def fixPdb2pqrPDB(filename_modified, filename_original, filename_output=None):
"""
Used to regenerate some data lost by PDB2PQR.
Parameters
----------
filename_modified : str
Name of the modified PDB file.
filename_original : str
Name of the original PDB file.
filename_output : str
Name of the fixed output PDB file.
Returns
-------
filename_output : str
The absolute path to the fixed output PDB file.
"""
pdb_original = _PDB(filename_original)
pqr_modified = _PDB(filename_modified)
for res_orig in pdb_original.filter("type=='amino_acid'"):
filter = "chainID=='{}'&resSeq=={}&iCode=='{}'".format(
res_orig.chainID, res_orig.resSeq, res_orig.iCode)
res_mod = pqr_modified.filter(filter)[0]
res_orig.clear()
res_orig.__init__(res_mod)
for atom in res_orig:
for attr in ["occupancy", "tempFactor", "element", "charge"]:
setattr(atom, attr, "")
pdb_original.missing_atoms = []
for bond in pdb_original.disulfide_bonds:
for res in bond:
if res.resName != "CYX":
_warnings.warn(
"Disulfide bond found at a residue not labelled "
"as CYX ({} {}{}{}). Please check your "
"structure. Correcting residue to CYX...".format(
res.resName, res.chainID, res.resSeq, res.iCode))
res.resName = "CYX"
pdb_original.reNumberAtoms()
if filename_output is None:
filename_output = _os.path.splitext(pdb_original.filename)[0] + \
"_modified.pdb"
return pdb_original.writePDB(filename_output)
def charmmguiTransform(filename, **kwargs):
"""
Adds missing residues to a PDB file.
Parameters
----------
filename : str
Name of the input PDB file.
kwargs
Keyword arguments to be passed to PDBReader.
Returns
-------
filename_output : str
Absolute path to the modified file.
"""
tgz = _tarfile.open(PDBReader(filename, **kwargs), "r:gz")
paths = []
for member in tgz:
if "model.pdb" in member.name.split("/")[-1]:
f = tgz.extractfile(member)
with open(member.name.split("/")[-1], "wb") as file:
file.write(f.read())
paths += [_os.path.abspath(member.name.split("/")[-1])]
tgz.close()
paths = sorted(paths)
pdb_obj = _PDB(paths[0])
chainID = paths[0].split("pro")[-1][0].upper()
for chain in pdb_obj:
chain.chainID = chainID
for path in paths[1:]:
pdb_add = _PDB(path)
chainID = paths[0].split("pro")[-1][0].upper()
for chain in pdb_add:
chain.chainID = chainID
pdb_obj += pdb_add
filename_output = _os.path.splitext(filename)[0] + "_charmmgui.pdb"
return fixCharmmguiPDB(pdb_obj, filename, filename_output=filename_output)
def fixCharmmguiPDB(pdb_modified, filename_original, filename_output=None):
"""
Used to regenerate some data lost by CHARMM-GUI.
Parameters
----------
pdb_modified : ProtoCaller.IO.PDB.PDB
PDB object containing all fixed residues created by CHARMM-GUI.
filename_original : str
Name of the original PDB file.
filename_output : str
Name of the fixed output PDB file.
Returns
-------
filename_output : str
The absolute path to the fixed output PDB file.
