def _pka_backend_internal(mol, pH):
tmpmol = mol.copy()
tmpmol.filter("noh")
pka_pdb = tempfile.NamedTemporaryFile(mode="w+", suffix=".pdb")
tmpmol.write(pka_pdb.name)
pka_options, _ = propka.lib.loadOptions('--pH', pH, '--quiet')
pka_molecule = propka.molecular_container.Molecular_container(pka_pdb.name, pka_options)
pka_pdb.close()
# calculating pKa values for ionizable residues -
pka_molecule.calculate_pka()
rd = PreparationData()
rd._importPKAs(pka_molecule)
return rd.data
def _buildResAndMol(pdb2pqr_protein):
# Here I parse the returned protein object and recreate a Molecule,
# because I need to access the properties.
logger.debug("Building Molecule object.")
name = []
resid = []
chain = []
insertion = []
coords = []
resname = []
segid = []
element = []
occupancy = []
beta = []
record = []
charge = []
prepData = PreparationData()
for i, residue in enumerate(pdb2pqr_protein.residues):
# if 'ffname' in residue.__dict__:
if getattr(residue, 'ffname', None):
curr_resname = residue.ffname
if len(curr_resname) >= 4:
curr_resname = curr_resname[-3:]
logger.debug("Residue %s has internal name %s, replacing with %s" %
(residue, residue.ffname, curr_resname))
else:
curr_resname = residue.name
prepData._setProtonationState(residue, curr_resname)
# Removed because not really useful
# if getattr(residue, 'patches', None):
# for patch in residue.patches:
# prepData._appendPatches(residue, patch)
# if patch != "PEPTIDE":
# logger.debug("Residue %s has patch %s set" % (residue, patch))
if getattr(residue, 'wasFlipped', 'UNDEF') != 'UNDEF':
prepData._setFlipped(residue, residue.wasFlipped)
prepData._set(residue, 'pdb2pqr_idx', i)
for atom in residue.atoms:
name.append(atom.name)
resid.append(residue.resSeq)
chain.append(residue.chainID)
insertion.append(residue.iCode)
coords.append([atom.x, atom.y, atom.z])
resname.append(curr_resname)
segid.append(atom.segID)
# Fixup element fields for added H (routines.addHydrogens)
elt = "H" if atom.added and atom.name.startswith("H") else atom.element
element.append(elt)
occupancy.append(0.0 if atom.added else atom.occupancy)
beta.append(99.0 if atom.added else atom.tempFactor)
charge.append(atom.charge)
record.append(atom.type)
if atom.added:
logger.debug("Coordinates of atom {:s} in residue {:s} were guessed".format(residue.__str__(),atom.name))
prepData._set(residue, 'guessedAtoms', atom.name, append=True)
mol_out = _fillMolecule(name, resname, chain, resid, insertion, coords, segid, element,
occupancy, beta, charge, record)
# mol_out.set("element", " ")
# Re-calculating elements
mol_out.element[:] = ''
mol_out.element = mol_out._guessMissingElements()
prepData._importPKAs(pdb2pqr_protein.pka_protein)
return mol_out, prepData
def _buildResAndMol(pdb2pqr_protein):
# Here I parse the returned protein object and recreate a Molecule,
# because I need to access the properties.
logger.debug("Building Molecule object.")
name = []
resid = []
chain = []
insertion = []
coords = []
resname = []
segid = []
element = []
occupancy = []
beta = []
record = []
charge = []
prepData = PreparationData()
for i, residue in enumerate(pdb2pqr_protein.residues):
# if 'ffname' in residue.__dict__:
if getattr(residue, 'ffname', None):
curr_resname = residue.ffname
if len(curr_resname) >= 4:
curr_resname = curr_resname[-3:]
logger.debug(
"Residue %s has internal name %s, replacing with %s" %
(residue, residue.ffname, curr_resname))
else:
curr_resname = residue.name
prepData._setProtonationState(residue, curr_resname)
# Removed because not really useful
# if getattr(residue, 'patches', None):
# for patch in residue.patches:
# prepData._appendPatches(residue, patch)
# if patch != "PEPTIDE":
# logger.debug("Residue %s has patch %s set" % (residue, patch))
if getattr(residue, 'wasFlipped', 'UNDEF') != 'UNDEF':
prepData._setFlipped(residue, residue.wasFlipped)
prepData._set(residue, 'pdb2pqr_idx', i)
for atom in residue.atoms:
name.append(atom.name)
resid.append(residue.resSeq)
chain.append(residue.chainID)
insertion.append(residue.iCode)
coords.append([atom.x, atom.y, atom.z])
resname.append(curr_resname)
segid.append(atom.segID)
# Fixup element fields for added H (routines.addHydrogens)
elt = "H" if atom.added and atom.name.startswith(
"H") else atom.element
element.append(elt)
occupancy.append(0.0 if atom.added else atom.occupancy)
beta.append(99.0 if atom.added else atom.tempFactor)
charge.append(atom.charge)
record.append(atom.type)
if atom.added:
logger.debug(
"Coordinates of atom {:s} in residue {:s} were guessed".
format(residue.__str__(), atom.name))
prepData._set(residue, 'guessedAtoms', atom.name, append=True)
mol_out = _fillMolecule(name, resname, chain, resid, insertion, coords,
segid, element, occupancy, beta, charge, record)
# mol_out.set("element", " ")
# Re-calculating elements
mol_out.element[:] = ''
mol_out.element = mol_out._guessMissingElements()
prepData._importPKAs(pdb2pqr_protein.pka_protein)
return mol_out, prepData