Intro to OEChem
Intro to OEChem
Intro to OEChem
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<strong>Intro</strong> <strong>to</strong> <strong>OEChem</strong><br />
product revue session<br />
Jeremy Yang<br />
CUP VIII, Feb 26-28, 2007
What is <strong>OEChem</strong>?<br />
• Programming <strong>to</strong>olkit for chemoinformatics<br />
• For molecular modelling and general use<br />
• Small and macromolecules<br />
• Well defined, supported and documented API<br />
• Foundation of higher level OE <strong>to</strong>olkits<br />
• Foundation of OE applications<br />
CUP VIII, Feb 26-28, 2007
Languages and platforms<br />
• Native C++ API<br />
• Python API (wrapper)<br />
• Java API (wrapper)<br />
CUP VIII, Feb 26-28, 2007
Documentation and references<br />
• <strong>OEChem</strong> { C++ | Python | Java } Theory<br />
manual<br />
• <strong>OEChem</strong> API manual<br />
• Example code<br />
– $OE_DIR/examples/oechem/<br />
– $OE_DIR/examples/oechem/docs-examples/<br />
– $OE_DIR/utilities/oechem/<br />
– $OE_DIR/wrappers/python/examples/<br />
– $OE_DIR/wrappers/python/doc-examples/<br />
• http://demo.eyesopen.com<br />
CUP VIII, Feb 26-28, 2007
Some key features<br />
• Multiconformer molecules<br />
• File format fluency and rigor<br />
• Smarts searching and beyond<br />
• MCSS<br />
• Smirks reaction processing<br />
• PDB expertise<br />
• Macromolecules<br />
• Professional, supported API<br />
CUP VIII, Feb 26-28, 2007
Example: mol2parts.py<br />
ims = oemolistream("1A00.pdb")<br />
oms = oemolostream("parts.sdf")<br />
partmol = OEGraphMol()<br />
for mol in ims.GetOEGraphMols():<br />
i,partlist = OEDetermineComponents(mol)<br />
pred = OEPartPredA<strong>to</strong>m(partlist)<br />
for j in range(1,i+1):<br />
pred.SelectPart(j)<br />
OESubsetMol(partmol,mol,pred)<br />
OEWriteMolecule(oms,partmol)<br />
CUP VIII, Feb 26-28, 2007
<strong>Intro</strong> <strong>to</strong> <strong>OEChem</strong>, Part 2:<br />
Practical examples, use cases<br />
CUP VIII, Feb 26-28, 2007
Reading and writing molecules<br />
• Formats<br />
• Format variants, OEFlavors<br />
• Multiconformer vs. single conf<br />
• Aromaticity, H-counts, valence models<br />
• Canonicalization<br />
• Interconversion of inconsistent formats<br />
• OEBinary<br />
• Error handling<br />
• See: convert.cpp, babel2.cpp, convert.py,<br />
convert webapp, Babel3 2.0<br />
CUP VIII, Feb 26-28, 2007
Fixing/standardizing molecules<br />
• C(=O)[OH] -> C(=O)[O-] , etc.<br />
• See:<br />
– fixmols.py<br />
– valencemodels.py<br />
– aromodels.cpp<br />
– aromatest.py<br />
– react.cpp, react.py<br />
– Filter 2.0.1<br />
CUP VIII, Feb 26-28, 2007
Analyzing molecules<br />
• rings<br />
• rotatable bonds<br />
• a<strong>to</strong>m types<br />
• stereo centers<br />
• polar hydrogens<br />
• aromaticity<br />
• hybridization<br />
• symmetry<br />
• See:<br />
– rings.py, rings.cpp<br />
– molanalyze.py<br />
– screen.py<br />
– molanalyze web app<br />
CUP VIII, Feb 26-28, 2007
Substructure searching<br />
• smarts matching<br />
• OEQMol matching<br />
• a<strong>to</strong>m and bond expressions<br />
• mol state dependence (arom/kek, H’s, etc.)<br />
• unique-a<strong>to</strong>mset and symmetric matching<br />
• See:<br />
– match.cpp, match.py<br />
– depict web app<br />
CUP VIII, Feb 26-28, 2007
MCSS - max common substructs<br />
• OE algorithm - “space state search”<br />
• OEMCSFuncs<br />
• a<strong>to</strong>m and bond expressions<br />
• mol state dependence (arom/kek, H’s, etc.)<br />
• ring issues<br />
• See:<br />
– mcss.cpp, mcss.py<br />
– molalign.py<br />
– mcss web app<br />
CUP VIII, Feb 26-28, 2007
3D handling and analysis<br />
• Measurement:<br />
length, angles,<br />
<strong>to</strong>rsions<br />
• Rotation and<br />
translation<br />
• Euler and Quaternion<br />
operations<br />
• RMSD<br />
• See:<br />
– rmsd.cpp, rmsd.py<br />
– rmsd_selftest.cpp<br />
– molgeom.cpp,<br />
molgeom.py<br />
– setro<strong>to</strong>r.py<br />
– add3dhyd.cpp<br />
– movemol.cpp<br />
– molalign.py<br />
– rmsd webapp<br />
CUP VIII, Feb 26-28, 2007
Macromolecules<br />
• residue perception<br />
• bond perception<br />
• ligand extraction<br />
• new in 1.4: OEBio<br />
• See:<br />
– pdb2lig.cpp, pdb2lig.py<br />
– resanalyze.py<br />
– bindanalyze.py<br />
– proteinalyze webapp<br />
CUP VIII, Feb 26-28, 2007
Combina<strong>to</strong>rics<br />
• building mols from fragments<br />
• fragmentation<br />
• ampersand notation smiles<br />
• enumerating stereoisomers<br />
• See:<br />
– frankenmol.py<br />
– frag.py<br />
– react.cpp,react.py<br />
– flipper.cpp,flipper.py<br />
CUP VIII, Feb 26-28, 2007
Canonicalization<br />
• canonical smiles<br />
• canonical Kekule smiles<br />
• canonical isomeric smiles<br />
• canonical fragment smiles<br />
• other canonical smiles<br />
• canonical molfiles<br />
• general canonicalization<br />
• See:<br />
– cansmi.py<br />
– canmol.py<br />
– canmol web app<br />
– tau<strong>to</strong>mers<br />
program<br />
CUP VIII, Feb 26-28, 2007
Non-structural data<br />
• SD data<br />
• generic data<br />
• OEBinary<br />
• bit vec<strong>to</strong>rs<br />
• See<br />
– rename.py<br />
– sdf2csv.py<br />
– bitvectest.cpp<br />
CUP VIII, Feb 26-28, 2007
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