std::string expandSuperatoms(const Settings& vars, const Molecule &molecule ) { logEnterFunction(); std::string molString; ArrayOutput so(molString); MolfileSaver ma(so); ma.saveMolecule(vars, molecule); if (!vars.general.ExpandAbbreviations) return molString; indigoSetOption("treat-x-as-pseudoatom", "true"); indigoSetOption("ignore-stereochemistry-errors", "true"); int mol = indigoLoadMoleculeFromString(molString.c_str()); if (mol == -1) { fprintf(stderr, "%s\n", indigoGetLastError()); return molString; } int expCount = indigoExpandAbbreviations(mol); if (expCount == -1) { fprintf(stderr, "%s\n", indigoGetLastError()); return molString; } std::string newMolfile = indigoMolfile(mol); indigoFree(mol); return newMolfile; }
int main (int argc, char *argv[]) { Params p; int obj = -1, reader = -1, writer = -1; int i = 0; char number[100]; char outfilename[4096]; const char *id; p.width = p.height = p.bond = p.mode = -1; p.id = p.string_to_load = p.file_to_load = NULL; p.hydro_set = p.query_set = p.smarts_set = 0; p.aromatization = NONE; p.comment_field = NULL; p.comment = NULL; p.comment_name = 0; if (argc <= 2) USAGE(); indigoSetErrorHandler(onError, 0); indigoSetOption("ignore-stereochemistry-errors", "on"); if (parseParams(&p, argc, argv) < 0) return -1; p.out_ext = OEXT_OTHER; if (strcmp(p.outfile_ext, "mol") == 0) p.out_ext = OEXT_MOL; else if (strcmp(p.outfile_ext, "sdf") == 0) p.out_ext = OEXT_SDF; else if (strcmp(p.outfile_ext, "rxn") == 0) p.out_ext = OEXT_RXN; else if (strcmp(p.outfile_ext, "rdf") == 0) p.out_ext = OEXT_RDF; else if (strcmp(p.outfile_ext, "cml") == 0) p.out_ext = OEXT_CML; // guess whether to layout or render by extension p.action = ACTION_LAYOUT; if (p.out_ext == OEXT_OTHER) { indigoSetOption("render-output-format", p.outfile_ext); p.action = ACTION_RENDER; } // read in the input reader = (p.file_to_load != NULL) ? indigoReadFile(p.file_to_load) : indigoReadString(p.string_to_load); if (p.mode == MODE_SINGLE_MOLECULE) { if (p.id != NULL) ERROR("on single input, setting '-id' is not allowed\n"); if (p.out_ext == OEXT_RXN) ERROR("reaction output specified for molecule input\n"); if (p.smarts_set) obj = indigoLoadSmarts(reader); else if (p.query_set) obj = indigoLoadQueryMolecule(reader); else obj = indigoLoadMolecule(reader); _prepare(obj, p.aromatization); if (p.action == ACTION_LAYOUT) { indigoLayout(obj); if (p.out_ext == OEXT_MOL) indigoSaveMolfileToFile(obj, p.outfile); else indigoSaveCmlToFile(obj, p.outfile); } else { _setComment(obj, &p); renderToFile(obj, p.outfile); } } else if (p.mode == MODE_SINGLE_REACTION) { if (p.id != NULL) ERROR("on single input, setting '-id' is not allowed\n"); if (p.out_ext == OEXT_MOL) ERROR("molecule output specified for reaction input\n"); if (p.smarts_set) obj = indigoLoadReactionSmarts(reader); else if (p.query_set) obj = indigoLoadQueryReaction(reader); else obj = indigoLoadReaction(reader); _prepare(obj, p.aromatization); if (p.action == ACTION_LAYOUT) { indigoLayout(obj); if (p.out_ext == OEXT_CML) indigoSaveCmlToFile(obj, p.outfile); else indigoSaveRxnfileToFile(obj, p.outfile); } else { _setComment(obj, &p); renderToFile(obj, p.outfile); } } else { int item; int have_percent_s = (strstr(p.outfile, "%s") != NULL); if (p.mode == MODE_MULTILINE_SMILES) obj = indigoIterateSmiles(reader); else if (p.mode == MODE_SDF) obj = indigoIterateSDF(reader); else if (p.mode == MODE_MULTIPLE_CML) obj = indigoIterateCML(reader); else if (p.mode == MODE_RDF) obj = indigoIterateRDF(reader); else { fprintf(stderr, "internal error: wrong branch\n"); return -1; } if ((p.out_ext == OEXT_MOL || p.out_ext == OEXT_RXN || p.out_ext == OEXT_OTHER) && !have_percent_s) ERROR("on multiple output, output file name must have '%%s'\n"); if (p.out_ext == OEXT_SDF || p.out_ext == OEXT_RDF || (p.out_ext == OEXT_CML && !have_percent_s)) { writer = indigoWriteFile(p.outfile); if (p.out_ext == OEXT_RDF) indigoRdfHeader(writer); if (p.out_ext == OEXT_CML) indigoCmlHeader(writer); } i = -1; while ((item = indigoNext(obj))) { int rc; ++i; if (writer > 0) printf("saving item #%d... ", i); else { if (p.id) { if (!indigoHasProperty(item, p.id)) { fprintf(stderr, "item #%d does not have %s, skipping\n", i, p.id); continue; } id = indigoGetProperty(item, p.id); snprintf(outfilename, sizeof(outfilename), p.outfile, id); } else { snprintf(number, sizeof(number), "%d", i); snprintf(outfilename, sizeof(outfilename), p.outfile, number); } printf("saving %s... ", outfilename); } indigoSetErrorHandler(0, 0); if (_prepare(item, p.aromatization) < 0) { printf("%s\n", indigoGetLastError()); indigoSetErrorHandler(onError, 0); continue; } if (p.action == ACTION_LAYOUT) { if (indigoLayout(item) < 0) { printf("%s\n", indigoGetLastError()); indigoSetErrorHandler(onError, 0); continue; } } if (writer > 0) { if (p.out_ext == OEXT_SDF) rc = indigoSdfAppend(writer, item); else if (p.out_ext == OEXT_RDF) rc = indigoRdfAppend(writer, item); else rc = indigoCmlAppend(writer, item); } else { if (p.action == ACTION_LAYOUT) { if (p.out_ext == OEXT_MOL) rc = indigoSaveMolfileToFile(item, outfilename); else if (p.out_ext == OEXT_RXN) rc = indigoSaveRxnfileToFile(item, outfilename); else ERROR("extension unexpected"); } else { _setComment(item, &p); rc = indigoRenderToFile(item, outfilename); } } if (rc < 0) { printf("%s\n", indigoGetLastError()); indigoSetErrorHandler(onError, 0); continue; } indigoFree(item); indigoSetErrorHandler(onError, 0); printf("\n"); } if (writer > 0) { if (p.out_ext == OEXT_CML) indigoCmlFooter(writer); indigoFree(writer); } } indigoFree(reader); indigoFree(obj); return 0; }