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; }
void renderMolecule(int structure, const char* folder, const char* file, int number, const char* title) { // render the molecule to file indigoLayout(structure); indigoSetOption("render-output-format", "png"); indigoSetOption("render-comment", title); indigoSetOption("render-comment-position", "top"); indigoSetOptionXY("render-image-size", 400, 500); indigoSetOptionColor("render-background-color", 1.0, 1.0, 1.0); char str[256]; if(number != -1) { sprintf(str, "%s/%d%s%s", folder, number, "_", file); } else if(strcmp(folder,"")!=0) { sprintf(str, "%s/%s", folder, file); } else { sprintf(str, "%s", file); } indigoRenderToFile(structure, str); }
void renderPair(int s1, int s2, const char* folder, const char* file, int number, const char* title) { int collection = indigoCreateArray(); indigoArrayAdd(collection, s1); indigoArrayAdd(collection, s2); indigoSetOption("render-output-format", "png"); indigoSetOption("render-comment", title); indigoSetOption("render-comment-position", "top"); indigoSetOptionXY("render-image-size", 800, 1000); indigoSetOptionColor("render-background-color", 1.0, 1.0, 1.0); char str[256]; if(number != -1) { sprintf(str, "./%s/%d%s%s%s", folder, number, "_", file, ".png"); } else { sprintf(str, "%s%s", file, ".png"); } indigoRenderGridToFile(collection, NULL, 2, str); indigoFree(collection); }
void _setComment (int obj, Params *p) { if (p->comment_name) { const char *name = indigoName(obj); if (name != NULL && *name != 0) { indigoSetOption("render-comment", name); return; } } if (p->comment_field != NULL) { if (indigoHasProperty(obj, p->comment_field)) { const char *prop = indigoGetProperty(obj, p->comment_field); if (prop != NULL && *prop != 0) { indigoSetOption("render-comment", prop); return; } } } if (p->comment != NULL && *p->comment != 0) { indigoSetOption("render-comment", p->comment); return; } }
int performFileAction(bool verbose, imago::Settings& vars, const std::string& imageName, const std::string& configName, const std::string& outputName) { logEnterFunction(); int result = 0; // ok mark imago::VirtualFS vfs; vars.general.StartTime = 0; // reset timelimit if (vars.general.ExtractCharactersOnly) { if (verbose) printf("Characters extraction from image '%s'\n", imageName.c_str()); } else { if (verbose) printf("Recognition of image '%s'\n", imageName.c_str()); } try { imago::Image image; if (vars.general.LogVFSEnabled) { imago::getLogExt().SetVirtualFS(vfs); } imago::ImageUtils::loadImageFromFile(image, imageName.c_str()); if (vars.general.ExtractCharactersOnly) { imago::Image out; imago::prefilterEntrypoint(vars, out, image); applyConfig(verbose, vars, configName); imago::ChemicalStructureRecognizer _csr; _csr.extractCharacters(vars, out); } else { RecognitionResult result = recognizeImage(verbose, vars, image, configName); imago::FileOutput fout(outputName.c_str()); fout.writeString(result.molecule.c_str()); if (imago::getLogExt().loggingEnabled()) { int molObj = indigoLoadMoleculeFromString(result.molecule.c_str()); if (molObj != -1) { indigoSetOption("render-output-format", "png"); indigoSetOption("render-background-color", "255, 255, 255"); std::string outputImg = imago::getLogExt().generateImageName(); indigoRenderToFile(molObj, outputImg.c_str()); imago::getLogExt().appendImageFile("Result image:", outputImg); indigoFree(molObj); } } } } catch (std::exception &e) { result = 2; // error mark puts(e.what()); } dumpVFS(vfs, "log_vfs.txt"); return result; }
