private void initIOSettings() { forceReadAs3DCoords = addSetting(new BooleanIOSetting("ForceReadAs3DCoordinates", IOSetting.Importance.LOW, "Should coordinates always be read as 3D?", "false")); interpretHydrogenIsotopes = addSetting(new BooleanIOSetting("InterpretHydrogenIsotopes", IOSetting.Importance.LOW, "Should D and T be interpreted as hydrogen isotopes?", "true")); addStereoElements = addSetting(new BooleanIOSetting("AddStereoElements", IOSetting.Importance.LOW, "Detect and create IStereoElements for the input.", "true")); }
private void initIOSettings() { forceReadAs3DCoords = addSetting(new BooleanIOSetting("ForceReadAs3DCoordinates", IOSetting.Importance.LOW, "Should coordinates always be read as 3D?", "false")); interpretHydrogenIsotopes = addSetting(new BooleanIOSetting("InterpretHydrogenIsotopes", IOSetting.Importance.LOW, "Should D and T be interpreted as hydrogen isotopes?", "true")); addStereoElements = addSetting(new BooleanIOSetting("AddStereoElements", IOSetting.Importance.LOW, "Detect and create IStereoElements for the input.", "true")); }
private void initIOSettings() { useRebondTool = addSetting(new BooleanIOSetting("UseRebondTool", IOSetting.Importance.LOW, "Should the PDBReader deduce bonding patterns?", "false")); readConnect = addSetting(new BooleanIOSetting("ReadConnectSection", IOSetting.Importance.LOW, "Should the CONECT be read?", "true")); useHetDictionary = addSetting(new BooleanIOSetting("UseHetDictionary", IOSetting.Importance.LOW, "Should the PDBReader use the HETATM dictionary for atom types?", "false")); }
private void initIOSettings() { forceReadAs3DCoords = new BooleanIOSetting("ForceReadAs3DCoordinates", IOSetting.Importance.LOW, "Should coordinates always be read as 3D?", "false"); addSetting(forceReadAs3DCoords); }
private void initIOSettings() { useRebondTool = addSetting(new BooleanIOSetting("UseRebondTool", IOSetting.Importance.LOW, "Should the PDBReader deduce bonding patterns?", "false")); readConnect = addSetting(new BooleanIOSetting("ReadConnectSection", IOSetting.Importance.LOW, "Should the CONECT be read?", "true")); useHetDictionary = addSetting(new BooleanIOSetting("UseHetDictionary", IOSetting.Importance.LOW, "Should the PDBReader use the HETATM dictionary for atom types?", "false")); }
private void initIOSettings() { readOptimizedStructureOnly = addSetting(new BooleanIOSetting("ReadOptimizedStructureOnly", IOSetting.Importance.LOW, "Should I only read the optimized structure from a geometry optimization?", "false")); }
private void initIOSettings() { readOptimizedStructureOnly = addSetting(new BooleanIOSetting("ReadOptimizedStructureOnly", IOSetting.Importance.LOW, "Should I only read the optimized structure from a geometry optimization?", "false")); }
private void initIOSettings() { forceReadAs3DCoords = addSetting(new BooleanIOSetting("ForceReadAs3DCoordinates", IOSetting.Importance.LOW, "Should coordinates always be read as 3D?", "false")); }
private void initIOSettings() { useAromaticityFlag = addSetting(new BooleanIOSetting("UseAromaticity", IOSetting.Importance.LOW, "Should aromaticity information be stored in the SMILES?", "false")); }
/** * Initializes IO settings.<br> * Please note with regards to "writeAromaticBondTypes": bond type values 4 through 8 are for SSS queries only, * so a 'query file' is created if the container has aromatic bonds and this settings is true. */ private void initIOSettings() { forceWriteAs2DCoords = addSetting(new BooleanIOSetting(OptForceWriteAs2DCoordinates, IOSetting.Importance.LOW, "Should coordinates always be written as 2D?", "false")); writeMajorIsotopes = addSetting(new BooleanIOSetting(OptWriteMajorIsotopes, IOSetting.Importance.LOW, "Write atomic mass of any non-null atomic mass including major isotopes (e.g. [12]C)", "true")); writeAromaticBondTypes = addSetting(new BooleanIOSetting(OptWriteAromaticBondTypes, IOSetting.Importance.LOW, "Should aromatic bonds be written as bond type 4?", "false")); writeQueryFormatValencies = addSetting(new BooleanIOSetting(OptWriteQueryFormatValencies, IOSetting.Importance.LOW, "Should valencies be written in the MDL Query format? (deprecated)", "false")); writeDefaultProps = addSetting(new BooleanIOSetting(OptWriteDefaultProperties, IOSetting.Importance.LOW, "Write trailing zero's on atom/bond property blocks even if they're not used.", "true")); }
