def split_molecule_components(
molecule: oechem.OEGraphMol) -> List[oechem.OEGraphMol]:
"""
Split an OpenEye Molecule into its bonded components.
Parameters
----------
molecule: oechem.OEGraphMol
An OpenEye molecule holding multiple components.
Returns
-------
: list of oechem.OEGraphMol
A list of OpenEye molecules holding the split components.
"""
# determine bonded components
number_of_components, part_list = oechem.OEDetermineComponents(molecule)
predicate = oechem.OEPartPredAtom(part_list)
# get bonded components
components = []
for i in range(number_of_components):
predicate.SelectPart(i + 1)
component = oechem.OEGraphMol()
oechem.OESubsetMol(component, molecule, predicate)
components.append(component)
return components
def get_binding_site(structure, ligand):
"""
"""
partlist = oechem.OEIntArray(structure.GetMaxAtomIdx())
# get all contacts between ligand and assembly
contacts = oechem.OEGetNearestNbrs(structure, ligand, 5.0)
binding_site_atom_idxs = set(contact.GetBgn().GetIdx()
for contact in contacts)
# create the partition map
for atom in structure.GetAtoms():
if atom.GetIdx() in binding_site_atom_idxs:
partlist[atom.GetIdx()] = 1
entitypred = oechem.OEPartPredAtom(partlist)
# select the binding site atoms
entitypred.SelectPart(1)
# create a new molecule for the entity
binding_site = oechem.OEGraphMol()
oechem.OESubsetMol(binding_site, structure, entitypred, False, False)
return binding_site
def main(argv=[__name__]):
if len(argv) != 3:
oechem.OEThrow.Usage("%s <infile> <outfile>" % argv[0])
ifs = oechem.oemolistream()
if not ifs.open(argv[1]):
oechem.OEThrow.Fatal("Unable to open %s for reading" % argv[1])
ofs = oechem.oemolostream()
if not ofs.open(argv[2]):
oechem.OEThrow.Fatal("Unable to open %s for writing" % argv[2])
for mol in ifs.GetOEGraphMols():
numparts, partlist = oechem.OEDetermineComponents(mol)
pred = oechem.OEPartPredAtom(partlist)
for i in range(1, numparts + 1):
pred.SelectPart(i)
partmol = oechem.OEGraphMol()
oechem.OESubsetMol(partmol, mol, pred)
oechem.OEWriteMolecule(ofs, partmol)
def PrepareReceptor(pdb,padding=4,outpath=""):
"""
Prepares a receptor from a pdb with a crystalized ligand
Padding controls the docking region.
If outpath is given, PrepareReceptor will write an openeye binary (oeb) of the receptor structure. This will be faster than rebuilding the receptor every time.
"""
print("STOP CALLING THIS FUNCTION")
exit()
com = oechem.OEGraphMol()
ifs = oechem.oemolistream()
if ifs.open(pdb):
oechem.OEReadPDBFile(ifs, com)
ifs.close()
"""
Sorry, this requires some explanation. Openeye wasn't recognizing the previously docked ligand, so I tried to find other ways.
The next blocks of code take our system and split it based on its connected components, for which its REQUIRED that our protein
only has a single chain. It assumes that the last component is the ligand. It then creates the ligand (lig) and protein (prot)
as separate molecules. Next, it finds the minimum and maximum 3D coordinates of the current ligand and produces a box around
it with the specified padding. Finally it uses this box to create a 'receptor' object into which ligands can be docked.
Only the receptor is returned.
Openeye's docking shouldn't be this involved, but I couldn't get it to run the typical 'hybrid' docking without error.
"""
oechem.OEDetermineConnectivity(com)
nparts, connect = oechem.OEDetermineComponents(com)
if(nparts != 2):
print("ERR in dock_conf::prepareReceptor. PDB doesn't have 2 connected components")
exit()
## TODO: What is a good way to catch errors?
# Get apo
pred = oechem.OEPartPredAtom(connect)
pred.SelectPart(nparts)
lig = oechem.OEGraphMol()
oechem.OESubsetMol(lig, com, pred)
print(lig)
# Get protein
pred = oechem.OEPartPredAtom(connect)
pred.SelectPart(1)
prot = oechem.OEGraphMol()
oechem.OESubsetMol(prot, com, pred)
# Get box dimensions by iterating over ligand
x_min = y_min = z_min = float('inf')
x_max = y_max = z_max = -float('inf')
crd = lig.GetCoords()
print("CRD", crd)
for atm in crd:
x,y,z = crd[atm]
if x < x_min:
x_min = x
if y < y_min:
y_min = y
if z < z_min:
z_min = z
if x > x_max:
x_max = x
if y > y_max:
y_max = y
if z > z_max:
z_max = z
x_min -= padding
y_min -= padding
z_min -= padding
x_max += padding
y_max += padding
z_max += padding
print(x_min,y_min,z_max, y_max)
# Now prepare the receptor
receptor = oechem.OEGraphMol()
box = oedocking.OEBox()
box.Setup(x_max, y_max, z_max, x_min, y_min, z_min)
oedocking.OEMakeReceptor(receptor, prot, box)
if not outpath == "":
oedocking.OEWriteReceptorFile(receptor,f'{outpath}/receptor.oeb')
return receptor