Depicting a Single Molecule

A program that converts a molecular structure 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 mol2img.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
   -ringdict : User-defined 2D ring dictionary

 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

 prepare depiction options :
   -clearcoords : Clear and regenerate 2D coordinates of molecule(s)
   -orientation : Set the preferred orientation of 2D coordinates
   -suppressH : Suppress explicit hydrogens of molecule(s)

Code

Download code

mol2img.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.

#############################################################################
# Converts a molecule structure into an image file.
# The output file format depends on its file extension.
#############################################################################

import sys
from openeye import oechem
from openeye import oedepict


def main(argv=[__name__]):

    itf = oechem.OEInterface(InterfaceData)
    oedepict.OEConfigureImageOptions(itf)
    oedepict.OEConfigurePrepareDepictionOptions(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.OEReadMolecule(ifs, mol):
        oechem.OEThrow.Fatal("Cannot read input file!")

    if itf.HasString("-ringdict"):
        rdfname = itf.GetString("-ringdict")
        if not oechem.OEInit2DRingDictionary(rdfname):
            oechem.OEThrow.Warning("Cannot use user-defined ring dictionary!")

    popts = oedepict.OEPrepareDepictionOptions()
    oedepict.OESetupPrepareDepictionOptions(popts, itf)

    oedepict.OEPrepareDepiction(mol, popts)

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

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

    return 0


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

InterfaceData = """
!BRIEF [-in] <input> [-out] <output image> [-ringdict] <rd file>

!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

  !PARAMETER -ringdict
    !ALIAS -rd
    !TYPE string
    !REQUIRED false
    !VISIBILITY simple
    !BRIEF User-defined 2D ring dictionary
    !DETAIL
        2D ring dictionaries can be generated by the following OEChem examples:
        C++    - createringdict.cpp
        Python - createringdict.py
        Java   - CreateRingDict.java
        C#     - CreateRingDict.cs
    !END

!END
"""

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

See also

• Molecule Depiction chapter

• OEConfigureImageOptions function

• OEConfigurePrepareDepictionOptions function

• OEConfigure2DMolDisplayOptions function

• OEIsRegisteredImageFile function

• OEPrepareDepictionOptions class

• OESetupPrepareDepictionOptions function

• OEPrepareDepiction function

• OEGetImageWidth and OEGetImageHeight functions

• OE2DMolDisplayOptions class

• OESetup2DMolDisplayOptions function

• OE2DMolDisplay class

• OERenderMolecule function

Examples

prompt> python mol2img.py -in nexium.ism -out image.png

will generate the image shown in Figure: Example of using the program with default parameters.

Example of using the program with default parameters

prompt> python mol2img.py -in nexium.ism -out image.png -atomcolor WhiteMonochrome

will generate the image shown in Figure: Example of using the program with the white monochrome atom coloring style.

Example of using the program with the white monochrome atom coloring style

prompt> python mol2img.py -in nexium.ism -out image.png -aromstyle Circle

will generate the image shown in Figure: Example of using the program with aromaticity style ‘Circle’.

Example of using the program with aromaticity style ‘Circle’

prompt> python mol2img.py -in nexium.ism -out image.png -atomstereostyle "AtomStereo|CIPAtomStereo"

will generate the image shown in Figure: Example of the mol2img program with CIP atom stereo option.

Example of using the program with CIP atom stereo option

prompt> python mol2img.py -in nexium.ism -out image.png -linewidth 4

will generate the image shown in Figure: Example of using the program with user-defined line width.

Example of using the program with user-defined line width

prompt> python mol2img.py -in nexium.ism -out image.png -superdisp All

will generate the image shown in Figure: Example of using the program with superatom style.

Example of using the program with superatom style

Note

The above program can generate 2D coordinates with user-defined 2D ring layouts when using the -ringdict parameter.

See also the 2D Coordinate Generation Examples section of the OEChem TK manual that shows examples about how to generate and utilize user-defined ring dictionaries.

See also

• Molecule Depiction chapter