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
applytransform.py	use a SMIRKS specification to perform individual reaction transformations on single molecules
applytransformiter.py	use a SMIRKS specification to perform individual reaction transformations on each input molecule
unimolrxn.py	perform a reaction
libgen.py	generate 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

3D Molecule Styling examples

Program	Description
basicStyle.py	applies a basic OE3DMolStyle to molecules
bFactorStyle.py	applies an OE3DMolStyle that focuses on B-Factor to molecules
styleHierarchy.py	applies multiple OE3DMolStyles to molecules, displaying the hierarchy between different OE3DMolStyles applied to the molecule, conformers, and atoms

Miscellaneous examples

Program	Description
oecheminfo.py	printing OEChem and format information
anisou.py	printing anisotropic B-factors
dots.py	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