def delete_shell(core_mol, del_mol, cut_off, in_out='in'):
"""
This function deletes molecules present in the passed argument
del_mol that are far (in_out=out) or close (in_out=in) than the
selected cutoff distance (in A) from the passed molecules core_mol
Parameters:
-----------
core_mol: OEMol molecule
The core molecules
del_mol: OEMol molecule
The molecules to be deleted if their distances from the core_mol
molecules are greater or closer that the selected cutoff distance
cut_off: python float number
The threshold distance in A used to mark atom for deletion
in_out: python string
A flag used to select if delete molecules far or close than
the cutoff distance from the core_mol
Return:
-------
reset_del: copy of del_mol where atoms have been deleted with
reset atom indexes
"""
if in_out not in ['in', 'out']:
raise ValueError(
"The passed in_out parameter is not recognized: {}".format(in_out))
# Copy the passed molecule to delete in
to_del = oechem.OEMol(del_mol)
# Create a OE bit vector mask for each atoms of the
# molecule to delete
bv = oechem.OEBitVector(to_del.GetMaxAtomIdx())
bv.NegateBits()
# Create the Nearest neighbours
nn = oechem.OENearestNbrs(to_del, cut_off)
for nbrs in nn.GetNbrs(core_mol):
# bv.SetBitOff(nbrs.GetBgn().GetIdx())
for atom in oechem.OEGetResidueAtoms(nbrs.GetBgn()):
bv.SetBitOff(atom.GetIdx())
# Invert selection mask
if in_out == 'in':
bv.NegateBits()
pred = oechem.OEAtomIdxSelected(bv)
for atom in to_del.GetAtoms(pred):
to_del.DeleteAtom(atom)
# It is necessary to reset the atom indexes of the molecule with
# delete atoms to avoid possible mismatching
reset_del = oechem.OEMol(to_del)
return reset_del
def LigandProteinCloseContacts(prot, lig, maxgap):
"""atoms in the protein within maxgap Angstroms of the ligand"""
oechem.OESuppressHydrogens(prot)
oechem.OESuppressHydrogens(lig)
DropLigandFromProtein(prot, lig)
nn = oechem.OENearestNbrs(prot, maxgap)
return list(nn.GetNbrs(lig))
def check_shell(core_mol, check_mol, cutoff):
"""
This function checks if at least one atomic distance from the passed
check_mol molecule to the core_mol molecule is less than the selected
cutoff distance in A.
Parameters:
-----------
core_mol: OEMol molecule
The core molecule
check_mol: OEMol molecule
The molecule to be checked if inside or outside a shell
surrounding the core_mole with radius equal to the cutoff
threshold
cut_off: python float number
The threshold distance in A used to mark atom inside or outside
the shell
Return:
-------
in_out: python boolean
True if at least one of check_mol atom distance from core_mole
is less than the selected cutoff threshold
"""
# Create a OE bit vector mask for each atoms of the
# molecule to be checked
bv = oechem.OEBitVector(check_mol.GetMaxAtomIdx())
# Create the Nearest neighbours
nn = oechem.OENearestNbrs(check_mol, cutoff)
# Check neighbours setting the atom bit mask
for nbrs in nn.GetNbrs(core_mol):
bv.SetBitOn(nbrs.GetBgn().GetIdx())
# Create predicate based on the atom bit mask
pred = oechem.OEAtomIdxSelected(bv)
# Checking flag
in_out = False
# If just one chem_mol atom is inside the cutoff distance return True
for atom in check_mol.GetAtoms(pred):
in_out = True
break
return in_out
def SetAverageBFactorOfNearbyProteinAtoms(ligand, protein, itag, maxdistance=4.0):
nn = oechem.OENearestNbrs(protein, maxdistance)
for latom in ligand.GetAtoms(oechem.OEIsHeavy()):
sumbfactor = 0.0
neighs = []
for neigh in nn.GetNbrs(latom):
ratom = neigh.GetBgn()
res = oechem.OEAtomGetResidue(ratom)
if ConsiderResidueAtom(ratom, res):
sumbfactor += res.GetBFactor()
neighs.append(ratom)
avgbfactor = 0.0
if len(neighs) > 0:
avgbfactor = sumbfactor / len(neighs)
latom.SetDoubleData(itag, avgbfactor)
def GetMinAndMaxBFactor(ligand, protein, maxdistance=4.0):
minbfactor = float("inf")
maxbfactor = float("-inf")
# Ligand atoms
for latom in ligand.GetAtoms(oechem.OEIsHeavy()):
res = oechem.OEAtomGetResidue(latom)
minbfactor = min(minbfactor, res.GetBFactor())
maxbfactor = max(maxbfactor, res.GetBFactor())
# Protein atoms close to ligand atoms
nn = oechem.OENearestNbrs(protein, maxdistance)
for latom in ligand.GetAtoms(oechem.OEIsHeavy()):
for neigh in nn.GetNbrs(latom):
ratom = neigh.GetBgn()
res = oechem.OEAtomGetResidue(ratom)
if ConsiderResidueAtom(ratom, res):
minbfactor = min(minbfactor, res.GetBFactor())
maxbfactor = max(maxbfactor, res.GetBFactor())
return minbfactor, maxbfactor
def around(dist, ls):
"""
This function select atom not far than the threshold distance from
the current selection. The threshold distance is in Angstrom
selection can be:
mask = '5.0 around ligand'
"""
# at = system.GetAtom(oechem.OEHasAtomIdx(idx))
# Atom set selection
atom_set_around = set()
# Create a OE bit vector mask for each atoms
bv_around = oechem.OEBitVector(system.GetMaxAtomIdx())
# Set the mask atom
for at in system.GetAtoms():
if at.GetIdx() in ls:
bv_around.SetBitOn(at.GetIdx())
# Predicate
pred = oechem.OEAtomIdxSelected(bv_around)
# Create the system molecule based on the atom mask
molecules = oechem.OEMol()
oechem.OESubsetMol(molecules, system, pred)
# Create the Nearest neighbours
nn = oechem.OENearestNbrs(system, float(dist))
for nbrs in nn.GetNbrs(molecules):
for atom in oechem.OEGetResidueAtoms(nbrs.GetBgn()):
if atom.GetIdx() in ls:
continue
atom_set_around.add(atom.GetIdx())
return atom_set_around
def DropLigandFromProtein(prot, lig):
"""delete atoms from the protein w/same coords as the ligand
as well as any waters"""
approximatelyTheSame = 0.05
nn = oechem.OENearestNbrs(prot, approximatelyTheSame)
# mark ligand atoms for deletion
bv = oechem.OEBitVector(prot.GetMaxAtomIdx())
for nbrs in nn.GetNbrs(lig):
r1 = oechem.OEAtomGetResidue(nbrs.GetBgn())
r2 = oechem.OEAtomGetResidue(nbrs.GetEnd())
if r1.GetModelNumber() == r2.GetModelNumber():
bv.SetBitOn(nbrs.GetBgn().GetIdx())
# mark waters for deletion too
for atom in prot.GetAtoms():
res = oechem.OEAtomGetResidue(atom)
if oechem.OEGetResidueIndex(res) == oechem.OEResidueIndex_HOH:
bv.SetBitOn(atom.GetIdx())
pred = oechem.OEAtomIdxSelected(bv)
for atom in prot.GetAtoms(pred):
prot.DeleteAtom(atom)
def __init__(self, prot_mol, cutoff=2.0):
self.near_nbr = oechem.OENearestNbrs(prot_mol, cutoff)
self.cutoff = cutoff