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); }
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; }