def Draw2DSurfaces(image, mol):
oedepict.OEPrepareDepiction(mol)
opts = oedepict.OE2DMolDisplayOptions(image.GetWidth(), image.GetHeight(),
oedepict.OEScale_AutoScale)
opts.SetTitleLocation(oedepict.OETitleLocation_Hidden)
opts.SetScale(oegrapheme.OEGetMoleculeSurfaceScale(mol, opts, 1.50))
disp = oedepict.OE2DMolDisplay(mol, opts)
Draw2DSurface(disp, oechem.OEHasAtomicNum(oechem.OEElemNo_C), 1.00,
oechem.OEBlack)
Draw2DSurface(disp, oechem.OEHasAtomicNum(oechem.OEElemNo_N), 1.25,
oechem.OEDarkBlue)
Draw2DSurface(disp, oechem.OEHasAtomicNum(oechem.OEElemNo_O), 1.50,
oechem.OEDarkRed)
oedepict.OERenderMolecule(image, disp)
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
# or its use.
# @ <SNIPPET>
from __future__ import print_function
from openeye import oechem
mol = oechem.OEGraphMol()
oechem.OESmilesToMol(mol, "c1cnc(O)cc1CCCBr")
print("Number of chain atoms =", end=" ")
print(oechem.OECount(mol, oechem.OENotAtom(oechem.OEAtomIsInRing())))
print("Number of aromatic nitrogens =", end=" ")
print(
oechem.OECount(
mol, oechem.OEAndAtom(oechem.OEIsNitrogen(),
oechem.OEIsAromaticAtom())))
print("Number of non-carbons =", end=" ")
print(
oechem.OECount(mol,
oechem.OENotAtom(oechem.OEHasAtomicNum(oechem.OEElemNo_C))))
print("Number of nitrogen and oxygen atoms =", end=" ")
print(
oechem.OECount(
mol,
oechem.OEOrAtom(oechem.OEHasAtomicNum(oechem.OEElemNo_N),
oechem.OEHasAtomicNum(oechem.OEElemNo_O))))
# @ </SNIPPET>
# 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.
from openeye import oechem
from openeye import oedepict
# @ <SNIPPET-ATOM-DISPLAY-LABEL>
mol = oechem.OEGraphMol()
oechem.OESmilesToMol(mol, "c1cc(N)cc(S(=O)(=O)O)c1")
oedepict.OEPrepareDepiction(mol)
width, height = 300, 200
opts = oedepict.OE2DMolDisplayOptions(width, height,
oedepict.OEScale_AutoScale)
disp = oedepict.OE2DMolDisplay(mol, opts)
for adisp in disp.GetAtomDisplays(oechem.OEHasAtomicNum(oechem.OEElemNo_C)):
if adisp.IsVisible():
adisp.SetLabel("C")
oedepict.OERenderMolecule("AtomDisplayLabel.png", disp)
# @ </SNIPPET-ATOM-DISPLAY-LABEL>
oedepict.OERenderMolecule("AtomDisplayLabel.pdf", disp)
# 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 openeye import oechem
# @ <SNIPPET-OEADDMOLS>
dstmol = oechem.OEGraphMol()
oechem.OESmilesToMol(dstmol, 'c1ccccc1 benzene')
srcmol = oechem.OEGraphMol()
oechem.OESmilesToMol(srcmol, 'c1cnccc1 pyridine')
amap, bmap = oechem.OEAddMols(dstmol, srcmol, "+")
print("%s %s" % (oechem.OEMolToSmiles(dstmol), dstmol.GetTitle()))
print(" ".join(str(a) for a in amap))
print(" ".join(str(b) for b in bmap))
# @ </SNIPPET-OEADDMOLS>
# @ <SNIPPET-OEADDMOL-ATOMMAP>
srcatom = srcmol.GetAtom(oechem.OEHasAtomicNum(oechem.OEElemNo_N))
dstatom = amap[srcatom.GetIdx()]
# @ </SNIPPET-OEADDMOL-ATOMMAP>
# @ <SNIPPET-OEADDMOL-BONDMAP>
srcbond = srcmol.GetBond(oechem.OEHasBondIdx(0))
dstbond = bmap[srcbond.GetIdx()]
# @ </SNIPPET-OEADDMOL-BONDMAP>
# @ </SNIPPET>
#!/usr/bin/env python
# (C) 2017 OpenEye Scientific Software Inc. All rights reserved.
#
# TERMS FOR USE OF SAMPLE CODE The software below ("Sample Code") is
# provided to current licensees or subscribers of OpenEye products or
# SaaS offerings (each a "Customer").
# Customer is hereby permitted to use, copy, and modify the Sample Code,
# 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, "c1c(Br)occ1CCC")
print("Carbon atoms:", end=" ")
for atom in mol.GetAtoms(oechem.OEHasAtomicNum(oechem.OEElemNo_C)):
print(atom.GetIdx(), end=" ")
print()
# @ </SNIPPET>
#!/usr/bin/env python
# (C) 2017 OpenEye Scientific Software Inc. All rights reserved.
#
# TERMS FOR USE OF SAMPLE CODE The software below ("Sample Code") is
# provided to current licensees or subscribers of OpenEye products or
# SaaS offerings (each a "Customer").
# Customer is hereby permitted to use, copy, and modify the Sample Code,
# 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, "c1cc[nH]c1CC2COCNC2")
# @ <SNIPPET-PRED-ATOMIC>
print("Number of oxygen atoms =",
oechem.OECount(mol, oechem.OEHasAtomicNum(oechem.OEElemNo_O)))
print("Number of oxygen atoms =", oechem.OECount(mol, oechem.OEIsOxygen()))
# @ </SNIPPET-PRED-ATOMIC>
# @ </SNIPPET>
