def read_receptor(fragid, assembly_state, protonation_state):
"""
Read the receptor for the given fragment
Parameters
----------
fragid : str
The XChem fragment ID
assembly_state : str
Assembly state ['monomer', 'dimer']
protonation_state : str
Protonation state ['neutral', 'charged']
Returns
-------
receptor : OEReceptor
The receptor
"""
from openeye import oechem
receptor = oechem.OEGraphMol()
suffix = '' if protonation_state == 'neutral' else '-thiolate'
receptor_filename = f'../../receptors/{assembly_state}/Mpro-{fragment}_0A_bound-receptor{suffix}.oeb.gz'
from openeye import oedocking
oedocking.OEReadReceptorFile(receptor, receptor_filename)
logging.info(f' Receptor has {receptor.NumAtoms()} atoms.')
return receptor
def main(argv=[__name__]):
if len(argv) != 3:
oechem.OEThrow.Usage("SetOuterContourVolume.py <receptor> <volume>")
receptor = oechem.OEGraphMol()
if not oedocking.OEReadReceptorFile(receptor, argv[1]):
oechem.OEThrow.Fatal("Unable to open receptor file")
outerContourVolume = float(argv[2])
# @ <SNIPPET-SET-OUTER-CONTOUR-VOLUME-1>
negativeImagePotential = oedocking.OEReceptorGetNegativeImageGrid(receptor)
gridElement = []
for i in range(negativeImagePotential.GetSize()):
gridElement.append(negativeImagePotential[i])
gridElement.sort()
gridElement.reverse()
countToVolume = pow(negativeImagePotential.GetSpacing(), 3)
ilevel = int((outerContourVolume / countToVolume) + 0.5)
outerContourLevel = gridElement[-1]
if ilevel < len(gridElement):
outerContourLevel = gridElement[ilevel]
oedocking.OEReceptorSetOuterContourLevel(receptor, outerContourLevel)
# @ </SNIPPET-SET-OUTER-CONTOUR-VOLUME-1>
if not oedocking.OEWriteReceptorFile(receptor, argv[1]):
oechem.OEThrow.Fatal("Unable to write updated receptor")
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 load_receptor(receptor_oeb_path):
"""Load an OpenEye receptor file in oeb format."""
if not os.path.exists(receptor_oeb_path):
raise FileNotFoundError('Could not find ', receptor_oeb_path)
receptor = oechem.OEGraphMol()
oedocking.OEReadReceptorFile(receptor, receptor_oeb_path)
return receptor
def dock_molecules(receptor_filename, molecules, filename):
"""
Dock the specified molecules, writing out to specified file
Parameters
----------
receptor_filename : str
Receptor .oeb.gz filename
molecules : list of openeye.oechem.OEMol
The read molecules to dock
filename : str
The filename to stream docked molecules to
"""
# Read the receptor
print('Loading receptor...')
from openeye import oechem, oedocking
receptor = oechem.OEGraphMol()
if not oedocking.OEReadReceptorFile(receptor, 'receptor.oeb.gz'):
oechem.OEThrow.Fatal("Unable to read receptor")
if oedocking.OEReceptorHasBoundLigand(receptor):
print("Receptor has a bound ligand")
else:
print("Receptor does not have bound ligand")
print('Initializing receptor...')
