Molecular Property Table

The OEFilter object allows for the calculation of all the molecular properties it uses during the filtering process without actually applying the filter. This may be useful for caching the OEFilter object results into a database. The OEFilter.SetTable method can be used to specify where to write a tab-delimited table of every property in the associated filter file. This example demonstrates how to write the tabular output to standard out.

Note

A tab-delimited file format was chosen to integrate better with Unix commandline utilities. For example, this allows for quick and easy filter experimentation with the awk command line utility. The following snippet will print the number of molecules (plus one for the header) with a molecular weight greater than 200.

> python molproptable.py -in drugs.sdf -filtertype Lead > drugs.txt
> cat drugs.txt | awk -F\t '{if ($12 > 200) { print $12 }}' | wc -l

Furthermore, all database programs have utilities for importing tab-delimited files. Loading the filter results into a third-party database would provide very speedy filter experimentation since the properties would only have to be calculated once and then cached in the database.

Command Line Interface

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

prompt> python molproptable.py --help

will generate the following output:

Simple parameter list
 filter options :
   -filtertype : filter type

 input/output options :
   -in : Input filename

 other options :
   -verbose : Error level of messages

Code

Download code

molproptable.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
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# subject to these terms. Cadence claims no rights to Customer's
# modifications. Modification of Sample Code is at Customer's sole and
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# 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.

#############################################################################
#  Generate a tabular output of molecular properties
#############################################################################
import sys
from openeye import oechem
from openeye import oemolprop


def main(argv=[__name__]):
    itf = oechem.OEInterface(InterfaceData)
    oemolprop.OEConfigureFilterParams(itf)

    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!")

    ftype = oemolprop.OEGetFilterType(itf)
    filt = oemolprop.OEFilter(ftype)

    ver = itf.GetInt("-verbose")
    oechem.OEThrow.SetLevel(ver)

    pwnd = False
    filt.SetTable(oechem.oeout, pwnd)

    for mol in ifs.GetOEGraphMols():
        filt(mol)


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

InterfaceData = '''
!BRIEF [-in] <input> [-verbose] <verbose>

!CATEGORY "input/output options :"

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

!END

!CATEGORY "other options :"

    !PARAMETER -verbose
    !TYPE int
    !REQUIRED false
    !LEGAL_RANGE 2 5
    !DEFAULT 4
    !VISIBILITY simple
    !BRIEF Error level of messages
    !DETAIL
        2 is Verbose
        3 is Info
        4 is Warning
        5 is Error
  !END

!END
'''

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

Examples

prompt> python molpropsdtable.py -in drugs.sdf -filtertype Lead