Append 2D ring dictionary

A program that adds new ring layouts to a ring dictionary that can be plugged into the 2D coordinates generation system.

Note

If a ring template already exists in the dictionary then the new template will be ignored i.e. currently ring templates can not be overwritten in the OE2DRingDictionary object.

Code

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appendringdict.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.

#############################################################################
# Appends rings to an existing 2D rings dictionary
#############################################################################

import sys
from openeye import oechem


def main(argv=[__name__]):

    itf = oechem.OEInterface(InterfaceData, argv)

    ifname = itf.GetString("-in")
    irdfname = itf.GetString("-inringdict")
    ordfname = itf.GetString("-outringdict")

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

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

    if not oechem.OEIsValid2DRingDictionary(irdfname):
        oechem.OEThrow.Fatal("Invalid ring dirctinary file!")

    ringdict = oechem.OE2DRingDictionary(irdfname)

    nrrings = ringdict.NumRings()

    dots = oechem.OEDots(10000, 100, "molecules")

    for mol in ifs.GetOEGraphMols():
        dots.Update()
        ringdict.AddRings(mol)

    dots.Total()

    nrnewrings = ringdict.NumRings() - nrrings
    oechem.OEThrow.Info("%d new ring templates have been added!" % nrnewrings)

    oechem.OEWrite2DRingDictionary(ordfname, ringdict)

    return 0


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

InterfaceData = """
!BRIEF [-in] <input> [-inringdict] <input ringdict> [-outringdict] <output ringdict>

!CATEGORY "input/output options :"

  !PARAMETER -in
    !ALIAS -i
    !TYPE string
    !REQUIRED true
    !KEYLESS 1
    !VISIBILITY simple
    !BRIEF Input 2D molecule filename
  !END

  !PARAMETER -inringdict
    !ALIAS -ird
    !TYPE string
    !REQUIRED true
    !KEYLESS 2
    !VISIBILITY simple
    !BRIEF Input ring dictionary OEB filename
    !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

  !PARAMETER -outringdict
    !ALIAS -ord
    !TYPE string
    !REQUIRED true
    !KEYLESS 3
    !VISIBILITY simple
    !BRIEF Output ring dictionary OEB filename
  !END

!END
"""


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