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; }
int parseParams (Params* p, int argc, char *argv[]) { int i; if (strcmp(argv[1], "-") == 0) { if (_isReaction(argv[2])) { p->mode = MODE_SINGLE_REACTION; p->string_to_load = argv[2]; } else { p->mode = MODE_SINGLE_MOLECULE; p->string_to_load = argv[2]; } if (argc <= 3) USAGE(); i = 3; } else { p->infile_ext[0] = 0; if (strlen(argv[1]) >= 4 && argv[1][strlen(argv[1]) - 4] == '.') { p->infile_ext[3] = 0; strncpy(p->infile_ext, argv[1] + strlen(argv[1]) - 3, 3); } else if (strlen(argv[1]) > 7 && argv[1][strlen(argv[1]) - 7] == '.') { p->infile_ext[6] = 0; strncpy(p->infile_ext, argv[1] + strlen(argv[1]) - 6, 6); } p->file_to_load = argv[1]; if (strcasecmp(p->infile_ext, "mol") == 0) p->mode = MODE_SINGLE_MOLECULE; else if (strcasecmp(p->infile_ext, "rxn") == 0) p->mode = MODE_SINGLE_REACTION; else if (strcasecmp(p->infile_ext, "smi") == 0) { int reaction; if (_isMultiline(argv[1], &reaction)) p->mode = MODE_MULTILINE_SMILES; else { if (reaction) p->mode = MODE_SINGLE_REACTION; else p->mode = MODE_SINGLE_MOLECULE; } } else if (strcasecmp(p->infile_ext, "cml") == 0) { int reaction; if (_isMultipleCML(argv[1], &reaction)) p->mode = MODE_MULTIPLE_CML; else { if (reaction) p->mode = MODE_SINGLE_REACTION; else p->mode = MODE_SINGLE_MOLECULE; } } else if (strcasecmp(p->infile_ext, "sdf") == 0 || strcasecmp(p->infile_ext, "sdf.gz") == 0) p->mode = MODE_SDF; else if (strcasecmp(p->infile_ext, "rdf") == 0 || strcasecmp(p->infile_ext, "rdf.gz") == 0) p->mode = MODE_RDF; else USAGE(); i = 2; } p->outfile = argv[i++]; if (strlen(p->outfile) < 5 || p->outfile[strlen(p->outfile) - 4] != '.') USAGE(); p->outfile_ext[3] = 0; strncpy(p->outfile_ext, p->outfile + strlen(p->outfile) - 3, 3); indigoSetOptionBool("treat-x-as-pseudoatom", 1); indigoSetOptionBool("render-coloring", 1); indigoSetOptionBool("render-highlight-color-enabled", 1); for (; i < argc; i++) { if (strcmp(argv[i], "-w") == 0) { if (++i == argc) { fprintf(stderr, "expecting number after -w\n"); return -1; } if (sscanf(argv[i], "%d", &p->width) != 1 || p->width <= 0) { fprintf(stderr, "%s is not a valid width\n", argv[i]); return -1; } } else if (strcmp(argv[i], "-h") == 0) { if (++i == argc) { fprintf(stderr, "expecting number after -h\n"); return -1; } if (sscanf(argv[i], "%d", &p->height) != 1 || p->height <= 0) { fprintf(stderr, "%s is not a valid height\n", argv[i]); return -1; } } else if (strcmp(argv[i], "-margins") == 0) { int horz, vert; if (i + 2 >= argc) { fprintf(stderr, "expecting two numbers after -margins\n"); return -1; } if (sscanf(argv[i + 1], "%d", &horz) != 1 || horz < 0) { fprintf(stderr, "%s is not a valid horizontal margin\n", argv[i]); return -1; } if (sscanf(argv[i + 2], "%d", &vert) != 1 || vert < 0) { fprintf(stderr, "%s is not a valid vertical margin\n", argv[i + 1]); return -1; } indigoSetOptionXY("render-margins", horz, vert); i += 2; } else if (strcmp(argv[i], "-thickness") == 0) { float rt; if (++i == argc) { fprintf(stderr, "expecting number after -thickness\n"); return -1; } if (sscanf(argv[i], "%f", &rt) != 