def generate_ph(pdb, args, df_constructor, ts):
ifs = Base.FileIOStream(pdb, 'r')
tlc = args.ligand_three_letter_code
pdb_reader = Biomol.PDBMoleculeReader(ifs)
pdb_mol = Chem.BasicMolecule()
print '- Reading input: ', pdb, ' ...'
if not pdb_reader.read(pdb_mol):
print '!! Could not read input molecule'
return
print '- Processing macromolecule', pdb, ' ...'
i = 0
while i < pdb_mol.getNumBonds():
bond = pdb_mol.getBond(i)
if Chem.isMetal(bond.atoms[0]) or Chem.isMetal(bond.atoms[1]):
pdb_mol.removeBond(i)
else:
i += 1
for a in pdb_mol.atoms:
Chem.setImplicitHydrogenCount(a, 0)
Chem.calcImplicitHydrogenCounts(pdb_mol, True)
Chem.perceiveHybridizationStates(pdb_mol, True)
Chem.makeHydrogenComplete(pdb_mol)
Chem.setAtomSymbolsFromTypes(pdb_mol, False)
Chem.calcImplicitHydrogenCounts(pdb_mol, True)
Biomol.setHydrogenResidueSequenceInfo(pdb_mol, False)
Chem.setRingFlags(pdb_mol, True)
Chem.setAromaticityFlags(pdb_mol, True)
Chem.generateHydrogen3DCoordinates(pdb_mol, True)
Chem.calcFormalCharges(pdb_mol, True)
ligand = Chem.Fragment()
print '- Extracting ligand ', tlc, ' ...'
for atom in pdb_mol.atoms:
if Biomol.getResidueCode(atom) == tlc:
Biomol.extractResidueSubstructure(atom, pdb_mol, ligand, False)
break
if ligand.numAtoms == 0:
print '!! Could not find ligand', tlc, 'in input file'
return
Chem.perceiveSSSR(ligand, True)
lig_env = Chem.Fragment()
Biomol.extractEnvironmentResidues(ligand, pdb_mol, lig_env, 7.0)
Chem.perceiveSSSR(lig_env, True)
print '- Constructing pharmacophore ...'
lig_pharm = Pharm.BasicPharmacophore()
env_pharm = Pharm.BasicPharmacophore()
pharm_gen = Pharm.DefaultPharmacophoreGenerator(True)
pharm_gen.generate(ligand, lig_pharm)
pharm_gen.generate(lig_env, env_pharm)
#Pharm.FilePMLFeatureContainerWriter('./test/lig_ph_' + str(ts) + '.pml').write(lig_pharm)
analyzer = Pharm.DefaultInteractionAnalyzer()
interactions = Pharm.FeatureMapping()
analyzer.analyze(lig_pharm, env_pharm, interactions)
df_constructor, interaction_at_ts = outputInteractions(
lig_pharm, env_pharm, interactions, df_constructor)
#Chem.FileSDFMolecularGraphWriter('./test/ligand_' + str(ts) + '.sdf').write(ligand)
return df_constructor, interaction_at_ts
def process():
if len(sys.argv) < 4:
print >> sys.stderr, 'Usage:', sys.argv[
0], '[input topology-file] [input coordinates-file] [output CDF-file]'
sys.exit(2)
print >> sys.stderr, '- Processing topology-file', sys.argv[
1], 'and coordinates-file', sys.argv[2], '...'
u = MDAnalysis.Universe(sys.argv[1], sys.argv[2])
cdf_mol = Chem.BasicMolecule()
cdf_mol.reserveMemoryForAtoms(len(u.atoms))
cdf_mol.reserveMemoryForBonds(len(u.bonds))
print >> sys.stderr, '- Num. atoms:', len(u.atoms)
print >> sys.stderr, '- Num. bonds:', len(u.bonds)
num_frames = len(u.trajectory)
print >> sys.stderr, '- Num. frames:', num_frames
# construct atoms
print >> sys.stderr, '- Building atoms ...'
waters = {}
i = 0
for md_atom in u.atoms:
atom = cdf_mol.addAtom()
sym = MDAnalysis.topology.guessers.guess_atom_element(md_atom.name)
Chem.setSymbol(atom, sym.title())
Chem.setImplicitHydrogenCount(atom, 0)
Biomol.setChainID(atom, md_atom.segid)
if md_atom.resname == 'WAT':
Biomol.setResidueCode(atom, 'HOH')
else:
Biomol.setResidueCode(atom, md_atom.resname)
if Biomol.getResidueCode(atom) == 'HOH':
if md_atom.resid in waters:
waters[md_atom.resid].append(i)
else:
waters[md_atom.resid] = [i]
Biomol.setResidueSequenceNumber(atom, int(md_atom.resid))
Biomol.setResidueAtomName(atom, md_atom.name)
# fix positive charge on arginin nitrogen
if md_atom.resname == 'ARG' and md_atom.name == 'NH2':
Chem.setFormalCharge(atom, 1)
coords = []
for coord in md_atom.position:
coords.append(float(coord))
Chem.set3DCoordinates(atom, coords)
coords_array = Math.Vector3DArray()
coords_array.reserve(num_frames)
Chem.set3DCoordinatesArray(atom, coords_array)
Chem.setPEOECharge(atom, float(md_atom.charge))
i += 1
Chem.setAtomTypesFromSymbols(cdf_mol, True)
# construct bonds
print >> sys.stderr, '- Building bonds ...'
for md_bond in u.bonds:
cdf_mol.addBond(int(md_bond.atoms[0].index),
int(md_bond.atoms[1].index))
print >> sys.stderr, '- Building water atom bonds ...'
for water in waters.values():
if len(water) < 2:
continue
for atom_idx in water:
if Chem.getType(cdf_mol.atoms[atom_idx]) == Chem.AtomType.O:
if atom.numBonds > 1:
break
for atom_idx2 in water:
if Chem.getType(
cdf_mol.atoms[atom_idx2]) == Chem.AtomType.H:
cdf_mol.addBond(atom_idx, atom_idx2)
break
# make sane biomolecule
Chem.perceiveSSSR(cdf_mol, True)
Chem.setRingFlags(cdf_mol, True)
Chem.perceiveBondOrders(cdf_mol, True)
Chem.perceiveHybridizationStates(cdf_mol, True)
Chem.setAromaticityFlags(cdf_mol, True)
Chem.calcFormalCharges(cdf_mol, True)
# read timsteps and write cdf
print >> sys.stderr, '- Importing coordinates ...'
i = 0
traj_coords = []
atom_coords = Math.Vector3D()
for ts in u.trajectory:
print >> sys.stderr, '- Processing time step', i, '...'
for md_atom in u.atoms:
del traj_coords[:]
for coord in md_atom.position:
traj_coords.append(float(coord))
coords_array = Chem.get3DCoordinatesArray(
cdf_mol.getAtom(int(md_atom.index)))
atom_coords[0] = traj_coords[0]
atom_coords[1] = traj_coords[1]
atom_coords[2] = traj_coords[2]
coords_array.addElement(atom_coords)
i += 1
print >> sys.stderr, '- Writing output file:'
if not Chem.FileCDFMolecularGraphWriter(sys.argv[3]).write(cdf_mol):
print >> sys.stderr, '!! Could not write output file'
sys.exit(2)
