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

• Convert molecule files
• Concatenating molecules
• Splitting multicomponent molecules
• Extract molecules by title
• Write out unique molecules (canonical SMILES)
• Write out unique molecules (InChI)
• Randomize atoms of molecules
• Generate canonical smiles
• Filter molecules by weight or heavy atom count
• Strip salts
• Extract rings
• Extract molecule scaffolds
• Extract random molecule subset
• Split molecule file
• Performing a reaction
• Library generation
• Perform substructure searches
• Generate database for fast substructure search
• Perform SMARTS search on substructure database file
• Align molecules by maximum common substructure
• Align molecules by clique match
• Align molecules by SMARTS match
• Align multi-conformer molecules
• Modifying SD tags
• Exporting SD data to a csv file
• Adding csv data as SD tags
• Renaming molecules by SD field
• Filter molecules by SD data
• Print OEChem and file format information
• Counting molecules
• Get molecule titles
• Print simple molecule information
• Print rotor count distribution
• Find minimum path in a molecule
• Print molecule atom names
• Extract 2D ring templates
• Create 2D ring dictionary
• Append 2D ring dictionary
• Generate 2D coordinates with user-defined ring templates
• Print anisotropic B-factors
• Print dots
• Define parameters
• Basic example of setting up an OE3DMolStyle on a molecule
• OE3DMolStyle focused on B-Factor styling
• OE3DMolStyle hierarchy between molecule, conformers, and atoms