OEChem Examples

The following table lists the currently available OEChem examples:

Molecule processing

Program Description
convert converting molecule files
catmols concatenating molecules
parts2mols splitting multicomponent molecules
molextract extracting molecules by title
uniqmol writing out unique molecules (canonical SMILES)
uniqinchi writing out unique molecules (InChI)
randomizeatoms randomizing atoms of molecules
cansmi generating canonical smiles
sizefilter filtering molecules by weight or heavy atom count
stripsalts stripping salt
ringsubset extracting rings
extractscaffold extracting molecule scaffolds
randomsample extracting random molecule subset

Reactions

Program Description
unimolrxn performing a reaction
libgen generating a library

Molecule searching

Program Description
molgrep performing substructure search

Molecule alignment

Program Description
mcs3dalign aligning molecules by maximum common substructure
cliquealign aligning molecules by clique match
smartsalign aligning molecules by SMARTS match
rmsd aligning multi-conformer molecules

SDF specific

Program Description
sdfmodprops modifying SD tags
sdf2csv exporting SD data to a csv file
csv2sdf adding csv data as SD tags
sdfrename renaming molecules by SD field
sdfilter filter molecules by SD data

Molecule information examples

Program Description
molcount counting molecules
gettitles getting molecule titles
molstats printing simple molecule information
rotorcount printing rotor count distribution
minpath finding minimum path in a molecule
printatomnames print molecule atom names

2D coordinate generation examples

Program Description
extractringtemplates extracting 2D ring templates
createringdict creating 2D ring dictionary
appendringdict appending 2D ring dictionary
generate2D generating 2D coordinates