def CanSmi(mol, isomeric, kekule):
oechem.OEFindRingAtomsAndBonds(mol)
oechem.OEAssignAromaticFlags(mol, oechem.OEAroModel_OpenEye)
smiflag = oechem.OESMILESFlag_Canonical
if isomeric:
smiflag |= oechem.OESMILESFlag_ISOMERIC
if kekule:
for bond in mol.GetBonds(oechem.OEIsAromaticBond()):
bond.SetIntType(5)
oechem.OECanonicalOrderAtoms(mol)
oechem.OECanonicalOrderBonds(mol)
oechem.OEClearAromaticFlags(mol)
oechem.OEKekulize(mol)
smi = oechem.OECreateSmiString(mol, smiflag)
return smi
def canonical_order_atoms(molecule, in_place=True):
"""
Canonical order of atom indices. This ensures the map indices are always in the same order.
Parameters
----------
molecule: oechem.OEMol
in_place: bool, optional, default True
If True, the order of atom indices will happen in place. If False, a copy of the molecule with reordered atom
indices will be returned.
Returns
-------
molecule: OEMol with canonical ordered atom indices.
"""
if not in_place:
molecule = copy.deepcopy(molecule)
oechem.OECanonicalOrderAtoms(molecule)
oechem.OECanonicalOrderBonds(molecule)
vatm = []
for atom in molecule.GetAtoms():
if atom.GetAtomicNum() != oechem.OEElemNo_H:
vatm.append(atom)
molecule.OrderAtoms(vatm)
vbnd = []
for bond in molecule.GetBonds():
if bond.GetBgn().GetAtomicNum() != oechem.OEElemNo_H and bond.GetEnd(
).GetAtomicNum() != oechem.OEElemNo_H:
vbnd.append(bond)
molecule.OrderBonds(vbnd)
molecule.Sweep()
for bond in molecule.GetBonds():
if bond.GetBgnIdx() > bond.GetEndIdx():
bond.SwapEnds()
if not in_place:
return molecule
def CanSmi(mol, isomeric, kekule):
"""
Returns the cannonical smile from the OEMol provided
:param mol: OEMolBase object
:param isomeric: force isometric
:param kekule: use kekule cleaning
:return: string of OESmiles
"""
oechem.OEFindRingAtomsAndBonds(mol)
oechem.OEAssignAromaticFlags(mol, oechem.OEAroModel_OpenEye)
smiflag = oechem.OESMILESFlag_Canonical
if isomeric:
smiflag |= oechem.OESMILESFlag_ISOMERIC
if kekule:
for bond in mol.GetBonds(oechem.OEIsAromaticBond()):
bond.SetIntType(5)
oechem.OECanonicalOrderAtoms(mol)
oechem.OECanonicalOrderBonds(mol)
oechem.OEClearAromaticFlags(mol)
oechem.OEKekulize(mol)
smi = oechem.OECreateSmiString(mol, smiflag)
return smi
def main(argv=[__name__]):
"""
itf = oechem.OEInterface()
oechem.OEConfigure(itf, InterfaceData)
if not oechem.OEParseCommandLine(itf, argv):
return 1
oname = itf.GetString("-out")
iname = itf.GetString("-in")
ext = oechem.OEGetFileExtension(oname)
if not oedepict.OEIsRegisteredImageFile(ext):
oechem.OEThrow.Fatal("Unknown image type!")
ofs = oechem.oeofstream()
if not ofs.open(oname):
oechem.OEThrow.Fatal("Cannot open output file!")
