@Override public IFingerprinter getBitFingerprinter() { return new KlekotaRothFingerprinter(); }
public static List<IFingerprinter> createListOfFingerprints() { return Arrays.asList( (IFingerprinter) new OpenBabelFingerprinter(), (IFingerprinter) new SubstructureFingerprinter(), (IFingerprinter) new MACCSFingerprinter(), (IFingerprinter) new PubchemFingerprinter(DefaultChemObjectBuilder.getInstance()), (IFingerprinter) new KlekotaRothFingerprinter(), (IFingerprinter) new ECFPFingerprinter() ); }
public static List<IFingerprinter> createExtendedListOfFingerprints() { return Arrays.asList( (IFingerprinter) new OpenBabelFingerprinter(), (IFingerprinter) new SubstructureFingerprinter(), (IFingerprinter) new MACCSFingerprinter(), (IFingerprinter) new PubchemFingerprinter(DefaultChemObjectBuilder.getInstance()), (IFingerprinter) new KlekotaRothFingerprinter(), (IFingerprinter) new SphericalFingerprint() ); }
public static List<IFingerprinter> createListOfAllFingerprints() { return Arrays.asList( (IFingerprinter) new OpenBabelFingerprinter(), // 55 (0..54) (IFingerprinter) new SubstructureFingerprinter(), // 307 (55..361) (IFingerprinter) new MACCSFingerprinter(),// 166 (362..527) (IFingerprinter) new PubchemFingerprinter( DefaultChemObjectBuilder.getInstance()), // 881 (528..1408) (IFingerprinter) new KlekotaRothFingerprinter(), // 4860 (1409..6269) (IFingerprinter) new SphericalFingerprint(), (IFingerprinter) new ECFPFingerprinter() ); }
public Fingerprinter getFingerprinter(ComputeOpts opts) throws CDKException { if (opts.isCfm() || opts.isKlekotha() || opts.isMaccs() || opts.isOpenbabel() || opts.isPubchem()) { ArrayList<IFingerprinter> fingerprinters = new ArrayList<IFingerprinter>(); if (opts.isOpenbabel()) fingerprinters.add(new OpenBabelFingerprinter()); if (opts.isMaccs()) fingerprinters.add(new MACCSFingerprinter()); if (opts.isPubchem()) fingerprinters.add(new PubchemFingerprinter(DefaultChemObjectBuilder.getInstance())); if (opts.isKlekotha()) fingerprinters.add(new KlekotaRothFingerprinter()); if (opts.isPath()) fingerprinters.add(new MarcusPathFingerprinter()); if (opts.isCfm()) fingerprinters.add(new CFMFingerprinter()); if (opts.isNeighbourhood()) fingerprinters.add(new NeighbourhoodFingerprinter()); return new Fingerprinter(fingerprinters); } else return new Fingerprinter(); }
private static List<IFingerprinter> getFingerprintList(ComputeOpts opts) { final List<IFingerprinter> list = new ArrayList<IFingerprinter>(); if (opts.isAll()) return Fingerprinter.createListOfAllFingerprints(); if (opts.isExtended()) return Fingerprinter.createExtendedListOfFingerprints(); if (opts.isOpenbabel()) { list.add(new OpenBabelFingerprinter()); list.add(new SubstructureFingerprinter()); } if (opts.isMaccs()) list.add(new MACCSFingerprinter()); if (opts.isPubchem()) list.add(new PubchemFingerprinter(DefaultChemObjectBuilder.getInstance())); if (opts.isKlekotha()) list.add(new KlekotaRothFingerprinter()); if (opts.isPath()) list.add(new MarcusPathFingerprinter()); if (opts.isNeighbourhood()) list.add(new NeighbourhoodFingerprinter()); if (opts.isSpherical()) list.add(new SphericalFingerprint()); if (list.size() > 0) { return list; } else { return Fingerprinter.createListOfFingerprints(); } }
public static IFingerprinter getFingerprinterByName(String name) { switch (name.toLowerCase()) { case "openbabel": return new OpenBabelFingerprinter(); case "substructure": return new SubstructureFingerprinter(); case "maccs": return new MACCSFingerprinter(); case "pubchem": return new PubchemFingerprinter(DefaultChemObjectBuilder.getInstance()); case "klekota": case "klekota_roth": return new KlekotaRothFingerprinter(); case "path": return new MarcusPathFingerprinter(); case "neighbours": return new NeighbourhoodFingerprinter(); case "spheres": return new SphericalFingerprint(); case "ecfp": return new ECFPFingerprinter(); default: throw new IllegalArgumentException("Unknown fingerprinter: " + name); } }
public static IFingerprinter getFingerprinter(CdkFingerprintVersion.USED_FINGERPRINTS fp) { switch (fp) { case OPENBABEL: return new OpenBabelFingerprinter(); case SUBSTRUCTURE: return new SubstructureFingerprinter(); case MACCS: return new MACCSFingerprinter(); case PUBCHEM: return new PubchemFingerprinter(DefaultChemObjectBuilder.getInstance()); case KLEKOTA_ROTH: return new KlekotaRothFingerprinter(); case ECFP: return new ECFPFingerprinter(); case CLASSYFIRE_SMARTS: return new ClassyFireSmartsFingerprint(); case SHORTEST_PATH: return new ShortestPathFingerprinter(); case BIOSMARTS: return new BiosmartsFingerprinter(); case RINGSYSTEMS: return new RingsystemFingerprinter(); default: throw new IllegalArgumentException(); } }