def create_box_receptor(
protein: oechem.OEGraphMol,
box_dimensions: Tuple[float, float, float, float, float, float],
) -> oechem.OEGraphMol:
"""
Create a box receptor for docking.
Parameters
----------
protein: oechem.OEGraphMol
An OpenEye molecule holding a prepared protein structure.
box_dimensions: tuple of float
The box dimensions in the order of xmax, ymax, zmax, xmin, ymin, zmin.
Returns
-------
receptor: oechem.OEGraphMol
An OpenEye molecule holding a receptor with defined binding site via box dimensions.
"""
from openeye import oedocking
# create receptor
box = oedocking.OEBox(*box_dimensions)
receptor = oechem.OEGraphMol()
oedocking.OEMakeReceptor(receptor, protein, box)
return receptor
def main(argv=[__name__]):
path = "receptor_pdbs/*.pdb" #input: pdbs from clustering
files = glob.glob(path)
for i in files:
centroid_number = i[-5:-4]
imstr = oechem.oemolistream(i)
proteinStructure = oechem.OEGraphMol()
oechem.OEReadMolecule(imstr, proteinStructure)
coordinates_dictionary = oechem.OEMolBase.GetCoords(proteinStructure)
x_coord = []
y_coord = []
z_coord = []
for key in coordinates_dictionary:
x = coordinates_dictionary[key][0]
y = coordinates_dictionary[key][1]
z = coordinates_dictionary[key][2]
x_coord.append(x)
y_coord.append(y)
z_coord.append(z)
x_max = max(x_coord)
x_min = min(x_coord)
y_max = max(y_coord)
y_min = min(y_coord)
z_max = max(z_coord)
z_min = min(z_coord)
box = oedocking.OEBox(
x_max, y_max, z_max, x_min, y_min,
z_min) #Box set using max and min coordinates of entire protein
receptor = oechem.OEGraphMol()
oedocking.OEMakeReceptor(receptor, proteinStructure, box)
oedocking.OEWriteReceptorFile(receptor, "receptor_oebs/receptor" +
str(centroid_number) +
".oeb") #output: receptor oebs
return 0
def create_receptor(protein_pdb_path, box):
"""Create an OpenEye receptor from a PDB file.
Parameters
----------
protein_pdb_path : str
Path to the receptor PDB file.
box : 1x6 array of float
The minimum and maximum values of the coordinates of the box
representing the binding site [xmin, ymin, zmin, xmax, ymax, zmax].
Returns
-------
receptor : openeye.oedocking.OEReceptor
The OpenEye receptor object.
"""
input_mol_stream = oechem.oemolistream(protein_pdb_path)
protein_oemol = oechem.OEGraphMol()
oechem.OEReadMolecule(input_mol_stream, protein_oemol)
box = oedocking.OEBox(*box)
receptor = oechem.OEGraphMol()
oedocking.OEMakeReceptor(receptor, protein_oemol, box)
return receptor
def create_box_receptor(protein,
xmax,
ymax,
zmax,
xmin,
ymin,
zmin,
receptor_save_path=None):
"""
Create a box receptor for docking.
Parameters
----------
protein: oechem.OEGraphMol
An oechem.OEGraphMol object holding a prepared protein structure.
xmax: float or int
Maximal number in x direction.
ymax: float or int
Maximal number in y direction.
zmax: float or int
Maximal number in z direction.
xmin: float or int
Minimal number in x direction.
ymin: float or int
Minimal number in x direction.
zmin: float or int
Minimal number in z direction.
receptor_save_path: str
File path for saving created receptor. If receptor_save_path is not provided, receptor will not be saved.
Returns
-------
receptor: oechem.OEGraphMol
An oechem.OEGraphMol object holding a receptor with defined binding site via box dimensions.