## INPUT PARAMETERS
#########################################################
#########################################################
mm = 'tyk2/og_pdbs'
qml = 'tyk2/forward_snapshots'
phase = 'solvent'
which_ligand = 'old'
dir_name = iname
ligand_pdbs_mm = glob.glob(f"{mm}/{dir_name}/{which_ligand}*{phase}.pdb")
print(len(ligand_pdbs_mm))
ligand_pdbs_qml = glob.glob(f"{qml}/{dir_name}/{which_ligand}*{phase}.pdb")
print(len(ligand_pdbs_qml))
#d = np.load('full_data_dict.npy', allow_pickle=True)
from_ligand, to_ligand = iname.replace('from', '').replace('to', '').replace('lig', '')
print(from_ligand)
print(to_ligand)
#key1 = (1, 8)
#key2 = ('solvent', which_ligand)
#########################################################
#########################################################
#d = d.flatten()[0]
#work = d[key1][key2]
#print(work)
for i, (mm_pdb_path, ani_pdb_path) in enumerate(zip(ligand_pdbs_mm, ligand_pdbs_qml)):
print(mm_pdb_path, ani_pdb_path)
if i == 0:
MM_mol = createOEMolFromSDF(mm_pdb_path, 0)
ANI_mol = createOEMolFromSDF(ani_pdb_path, 0)
else:
# there absolutely must be a better/faster way of doing this because this is ugly and slow
MM_mol.NewConf(createOEMolFromSDF(mm_pdb_path, 0))
ANI_mol.NewConf(createOEMolFromSDF(ani_pdb_path, 0))
"""
ofs = oechem.oeofstream()
oname = f"tor_out"
ext = oechem.OEGetFileExtension(oname)
mm_pdb_path = f"og_lig0_solvent.pdb"
ani_pdb_path = f"forward_lig0.solvent.pdb"
MM_mol = createOEMolFromSDF(mm_pdb_path, 0)
ANI_mol = createOEMolFromSDF(ani_pdb_path, 0)
mol = MM_mol
mol2 = ANI_mol
for m in [mol, mol2]:
oechem.OESuppressHydrogens(m)
oechem.OECanonicalOrderAtoms(m)
oechem.OECanonicalOrderBonds(m)
m.Sweep()
refmol = None
stag = "dihedral_histogram"
itag = oechem.OEGetTag(stag)
nrbins = 20
print(mol.NumConfs())
print(mol2.NumConfs())
get_dihedrals(mol, itag)
set_dihedral_histograms(mol, itag, nrbins)
get_dihedrals(mol2, itag)
#set_weighted_dihedral_histograms(mol2, itag, work, nrbins)
set_dihedral_histograms(mol2, itag, nrbins)
width, height = 800, 400
image = oedepict.OEImage(width, height)
moffset = oedepict.OE2DPoint(0, 0)
mframe = oedepict.OEImageFrame(image, width * 0.70, height, moffset)
doffset = oedepict.OE2DPoint(mframe.GetWidth(), height * 0.30)
dframe = oedepict.OEImageFrame(image, width * 0.30, height * 0.5, doffset)
flexibility = True
colorg = get_color_gradient(nrbins, flexibility)
opts = oedepict.OE2DMolDisplayOptions(mframe.GetWidth(),
mframe.GetHeight(),
oedepict.OEScale_AutoScale)
depict_dihedrals(mframe, dframe, mol, mol2, refmol, opts, itag, nrbins,
colorg)
if flexibility:
lopts = oedepict.OELegendLayoutOptions(
oedepict.OELegendLayoutStyle_HorizontalTopLeft,
oedepict.OELegendColorStyle_LightBlue,
oedepict.OELegendInteractiveStyle_Hover)
lopts.SetButtonWidthScale(1.2)
lopts.SetButtonHeightScale(1.2)
lopts.SetMargin(oedepict.OEMargin_Right, 40.0)
lopts.SetMargin(oedepict.OEMargin_Bottom, 80.0)
legend = oedepict.OELegendLayout(image, "Legend", lopts)
legend_area = legend.GetLegendArea()
draw_color_gradient(legend_area, colorg)
oedepict.OEDrawLegendLayout(legend)
iconscale = 0.5
oedepict.OEAddInteractiveIcon(image, oedepict.OEIconLocation_TopRight,
iconscale)
oedepict.OEDrawCurvedBorder(image, oedepict.OELightGreyPen, 10.0)
oedepict.OEWriteImage(ofs, ext, image)
return 0
if args.UseOpenEye == 'Y' and not step_complete(charged_FN):
from openeye import oechem
from openeye import oequacpac
mol = oechem.OEGraphMol()
if os.path.isfile(args.inp):
ifs = oechem.oemolistream(args.inp)
oechem.OEReadMolecule(ifs, mol)
ifs.close()
else:
# Create a OpenEye molecule object from the SMILES string
if not oechem.OESmilesToMol(mol, smi):
raise Exception('Invalid SMILES string', smi)
oechem.OECanonicalOrderAtoms(mol)
oechem.OECanonicalOrderBonds(mol)
# Assign a reasonable protomer
if args.RetainProtonation:
for atom in mol.GetAtoms():
atom.SetImplicitHCount(0)
else:
if not oequacpac.OEGetReasonableProtomer(mol):
print 'Failed to get a reasonable protomer at pH 7.4'
oechem.OEAssignAromaticFlags(mol, oechem.OEAroModelOpenEye)
if not args.RetainProtonation:
oechem.OEAddExplicitHydrogens(mol)
# 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
src = oechem.OEGraphMol()
oechem.OESmilesToMol(src, "c1ccccc1")
# make holes in the molecule index space and juggle things around
oechem.OEAddExplicitHydrogens(src)
oechem.OESuppressHydrogens(src)
oechem.OEAddExplicitHydrogens(src)
oechem.OECanonicalOrderAtoms(src)
atommap = oechem.OEAtomArray(src.GetMaxAtomIdx())
dst = oechem.OEGraphMol()
oechem.OECopyMol(dst, src, atommap)
for srcatom in src.GetAtoms():
dstatom = atommap[srcatom.GetIdx()]
print(srcatom.GetIdx(), " -> ", dstatom.GetIdx())
# @ </SNIPPET>