OEChem Examples

The following table lists the currently available OEChem TK examples:

Molecule processing

Program

Description

convert.py

converting molecule files

catmols.py

concatenating molecules

parts2mols.py

splitting multicomponent molecules

molextract.py

extracting molecules by title

uniqmol.py

writing out unique molecules (canonical SMILES)

uniqinchi.py

writing out unique molecules (InChI)

randomizeatoms.py

randomizing atoms of molecules

cansmi.py

generating canonical smiles

sizefilter.py

filtering molecules by weight or heavy atom count

stripsalts.py

stripping salt

ringsubset.py

extracting rings

extractscaffold.py

extracting molecule scaffolds

randomsample.py

extracting random molecule subset

molchunk.py

split molecule file into N chunks or chunks of size N

Reactions

Program

Description

unimolrxn.py

performing a reaction

libgen.py

generating a library

Molecule searching

Program

Description

molgrep.py

performing substructure search

makefastss.py

generating database for fast substructure search

searchfastss.py

performing search on substructure database file

Molecule alignment

Program

Description

mcs3dalign.py

aligning molecules by maximum common substructure

cliquealign.py

aligning molecules by clique match

smartsalign.py

aligning molecules by SMARTS match

rmsd.py

aligning multi-conformer molecules

SDF specific

Program

Description

sdfmodprops.py

modifying SD tags

sdf2csv.py

exporting SD data to a csv file

csv2sdf.py

adding csv data as SD tags

sdfrename.py

renaming molecules by SD field

sdfilter.py

filter molecules by SD data

Molecule information examples

Program

Description

molcount.py

counting molecules

gettitles.py

get molecule titles

molstats.py

printing simple molecule information

rotorcount.py

printing rotor count distribution

minpath.py

finding minimum path in a molecule

printatomnames.py

print molecule atom names

2D coordinate generation examples

Program

Description

extractringtemplates.py

extracting 2D ring templates

createringdict.py

creating 2D ring dictionary

appendringdict.py

appending 2D ring dictionary

generate2D.py

generating 2D coordinates