MolFromSmiles seems to consume all available memory (and beyond) with certain Smiles strings when sanitize is set to True (the default). This also affects the postgresql cartridge. I am using version 2012_06_1.
Below is an example: #!/usr/bin/env python """ example of rdkit consuming infinite amount of memory Pubchem compound CID 57383442 http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=57383442 """ from rdkit import Chem smi = 'CCCOc1c2CNC(=O)c3cc(cc(c3)C(=O)NCc3cc4cc(CNC(=O)c5cc(C(=O)NCc1cc(c2)c1cc2CNC(=O)c6cc(cc(c6)C(=O)NCc6cc4cc(CNC(=O)c4cc(C(=O)NCc(c1)c2OCCC)cc(c4)C(=O)NC(COCCC(=O)O)(COCCC(=O)O)COCCC(=O)O)c6OCCC)C(=O)NC(COCCC(=O)O)(COCCC(=O)O)COCCC(=O)O)cc(c5)C(=O)NC(COCCC(=O)O)(COCCC(=O)O)COCCC(=O)O)c3OCCC)C(=O)NC(COCCC(=O)O)(COCCC(=O)O)COCCC(=O)O' print "Calling MolFromSmiles WITHOUT sanitize" m = Chem.MolFromSmiles(smi, sanitize=False ) print "Calling MolFromSmiles WITH sanitize" m = Chem.MolFromSmiles(smi, sanitize=True ) print "It worked?" # end of script
rdkit_bug.py
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