def otherinteractions(resdict, residuechoice, protein, ligand):
for residue in OBResidueIter(protein):
residuename = residue.GetName()
if residuename in residuechoice:
for atom in OBResidueAtomIter(residue):
if not atom.IsHydrogen():
for atomlig in OBMolAtomIter(ligand):
if not atomlig.IsHydrogen():
distance = atom.GetDistance(atomlig)
if distance <= 4.5:
if isnonpolar(atomlig) & isnonpolar(atom):
resdict[residuename] |= bitarray('1000000')
if distance <= 4.0:
setformalcharge(atom)
setformalcharge(atomlig)
if (atom.GetFormalCharge()>0) & (atomlig.GetFormalCharge()<0):
resdict[residuename] |= bitarray('0000010')
if (atom.GetFormalCharge()<0) & (atomlig.GetFormalCharge()>0):
resdict[residuename] |= bitarray('0000001')
if distance <= 3.5:
if atom.IsHbondDonor() & atomlig.IsHbondAcceptor():
donorresidue = atom.GetResidue()
for atomres in OBResidueAtomIter(donorresidue):
if atomres.IsHbondDonorH() & atomres.IsConnected(atom):
angle = atom.GetAngle(atomres, atomlig)
if angle>135.0:
resdict[residuename] |= bitarray('0001000')
if atom.IsHbondAcceptor() & atomlig.IsHbondDonor():
for atomres in OBMolAtomIter(ligand):
if atomres.IsHbondDonorH() & atomres.IsConnected(atomlig):
angle = atomlig.GetAngle(atomres, atom)
if angle>135.0:
resdict[residuename] |= bitarray('0000100')
def hbonddockprot(resdict, residuechoice, protein, ligand):
for residue in OBResidueIter(protein):
residuename = residue.GetName()
if residuename in residuechoice:
for atom in OBResidueAtomIter(residue):
if not atom.IsHydrogen():
for atomlig in OBMolAtomIter(ligand):
if not atomlig.IsHydrogen():
distance = atom.GetDistance(atomlig)
if distance <= 3.5:
if atom.IsHbondDonor(
) & atomlig.IsHbondAcceptor():
for neighborDon in OBAtomAtomIter(atom):
if neighborDon.IsHydrogen():
angle = atom.GetAngle(
neighborDon, atomlig)
if angle > 135.0:
resdict[
residuename] |= bitarray(
'0001000')
if atom.IsHbondAcceptor(
) & atomlig.IsHbondDonor():
for neighborDon in OBAtomAtomIter(atomlig):
if neighborDon.IsHydrogen():
angle = atomlig.GetAngle(
neighborDon, atom)
if angle > 135.0:
resdict[
residuename] |= bitarray(
'0000100')
def otherinteractions(resdict, residuechoice, protein, ligand,
backboneatomlist):
for residue in OBResidueIter(protein):
residuename = residue.GetName()
if residuename in residuechoice:
for atom in OBResidueAtomIter(residue):
if not atom.IsHydrogen():
for atomlig in OBMolAtomIter(ligand):
if not atomlig.IsHydrogen():
distance = atom.GetDistance(atomlig)
if distance <= 4.5:
if isnonpolar(atomlig) & isnonpolar(atom):
#print "POLAR"
resdict[residuename] |= bitarray('1000000')
if distance <= 4.0:
setformalcharge(atom, backboneatomlist)
fakebbatomlist = []
setformalcharge(atomlig, fakebbatomlist)
if (atom.GetFormalCharge() > 0) & (
atomlig.GetFormalCharge() < 0):
#print "NEGATIVE"
resdict[residuename] |= bitarray(
'0000010')
if (atom.GetFormalCharge() < 0) & (
atomlig.GetFormalCharge() > 0):
#print "POSITIVE"
resdict[residuename] |= bitarray(
'0000001')
if distance <= 3.5:
if atom.IsHbondDonor(
) & atomlig.IsHbondAcceptor():
for neighborDon in OBAtomAtomIter(
atom):
if neighborDon.IsHydrogen():
