def main(pathway, pdb_with_connects, ligand_chain="L", outfilename=None):
pdb = pm.PDB(pdb_with_connects, chain=ligand_chain)
ligand = "".join(pdb.get_atoms_of_chain())
connects = "".join(pdb.read_conect())
ligand_with_connects = ligand + connects
# Temporary file to extract the indexes of the ligand
with open("ligand_with_connects_tmp.pdb", "w") as out:
out.write(ligand_with_connects)
pdb = pm.PDB(in_pdb="ligand_with_connects_tmp.pdb", chain=ligand_chain)
names_dictionary = pdb.get_names_dictionary()
os.remove("ligand_with_connects_tmp.pdb")
pathway_snapshots = utilities.getSnapshots(pathway)
new_pathway = []
sys.stderr.write("Rebuilding indexes...\n")
for snap in pathway_snapshots:
with open("snap_tmp.pdb", "w") as out:
out.write(snap)
pdb = pm.PDB(in_pdb="snap_tmp.pdb", chain=ligand_chain)
os.remove("snap_tmp.pdb")
ligand = pdb.get_atoms_of_chain()
complex_no_ligand = sorted(
list(set(pdb.read_atoms_section()) ^ set(ligand)))
new_ligand = []
for index, name in names_dictionary.items():
for line in ligand:
pdb_name = pm.get_atom_pdb_name_from_line(line).strip()
if name == pdb_name:
new_line = pm.set_index_to_line(line, index)
new_ligand.append(new_line)
new_ligand_with_connects = "".join(new_ligand) + connects
new_complex = "".join(complex_no_ligand) + new_ligand_with_connects
new_pathway.append(new_complex)
sys.stderr.write("Writing connects...\n")
if not outfilename:
outfilename = "{}_connected.pdb".format(pathway.split(".pdb")[0])
if os.path.exists(outfilename):
os.remove(outfilename)
for n, model in enumerate(new_pathway):
with open(outfilename, "a") as output:
output.write("MODEL {}\n".format(n))
output.write(model)
output.write("ENDMDL\n")
def test_file_content(self):
result_files = glob.glob("results_testing_convert/pdbs/*")
chains = []
resnames = []
resnums = []
for pdb in result_files:
pdb_class = pdbm.PDB(pdb)
for line in pdb_class.read_atoms_section():
chains.append(pdbm.get_chain_from_line(line))
resnames.append(pdbm.get_resname_from_line(line).strip())
resnums.append(pdbm.get_resnum_from_line(line).strip())
assert list(set(chains)) == [self.CHAIN] and list(set(resnames)) == [self.RESNAME] \
and list(set(resnums)) == [str(self.RESNUM)]
def prepare_frag_pele_instructions(self):
instructions = []
lib_manager.LibraryChecker.check_library_format(self)
for pdb in self.library_files:
try:
atom_idx = self.select_atom_to_grow(pdb)
pdb_obj = pdb_modifier.PDB(pdb)
instruction_line = "{} {} {}".format(
os.path.abspath(pdb), self.heavy_atom_pdb_complex,
pdb_obj.find_pdb_atom_name_of_idx(atom_idx).strip())
print(instruction_line)
instructions.append(instruction_line)
except Exception as e:
print(e)
self.instructions = "\n".join(instructions)
def prepare_library(self, chain, resname, resnum):
if self.format == ".pdb":
for pdb in self.get_files():
pdb_object = pdb_modifier.PDB(in_pdb=pdb, chain=chain, resname=resname, resnum=resnum)
pdb_object.modify_pdb()
pdb_object.overwrite_pdb()
def get_names_dictionary_from_ligand(self):
if not os.path.exists("tmp/ligand.pdb"):
self.tmp_ligand()
pdb_ligand = pdm.PDB("tmp/ligand.pdb", self.chain)
dictionary_names = pdb_ligand.get_names_dictionary()
return dictionary_names