OEChem Examples

The following table lists the currently available OEChem TK 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

molchunk

split molecule file into N chunks or chunks of size N

Reactions

Program

Description

unimolrxn

performing a reaction

libgen

generating a library

Molecule searching

Program

Description

molgrep

performing substructure search

makefastss

generating database for fast substructure search

searchfastss

performing search on substructure database file

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

3D Molecule Styling examples

Program

Description

basicStyle

applies a basic OE3DMolStyle to molecules

bFactorStyle

applies an OE3DMolStyle that focuses on B-Factor to molecules

styleHierarchy

applies multiple OE3DMolStyles to molecules, displaying the hierarchy between different OE3DMolStyles applied to the molecule, conformers, and atoms

Miscellaneous examples

Program

Description

oecheminfo

printing OEChem and format information

anisou

printing anisotropic B-factors

dots

printing dots

options

defining parameters

Examples