Depicting MDL Reaction

A program that converts an MDL reaction into an image file.

Command Line Interface

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

prompt> python mdlreaction2img.py --help

will generate the following output:

Simple parameter list

 image options :
   -height : Height of output image
   -width : Width of output image

 input/output options :
   -in : Input filename
   -out : Output filename

 molecule display options :
   -aromstyle : Aromatic ring display style
   -atomcolor : Atom coloring style
   -atomlabelfontscale : Atom label font scale
   -atomprop : Atom property display
   -atomstereostyle : Atom stereo display style
   -bondcolor : Bond coloring style
   -bondprop : Bond property display
   -bondstereostyle : Bond stereo display style
   -hydrstyle : Hydrogen display style
   -linewidth : Default bond line width
   -protgroupdisp : Protective group display style
   -scale : Scaling of the depicted molecule
   -superdisp : Super atom display style
   -titleloc : Location of the molecule title

Code

Download code

mdlreaction2img.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").
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# 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.

#############################################################################
# Converts an MDL reaction into an image file.
# The output file format is depends on its file extension.
#############################################################################

import sys
from openeye import oechem
from openeye import oedepict


def main(argv=[__name__]):

    itf = oechem.OEInterface()
    oechem.OEConfigure(itf, InterfaceData)
    oedepict.OEConfigureImageOptions(itf)
    oedepict.OEConfigure2DMolDisplayOptions(itf)

    if not oechem.OEParseCommandLine(itf, argv):
        oechem.OEThrow.Fatal("Unable to interpret command line!")

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

    ext = oechem.OEGetFileExtension(oname)
    if not oedepict.OEIsRegisteredImageFile(ext):
        oechem.OEThrow.Fatal("Unknown image type!")

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

    ofs = oechem.oeofstream()
    if not ofs.open(oname):
        oechem.OEThrow.Fatal("Cannot open output file!")

    mol = oechem.OEGraphMol()
    if not oechem.OEReadMDLReactionQueryFile(ifs, mol):
        oechem.OEThrow.Fatal("Cannot read mdl reaction!")

    clearcoords, suppressH = False, False
    oedepict.OEPrepareDepiction(mol, clearcoords, suppressH)

    width, height = oedepict.OEGetImageWidth(itf), oedepict.OEGetImageHeight(itf)
    opts = oedepict.OE2DMolDisplayOptions(width, height, oedepict.OEScale_AutoScale)
    oedepict.OESetup2DMolDisplayOptions(opts, itf)

    disp = oedepict.OE2DMolDisplay(mol, opts)
    oedepict.OERenderMolecule(ofs, ext, disp)

    return 0


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

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

!CATEGORY "input/output options :"

    !PARAMETER -in
      !ALIAS -i
      !TYPE string
      !REQUIRED true
      !KEYLESS 1
      !VISIBILITY simple
      !BRIEF Input filename
    !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

• MDL Reaction Depiction chapter

• OEConfigureImageOptions function

• OEConfigure2DMolDisplayOptions function

• OEIsRegisteredImageFile function

• OEReadMDLReactionQueryFile function

• OEPrepareDepiction function

• OEGetImageWidth and OEGetImageHeight functions

• OE2DMolDisplayOptions class

• OESetup2DMolDisplayOptions function

• OE2DMolDisplay class

• OERenderMolecule function

Examples

prompt> python mdlreaction2img.py -in mdlreaction.sdf -out image.png

will generate the following image: Figure: Example of depicting an MDL reaction

Example of depicting an MDL reaction

prompt> python mdlreaction2img.py -in mdlreaction.sdf -out image.png -atomprop MapIdx

will generate the following image: Figure: Example of depicting an MDL reaction with atom map indices

Example of depicting an MDL reaction with atom map indices

See also

• MDL Reaction Depiction chapter