def writeFilenameExtractedCoordinates(filename,
params,
pathFolder,
constants,
topology,
indexes=None):
"""
Process the coordinates of a trajectory
"""
if params.dihedrals:
coords = calculateDihedrals(filename, params, topology)
if params.dihedrals_projection:
coords = projectDihedrals(coords)
outputFilename = getOutputFilename(
constants.extractedTrajectoryFolder, filename,
constants.baseExtractedTrajectoryName)
writeToFile(coords, outputFilename % pathFolder)
return
ext = utilities.getFileExtension(filename)
if ext == ".pdb":
allCoordinates = loadAllResnameAtomsInPdb(filename, params)
if params.writeLigandTrajectory:
outputFilename = os.path.join(
pathFolder, constants.ligandTrajectoryBasename %
extractFilenumber(filename))
with open(outputFilename, 'w') as f:
f.write("\nENDMDL\n".join(allCoordinates))
if params.protein_CA:
coords = getLigandAlphaCarbonsCoords(allCoordinates,
params.lig_resname)
elif params.sidechains:
coords = getLigandAlphaCarbonsCoords(allCoordinates,
params.lig_resname,
sidechains=params.sidechains)
else:
if params.com:
coords = getPDBCOM(allCoordinates, params.lig_resname)
elif params.contact_map:
coords = np.array(
extractContactMapCoordinatesPDB(allCoordinates, params))
coords = utils.contactMap(coords, int(coords.shape[1] / 3))
else:
coords = getAtomCoord(allCoordinates, params.lig_resname,
params.atomIds)
elif ext in MDTRAJ_FORMATS:
if not indexes:
raise ValueError("Empty selection!!!")
if params.contact_map:
coords = contactMapNonPDB(filename, params, topology, indexes)
else:
coords = extractCoordinatesXTCFile(filename, params, topology,
indexes)
else:
raise ValueError("Unrecongnized file extension for %s" % filename)
outputFilename = getOutputFilename(constants.extractedTrajectoryFolder,
filename,
constants.baseExtractedTrajectoryName)
writeToFile(coords, outputFilename % pathFolder)
def getTopologyObject(topology_file):
ext = utilities.getFileExtension(topology_file)
if ext == ".pdb":
return TopologyCompat(topology_file)
elif ext == ".pkl":
return utilities.readClusteringObject(topology_file)
else:
raise ValueError(
"The topology parameter needs to be the path to a pickled Topology object or a pdb!"
)
def extractSidechainIndexes(params, pool=None):
trajs = glob.glob(params.sidechain_folder)
sidechains_trajs = []
workers = []
for traj in trajs:
ext = utilities.getFileExtension(traj)
if ext == ".pdb":
if PRODY:
if pool is None:
sidechains_trajs.extend(
extractSidechainIndexes_prody(traj,
params.lig_resname))
else:
workers.append(
pool.apply_async(extractSidechainIndexes_prody,
args=(traj, params.lig_resname)))
else:
if pool is None:
sidechains_trajs.extend(
extractSidechainIndexes_mdtraj(traj,
params.lig_resname))
else:
workers.append(
pool.apply_async(extractSidechainIndexes_mdtraj,
args=(traj, params.lig_resname)))
elif ext in MDTRAJ_FORMATS:
epoch, traj_num = get_epoch_traj_num(traj)
if pool is None:
sidechains_trajs.extend(
extractSidechainIndexes_mdtraj(
traj,
params.lig_resname,
topology=params.topology.getTopologyFile(
epoch, traj_num)))
else:
workers.append(
pool.apply_async(
extractSidechainIndexes_mdtraj(traj,
params.lig_resname,
params.topology)))
else:
raise ValueError("Unrecongnized file extension for %s" % traj)
for w in workers:
sidechains_trajs.extend(w.get())
return list(set(sidechains_trajs))
def writeFilenameExtractedCoordinates(filename,
lig_resname,
atom_Ids,
pathFolder,
writeLigandTrajectory,
constants,
writeCA,
sidechains,
topology=None,
indexes=None):
"""
Process the coordinates of a trajectory
"""
ext = utilities.getFileExtension(filename)
if ext == ".pdb":
allCoordinates = loadAllResnameAtomsInPdb(filename, lig_resname,
writeCA, sidechains)
if writeLigandTrajectory:
outputFilename = os.path.join(
pathFolder, constants.ligandTrajectoryBasename %
extractFilenumber(filename))
with open(outputFilename, 'w') as f:
f.write("\nENDMDL\n".join(allCoordinates))
if writeCA:
coords = getLigandAlphaCarbonsCoords(allCoordinates, lig_resname)
elif sidechains:
coords = getLigandAlphaCarbonsCoords(allCoordinates,
lig_resname,
sidechains=sidechains)
else:
if atom_Ids is None or len(atom_Ids) == 0:
coords = getPDBCOM(allCoordinates, lig_resname)
else:
coords = getAtomCoord(allCoordinates, lig_resname, atom_Ids)
elif ext in MDTRAJ_FORMATS:
coords = extractCoordinatesXTCFile(filename, lig_resname, atom_Ids,
writeCA, topology, indexes,
sidechains)
else:
raise ValueError("Unrecongnized file extension for %s" % filename)
outputFilename = getOutputFilename(constants.extractedTrajectoryFolder,
filename,
constants.baseExtractedTrajectoryName)
writeToFile(coords, outputFilename % pathFolder)