Generating 2D coordinates

A program that assigns 2D coordinates to molecule(s).

Command Line Interface

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

prompt> python depict.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

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

Code

Download code

depict.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
#############################################################################

import sys
from openeye import oechem
from openeye import oedepict


def main(argv=[__name__]):

    itf = oechem.OEInterface(InterfaceData)
    oedepict.OEConfigurePrepareDepictionOptions(itf,
                                                oedepict.OEPrepareDepictionSetup_SuppressHydrogens |
                                                oedepict.OEPrepareDepictionSetup_DepictOrientation)

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

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

    ofs = oechem.oemolostream(".sdf")
    if itf.HasString("-out"):
        oname = itf.GetString("-out")
        if not ofs.open(oname):
            oechem.OEThrow.Fatal("Cannot open output file!")
        if not oechem.OEIs2DFormat(ofs.GetFormat()):
            oechem.OEThrow.Fatal("Invalid output format for 2D coordinates")

    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)
    popts.SetClearCoords(True)

    for mol in ifs.GetOEGraphMols():
        oedepict.OEPrepareDepiction(mol, popts)
        oechem.OEWriteMolecule(ofs, mol)

    return 0


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

InterfaceData = """
!BRIEF [-in] <input> [-out] <output> [-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 false
    !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

• OEConfigurePrepareDepictionOptions function

• OEIs2DFormat function

• OEPrepareDepictionOptions class

• OESetupPrepareDepictionOptions function

• OEPrepareDepiction function

Example

prompt> python depict.py .ism .mol

C(=O)N

will generate the following output:

  -OEChem-07031123462D

  3  2  0     0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5000   -0.8660    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
M  END

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.