"""
# Standard libraries
import pathlib
# External libraries
from openeye import oechem, oedocking
# create receptor
box = oedocking.OEBox(xmax, ymax, zmax, xmin, ymin, zmin)
receptor = oechem.OEGraphMol()
oedocking.OEMakeReceptor(receptor, protein, box)
# save receptor
if receptor_save_path is not None:
oedocking.OEWriteReceptorFile(
receptor, str(pathlib.Path(receptor_save_path).absolute()))
return receptor
def create_receptor(output_name, pdb_file, bp_min, bp_max):
check_oeb = output_name
proteinStructure = oechem.OEGraphMol()
ifs = oechem.oemolistream(pdb_file)
ifs.SetFormat(oechem.OEFormat_PDB)
oechem.OEReadMolecule(ifs, proteinStructure)
box = oedocking.OEBox(*bp_max, *bp_min)
receptor = oechem.OEGraphMol()
s = oedocking.OEMakeReceptor(receptor, proteinStructure, box)
oedocking.OEWriteReceptorFile(receptor, check_oeb)
def __init__(self, pdb_file, xmax, ymax, zmax, xmin, ymin, zmin):
self.receptor = oechem.OEGraphMol()
self.scorers = oedocking.OEScore(oedocking.OEScoreType_Chemgauss4)
proteinStructure = oechem.OEGraphMol()
ifs = oechem.oemolistream(pdb_file)
ifs.SetFormat(oechem.OEFormat_PDB)
oechem.OEReadMolecule(ifs, proteinStructure)
box = oedocking.OEBox(xmax, ymax, zmax, xmin, ymin, zmin)
receptor = oechem.OEGraphMol()
s = oedocking.OEMakeReceptor(receptor, proteinStructure, box)
self.scorers.Initialize(receptor)
def main(argv=[__name__]):
if len(argv) != 3:
oechem.OEThrow.Usage("%s <receptor> <ligand>" % argv[0])
# @ <SNIPPET-SCORE-BOX-1>
protein = oechem.OEGraphMol()
imstr = oechem.oemolistream(argv[1])
oechem.OEReadMolecule(imstr, protein)
pose = oechem.OEGraphMol()
imstr.open(argv[2])
oechem.OEReadMolecule(imstr, pose)
addbox = 4.0
box = oedocking.OEBox()
oedocking.OESetupBox(box, pose, addbox)
oescore = oedocking.OEScore()
oescore.Initialize(protein, box)
def __init__(self, pdb_file, xmax, ymax, zmax, xmin, ymin, zmin):
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),
}
proteinStructure = oechem.OEGraphMol()
ifs = oechem.oemolistream(pdb_file)
ifs.SetFormat(oechem.OEFormat_PDB)
oechem.OEReadMolecule(ifs, proteinStructure)
box = oedocking.OEBox(xmax, ymax, zmax, xmin, ymin, zmin)
receptor = oechem.OEGraphMol()
s = oedocking.OEMakeReceptor(receptor, proteinStructure, box)
for _, score in self.scorers.items():
assert (s != False)
score.Initialize(receptor)
def make_receptor( pdb):
from openeye import oedocking, oechem
import os.path
file_name = str(os.path.basename(pdb))
check_oeb = conf['cache'] + file_name.split(".")[0] + ".oeb"
if os.path.isfile(check_oeb):
g = oechem.OEGraphMol()
oedocking.OEReadReceptorFile(g, check_oeb)
return g
else:
proteinStructure = oechem.OEGraphMol()
ifs = oechem.oemolistream(pdb)
ifs.SetFormat(oechem.OEFormat_PDB)
oechem.OEReadMolecule(ifs, proteinStructure)
box = oedocking.OEBox(*conf['bp_max'], *conf['bp_min'])
receptor = oechem.OEGraphMol()
s = oedocking.OEMakeReceptor(receptor, proteinStructure, box)
oedocking.OEWriteReceptorFile(receptor, check_oeb)
assert (s != False)
return receptor
def main(argv=[__name__]):
if len(sys.argv) != 8:
oechem.OEThrow.Usage("MakeReceptorFromBox.py \
<protein> <xmax> <ymax> <zmax> <xmin> <ymin> <zmin>"
)
xmax = float(sys.argv[2])
ymax = float(sys.argv[3])
zmax = float(sys.argv[4])
xmin = float(sys.argv[5])
ymin = float(sys.argv[6])
zmin = float(sys.argv[7])
# @ <SNIPPET-MAKE-RECEPTOR-WITH-BOX-1>
imstr = oechem.oemolistream(sys.argv[1])
proteinStructure = oechem.OEGraphMol()
oechem.OEReadMolecule(imstr, proteinStructure)
box = oedocking.OEBox(xmax, ymax, zmax, xmin, ymin, zmin)
receptor = oechem.OEGraphMol()
oedocking.OEMakeReceptor(receptor, proteinStructure, box)
# @ </SNIPPET-MAKE-RECEPTOR-WITH-BOX-1>
oedocking.OEWriteReceptorFile(receptor, "receptor.oeb.gz")
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
