Open Babel: An open chemical toolbox

Open Babel: An open chemical toolbox Noel M. O’Boyle Michael Banck Craig A. James Chris Morley Tim Vandermeersch Geoffrey Hutchison

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Open Babel: An open chemical toolbox 2011 Journal of Cheminformatics 10.1186/1758-2946-3-33 o-boyle2011-open-babel-an-open-chemical-toolbo o-boyle2011-open-babel-an-open-chemical-toolbo.txt, the project's staged copy a1b4a7260041030a9eae734d6cdd159895fb1086 cc-by chemistry

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0 spans located by searching the stored text for the quote's exact words, allowing any whitespace between them the interconversion of chemical structures between file formats, and the 111 formats Open Babel implements Quotation withheld because this record is not cleared for redistribution. how a single toolkit can read and write the many incompatible representations of molecular data Quotation withheld because this record is not cleared for redistribution. Open Babel itself, described for the first time, with a round-trip validation taking the error rate from 8% to 0.01% Quotation withheld because this record is not cleared for redistribution. method Quotation withheld because this record is not cleared for redistribution. the proliferation of incompatible chemical file formats, which a standard failed to resolve Quotation withheld because this record is not cleared for redistribution. system-or-tool-building system-or-tool-building Quotation withheld because this record is not cleared for redistribution. mechanisms BOND CONNECTIVITY FROM GEOMETRY ALONE: atoms closer than the sum of their covalent radii plus 0.45 angstrom are bonded, which is what lets formats that store no bonding at all be read as molecules Quotation withheld because this record is not cleared for redistribution. mechanisms AROMATICITY IS WITHHELD UNLESS A KEKULE PATTERN EXISTS: the ring is only called aromatic when a well-defined valence-bond assignment can be found, so the label is earned by a construction rather than asserted from ring membership Quotation withheld because this record is not cleared for redistribution. mechanisms AN EXPONENTIAL SEARCH WITH A DELIBERATE GIVE-UP: kekulisation terminates at 30 levels of recursion or 15 seconds, so a large fused ring system returns no answer rather than hanging Quotation withheld because this record is not cleared for redistribution. mechanisms SUBSTRUCTURE SEARCH BY HASHED BIT-STRING: every linear and ring substructure of length 1 to 7 is mapped onto 1024 bits, so a query's bits must all be set in any target that contains it Quotation withheld because this record is not cleared for redistribution. TWO round-trip failures remain at 0.01%, and the paper names both: a kekulisation error in a polycyclic aromatic with heteroatoms, and a bridgehead-carbon stereochemistry case Quotation withheld because this record is not cleared for redistribution. Molecules outside the pharmaceutical mainstream - radicals, organometallics, inorganics, coordinate and 3-center 2-electron bonds - are stated to be poorly supported, and not only by this toolkit Quotation withheld because this record is not cleared for redistribution. Kekulisation is exponential and is CUT OFF at 30 levels of recursion or 15 seconds, so large fused ring systems are a known non-answer Quotation withheld because this record is not cleared for redistribution. The standard that was meant to remove the problem did not take: CML exists and is not widely used, which is the premise the whole toolkit rests on Quotation withheld because this record is not cleared for redistribution. a round-trip over 18,084 PubChem3D structures: SDF to SMILES to canonical SMILES, compared against SDF straight to canonical SMILES eliminates: errors anywhere in reading SDF, reading and writing SMILES, and canonicalisation - by making two routes to the same answer disagree · outcome (stated by the tagger, no quotation): held Quotation withheld because this record is not cleared for redistribution. a nightly test suite of 60 programs, each with tens to hundreds of tests eliminates: regressions between releases · outcome (stated by the tagger, no quotation): held Quotation withheld because this record is not cleared for redistribution. Open Babel Open Babel Quotation withheld because this record is not cleared for redistribution. interconversion interconversion Quotation withheld because this record is not cleared for redistribution. Chemical Markup Language Chemical Markup Language Quotation withheld because this record is not cleared for redistribution. canonical representation canonical representation Quotation withheld because this record is not cleared for redistribution. canonical numbering canonical numbering Quotation withheld because this record is not cleared for redistribution. canonicalization canonicalization Quotation withheld because this record is not cleared for redistribution. kekulization kekulization Quotation withheld because this record is not cleared for redistribution. stereochemistry stereochemistry Quotation withheld because this record is not cleared for redistribution. aromaticity aromaticity Quotation withheld because this record is not cleared for redistribution. covalent radii covalent radii Quotation withheld because this record is not cleared for redistribution. Tanimoto coefficient Tanimoto coefficient Quotation withheld because this record is not cleared for redistribution. substructures substructures Quotation withheld because this record is not cleared for redistribution. structural similarity structural similarity Quotation withheld because this record is not cleared for redistribution. XML dialect XML dialect Quotation withheld because this record is not cleared for redistribution. SMILES SMILES Quotation withheld because this record is not cleared for redistribution. test suite test suite Quotation withheld because this record is not cleared for redistribution. OELib OELib Quotation withheld because this record is not cleared for redistribution. OEChem OEChem Quotation withheld because this record is not cleared for redistribution. file formats file formats Quotation withheld because this record is not cleared for redistribution. canonical representation - A CHOICE, NOT A FACT ABOUT THE MOLECULE: the same structure has N! orderings that encode exactly the same information, and canonicalisation picks one so it can be used as a database key Quotation withheld because this record is not cleared for redistribution. failure - IN THIS PAPER A ROUND-TRIP DISAGREEMENT, not a wrong answer: two routes to the same canonical SMILES are compared against each other, and the second of the two residual failures is a case where BOTH strings are correct and the algorithm merely failed to choose Quotation withheld because this record is not cleared for redistribution. Chemical Markup Language —is-a→ XML dialect Chemical Markup Language XML dialect strength of the relation: 1 Quotation withheld because this record is not cleared for redistribution. structural similarity —operationalised-as→ Tanimoto coefficient structural similarity Tanimoto coefficient strength of the relation: 1 Quotation withheld because this record is not cleared for redistribution.

The full text of this article is not redistributable, so it is not included here. The evidence sentences are withheld with it; the tag layer and its grounding status remain. The article itself is at https://doi.org/10.1186/1758-2946-3-33.