Depicting Active Site Interactions

A program that depicts receptor-ligand interactions.

See also

• Visualizing Protein-Ligand Interactions OpenEye Python Cookbook example

Command Line Interface

A description of the command line interface can be obtained by executing the program with the –help argument.

prompt> python complex2img.py --help

will generate the following output:

[-complex] <input> [-out] <output image>

Simple parameter list
    -height : Height of output image
    -width : Width of output image

    SplitMolComplex options :
      -ligandname : Ligand name

    input/output options
      -complex : Input filename of the protein complex
      -out : Output filename

    molecule display options
      -aromstyle : Aromatic ring display style

Code

Download code

complex2img.py

#!/usr/bin/env python
# (C) 2022 Cadence Design Systems, Inc. (Cadence) 
# All rights reserved.
# TERMS FOR USE OF SAMPLE CODE The software below ("Sample Code") is
# provided to current licensees or subscribers of Cadence products or
# SaaS offerings (each a "Customer").
# Customer is hereby permitted to use, copy, and modify the Sample Code,
# subject to these terms. Cadence claims no rights to Customer's
# modifications. Modification of Sample Code is at Customer's sole and
# exclusive risk. Sample Code may require Customer to have a then
# current license or subscription to the applicable Cadence 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 Cadence be
# liable for any damages or liability in connection with the Sample Code
# or its use.

#############################################################################
# Depicts the interactions of an active site
#############################################################################

import sys
from openeye import oechem
from openeye import oedepict
from openeye import oegrapheme


def main(argv=[__name__]):

    itf = oechem.OEInterface()
    oechem.OEConfigure(itf, InterfaceData)
    oedepict.OEConfigureImageWidth(itf, 900.0)
    oedepict.OEConfigureImageHeight(itf, 600.0)
    oedepict.OEConfigure2DMolDisplayOptions(itf, oedepict.OE2DMolDisplaySetup_AromaticStyle)
    oechem.OEConfigureSplitMolComplexOptions(itf, oechem.OESplitMolComplexSetup_LigName)

    if not oechem.OEParseCommandLine(itf, argv):
        return 1

    iname = itf.GetString("-complex")
    oname = itf.GetString("-out")

    ifs = oechem.oemolistream()
    if not ifs.open(iname):
        oechem.OEThrow.Fatal("Cannot open input file!")

    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!")

    complexmol = oechem.OEGraphMol()
    if not oechem.OEReadMolecule(ifs, complexmol):
        oechem.OEThrow.Fatal("Unable to read molecule from %s" % iname)

    if not oechem.OEHasResidues(complexmol):
        oechem.OEPerceiveResidues(complexmol, oechem.OEPreserveResInfo_All)

    # Separate ligand and protein

    sopts = oechem.OESplitMolComplexOptions()
    oechem.OESetupSplitMolComplexOptions(sopts, itf)

    ligand = oechem.OEGraphMol()
    protein = oechem.OEGraphMol()
    water = oechem.OEGraphMol()
    other = oechem.OEGraphMol()

    pfilter = sopts.GetProteinFilter()
    wfilter = sopts.GetWaterFilter()
    sopts.SetProteinFilter(oechem.OEOrRoleSet(pfilter, wfilter))
    sopts.SetWaterFilter(oechem.OEMolComplexFilterFactory(
                         oechem.OEMolComplexFilterCategory_Nothing))

    oechem.OESplitMolComplex(ligand, protein, water, other, complexmol, sopts)

    if ligand.NumAtoms() == 0:
        oechem.OEThrow.Fatal("Cannot separate complex!")

    # Perceive interactions

    asite = oechem.OEInteractionHintContainer(protein, ligand)
    if not asite.IsValid():
        oechem.OEThrow.Fatal("Cannot initialize active site!")
    asite.SetTitle(ligand.GetTitle())

    oechem.OEPerceiveInteractionHints(asite)

    oegrapheme.OEPrepareActiveSiteDepiction(asite)

    # Depict active site with interactions

    width, height = oedepict.OEGetImageWidth(itf), oedepict.OEGetImageHeight(itf)
    image = oedepict.OEImage(width, height)

    cframe = oedepict.OEImageFrame(image, width * 0.80, height, oedepict.OE2DPoint(0.0, 0.0))
    lframe = oedepict.OEImageFrame(image, width * 0.20, height,
                                   oedepict.OE2DPoint(width * 0.80, 0.0))

    opts = oegrapheme.OE2DActiveSiteDisplayOptions(cframe.GetWidth(), cframe.GetHeight())
    oedepict.OESetup2DMolDisplayOptions(opts, itf)

    adisp = oegrapheme.OE2DActiveSiteDisplay(asite, opts)
    oegrapheme.OERenderActiveSite(cframe, adisp)

    lopts = oegrapheme.OE2DActiveSiteLegendDisplayOptions(10, 1)
    oegrapheme.OEDrawActiveSiteLegend(lframe, adisp, lopts)

    oedepict.OEWriteImage(oname, image)

    return 0


#############################################################################
# INTERFACE
#############################################################################

InterfaceData = '''
!BRIEF [-complex] <input> [-out] <output image>

!CATEGORY "input/output options :"

  !PARAMETER -complex
    !ALIAS -c
    !TYPE string
    !KEYLESS 1
    !REQUIRED true
    !VISIBILITY simple
    !BRIEF Input filename of the protein complex
  !END

  !PARAMETER -out
    !ALIAS -o
    !TYPE string
    !REQUIRED true
    !KEYLESS 2
    !VISIBILITY simple
    !BRIEF Output filename
  !END

!END
'''

if __name__ == "__main__":
    sys.exit(main(sys.argv))

See also

• OESplitMolComplex function in OEChem TK

• OEInteractionHintContainer class in OEChem TK

• OEPerceiveInteractionHints function in OEChem TK

• OEPrepareActiveSiteDepiction function

• OE2DActiveSiteDisplayOptions class

• OE2DActiveSiteDisplay class and OERenderActiveSite function

• OEDrawActiveSiteLegend function

Examples

prompt> python complex2img.py -complex pdb1br6.ent -out 1br6-PT1.png

will generate the image shown in Figure: Example of depicting the receptor-ligand interaction (PDB: 1br6).

Example of depicting the receptor-ligand interactions (PDB: 1br6)

prompt> python complex2img.py -complex pdb1eoc.ent -out 1eoc-4NC.png

will generate the image shown in Figure: Example of depicting the receptor-ligand interaction (PDB: 1eoc).

Example of depicting the receptor-ligand interactions (PDB: 1eoc)