1 || rt < 0) { fprintf(stderr, "%s is not a valid relative thickness\n", argv[i]); return -1; } indigoSetOptionFloat("render-relative-thickness", rt); } else if (strcmp(argv[i], "-linewidth") == 0) { float rt; if (++i == argc) { fprintf(stderr, "expecting number after -linewidth\n"); return -1; } if (sscanf(argv[i], "%f", &rt) != 1 || rt < 0) { fprintf(stderr, "%s is not a valid line width value\n", argv[i]); return -1; } indigoSetOptionFloat("render-bond-line-width", rt); } else if (strcmp(argv[i], "-bond") == 0) { if (++i == argc) { fprintf(stderr, "expecting number after -bond\n"); return -1; } if (sscanf(argv[i], "%d", &p->bond) != 1 || p->bond <= 0) { fprintf(stderr, "%s is not a valid bond length\n", argv[i]); return -1; } } else if (strcmp(argv[i], "-coloring") == 0) { if (++i == argc) { fprintf(stderr, "expecting 'on' or 'off' after -coloring\n"); return -1; } if (strcasecmp(argv[i], "on") == 0) indigoSetOptionBool("render-coloring", 1); else if (strcasecmp(argv[i], "off") == 0) indigoSetOptionBool("render-coloring", 0); else { fprintf(stderr, "expecting 'on' or 'off' after -coloring\n"); return -1; } } else if (strcmp(argv[i], "-hlthick") == 0) { indigoSetOptionBool("render-highlight-thickness-enabled", 1); } else if (strcmp(argv[i], "-hlcolor") == 0) { float r, g, b; if (i + 3 >= argc) { fprintf(stderr, "expecting 3 numbers after -hlcolor\n"); return -1; } if (parseColor(argv, i, &r, &g, &b) != 0) return -1; indigoSetOptionBool("render-highlight-color-enabled", 1); indigoSetOptionColor("render-highlight-color", r, g, b); i += 3; } else if (strcmp(argv[i], "-bgcolor") == 0) { float r, g, b; if (i + 3 >= argc) { fprintf(stderr, "expecting 3 numbers after -bgcolor\n"); return -1; } if (parseColor(argv, i, &r, &g, &b) != 0) return -1; indigoSetOptionColor("render-background-color", r, g, b); i += 3; } else if (strcmp(argv[i], "-basecolor") == 0) { float r, g, b; if (i + 3 >= argc) { fprintf(stderr, "expecting 3 numbers after -basecolor\n"); return -1; } if (parseColor(argv, i, &r, &g, &b) != 0) return -1; indigoSetOptionColor("render-base-color", r, g, b); i += 3; } else if (strcmp(argv[i], "-aamcolor") == 0) { float r, g, b; if (i + 3 >= argc) { fprintf(stderr, "expecting 3 numbers after -aamcolor\n"); return -1; } if (parseColor(argv, i, &r, &g, &b) != 0) return -1; indigoSetOptionColor("render-aam-color", r, g, b); i += 3; } else if (strcmp(argv[i], "-dsgcolor") == 0) { float r, g, b; if (i + 3 >= argc) { fprintf(stderr, "expecting 3 numbers after -aamcolor\n"); return -1; } if (parseColor(argv, i, &r, &g, &b) != 0) return -1; indigoSetOptionColor("render-data-sgroup-color", r, g, b); i += 3; } else if (strcmp(argv[i], "-hydro") == 0) { if (++i == argc) { fprintf(stderr, "expecting an identifier after -hydro\n"); return -1; } indigoSetOption("render-implicit-hydrogens-visible", argv[i]); p->hydro_set = 1; } else if (strcmp(argv[i], "-label") == 0) { if (++i == argc) { fprintf(stderr, "expecting an identifier after -label\n"); return -1; } indigoSetOption("render-label-mode", argv[i]); } else if (strcmp(argv[i], "-arom") == 0) { p->aromatization = AROM; } else if (strcmp(argv[i], "-dearom") == 0) { p->aromatization = DEAROM; } else if (strcmp(argv[i], "-stereo") == 0) { if (++i == argc) { fprintf(stderr, "expecting an