dockMethod = oedocking.OEDockMethod_Hybrid2
dockResolution = oedocking.OESearchResolution_High
dock = oedocking.OEDock(dockMethod, dockResolution)
success = dock.Initialize(receptor)
# Set up Omega
from openeye import oeomega
omegaOpts = oeomega.OEOmegaOptions(oeomega.OEOmegaSampling_Dense)
#omegaOpts = oeomega.OEOmegaOptions()
omega = oeomega.OEOmega(omegaOpts)
omega.SetStrictStereo(False)
# Dock molecules
with oechem.oemolostream(filename) as ofs:
from tqdm import tqdm
for mol in tqdm(molecules):
dockedMol = oechem.OEGraphMol()
# Expand conformers
omega.Build(mol)
# Dock molecule
retCode = dock.DockMultiConformerMolecule(dockedMol, mol)
if (retCode != oedocking.OEDockingReturnCode_Success):
oechem.OEThrow.Fatal("Docking Failed with error code " + oedocking.OEDockingReturnCodeGetName(retCode))
# Store docking data
sdtag = oedocking.OEDockMethodGetName(dockMethod)
oedocking.OESetSDScore(dockedMol, dock, sdtag)
dock.AnnotatePose(dockedMol)
# Write molecule
oechem.OEWriteMolecule(ofs, dockedMol)
def main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData)
if not oechem.OEParseCommandLine(itf, argv):
return 1
imstr = oechem.oemolistream(itf.GetString("-in"))
omstr = oechem.oemolostream(itf.GetString("-out"))
receptors = []
for receptor_filename in itf.GetStringList("-receptors"):
receptor = oechem.OEGraphMol()
if not oedocking.OEReadReceptorFile(receptor, receptor_filename):
oechem.OEThrow.Fatal("Unable to read receptor from %s" %
receptor_filename)
receptors.append(receptor)
poser = oedocking.OEPosit()
for receptor in receptors:
poser.AddReceptor(receptor)
for mcmol in imstr.GetOEMols():
print("posing", mcmol.GetTitle())
result = oedocking.OESinglePoseResult()
ret_code = poser.Dock(result, mcmol)
if ret_code == oedocking.OEDockingReturnCode_Success:
posedMol = result.GetPose()
oechem.OESetSDData(posedMol, poser.GetName(),
str(result.GetProbability()))
oechem.OESetSDData(posedMol, "Receptor Index",
str(result.GetReceptorIndex()))
oechem.OEWriteMolecule(omstr, posedMol)
else:
errMsg = oedocking.OEDockingReturnCodeGetName(ret_code)
oechem.OEThrow.Warning("%s: %s" % (mcmol.GetTitle(), errMsg))
return 0
def main(argv):
if len(argv) != 2:
oechem.OEThrow.Usage("%s <receptor>" % argv[0])
receptor = oechem.OEGraphMol()
oedocking.OEReadReceptorFile(receptor, argv[1])
# @ <SNIPPET-RECEPTOR-BOUND-LIGAND-EDITING-1>
if oedocking.OEReceptorHasBoundLigand(receptor):
print("Receptor has a bound ligand")
else:
print("Receptor does not have bound ligand")
# @ </SNIPPET-RECEPTOR-BOUND-LIGAND-EDITING-1>
# @ <SNIPPET-RECEPTOR-BOUND-LIGAND-EDITING-2>
ligand = oechem.OEGraphMol()
if oedocking.OEReceptorHasBoundLigand(receptor):
ligand = oedocking.OEReceptorGetBoundLigand(receptor)
# @ </SNIPPET-RECEPTOR-BOUND-LIGAND-EDITING-2>
# @ <SNIPPET-RECEPTOR-BOUND-LIGAND-EDITING-3>
oedocking.OEReceptorSetBoundLigand(receptor, ligand)
# @ </SNIPPET-RECEPTOR-BOUND-LIGAND-EDITING-3>
# @ <SNIPPET-RECEPTOR-BOUND-LIGAND-EDITING-4>
oedocking.OEReceptorClearBoundLigand(receptor)
def dock_molecules_to_receptor(receptor_filename):
"""
Dock the specified molecules, writing out to specified file
Parameters
----------
receptor_filename : str
Receptor .oeb.gz filename
fragment : str
The fragment name to dock to
"""
import os
# Read the receptor
from openeye import oechem, oedocking
receptor = oechem.OEGraphMol()
if not oedocking.OEReadReceptorFile(receptor, receptor_filename):
oechem.OEThrow.Fatal("Unable to read receptor")
if not oedocking.OEReceptorHasBoundLigand(receptor):
raise Exception("Receptor does not have bound ligand")
#print('Initializing receptor...')
dockMethod = oedocking.OEDockMethod_Hybrid2
dockResolution = oedocking.OESearchResolution_Default
dock = oedocking.OEDock(dockMethod, dockResolution)
success = dock.Initialize(receptor)
# Set up Omega
#print('Expanding conformers...')
from openeye import oeomega
#omegaOpts = oeomega.OEOmegaOptions(oeomega.OEOmegaSampling_Dense)
omegaOpts = oeomega.OEOmegaOptions()
omega = oeomega.OEOmega(omegaOpts)
omega.SetStrictStereo(False)
# Dock molecules
docked_molecules = list()
for mol in molecules:
dockedMol = oechem.OEGraphMol()
# Expand conformers
omega.Build(mol)
# Dock molecule
#print(f'Docking {mol.NumConfs()} conformers...')
