/** * Sets the setting for a certain question. The setting * is of type String, and any string is accepted. */ @Override public void setSetting(String setting) throws CDKException { // anything is accepted super.setSetting(setting); }
/** * Sets the setting for a certain question. The setting * is of type String, and any string is accepted. */ @Override public void setSetting(String setting) throws CDKException { // anything is accepted super.setSetting(setting); }
/** * Processes the IOSettings by listing the question, giving the options * and asking the user to provide their choice. * * <p>Note: if the input reader is <code>null</code>, then the method * does not wait for an answer, and takes the default. */ @Override public void processIOSettingQuestion(IOSetting setting) { String questionName = setting.getName(); if (props != null) { String propValue = props.getProperty(questionName, setting.getSetting()); try { setting.setSetting(propValue); } catch (CDKException exception) { String message = "Submitted Value (" + propValue + ") is not valid!"; out.println(message); } } }
/** * Processes the IOSettings by listing the question, giving the options * and asking the user to provide their choice. * * <p>Note: if the input reader is <code>null</code>, then the method * does not wait for an answer, and takes the default. */ @Override public void processIOSettingQuestion(IOSetting setting) { String questionName = setting.getName(); if (props != null) { String propValue = props.getProperty(questionName, setting.getSetting()); try { setting.setSetting(propValue); } catch (CDKException exception) { String message = "Submitted Value (" + propValue + ") is not valid!"; out.println(message); } } }
private ISimpleChemObjectReader getReader(File file, String extension) throws IOException, CDKException { if (file.isDirectory()) { throw new IOException( "Input path " + file + " is a directory, not a file"); } switch (extension) { case "mol": return new MDLV2000Reader( new FileReader(file), IChemObjectReader.Mode.RELAXED); case "sdf": return new MDLV2000Reader( new FileReader(file)); case "cml": return new CMLReader(new FileInputStream(file)); case "ml2": return new Mol2Reader(new FileReader(file)); case "pdb": PDBReader reader = new PDBReader(new FileReader(file)); reader.getSetting("UseRebondTool").setSetting("false"); // UseRebondTool reader.getSetting("ReadConnectSection").setSetting("true"); // ReadConnectSection return reader; } return null; }
answer = "true"; setting.setSetting(answer); } else { setting.setSetting(answer);
answer = "true"; setting.setSetting(answer); } else { setting.setSetting(answer);
@Override public void processIOSettingQuestion(IOSetting setting) { if ("ForceReadAs3DCoordinates".equals(setting.getName())) { try { setting.setSetting("true"); } catch (CDKException e) { logger.error("Could not set forceReadAs3DCoords setting: ", e.getMessage()); logger.debug(e); } } }
setting.setSetting(answer); } catch (CDKException exception) {
setting.setSetting(answer); } catch (CDKException exception) {
/** *{@inheritDoc} */ @Override public void addSettings(Collection<IOSetting> settings) { for (IOSetting setting : settings) { if (hasSetting(setting.getName())) { try { getSetting(setting.getName()).setSetting(setting.getSetting()); } catch (CDKException ex) { // setting value was invalid (ignore as we already have a value for this setting // and we can't throw CDKException as IChemObject is in interfaces module) } } else { addSetting(setting); } } }
@Test public void writeAsATOM() throws CDKException, IOException { IAtomContainer mol = singleAtomMolecule(); StringWriter stringWriter = new StringWriter(); PDBWriter writer = new PDBWriter(stringWriter); writer.getSetting("WriteAsHET").setSetting("false"); writer.writeMolecule(mol); writer.close(); String asString = stringWriter.toString(); Assert.assertTrue(asString.indexOf("ATOM") != -1); }
/** *{@inheritDoc} */ @Override public void addSettings(Collection<IOSetting> settings) { for (IOSetting setting : settings) { if (hasSetting(setting.getName())) { try { getSetting(setting.getName()).setSetting(setting.getSetting()); } catch (CDKException ex) { // setting value was invalid (ignore as we already have a value for this setting // and we can't throw CDKException as IChemObject is in interfaces module) } } else { addSetting(setting); } } }
@Test public void writeAsHET() throws CDKException, IOException { IAtomContainer mol = singleAtomMolecule(); StringWriter stringWriter = new StringWriter(); PDBWriter writer = new PDBWriter(stringWriter); writer.getSetting("WriteAsHET").setSetting("true"); writer.writeMolecule(mol); writer.close(); String asString = stringWriter.toString(); Assert.assertTrue(asString.indexOf("HETATM") != -1); }
public IChemFile getChemFile(ISimpleChemObjectReader reader, boolean useRebond) throws Exception { Assert.assertNotNull(reader); reader.getSetting("UseRebondTool").setSetting(String.valueOf(useRebond)); IChemFile chemFile = (IChemFile) reader.read(new ChemFile()); Assert.assertNotNull(chemFile); return chemFile; }
@Test public void skipDefaultProps() throws Exception { StringWriter sw = new StringWriter(); try (MDLV2000Reader mdlr = new MDLV2000Reader(getClass().getResourceAsStream("/data/mdl/tetrahedral-parity-withImplH.mol")); MDLV2000Writer mdlw = new MDLV2000Writer(sw)) { mdlw.getSetting(MDLV2000Writer.OptWriteDefaultProperties) .setSetting("false"); mdlw.write(mdlr.read(new AtomContainer())); String output = sw.toString(); assertThat(output, containsString("\n" + " 5 4 0 0 1 0 0 0 0 0999 V2000\n" + " 0.0000 0.0000 0.0000 C 0 0 1 0 0 0\n" + " 0.0000 0.0000 0.0000 C 0 0\n" + " 0.0000 0.0000 0.0000 C 0 0\n" + " 0.0000 0.0000 0.0000 O 0 0\n" + " 0.0000 0.0000 0.0000 C 0 0\n" + " 1 2 1 0\n" + " 2 3 1 0\n" + " 1 4 1 0\n" + " 1 5 1 0\n" + "M END")); } } }
@Test public void ignoreCarbon12() throws Exception { IAtomContainer mol = builder.newAtomContainer(); IAtom atom = builder.newAtom(); atom.setSymbol("C"); atom.setMassNumber(12); mol.addAtom(atom); StringWriter sw = new StringWriter(); try (MDLV2000Writer mdlw = new MDLV2000Writer(sw)) { mdlw.getSetting(MDLV2000Writer.OptWriteMajorIsotopes) .setSetting("false"); mdlw.write(mol); } assertThat(sw.toString(), not(containsString("M ISO 1 1 12"))); }
reader.getSetting("UseRebondTool").setSetting("false"); // UseRebondTool reader.getSetting("ReadConnectSection").setSetting("true"); // ReadConnectSection