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)
# if 'patches' in residue.__dict__:
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:
# Fixup element fields for added H (routines.addHydrogens)
elt = "H" if atom.added and atom.name.startswith("H") else atom.element
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)
element.append(elt)
occupancy.append(atom.occupancy)
beta.append(atom.tempFactor)
charge.append(atom.charge)
record.append(atom.type)
mol_out = _fillMolecule(name, resname, chain, resid, insertion, coords, segid, element,
occupancy, beta, charge, record)
prepData._importPKAs(pdb2pqr_protein.pka_protein)
return mol_out, prepData