identifier after -stereo\n"); return -1; } indigoSetOption("render-stereo-style", argv[i]); } else if (strcmp(argv[i], "-cdbwsa") == 0) { indigoSetOptionBool("render-center-double-bond-when-stereo-adjacent", 1); } else if (strcmp(argv[i], "-query") == 0) { p->query_set = 1; } else if (strcmp(argv[i], "-smarts") == 0) { p->smarts_set = 1; } else if (strcmp(argv[i], "-id") == 0) { if (++i == argc) { fprintf(stderr, "expecting an identifier after -id\n"); return -1; } p->id = argv[i]; } else if (strcmp(argv[i], "-catalysts") == 0) { if (++i == argc) { fprintf(stderr, "expecting an identifier after -catalysts\n"); return -1; } indigoSetOption("render-catalysts-placement", argv[i]); } else if (strcmp(argv[i], "-comment") == 0) { if (++i == argc) { fprintf(stderr, "expecting an identifier after -comment\n"); return -1; } p->comment = argv[i]; } else if (strcmp(argv[i], "-commentoffset") == 0) { int offset; if (++i >= argc) { fprintf(stderr, "expecting an integer after -commentoffset\n"); return -1; } if (sscanf(argv[i], "%d", &offset) != 1 || offset < 0) { fprintf(stderr, "%s is not a valid comment offset\n", argv[i]); return -1; } indigoSetOptionInt("render-comment-offset", offset); } else if (strcmp(argv[i], "-commentfield") == 0) { if (++i == argc) { fprintf(stderr, "expecting an identifier after -commentfield\n"); return -1; } p->comment_field = argv[i]; } else if (strcmp(argv[i], "-commentname") == 0) { p->comment_name = 1; } else if (strcmp(argv[i], "-commentsize") == 0) { int commentsize; if (++i == argc) { fprintf(stderr, "expecting number after -commentsize\n"); return -1; } if (sscanf(argv[i], "%d", &commentsize) != 1 || commentsize <= 0) { fprintf(stderr, "%s is not a valid font size\n", argv[i]); return -1; } indigoSetOptionFloat("render-comment-font-size", (float)commentsize); } else if (strcmp(argv[i], "-commentcolor") == 0) { float r, g, b; if (i + 3 >= argc) { fprintf(stderr, "expecting 3 numbers after -commentcolor\n"); return -1; } if (parseColor(argv, i, &r, &g, &b) != 0) return -1; indigoSetOptionColor("render-comment-color", r, g, b); i += 3; } else if (strcmp(argv[i], "-commentalign") == 0) { if (++i == argc) { fprintf(stderr, "expecting an identifier after -commentalign\n"); return -1; } indigoSetOption("render-comment-alignment", argv[i]); } else if (strcmp(argv[i], "-commentpos") == 0) { if (++i == argc) { fprintf(stderr, "expecting an identifier after -commentpos\n"); return -1; } indigoSetOption("render-comment-position", argv[i]); } else if (strcmp(argv[i], "-atomnumbers") == 0) indigoSetOptionBool("render-atom-ids-visible", 1); else if (strcmp(argv[i], "-bondnumbers") == 0) indigoSetOptionBool("render-bond-ids-visible", 1); else if (strcmp(argv[i], "-onebased") == 0) indigoSetOptionBool("render-atom-bond-ids-from-one", 1); else if (strcmp(argv[i], "-help") == 0) { usage(); return 0; } else { fprintf(stderr, "unknown option: %s\n", argv[i]); return -1; } } if (p->bond > 0) indigoSetOptionFloat("render-bond-length", (float)p->bond); if (p->width > 0) indigoSetOptionInt("render-image-width", p->width); if (p->height > 0) indigoSetOptionInt("render-image-height", p->height); if (p->hydro_set && p->query_set) { fprintf(stderr, "-hydro conflicts with -query (implicit hydrogens do not exist in queries)\n"); } return 0; }