retCode = dock.DockMultiConformerMolecule(dockedMol, mol)
if (retCode != oedocking.OEDockingReturnCode_Success):
print("Docking Failed with error code " + oedocking.OEDockingReturnCodeGetName(retCode))
continue
# Store docking data
sdtag = oedocking.OEDockMethodGetName(dockMethod)
oedocking.OESetSDScore(dockedMol, dock, sdtag)
dock.AnnotatePose(dockedMol)
docked_molecules.append( oechem.OEMol(dockedMol) )
return docked_molecules
def receptor_from_file(receptor_filename):
receptor = oechem.OEGraphMol()
if not oedocking.OEReadReceptorFile(receptor, receptor_filename):
oechem.OEThrow.Fatal("Unable to read receptor")
if not oedocking.OEReceptorHasBoundLigand(receptor):
raise Exception("Receptor does not have bound ligand")
return receptor
def PrepareReceptorFromBinary(filename):
"""
If a receptor.oeb has been created, use this version.
If not, run 'PrepareReceptor' and a receptor.oeb will be created.
"""
receptor = oechem.OEGraphMol()
oedocking.OEReadReceptorFile(receptor,filename)
return receptor
def DockConf(pdb_file, mol, MAX_POSES = 5):
receptor = oechem.OEGraphMol()
oedocking.OEReadReceptorFile(receptor, pdb_file)
dock = oedocking.OEDock()
dock.Initialize(receptor)
lig = oechem.OEMol()
err = dock.DockMultiConformerMolecule(lig,mol,MAX_POSES)
return dock, lig, receptor
def PrepareReceptorFromBinary(filename):
"""
Gets receptor
:param filename: file name of .oeb or .oeb.gz of prepared receptor for OE
:return: OEMol receptor for docking
"""
receptor = oechem.OEMol()
oedocking.OEReadReceptorFile(receptor, filename)
return receptor
def __init__(self, receptor: utils.FilePath):
self.receptor_file = receptor
omegaOpts = oeomega.OEOmegaOptions()
omegaOpts.SetStrictStereo(False)
self.omega = oeomega.OEOmega(omegaOpts)
oechem.OEThrow.SetLevel(10000)
oereceptor = oechem.OEGraphMol()
oedocking.OEReadReceptorFile(oereceptor, self.receptor_file)
self.dock = oedocking.OEDock()
self.dock.Initialize(oereceptor)
def DockConf(pdb_file, mol, MAX_POSES=1, dock=None):
if dock is None:
receptor = oechem.OEGraphMol()
oedocking.OEReadReceptorFile(receptor, pdb_file)
dock = oedocking.OEDock(oedocking.OEScoreType_Chemgauss4,
oedocking.OESearchResolution_High)
dock.Initialize(receptor)
else:
receptor = None
lig = DockConf_(dock, mol, MAX_POSES=MAX_POSES)
return lig, receptor
def __init__(self, pdb_file):
self.receptor = oechem.OEGraphMol()
self.scorers = [oedocking.OEScore(oedocking.OEScoreType_Shapegauss),
oedocking.OEScore(oedocking.OEScoreType_Chemscore),
oedocking.OEScore(oedocking.OEScoreType_Chemgauss3),
oedocking.OEScore(oedocking.OEScoreType_Chemgauss4),
]
self.score = oedocking.OEScore(oedocking.OEScoreType_Chemgauss4)
oedocking.OEReadReceptorFile(self.receptor, pdb_file)
for score in self.scorers:
score.Initialize(self.receptor)
def __init__(self, pdb_file):
self.receptor = oechem.OEGraphMol()
self.scorers = {
'Shapegauss': oedocking.OEScore(oedocking.OEScoreType_Shapegauss),
'Chemscore': oedocking.OEScore(oedocking.OEScoreType_Chemscore),
'Chemgauss': oedocking.OEScore(oedocking.OEScoreType_Chemgauss),
'Chemgauss3': oedocking.OEScore(oedocking.OEScoreType_Chemgauss3),
'Chemgauss4': oedocking.OEScore(oedocking.OEScoreType_Chemgauss4),