angle = atom.GetAngle(
neighborDon, atomlig)
if angle > 135.0:
resdict[
residuename] |= bitarray(
'0001000')
# donorresidue = atom.GetResidue()
# for atomres in OBResidueAtomIter(donorresidue):
# if atomres.IsHydrogen() & atomres.IsConnected(atom):
# angle = atom.GetAngle(atomres, atomlig)
# if angle>135.0:
# resdict[residuename] |= bitarray('0001000')
if atom.IsHbondAcceptor(
) & atomlig.IsHbondDonor():
for neighborDon in OBAtomAtomIter(
atomlig):
if neighborDon.IsHydrogen():
#print True
angle = atomlig.GetAngle(
neighborDon, atom)
#print angle
if angle > 135.0:
#print "ACCEPTOR"
resdict[
residuename] |= bitarray(
'0000100')
def InitializeFragment(self, atomicNum):
mol=OBMol()
atom=Atom(self, atomicNum)
for mol in self.miner.GetAllMolecules():
for a in OBMolAtomIter(mol):
if atom.Match(a):
self.embedings.append(Embeding({atom.atomIndex : a.GetIdx()}, molecule=mol, fragment=self))
def hbonddockprot(resdict, residuechoice, protein, ligand):
for residue in OBResidueIter(protein):
if residue.GetName() in residuechoice:
for atom in OBResidueAtomIter(residue):
if not atom.IsHydrogen():
for atomlig in OBMolAtomIter(ligand):
if not atomlig.IsHydrogen():
distance = atom.GetDistance(atomlig)
if distance <= 3.5:
if atom.IsHbondDonor() & atomlig.IsHbondAcceptor():
donorresidue = atom.GetResidue()
for atomres in OBResidueAtomIter(donorresidue):
if atomres.IsHbondDonorH() & atomres.IsConnected(atom):
angle = atom.GetAngle(atomres, atomlig)
if angle>135.0:
resdict[residue.GetName()] |= bitarray('0001000')
if atom.IsHbondAcceptor() & atomlig.IsHbondDonor():
for atomres in OBMolAtomIter(ligand):
if atomres.IsHbondDonorH() & atomres.IsConnected(atomlig):
angle = atomlig.GetAngle(atomres, atom)
if angle>135.0:
resdict[residue.GetName()] |= bitarray('0000100')
def type_mof(filename, output_dir, ff="uff", output_files=True):
obconversion = OBConversion()
obconversion.SetInAndOutFormats("cif", "xyz")
obmol = OBMol()
# Read MOF file and unit cell and write xyz file
obconversion.ReadFile(obmol, filename)
unitcell = openbabel.toUnitCell(obmol.GetData(openbabel.UnitCell))
uc = [
unitcell.GetA(),
unitcell.GetB(),
unitcell.GetC(),
unitcell.GetAlpha(),
unitcell.GetBeta(),
unitcell.GetGamma()
]
obconversion.WriteFile(obmol, 'mof_tmp.xyz')
# Replicate unit cell using angstrom
mol = Molecule(read='mof_tmp.xyz')
mol.set_cell(uc)
n_atoms = len(mol.atoms)
mol333 = mol.replicate([3, 3, 3], center=True)
print(mol333.cell)
mol333.write('mof333.cif', cell=mol333.cell.to_list())
# Type FF
obconversion.ReadFile(obmol, 'mof333.cif')
ff = OBForceField.FindForceField("UFF")
if not ff.Setup(obmol):
print("Error: could not setup force field")
ff.GetAtomTypes(obmol)
# Get atom types for the middle cell
types = []
for atom_idx, obatom in enumerate(OBMolAtomIter(obmol)):
if atom_idx >= n_atoms * 13 and atom_idx < n_atoms * 14:
ff_atom_type = obatom.GetData("FFAtomType").GetValue()
types.append(ff_atom_type)
if output_files:
mof_name = os.path.splitext(os.path.basename(filename))[0]
with open(os.path.join(output_dir, mof_name + "-obabel.log"),
'w') as f:
f.write("NOTE: types order is the same as the CIF input file.\n")
