rdkit-orig
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rdkit
Older clone of the RDKit subversion repository at http://sourceforge.net/projects/rdkit/
the true negative rate calculated by scoring.py's ROC calculation is in fact the false positive rate.
Thread here: http://www.mail-archive.com/[email protected]/msg02934.html ``` In [2]: mol1 = Chem.MolFromSmiles("Fc1ccc(cc1)[C@@]3(OCc2cc(C#N)ccc23)CCCN(C)C") In [3]: mol2 = Chem.MolFromSmiles("Fc1ccc(cc1)[C@]3(OCc2cc(C#N)ccc23)CCCN(C)C") In [4]: from rdkit.Chem import MCS In [6]: MCS.FindMCS((mol1,mol2)) Out[6]: MCSResult(numAtoms=24, numBonds=26, smarts='[F]-[#6]:1:[#6]:[#6]:[#6](-[#6]-2(-[#6]-[#6]-[#6]-[#7](-[#6])-[#6])-[#8]-[#6]-[#6]:3:[#6]:[#6](:[#6]:[#6]:[#6]:3-2)-[#6]#[#7]):[#6]:[#6]:1', completed=1) ```
SDFs provided by the PDB (Protein Data Bank) have a slightly different format than what RDKit is expecting. Example file that would fail with the old code http://www.rcsb.org/pdb/download/downloadLigandFiles.do?ligandIdList=XK2&structIdList=1HVR&instanceType=all&excludeUnobserved=false&includeHydrogens=false The old...
The way things are currently broken with "make clean" should be fixed.
Easy enough to copy in from ROMol.i
Reported by Sabrina Syeda. Thread here: http://www.mail-archive.com/[email protected]/msg03080.html ``` python >>rxn = AllChem.ReactionFromSmarts('[CX4:4][CH1:3]=[CH1:2][CX4:5].[Br:1]>>[C:5][C:2]=[C:3][C:4][Br:1]') >>rxn.Initialize() >>r = [Chem.MolFromSmiles('CCC\C=C\C(C)C'), Chem.MolFromSmiles('Br')] >>ps = rxn.RunReactants(tuple(r)) >> for p in ps: ...: for m in p:...
reported by Jan Holst Jensen ``` > For example: InChI strings generated for spiro.mol (spiro.mol - attached): > > IUPAC: > InChI=1S/2C9H14Cl2/c2*1-7(10)3-9(4-7)5-8(2,11)6-9/h2*3-6H2,1-2H3/t2*7-,8-,9-/m10/s1 > RDKit: InChI=1S/2C9H14Cl2/c2*1-7(10)3-9(4-7)5-8(2,11)6-9/h2*3-6H2,1-2H3 This one still doesn't recognize...
Request from Roger Sayle. Idea is to remove all atoms, bonds, and properties.
The hard bits are already there in $RDBASE/rdkit/Chem/ChemUtils/TemplateExpand.py, it just needs a more user-friendly API and an example or two. This would be a good one from the cookbook based...
Not calling the `flush` method of an `SDWriter` initialized on a file object may produce an unhandled exception and terminate the interpreter: ``` python In [7]: with open('xyz.sdf', 'w') as...