}
oedocking.OEReadReceptorFile(self.receptor, pdb_file)
for _, score in self.scorers.items():
score.Initialize(self.receptor)
def main(argv=[__name__]):
if len(argv) != 3:
oechem.OEThrow.Usage("%s <receptor> <poses>" % argv[0])
receptor = oechem.OEGraphMol()
oedocking.OEReadReceptorFile(receptor, argv[1])
oescore = oedocking.OEScore()
oescore.Initialize(receptor)
poses = oechem.OEGraphMol()
imstr = oechem.oemolistream(argv[2])
for poses in imstr.GetOEMols():
TagPoses(oescore, poses, oescore.GetName())
def main(args):
smiles = args.s
receptor_name = args.r
hostname = args.a
port = args.p
receptor = oechem.OEGraphMol()
oedocking.OEReadReceptorFile(receptor, args.r)
client = DockingClient(hostname, port)
score = client(smiles, receptor_name, receptor=receptor)
print(score)
return 0
def main(argv=[__name__]):
if len(argv) != 3:
oechem.OEThrow.Usage("%s <receptor> <conformers>" % argv[0])
receptor = oechem.OEGraphMol()
oedocking.OEReadReceptorFile(receptor, argv[1])
dock = oedocking.OEDock()
dock.Initialize(receptor)
conformers = oechem.OEMol()
imstr = oechem.oemolistream(argv[2])
for conformers in imstr.GetOEMols():
poses = oechem.OEMol()
dock.DockMultiConformerMolecule(poses, conformers)
TagPoses(dock, poses, dock.GetName())
def __init__(self, prefix: str, receptor_file: os.PathLike):
"""
:param prefix: Prefix to identify scoring function instance (e.g., Risperidone)
:param receptor_file: Path to receptor file (.oeb).
"""
logger.warning("This code has not been tested (at all!)")
self.prefix = prefix
self.receptor_file = receptor_file
omegaOpts = oeomega.OEOmegaOptions()
omegaOpts.SetStrictStereo(False)
self.omega = oeomega.OEOmega(omegaOpts)
oechem.OEThrow.SetLevel(10000)
oereceptor = oechem.OEGraphMol()
oedocking.OEReadReceptorFile(oereceptor, self.receptor_file)
self.oedock = oedocking.OEDock()
self.oedock.Initialize(oereceptor)
def begin(self):
receptor = oechem.OEGraphMol()
self.args.receptor = utils.download_dataset_to_file(self.args.receptor)
if not oedocking.OEReadReceptorFile(receptor, str(self.args.receptor)):
raise Exception("Unable to read receptor from {0}".format(self.args.receptor))
# Initialize Docking
dock_method = oedocking.OEDockMethod_Hybrid
if not oedocking.OEReceptorHasBoundLigand(receptor):
oechem.OEThrow.Warning("No bound ligand, switching OEDockMethod to ChemGauss4.")
dock_method = oedocking.OEDockMethod_Chemgauss4
dock_resolution = oedocking.OESearchResolution_Default
self.sdtag = oedocking.OEDockMethodGetName(dock_method)
self.dock = oedocking.OEDock(dock_method, dock_resolution)
if not self.dock.Initialize(receptor):
raise Exception("Unable to initialize Docking with {0}".format(self.args.receptor))
def main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData)
# @ <SNIPPET-RESCORE-POSES-CONFIGURE>
oedocking.OEScoreTypeConfigure(itf, "-score")
# @ </SNIPPET-RESCORE-POSES-CONFIGURE>
if not oechem.OEParseCommandLine(itf, argv):
return 1
receptor = oechem.OEGraphMol()
if not oedocking.OEReadReceptorFile(receptor, itf.GetString("-receptor")):
oechem.OEThrow.Fatal("Unable to read receptor")
imstr = oechem.oemolistream()
if not imstr.open(itf.GetString("-in")):
