def main(argv):
if len(argv) != 2:
oechem.OEThrow.Usage("%s <receptor>" % argv[0])
receptor = oechem.OEGraphMol()
oedocking.OEReadReceptorFile(receptor, argv[1])
# @ <SNIPPET-RECEPTOR-PROTEIN-CONSTRAINT-EDITING-1>
for constraint in oedocking.OEReceptorGetProteinConstraints(receptor):
print("Atom %i has a constraint" % constraint.GetAtom().GetIdx())
# @ </SNIPPET-RECEPTOR-PROTEIN-CONSTRAINT-EDITING-1>
# @ <SNIPPET-RECEPTOR-PROTEIN-CONSTRAINT-EDITING-2>
for constraint in oedocking.OEReceptorGetProteinConstraints(receptor):
print("Protein constraint on atom %d" % constraint.GetAtom().GetIdx())
print(" Type : %s" % oedocking.OEProteinConstraintTypeGetName(constraint.GetType()))
print(" Name : %s" % constraint.GetName())
# @ </SNIPPET-RECEPTOR-PROTEIN-CONSTRAINT-EDITING-2>
for heavyAtom in receptor.GetAtoms(oechem.OENotAtom(oechem.OEIsHydrogen())):
# @ <SNIPPET-RECEPTOR-PROTEIN-CONSTRAINT-EDITING-3>
proteinConstraint = oedocking.OEProteinConstraint()
proteinConstraint.SetAtom(heavyAtom)
proteinConstraint.SetType(oedocking.OEProteinConstraintType_Contact)
proteinConstraint.SetName("Example constraint")
oedocking.OEReceptorSetProteinConstraint(receptor, proteinConstraint)
# @ </SNIPPET-RECEPTOR-PROTEIN-CONSTRAINT-EDITING-3>
break
# @ <SNIPPET-RECEPTOR-PROTEIN-CONSTRAINT-EDITING-4>
oedocking.OEReceptorClearProteinConstraints(receptor)
def noh(ls, dsets):
"""
This function remove hydrogens from the selection
"""
data_set = build_set(ls[1], dsets)
noh_set = set()
pred = oechem.OEIsHydrogen()
for idx in data_set:
atom = system.GetAtom(oechem.OEHasAtomIdx(idx))
if not pred(atom):
noh_set.add(idx)
return noh_set
def _OEFixConnectionNH(protein):
"""
Temporary fix, thanks to Jesper!
"""
for atom in protein.GetAtoms(
oechem.OEAndAtom(oespruce.OEIsModeledAtom(),
oechem.OEIsNitrogen())):
if oechem.OEGetPDBAtomIndex(atom) == oechem.OEPDBAtomName_N:
expected_h_count = 1
if oechem.OEGetResidueIndex(atom) == oechem.OEResidueIndex_PRO:
expected_h_count = 0
if atom.GetTotalHCount() != expected_h_count:
oechem.OESuppressHydrogens(atom)
atom.SetImplicitHCount(1)
oechem.OEAddExplicitHydrogens(protein, atom)
for nbr in atom.GetAtoms(oechem.OEIsHydrogen()):
oechem.OESet3DHydrogenGeom(protein, nbr)
def has_undesirable_elements(mol):
'''
returns True if molecule contains any element other than
H, C, N, O, F, S, Cl, or P
@param mol:
@type mol: OEGraphMol
@return: bool
'''
atomsHC = oechem.OEOrAtom(oechem.OEIsHydrogen(), oechem.OEIsCarbon())
atomsNO = oechem.OEOrAtom(oechem.OEIsNitrogen(), oechem.OEIsOxygen())
atomsFS = oechem.OEOrAtom(oechem.OEHasAtomicNum(9), oechem.OEIsSulfur())
atomsHCNO = oechem.OEOrAtom(atomsHC, atomsNO)
atomsHCNOFS = oechem.OEOrAtom(atomsHCNO, atomsFS)
atomsHCNOFSCl = oechem.OEOrAtom(atomsHCNOFS, oechem.OEHasAtomicNum(17))
atomsHCNOFSClP = oechem.OEOrAtom(atomsHCNOFSCl, oechem.OEIsPhosphorus())
undesirable_atom = mol.GetAtom(oechem.OENotAtom(atomsHCNOFSClP))
if undesirable_atom is not None:
return True
return False