Depicting Molecules in Multi-Page

A program that converts molecular structures into a multipage PDF image.

Command Line Interface

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

prompt> python mols2pdf.py --help

will generate the following output:

Simple parameter list
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)

report options :
  -colsperpage : Number of columns per page
  -pageheight : Page height
  -pageorientation : Page orientation
  -pagesize : Page size
  -pagewidth : Page width
  -rowsperpage : Number of rows per page

Code

Download code

mols2pdf.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 molecules into a multi-page PDF document.
#############################################################################

import sys
from openeye import oechem
from openeye import oedepict


def main(argv=[__name__]):

    itf = oechem.OEInterface(InterfaceData)
    oedepict.OEConfigureReportOptions(itf)
    oedepict.OEConfigurePrepareDepictionOptions(itf)
    oedepict.OEConfigure2DMolDisplayOptions(itf)

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

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

    oname = itf.GetString("-out")
    ext = oechem.OEGetFileExtension(oname)
    if ext != "pdf":
        oechem.OEThrow.Fatal("Output must be PDF format.")

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

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

    ropts = oedepict.OEReportOptions()
    oedepict.OESetupReportOptions(ropts, itf)
    ropts.SetFooterHeight(25.0)
    report = oedepict.OEReport(ropts)

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

    dopts = oedepict.OE2DMolDisplayOptions()
    oedepict.OESetup2DMolDisplayOptions(dopts, itf)
    dopts.SetDimensions(report.GetCellWidth(), report.GetCellHeight(), oedepict.OEScale_AutoScale)

    for mol in ifs.GetOEGraphMols():
        cell = report.NewCell()
        oedepict.OEPrepareDepiction(mol, popts)
        disp = oedepict.OE2DMolDisplay(mol, dopts)
        oedepict.OERenderMolecule(cell, disp)

    font = oedepict.OEFont(oedepict.OEFontFamily_Default, oedepict.OEFontStyle_Bold, 12,
                           oedepict.OEAlignment_Center, oechem.OEBlack)
    for pagenum, footer in enumerate(report.GetFooters()):
        text = "Page %d of %d" % (pagenum + 1, report.NumPages())
        oedepict.OEDrawTextToCenter(footer, text, font)

    oedepict.OEWriteReport(ofs, ext, report)

    return 0


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

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