def extractIndexesTopology(topology, lig_resname, atoms, writeCA, sidechains):
selection = []
if atoms:
atoms_set = set(atoms)
template = "%s:%s:%s"
iline = 0
bool_sidechains = bool(sidechains)
with open(topology) as f:
for line in f:
if not (line.startswith("ATOM") or line.startswith("HETATM")):
continue
if atoms:
serial_num = line[6:11].strip()
atom_name = line[12:16].strip()
residue_name = line[17:20].strip()
if template % (serial_num, atom_name,
residue_name) in atoms_set:
selection.append(iline)
elif (line[17:20] == lig_resname
or utils.isAlphaCarbon(line, writeCA) or utils.isSidechain(
line, bool_sidechains,
sidechains)) and line[76:80].strip().upper() != "H":
selection.append(iline)
iline += 1
return selection
def loadAllResnameAtomsInPdb(filename, lig_resname, writeCA, sidechains):
prunedFileContent = []
sidechains_bool = bool(sidechains)
with open(filename) as f:
prunedSnapshot = []
for line in f:
if utils.is_model(line):
prunedFileContent.append("".join(prunedSnapshot))
prunedSnapshot = []
elif line[17:20] == lig_resname or utils.isAlphaCarbon(
line, writeCA) or utils.isSidechain(
line, sidechains_bool, sidechains):
prunedSnapshot.append(line)
if prunedSnapshot:
prunedFileContent.append("".join(prunedSnapshot))
return prunedFileContent
def extractIndexesTopology_CM(topology, lig_resname, CM_mode, use_extra_atoms):
selection = []
iline = 0
if CM_mode == "p-p":
check_ligand = False
else:
check_ligand = True
with open(topology) as f:
for line in f:
if not (line.startswith("ATOM") or line.startswith("HETATM")):
continue
if line[76:80].strip().upper() != "H" and (
check_ligand and line[17:20] == lig_resname
or utils.isAlphaCarbon(line, True) or use_extra_atoms
and utils.extraAtomCheck(line, EXTRA_ATOMS)):
selection.append(iline)
iline += 1
return selection
def loadAllResnameAtomsInPdb(filename, params):
prunedFileContent = []
sidechains_bool = bool(params.sidechains)
with open(filename) as f:
prunedSnapshot = []
for line in f:
if utils.is_model(line):
prunedFileContent.append("".join(prunedSnapshot))
prunedSnapshot = []
elif utils.is_end(line) or utils.is_remark(line) or utils.is_cryst(
line):
continue
elif line[17:20] == params.lig_resname or utils.isAlphaCarbon(
line, params.protein_CA
or params.contact_map) or utils.isSidechain(
line, sidechains_bool, params.sidechains) or (
params.contact_map and params.extra_atoms
and utils.extraAtomCheck(line, EXTRA_ATOMS)):
prunedSnapshot.append(line)
if prunedSnapshot:
prunedFileContent.append("".join(prunedSnapshot))
return prunedFileContent