f.write("types= %s" % str(types))
uniq_types = sorted(set(types))
return [str(i) for i in uniq_types]
def Initialize(self):
"""Initializes the search"""
self.initialFragments=[]
self.rings={}
self.atomCount={}
self.canonicalPruningSet={}
candidates=[]
ringCandidates=[]
for mol in self.GetAllMolecules():
mol.rings=self.rings[mol]=list(mol.GetSSSR())
for ring in mol.rings:
ring.fingerprint=set([mol.GetAtom(i).GetAtomicNum() for i in ring._path])
## for ring in mol.rings:
## candidates.append(FragmentExtensionByRing([ring],[Embeding(molecule=mol)]))
for mol in self.GetAllMolecules():
for atom in OBMolAtomIter(mol):
self.atomCount[atom.GetAtomicNum()]= self.atomCount[atom.GetAtomicNum()]+1 if atom.GetAtomicNum() in self.atomCount else 1
if not (atom.GetAtomicNum()==6 and atom.IsInRing()):
candidates.append(FragmentExtensionByAtom(atom.GetAtomicNum(), atom.IsAromatic(), [atom.GetIdx()], [Embeding(molecule=mol)]))
groups=[]
candidates.sort(lambda a,b: cmp(self.atomCount[a.atomicNum], self.atomCount[b.atomicNum]))
for extension in candidates:
for ext in groups:
if type(ext)==type(extension) and ext.IsEquivalent(extension):
ext.MergeFrom(extension)
break
else:
groups.append(extension)
lst=self.atomCount.items()
lst.sort(lambda a,b:cmp(a[1], b[1]))
self.initialFragments=[]
lst=[t[0] for t in lst]
for extension in groups:
if type(extension)==FragmentExtensionByAtom:
f=Fragment(miner=self, excludeAtomList=lst[:lst.index(extension.atomicNum)])
else:
f=Fragment(miner=self)
extension.Extend(f)
self.initialFragments.append(f)
## self.initialFragments.reverse()
## excludeList=[]
## for atom, c in lst:
## f=Fragment(miner=self, excludeAtomList=excludeList)
## f.InitializeFragment(atom)
## self.initialFragments.append(f)
## excludeList.append(atom)
self.activeSet=set(self.active)
self.inactiveSet=set(self.inactive)
def get_atomic_fragments_from_mol(xyz):
"""Get the fragments around each atom
Args:
xyz (string): XYZ file for the
"""
# Read in the molecule
mol = OBMol()
converter.ReadString(mol, xyz)
# Determine ring types
OBRingTyper().AssignTypes(mol)
# For each atom, get its local environment
return [get_atomic_environment(atom) for atom in OBMolAtomIter(mol)]
def otherinteractions2(resdict, residuechoice, protein, ligand,
backboneatomlist):
RigidHdonors = ['HIS', 'GLN', 'ASN', 'ARG', 'TRP']
for residue in OBResidueIter(protein):
residuename = residue.GetName()
if residuename in residuechoice:
for atom in OBResidueAtomIter(residue):
if not atom.IsHydrogen():
for atomlig in OBMolAtomIter(ligand):
print atomlig
if not atomlig.IsHydrogen():
distance = atom.GetDistance(atomlig)
if distance <= 4.5:
if isnonpolar(atomlig) & isnonpolar(atom):
resdict[residuename] |= bitarray('1000000')
if distance <= 4.0:
setformalcharge(atom, backboneatomlist)
fakebbatomlist = []
setformalcharge(atomlig, fakebbatomlist)
if (atom.GetFormalCharge() > 0) & (
atomlig.GetFormalCharge() < 0):
resdict[residuename] |= bitarray(
'0000010')
if (atom.GetFormalCharge() < 0) & (
atomlig.GetFormalCharge() > 0):
resdict[residuename] |= bitarray(
'0000001')
if distance <= 3.5:
if residuename[:3] in RigidHdonors:
