def _get_design_unit(
self,
protein_structure: oechem.OEGraphMol,
design_unit_identifier: str,
electron_density: Union[oegrid.OESkewGrid, None] = None,
ligand_name: Union[str, None] = None,
) -> oechem.OEDesignUnit:
"""
Get an OpenEye design unit from a protein ligand complex.
Parameters
----------
protein_structure: oechem.OEGraphMol
An OpenEye molecule holding the protein that might be in
complex with a ligand.
design_unit_identifier: str
A unique identifier describing the design unit.
electron_density: oegrid.OESkewGrid or None
An OpenEye grid holding the electron density of the protein ligand complex.
ligand_name: str or None
Residue name of the ligand in complex with the protein structure.
Returns
-------
: oechem.OEDesignUnit
The design unit.
"""
from openeye import oechem
from ..modeling.OEModeling import prepare_complex, prepare_protein
from ..utils import LocalFileStorage
design_unit_path = LocalFileStorage.featurizer_result(
self.__class__.__name__, f"{design_unit_identifier}_design_unit",
"oedu")
if design_unit_path.is_file():
logging.debug("Reading design unit from file ...")
design_unit = oechem.OEDesignUnit()
oechem.OEReadDesignUnit(str(design_unit_path), design_unit)
else:
logging.debug("Generating design unit ...")
if ligand_name is None:
design_unit = prepare_protein(protein_structure,
self.loop_db,
cap_termini=False)
else:
design_unit = prepare_complex(
protein_structure,
electron_density,
self.loop_db,
ligand_name=ligand_name,
cap_termini=False,
)
logging.debug("Writing design unit ...")
oechem.OEWriteDesignUnit(str(design_unit_path), design_unit)
return design_unit
def deserialize(du_bytes):
design_unit = oechem.OEDesignUnit()
if not oechem.OEReadDesignUnitFromBytes(design_unit, du_bytes):
raise ValueError(
"It was not possible to deserialize the Design Unit")
return design_unit
def _get_design_unit(
self,
complex_structure: oechem.OEGraphMol,
design_unit_identifier: str,
electron_density: Union[oegrid.OESkewGrid, None],
) -> oechem.OEDesignUnit:
"""
Get an OpenEye design unit from a protein ligand complex.
Parameters
----------
complex_structure: oechem.OEGraphMol
An OpenEye molecule holding the protein in complex with a ligand.
design_unit_identifier: str
A unique identifier describing the design unit.
electron_density: oegrid.OESkewGrid or None
An OpenEye grid holding the electron density of the protein ligand complex.
Returns
-------
: oechem.OEDesignUnit
The design unit.
"""
from openeye import oechem
from ..modeling.OEModeling import prepare_complex
from ..utils import LocalFileStorage
design_unit_path = LocalFileStorage.featurizer_result(
self.__class__.__name__, f"{design_unit_identifier}_design_unit",
"oedu") # TODO: the file name needs to be unique
if design_unit_path.is_file():
logging.debug("Reading design unit from file ...")
design_unit = oechem.OEDesignUnit()
oechem.OEReadDesignUnit(str(design_unit_path), design_unit)
else:
logging.debug("Generating design unit ...")
design_unit = prepare_complex(complex_structure, electron_density,
self.loop_db)
logging.debug("Writing design unit ...")
oechem.OEWriteDesignUnit(str(design_unit_path), design_unit)
return design_unit
# 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.
import sys
from openeye import oechem
from openeye import oedepict
from openeye import oegrapheme
###############################################################
# USED TO GENERATE CODE SNIPPETS FOR THE GRAPHEME DOCUMENTATION
###############################################################
if len(sys.argv) != 2:
oechem.OEThrow.Usage("%s <design unit>" % sys.argv[0])
filename = sys.argv[1]
# @ <SNIPPET-DRAW-IRIDIUM-DATA>
du = oechem.OEDesignUnit()
if not oechem.OEReadDesignUnit(filename, du):
oechem.OEThrow.Fatal("Cannot read design unit!")
image = oedepict.OEImage(250, 250)
oegrapheme.OEDrawIridiumData(image, du)
oedepict.OEDrawBorder(image, oedepict.OELightGreyPen)
oedepict.OEWriteImage("DrawIridiumData.svg", image)
# @ </SNIPPET-DRAW-IRIDIUM-DATA>
oedepict.OEWriteImage("DrawIridiumData.pdf", image)
def read_design_unit(fname):
du = oechem.OEDesignUnit()
oechem.OEReadDesignUnit(fname, du)
return du
oechem.OEPlaceHydrogens(mol)
return mol
def read_design_unit(fname):
du = oechem.OEDesignUnit()
oechem.OEReadDesignUnit(fname, du)
return du
if len(sys.argv) != 3:
oechem.OEThrow.Usage("{} <du file> <lig file>".format(sys.argv[0]))
du = read_design_unit(sys.argv[1])
lig = read_graph_mol(sys.argv[2])
# @ <SNIPPET-OEUpdateDesignUnit>
if not oechem.OEUpdateDesignUnit(du, lig,
oechem.OEDesignUnitComponents_Ligand):
oechem.OEThrow.Fatal(
"Error: Could not add the ligand to the OEDesignUnit.")
# @ </SNIPPET-OEUpdateDesignUnit>
# @ <SNIPPET-OESubsetDesignUnit>
ligProtDU = oechem.OEDesignUnit()
components = oechem.OEDesignUnitComponents_Protein | oechem.OEDesignUnitComponents_Ligand
if not oechem.OESubsetDesignUnit(ligProtDU, du, components):
oechem.OEThrow.Fatal(
"Error: Could create a subset of the reference OEDesignUnit.")
# @ </SNIPPET-OESubsetDesignUnit>