inchi¶
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createInChIStruct
(mets, sdfFileName)[source]¶ Converts metabolite structures in SDF to InChI strings with OpenBabel, and maps InChIs to mets.
Usage
inchiStruct = createInChIStruct(mets, sdfFileName)Inputs
- mets – m x 1 cell array of metabolite identifiers (e.g., BiGG abbreviations).
- sdfFileName – SDF with structures of metabolites in mets. Metabolite identifiers in the SDF are assumed to be the same as in mets.
Output
- inchiStruct –
Structure with following fields:
- .standard - Standard InChIs with no isotope, stereo or charge layers.
- .standardWithStereo - Standard InChIs with stereo layers.
- .standardWithStereoAndCharge - Standard InChIs with stereo and charge layers
- .nonstandard - Nonstandard InChI with all layers.
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sdf2inchi
(sdfFileName, options)[source]¶ Converts metabolite structures in an SDF to a cell array of InChI strings with OpenBabel.
Usage
[inchi, metList] = sdf2inchi(sdfFileName, options)Input
- sdfFileName – Path to SDF file.
Optional input
- options – Write options for InChI strings. See InChI documentation for details. If no options are specified the function will output standard InChI.
Outputs
- inchi – Cell array of InChI strings for metabolites in the SDF file.
- metList – Cell array of metabolite identifiers (first line of each molfile in SDF). Will be empty unless write option t is used (i.e., options >= ‘-xt’).