Creating mmcif file from an input DU

This example shows how to write an output mmcif file from a spruce generated design unit.

Command Line Interface

This example uses an input design unit (oedu) file, and will output a mmcif file from it to a temporary directory (see OEMakeDesignUnits for details on the API).

prompt> du2mmcif <input design unit>

Code

Download code

du2mmcif.py and both the 1TQN_A__DU__HEM_A-508.oedu (the input design unit),

#!/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.


import sys
import os
from openeye import oechem
from openeye import oegrid
from openeye import oespruce


def main(argv=sys.argv):
    if len(argv) > 2:
        oechem.OEThrow.Usage("%s <infile>" % argv[0])
    ifs = oechem.oemolistream()
    ifile = argv[1]
    ofile = os.path.basename(ifile)[:-5] + ".cif"

    ofs = oechem.oemolostream(ofile)
    ofs.SetFlavor(oechem.OEFormat_MMCIF, oechem.OEOFlavor_MMCIF_Default)   

    du = oechem.OEDesignUnit() 
    if not oechem.OEReadDesignUnit(ifile, du):
        oechem.OEThrow.Fatal("Cannot read design unit!")
    complex = oechem.OEGraphMol()
    du.GetComponents(complex, oechem.OEDesignUnitComponents_All ^ oechem.OEDesignUnitComponents_PackingResidues)
    du.GetPDBMetaData(complex)
    oechem.OEWriteMolecule(ofs, complex)
    ofs.close()

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

Example

prompt> du2mmcif.py 1TQN_A__DU__HEM_A-508.oedu