def isEtherRotor(bond):
if bond.GetOrder() != 1:
return False
atomB = bond.GetBgn()
atomE = bond.GetEnd()
isEtherOxygen = oechem.OEMatchAtom("[OX2][C,c]")
return (atomB.IsCarbon()
and isEtherOxygen(atomE)) or (atomE.IsCarbon()
and isEtherOxygen(atomB))
def findIntraHB(mol):
"""
WORDS
Parameters
----------
mol
Returns
-------
Hbond_list: 2D list. Each sublist is a unique possible intra HB pair.
Sublist is ordered by donor atom index, H atom index, acceptor index,
Hbond distance in Angstroms, Hbond angle in degrees (sublist length 5).
"""
def getAtomCoords(mol, idx):
atom = mol.GetAtom(oechem.OEHasAtomIdx(idx))
xyz = oechem.OEFloatArray(3)
mol.GetCoords(atom, xyz)
return np.array([xyz[0], xyz[1], xyz[2]])
# .........!!!!!!!!!!!!!!!!!!!!
# definitions of donor acceptor:
# https://docs.eyesopen.com/toolkits/python/molproptk/molprops_sub.html
# how to match to donor atom
# https://docs.eyesopen.com/toolkits/python/oechemtk/genericdata.html
# match to atom that's N or O with at least one H attached
IsDonorAtom = oechem.OEMatchAtom("[!H0;#7,#8]")
IsAcceptorAtom = oechem.OEMatchAtom("[#7,#8]")
# defaults from SetMaxHBondDistance and SetMaxDonorAngle
# https://docs.eyesopen.com/toolkits/python/oechemtk/OEBioClasses/OEPerceiveInteractionOptions.html
Hbond_angle_cutoff = 50.0
Hbond_dist_cutoff = 3.2
# Make list of H atoms, their donor atoms and possible Acceptor atoms
HD_atom_idx_list = []
A_atom_idx_list = []
HD_D_idx_dict = {} # HD means H atom bonded to Donor atom (D), A=acceptor
for atom in mol.GetAtoms():
idx = atom.GetIdx()
if atom.GetAtomicNum() == 1: # hydrogen atoms
for nn_atom in atom.GetAtoms(): # nn_atom=nearest neighbour atom
if IsDonorAtom(nn_atom):
HD_atom_idx_list.append(
idx) # list of H atoms bonded to D atoms
HD_D_idx_dict[idx] = nn_atom.GetIdx(
) # dictionary of H atom idx and its D atom idx
if IsAcceptorAtom(atom):
A_atom_idx_list.append(idx) # list of A atoms
# Check distance and angle between HD and A atoms and make list of H bonds (atoms involved, angle and distance)
Hbond_list = []
for HD_atom_idx in HD_atom_idx_list:
HD_atom = mol.GetAtom(oechem.OEHasAtomIdx(HD_atom_idx))
D_atom_idx = HD_D_idx_dict[HD_atom_idx]
D_atom = mol.GetAtom(oechem.OEHasAtomIdx(D_atom_idx))
HD_atom_coords = getAtomCoords(mol, D_atom_idx)
for A_atom_idx in A_atom_idx_list:
if A_atom_idx == D_atom_idx: # don't consider the H atom's D atom as A atom
pass
else:
A_atom_coords = getAtomCoords(mol, A_atom_idx)
A_atom = mol.GetAtom(oechem.OEHasAtomIdx(A_atom_idx))
Hbond_angle = degrees(
oechem.OEGetAngle(mol, D_atom, HD_atom, A_atom))
Hbond_dist = np.linalg.norm(HD_atom_coords - A_atom_coords)
if Hbond_angle > Hbond_angle_cutoff and Hbond_dist < Hbond_dist_cutoff:
Hbond_list.append([
D_atom_idx, HD_atom_idx, A_atom_idx, Hbond_dist,
Hbond_angle
])
return Hbond_list
# subject to these terms. OpenEye claims no rights to Customer's
# modifications. Modification of Sample Code is at Customer's sole and
# exclusive risk. Sample Code may require Customer to have a then
# current license or subscription to the applicable OpenEye offering.
# THE SAMPLE CODE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED. OPENEYE DISCLAIMS ALL WARRANTIES, INCLUDING, BUT
# NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
# PARTICULAR PURPOSE AND NONINFRINGEMENT. In no event shall OpenEye be
# liable for any damages or liability in connection with the Sample Code
# or its use.
# @ <SNIPPET>
from __future__ import print_function
from openeye import oechem
IsDonorAtom = oechem.OEMatchAtom("[!H0;#7,#8]")
mol = oechem.OEGraphMol()
oechem.OESmilesToMol(mol, "c1c(Cl)cncc1C(=O)O")
for atom in mol.GetAtoms():
atom.SetData("isdonor", IsDonorAtom(atom))
class IsDonorAtomPred(oechem.OEUnaryAtomPred):
def __call__(self, atom):
return atom.GetData("isdonor")
print("Donor atoms:", end=" ")
for atom in mol.GetAtoms(IsDonorAtomPred()):
# subject to these terms. OpenEye claims no rights to Customer's
# modifications. Modification of Sample Code is at Customer's sole and
# exclusive risk. Sample Code may require Customer to have a then
# current license or subscription to the applicable OpenEye offering.
# THE SAMPLE CODE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED. OPENEYE DISCLAIMS ALL WARRANTIES, INCLUDING, BUT
# NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
# PARTICULAR PURPOSE AND NONINFRINGEMENT. In no event shall OpenEye be
# liable for any damages or liability in connection with the Sample Code
# or its use.
# @ <SNIPPET>
from __future__ import print_function
from openeye import oechem
mol = oechem.OEGraphMol()
oechem.OESmilesToMol(mol, "C1(Cl)C(N)C(F)OC1C(=O)NCCCN")
NonAmideNitrogenPred = oechem.OEMatchAtom("[N;!$(NC=O)]")
print("Number of non-amide nitrogen =",
oechem.OECount(mol, NonAmideNitrogenPred))
FiveMemberedRingOxygenPred = oechem.OEMatchAtom("[O;r5]")
print("Number of 5-membered ring oxygen =",
oechem.OECount(mol, FiveMemberedRingOxygenPred))
CarbonAttachedToHalogenPred = oechem.OEMatchAtom("[#6][Cl,Br,F]")
print("Number of carbon attached to halogen =",
oechem.OECount(mol, CarbonAttachedToHalogenPred))
# @ </SNIPPET>