if atom.IsHbondDonor(
) & atomlig.IsHbondAcceptor():
for neighborDon in OBAtomAtomIter(
atom):
if neighborDon.IsHydrogen(
):
angle = atom.GetAngle(
neighborDon,
atomlig)
if angle > 135.0:
resdict[
residuename] |= bitarray(
'0001000')
elif atom.GetIdx() in backboneatomlist:
if atom.IsHbondDonor(
) & atomlig.IsHbondAcceptor():
for neighborDon in OBAtomAtomIter(
atom):
if neighborDon.IsHydrogen(
):
angle = atom.GetAngle(
neighborDon,
atomlig)
if angle > 135.0:
resdict[
residuename] |= bitarray(
'0001000')
if atom.IsHbondAcceptor(
) & atomlig.IsHbondDonor():
for neighborDon in OBAtomAtomIter(
atomlig):
if neighborDon.IsHydrogen():
angle = atomlig.GetAngle(
neighborDon, atom)
if angle > 135.0:
resdict[
residuename] |= bitarray(
'0000100')
def otherinteractions(l_bit, l_res_choices, st_protein, st_lig,
l_serial_atom_backbone):
for residue in OBResidueIter(st_protein):
residuename = residue.GetName()
if residuename in l_res_choices:
for atom in OBResidueAtomIter(residue):
if not atom.IsHydrogen():
for atomlig in OBMolAtomIter(st_lig):
if not atomlig.IsHydrogen():
distance = atom.GetDistance(atomlig)
if distance <= 4.5:
if isnonpolar(atomlig) & isnonpolar(atom):
l_bit[residuename] |= bitarray('1000000')
if distance <= 4.0:
setformalcharge(atom,
l_serial_atom_backbone)
fakebbatomlist = []
setformalcharge(atomlig, fakebbatomlist)
if (atom.GetFormalCharge() > 0) & (
atomlig.GetFormalCharge() < 0):
l_bit[residuename] |= bitarray(
'0000010')
if (atom.GetFormalCharge() < 0) & (
atomlig.GetFormalCharge() > 0):
l_bit[residuename] |= bitarray(
'0000001')
if distance <= 3.5:
if atom.IsHbondDonor(
) & atomlig.IsHbondAcceptor():
for neighborDon in OBAtomAtomIter(
atom):
if neighborDon.IsHydrogen():
for neighborAcc in OBAtomAtomIter(
atomlig):
angle = neighborAcc.GetAngle(
atomlig,
neighborDon)
if angle > 135.0:
l_bit[
residuename] |= bitarray(
'0001000')
# donorresidue = atom.GetResidue()
# for atomres in OBResidueAtomIter(donorresidue):
# if atomres.IsHydrogen() & atomres.IsConnected(atom):
# angle = atom.GetAngle(atomres, atomlig)
# if angle>135.0:
# l_bit[residuename] |= bitarray('0001000')
if atom.IsHbondAcceptor(
) & atomlig.IsHbondDonor():
for neighborDon in OBAtomAtomIter(
atomlig):
if neighborDon.IsHydrogen():
for neighborAcc in OBAtomAtomIter(
atom):
angle = neighborAcc.GetAngle(
atom, neighborDon)
if angle > 135.0:
l_bit[
residuename] |= bitarray(
'0000100')
```
"""
import sys
sys.path.insert(0, "/usr/local/lib/python3.6/site-packages")
import os
from openbabel import OBMol, OBConversion, OBMolAtomIter, OBForceField
mof = "csdac-linkers-cml/uio66-HNC3-alkane.cml"
obconversion = OBConversion()
obconversion.SetInAndOutFormats("cml", "cml")
obmol = OBMol()
obconversion.ReadFile(obmol, mof)
ff = OBForceField.FindForceField("UFF")
ff.SetLogToStdOut()
ff.SetLogLevel(3)
if not ff.Setup(obmol):
print("Error: could not setup force field")
ff.GetAtomTypes(obmol)
for atom_idx, obatom in enumerate(OBMolAtomIter(obmol)):
ff_atom_type = obatom.GetData("FFAtomType").GetValue()
print(ff_atom_type)
print(ff.Energy(True))
print(ff.E_Torsion())
print(obmol.GetEnergy())