecule/molecule.py in _readTraj(self, filename, skip, frames, append, mdtraj)
914 traj.coords = traj.coords[:, :, frames[i]]
915 else:
--> 916 traj = XTCread(f, frames[i])
917 self.fileloc.append([f, int(frames[i])])
918
/path/to/htmd/molecule/xtc.py in XTCread(filename, frames)
52
53 def XTCread(filename, frames=None):
---> 54 lib = xtc_lib()
55 nframes = pack_ulong_buffer([0])
56 natoms = pack_int_buffer([0])
/path/to/htmd/molecule/xtc.py in xtc_lib()
35 def xtc_lib():
36 lib = {}
---> 37 libdir = htmd.home(libDir=True)
38
39 import platform
/path/to/htmd/home.py in home(dataDir, libDir)
45 return os.path.join(libdir, "pro", platform.system())
46 else:
---> 47 raise FileNotFoundError('Could not find libs.')
48 else:
49 return homeDir
FileNotFoundError: Could not find libs.