/** * Construct a INChI reader from a Reader object. * * @param input the Reader with the content */ public INChIPlainTextReader(Reader input) { this.init(); setReader(input); inchiTool = new INChIContentProcessorTool(); }
private void initIOSettings() { paramWriteData = addSetting(new BooleanIOSetting("writeProperties", IOSetting.Importance.LOW, "Should molecule properties be written as non-structural data", "true")); paramWriteV3000 = addSetting(new BooleanIOSetting("writeV3000", IOSetting.Importance.LOW, "Write all records as V3000", "false")); addSettings(new MDLV2000Writer().getSettings()); addSettings(new MDLV3000Writer().getSettings()); }
/** * Constructs a ReaderFactory which tries to detect the format in the * first given number of chars. * * @param headerLength length of the header in number of chars */ public ReaderFactory(int headerLength) { formatFactory = new FormatFactory(headerLength); this.headerLength = headerLength; }
/** * Constructs a new CDKSourceCodeWriter. * * @param out The Writer to write to */ public CDKSourceCodeWriter(Writer out) { initIOSettings(); try { setWriter(out); } catch (Exception exc) { } }
/** * Registers a format for detection. */ public void registerFormat(IChemFormatMatcher format) { formatFactory.registerFormat(format); }
public void customizeJob() { for (IOSetting setting : getSettings()) { fireIOSettingQuestion(setting); } }
/** * Reads CML from an java.io.InputStream, for example the FileInputStream. * * @param input InputStream type input */ public CMLReader(InputStream input) { this.input = input; init(); }
/** * Construct a new reader from a Reader type object. * * @param input reader from which input is read */ public PCCompoundXMLReader(Reader input) throws Exception { setReader(input); }
private void customizeJob() { fireIOSettingQuestion(write2DCoordinates); fireIOSettingQuestion(write3DCoordinates); fireIOSettingQuestion(builder); }
/** * Construct a new reader from a Reader type object. * * @param input reader from which input is read */ public PCSubstanceXMLReader(Reader input) throws Exception { setReader(input); }
/** * Constructor for the IChIHandler. **/ public INChIHandler(IChemObjectBuilder bldr) { this.builder = bldr; this.inchiTool = new INChIContentProcessorTool(); }
/** * {@inheritDoc} */ @Override public void close() throws IOException { if (writer != null) writer.close(); }
/** * Constructs a ReaderFactory which tries to detect the format in the * first given number of chars. * * @param headerLength length of the header in number of chars */ public ReaderFactory(int headerLength) { formatFactory = new FormatFactory(headerLength); this.headerLength = headerLength; }
/** * Constructs a new CDKSourceCodeWriter. * * @param out The Writer to write to */ public CDKSourceCodeWriter(Writer out) { initIOSettings(); try { setWriter(out); } catch (Exception exc) { } }
/** * Registers a format for detection. */ public void registerFormat(IChemFormatMatcher format) { formatFactory.registerFormat(format); }
/** * Reads CML from an java.io.InputStream, for example the FileInputStream. * * @param input InputStream type input */ public CMLReader(InputStream input) { this.input = input; init(); }
/** * Construct a new reader from a Reader type object. * * @param input reader from which input is read */ public PCCompoundXMLReader(Reader input) throws Exception { setReader(input); }
private void customizeJob() { fireIOSettingQuestion(write2DCoordinates); fireIOSettingQuestion(write3DCoordinates); fireIOSettingQuestion(builder); }
/** * Define this CMLReader to take the input from a java.io.Reader * class. Possible readers are (among others) StringReader and FileReader. * * @param url String url which points to the file to be read */ public CMLReader(String url) { this.init(); this.url = url; }
/** * Define this CMLReader to take the input from a java.io.Reader * class. Possible readers are (among others) StringReader and FileReader. * * @param url String url which points to the file to be read */ public CMLReader(String url) { this.init(); this.url = url; }