Print simple molecule information
A program that prints some simple molecule information for a database of molecules. This includes the title, molecular weight, number of atoms, number of heavy atoms, number of ring atoms, number of rotors and number of conformers.
Example
prompt> molstats.py input.oeb.gz
Code
Download code
#!/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.
#############################################################################
# Output some basic molecule properties
#############################################################################
import sys
from openeye import oechem
def main(argv=[__name__]):
if len(argv) != 2:
oechem.OEThrow.Usage("%s <infile>" % argv[0])
ifs = oechem.oemolistream()
if not ifs.open(argv[1]):
oechem.OEThrow.Fatal("Unable to open %s for reading" % argv[1])
print("Title MolWt NumAtoms NumHeavyAtoms NumRingAtoms NumRotors NumConfs")
for mol in ifs.GetOEMols():
title = mol.GetTitle()
if not title:
title = "Untitled"
print("%s %.3f %d %d %d %d %d" % (title,
oechem.OECalculateMolecularWeight(mol),
mol.NumAtoms(),
oechem.OECount(mol, oechem.OEIsHeavy()),
oechem.OECount(mol, oechem.OEAtomIsInRing()),
oechem.OECount(mol, oechem.OEIsRotor()),
mol.NumConfs()))
if __name__ == "__main__":
sys.exit(main(sys.argv))
See also
OEIsHeavy functor
OEIsRotor functor
OECalculateMolecularWeightfunction