oechem.OEThrow.Fatal("Unable to open input file of ligands")
omstr = oechem.oemolostream()
if not omstr.open(itf.GetString("-out")):
oechem.OEThrow.Fatal("Unable to open out file for rescored ligands")
# @ <SNIPPET-RESCORE-POSES-GET-VALUE>
scoreType = oedocking.OEScoreTypeGetValue(itf, "-score")
# @ </SNIPPET-RESCORE-POSES-GET-VALUE>
# @ <SNIPPET-RESCORE-POSES-SETUP-SCORE>
score = oedocking.OEScore(scoreType)
# @ </SNIPPET-RESCORE-POSES-SETUP-SCORE>
# @ <SNIPPET-RESCORE-POSES-INITIALIZE>
score.Initialize(receptor)
# @ </SNIPPET-RESCORE-POSES-INITIALIZE>
for ligand in imstr.GetOEMols():
if itf.GetBool("-optimize"):
# @ <SNIPPET-RESCORE-POSES-OPTIMIZE>
score.SystematicSolidBodyOptimize(ligand)
# @ </SNIPPET-RESCORE-POSES-OPTIMIZE>
# @ <SNIPPET-RESCORE-POSES-ANNOTATE>
score.AnnotatePose(ligand)
# @ </SNIPPET-RESCORE-POSES-ANNOTATE>
sdtag = score.GetName()
# @ <SNIPPET-RESCORE-POSES-ASSIGN-SCORE>
oedocking.OESetSDScore(ligand, score, sdtag)
# @ </SNIPPET-RESCORE-POSES-ASSIGN-SCORE>
# @ <SNIPPET-RESCORE-POSES-SCORE-SORTING>
oechem.OESortConfsBySDTag(ligand, sdtag,
score.GetHighScoresAreBetter())
# @ </SNIPPET-RESCORE-POSES-SCORE-SORTING>
oechem.OEWriteMolecule(omstr, ligand)
return 0
def main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData)
# @ <SNIPPET-DOCK-MOLECULES-CONFIGURE>
oedocking.OEDockMethodConfigure(itf, "-method")
oedocking.OESearchResolutionConfigure(itf, "-resolution")
# @ </SNIPPET-DOCK-MOLECULES-CONFIGURE>
if not oechem.OEParseCommandLine(itf, argv):
return 1
imstr = oechem.oemolistream(itf.GetString("-in"))
omstr = oechem.oemolostream(itf.GetString("-out"))
receptor = oechem.OEGraphMol()
if not oedocking.OEReadReceptorFile(receptor, itf.GetString("-receptor")):
oechem.OEThrow.Fatal("Unable to read receptor")
# @ <SNIPPET-DOCK-MOLECULES-GET-VALUE>
dockMethod = oedocking.OEDockMethodGetValue(itf, "-method")
dockResolution = oedocking.OESearchResolutionGetValue(itf, "-resolution")
# @ </SNIPPET-DOCK-MOLECULES-GET-VALUE>
# @ <SNIPPET-DOCK-MOLECULES-SETUP>
dock = oedocking.OEDock(dockMethod, dockResolution)
# @ </SNIPPET-DOCK-MOLECULES-SETUP>
# @ <SNIPPET-DOCK-MOLECULES-INITIALIZE>
dock.Initialize(receptor)
# @ </SNIPPET-DOCK-MOLECULES-INITIALIZE>
for mcmol in imstr.GetOEMols():
print("docking", mcmol.GetTitle())
dockedMol = oechem.OEGraphMol()
# @ <SNIPPET-DOCK-MOLECULES-DOCK>
retCode = dock.DockMultiConformerMolecule(dockedMol, mcmol)
if (retCode != oedocking.OEDockingReturnCode_Success):
oechem.OEThrow.Fatal("Docking Failed with error code " + oedocking.OEDockingReturnCodeGetName(retCode))
# @ </SNIPPET-DOCK-MOLECULES-DOCK>
sdtag = oedocking.OEDockMethodGetName(dockMethod)
# @ <SNIPPET-DOCK-MOLECULES-ASSIGN-SCORE>
oedocking.OESetSDScore(dockedMol, dock, sdtag)
# @ </SNIPPET-DOCK-MOLECULES-ASSIGN-SCORE>
# @ <SNIPPET-DOCK-MOLECULES-ANNOTATE>
dock.AnnotatePose(dockedMol)
# @ </SNIPPET-DOCK-MOLECULES-ANNOTATE>
oechem.OEWriteMolecule(omstr, dockedMol)
return 0
def __init__(self, prefix: str, receptor_file: str):
"""
Scoring function class to perform OpenEye docking (FRED)
:param prefix: Name (to help keep track metrics, if using a scoring function class more than once)
:param receptor_file: Path to oe receptor file.