"""
pdb_original = _PDB(filename_original)
for miss_res in pdb_original.missing_residues:
filter = "chainID=='{}'&resSeq=={}&iCode=='{}'".format(
miss_res.chainID, miss_res.resSeq, miss_res.iCode)
fixed_res = _copy.copy(pdb_modified.filter(filter)[0])
fixed_res.chainID = miss_res.chainID
fixed_res.resSeq = miss_res.resSeq
if fixed_res.resName != miss_res.resName:
_warnings.warn("Mismatch between original residue name ({}) "
"and the residue name output by CHARMM-GUI ({}) in "
"chain {}, residue number {}.".format(
miss_res.resName, fixed_res.resName,
miss_res.chainID, miss_res.resSeq))
chain = pdb_original.filter("chainID=='{}'".format(miss_res.chainID),
type="chains")[0]
if miss_res > chain[-1]:
chain.append(fixed_res)
else:
for i, res in enumerate(chain):
if res > miss_res:
chain.insert(i, fixed_res)
break
pdb_original.missing_residues = []
pdb_original.reNumberAtoms()
pdb_original.reNumberResidues()
if filename_output is None:
filename_output = _os.path.splitext(pdb_original.filename)[0] + \
"_modified.pdb"
return pdb_original.writePDB(filename_output)
def fixPDBFixerPDB(filename_modified,
filename_original,
replace_nonstandard_residues,
add_missing_residues,
add_missing_atoms,
filename_output=None):
"""
Used to regenerate some data lost by PDBFixer.
Parameters
----------
filename_modified : str
Name of the modified PDB file.
filename_original : str
Name of the original PDB file.
replace_nonstandard_residues : bool
Whether to replace nonstandard residues with their standard equivalents.
add_missing_residues : bool
Whether to add missing residues.
add_missing_atoms : bool
Whether to add missing atoms.
filename_output : str
Name of the fixed output PDB file.
Returns
-------
filename_output : str
The absolute path to the fixed output PDB file.
"""
pdb_original = _PDB(filename_original)
pdb_modified = _PDB(filename_modified)
all_res_mod = pdb_modified.totalResidueList()
if add_missing_residues:
all_res_orig = pdb_original.totalResidueList()
else:
if replace_nonstandard_residues:
all_res_orig = pdb_original.filter("type in ['amino_acid', "
"'amino_acid_modified']")
else:
all_res_orig = pdb_original.filter("type=='amino_acid'")
_PDB.sortResidueList(all_res_orig)
if len(all_res_orig) != len(all_res_mod):
raise ValueError(
"Mismatch between original number of residues ({}) "
"and number of residues output by PDBFixer ({}).".format(
len(all_res_orig), len(all_res_mod)))
if replace_nonstandard_residues:
for mod_res in pdb_original.modified_residues:
fixed_res = all_res_mod[all_res_orig.index(mod_res)]
fixed_res.chainID = mod_res.chainID
fixed_res.resSeq = mod_res.resSeq
fixed_res.iCode = mod_res.iCode
mod_res.clear()
mod_res.__init__(fixed_res)
pdb_original.modified_residues = []
if add_missing_residues:
for miss_res in pdb_original.missing_residues:
fixed_res = _copy.copy(all_res_mod[all_res_orig.index(miss_res)])
fixed_res.chainID = miss_res.chainID
fixed_res.resSeq = miss_res.resSeq
if fixed_res.resName != miss_res.resName:
_warnings.warn("Mismatch between original residue name ({}) "
"and the residue name output by PDBFixer ({}) "
"in chain {}, residue number {}.".format(
miss_res.resName, fixed_res.resName,
miss_res.chainID, miss_res.resSeq))
chain = pdb_original.filter("chainID=='{}'".format(
miss_res.chainID),
type="chains")[0]
if miss_res > chain[-1]:
chain.append(fixed_res)
else:
for i, res in enumerate(chain):
if res > miss_res:
chain.insert(i, fixed_res)
break
pdb_original.missing_residues = []
if add_missing_atoms:
for missing_atom in pdb_original.missing_atoms:
filter = "chainID=='{}'&resSeq=={}&iCode=='{}'".format(
missing_atom.chainID, missing_atom.resSeq, missing_atom.iCode)
res = pdb_original.filter(filter)[0]
fixed_res = all_res_mod[all_res_orig.index(res)]
fixed_res.chainID = missing_atom.chainID
fixed_res.resSeq = missing_atom.resSeq
res.__init__(fixed_res)
pdb_original.missing_atoms = []
pdb_original.reNumberAtoms()
if add_missing_residues:
pdb_original.reNumberResidues()
if filename_output is None:
filename_output = _os.path.splitext(pdb_original.filename)[0] + \
"_modified.pdb"
return pdb_original.writePDB(filename_output)