Generate 2D coordinates with user-defined ring templates

A program that generates 2D coordinates with user-defined ring layouts.
Code

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generate2D.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.

#############################################################################
# Generates 2D coordinates using user-defined ring templates
#############################################################################

import sys
from openeye import oechem


def main(argv=[__name__]):

    itf = oechem.OEInterface(InterfaceData, argv)

    ifname = itf.GetString("-in")
    ofname = itf.GetString("-out")

    ifs = oechem.oemolistream()
    if not ifs.open(ifname):
        oechem.OEThrow.Fatal("Unable to open %s for reading!" % ifname)

    ofs = oechem.oemolostream()
    if not ofs.open(ofname):
        oechem.OEThrow.Fatal("Unable to open %s for writing!" % ofname)

    if not oechem.OEIs2DFormat(ofs.GetFormat()):
        oechem.OEThrow.Fatal("Invalid output file format for 2D coordinates!")

    if itf.HasString("-ringdict"):
        rdfname = itf.GetString("-ringdict")

        if not oechem.OEIsValid2DRingDictionary(rdfname):
            oechem.OEThrow.Warning("Invalid 2D ring dictionary file!")
        else:
            oechem.OEInit2DRingDictionary(rdfname)

    for mol in ifs.GetOEGraphMols():
        oechem.OEGenerate2DCoordinates(mol)
        oechem.OEWriteMolecule(ofs, mol)

    return 0


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

InterfaceData = """
!BRIEF [-in] <input> [-out] <output> [-ringdict] <ringdict 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 Ring dictionary file
    !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))