"""
logger.warning("This code has not been tested (at all!)")
self.prefix = prefix
self.receptor_file = receptor_file
omegaOpts = oeomega.OEOmegaOptions()
omegaOpts.SetStrictStereo(False)
self.omega = oeomega.OEOmega(omegaOpts)
oechem.OEThrow.SetLevel(10000)
oereceptor = oechem.OEGraphMol()
oedocking.OEReadReceptorFile(oereceptor, self.receptor_file)
self.oedock = oedocking.OEDock()
self.oedock.Initialize(oereceptor)
def main(argv=[__name__]):
if len(argv) != 3:
oechem.OEThrow.Usage("%s <receptor> <ligand>" % argv[0])
receptor = oechem.OEGraphMol()
oedocking.OEReadReceptorFile(receptor, argv[1])
oescore = oedocking.OEScore()
oescore.Initialize(receptor)
imstr = oechem.oemolistream(argv[2])
mcmol = oechem.OEMol()
oechem.OEReadMolecule(imstr, mcmol)
for pose in mcmol.GetConfs():
PrintScore(oescore, pose)
for atom in pose.GetAtoms():
PrintAtomScore(oescore, pose, atom)
def main(argv=[__name__]):
if len(argv) != 2:
oechem.OEThrow.Usage("ToggleInterContour.py <receptor>")
receptor = oechem.OEGraphMol()
if not oedocking.OEReadReceptorFile(receptor, argv[1]):
oechem.OEThrow.Fatal("Cannot read receptor")
# @ <SNIPPET-TOGGLE-INNER-CONTOUR-1>
innerContourLevel = oedocking.OEReceptorGetInnerContourLevel(receptor)
oedocking.OEReceptorSetInnerContourLevel(receptor, -innerContourLevel)
# @ </SNIPPET-TOGGLE-INNER-CONTOUR-1>
if innerContourLevel > 0.0:
oechem.OEThrow.Info("Toggling inner contour off")
else:
oechem.OEThrow.Info("Toggling inner contour on")
if not oedocking.OEWriteReceptorFile(receptor, argv[1]):
oechem.OEThrow.Fatal("Unable to write receptor")
def main(argv=[__name__]):
if len(argv) != 2:
oechem.OEThrow.Usage("%s <receptor>" % argv[0])
receptor = oechem.OEGraphMol()
oedocking.OEReadReceptorFile(receptor, argv[1])
# @ <SNIPPET-RECEPTOR-EXTRA-MOLECULES-EDITING-1>
count = 0
newExtraMolList = []
for extraMol in oedocking.OEReceptorGetExtraMols(receptor):
if count == 0:
oedocking.OEReceptorSetBoundLigand(receptor, extraMol)
else:
newExtraMolList.append(extraMol)
count += 1
oedocking.OEReceptorClearExtraMols(receptor)
for extraMol in newExtraMolList:
oedocking.OEReceptorAddExtraMol(receptor, extraMol)
def main(argv=[__name__]):
if len(sys.argv) != 2:
oechem.OEThrow.Usage("ReceptorOuterContourVolume.py <receptor>")
receptor = oechem.OEGraphMol()
if not oedocking.OEReadReceptorFile(receptor, sys.argv[1]):
oechem.OEThrow.Fatal("%s is not a valid receptor", argv[1])
# @ <SNIPPET-RECEPTOR-OUTER-CONTOUR-VOLUME-1>
negativeImagePotential = oedocking.OEReceptorGetNegativeImageGrid(receptor)
outerContourLevel = oedocking.OEReceptorGetOuterContourLevel(receptor)
outerCount = 0
for i in range(negativeImagePotential.GetSize()):
if negativeImagePotential[i] >= outerContourLevel:
outerCount += 1
countToVolume = pow(negativeImagePotential.GetSpacing(), 3)
print(outerCount * countToVolume, " cubic angstroms")
def load_receptor(receptor_oeb_path):
"""Load an OpenEye receptor file in oeb format.
Parameters
----------
receptor_oeb_path : str
Receptor in OpenEye oeb binary format
Returns
-------
receptor : openeye.oedocking.OEReceptor
The OpenEye receptor object
"""
from openeye import oechem, oedocking
import os
if not os.path.exists(receptor_oeb_path):
raise FileNotFoundError('Could not find ', receptor_oeb_path)
receptor = oechem.OEGraphMol()
oedocking.OEReadReceptorFile(receptor, receptor_oeb_path)
return receptor
def read_receptor(fragid):
"""
Read the receptor for the given fragment
Parameters
----------
fragid : str
The XChem fragment ID
Returns
-------
receptor : OEReceptor
The receptor
"""
from openeye import oechem
receptor = oechem.OEGraphMol()
receptor_filename = f'../../receptors/monomer/Mpro-{fragment}_0A_bound-receptor.oeb.gz'
from openeye import oedocking
oedocking.OEReadReceptorFile(receptor, receptor_filename)
print(f' Receptor has {receptor.NumAtoms()} atoms.')
return receptor