/** * Initializes IO settings.<br> * Please note with regards to "writeAromaticBondTypes": bond type values 4 * through 8 are for SSS queries only, so a 'query file' is created if the * container has aromatic bonds and this settings is true. */ private void initIOSettings() { forceWriteAs2DCoords = addSetting(new BooleanIOSetting(OptForceWriteAs2DCoordinates, IOSetting.Importance.LOW, "Should coordinates always be written as 2D?", "false")); writeMajorIsotopes = addSetting(new BooleanIOSetting(OptWriteMajorIsotopes, IOSetting.Importance.LOW, "Write atomic mass of any non-null atomic mass including major isotopes (e.g. [12]C)", "true")); writeAromaticBondTypes = addSetting(new BooleanIOSetting(OptWriteAromaticBondTypes, IOSetting.Importance.LOW, "Should aromatic bonds be written as bond type 4?", "false")); writeQueryFormatValencies = addSetting(new BooleanIOSetting(OptWriteQueryFormatValencies, IOSetting.Importance.LOW, "Should valencies be written in the MDL Query format? (deprecated)", "false")); writeDefaultProps = addSetting(new BooleanIOSetting(OptWriteDefaultProperties, IOSetting.Importance.LOW, "Write trailing zero's on atom/bond property blocks even if they're not used.", "true")); }
/** * Creates a PDB writer. * * @param out the stream to write the PDB file to. */ public PDBWriter(Writer out) { try { if (out instanceof BufferedWriter) { writer = (BufferedWriter) out; } else { writer = new BufferedWriter(out); } } catch (Exception exc) { } writeAsHET = addSetting(new BooleanIOSetting("WriteAsHET", IOSetting.Importance.LOW, "Should the output file use HETATM", "false")); useElementSymbolAsAtomName = addSetting(new BooleanIOSetting("UseElementSymbolAsAtomName", IOSetting.Importance.LOW, "Should the element symbol be written as the atom name", "false")); writeCONECTRecords = addSetting(new BooleanIOSetting("WriteCONECT", IOSetting.Importance.LOW, "Should the bonds be written as CONECT records?", "true")); writeTERRecord = addSetting(new BooleanIOSetting("WriteTER", IOSetting.Importance.LOW, "Should a TER record be put at the end of the atoms?", "false")); writeENDRecord = addSetting(new BooleanIOSetting("WriteEND", IOSetting.Importance.LOW, "Should an END record be put at the end of the file?", "true")); }
/** * Creates a PDB writer. * * @param out the stream to write the PDB file to. */ public PDBWriter(Writer out) { try { if (out instanceof BufferedWriter) { writer = (BufferedWriter) out; } else { writer = new BufferedWriter(out); } } catch (Exception exc) { } writeAsHET = addSetting(new BooleanIOSetting("WriteAsHET", IOSetting.Importance.LOW, "Should the output file use HETATM", "false")); useElementSymbolAsAtomName = addSetting(new BooleanIOSetting("UseElementSymbolAsAtomName", IOSetting.Importance.LOW, "Should the element symbol be written as the atom name", "false")); writeCONECTRecords = addSetting(new BooleanIOSetting("WriteCONECT", IOSetting.Importance.LOW, "Should the bonds be written as CONECT records?", "true")); writeTERRecord = addSetting(new BooleanIOSetting("WriteTER", IOSetting.Importance.LOW, "Should a TER record be put at the end of the atoms?", "false")); writeENDRecord = addSetting(new BooleanIOSetting("WriteEND", IOSetting.Importance.LOW, "Should an END record be put at the end of the file?", "true")); }
private void initIOSettings() { write2DCoordinates = addSetting(new BooleanIOSetting("write2DCoordinates", IOSetting.Importance.LOW, "Should 2D coordinates be added?", "true")); write3DCoordinates = addSetting(new BooleanIOSetting("write3DCoordinates", IOSetting.Importance.LOW, "Should 3D coordinates be added?", "true")); builder = addSetting(new StringIOSetting("builder", IOSetting.Importance.LOW, "Which IChemObjectBuilder should be used?", "DefaultChemObjectBuilder")); }
private void initIOSettings() { write2DCoordinates = addSetting(new BooleanIOSetting("write2DCoordinates", IOSetting.Importance.LOW, "Should 2D coordinates be added?", "true")); write3DCoordinates = addSetting(new BooleanIOSetting("write3DCoordinates", IOSetting.Importance.LOW, "Should 3D coordinates be added?", "true")); builder = addSetting(new StringIOSetting("builder", IOSetting.Importance.LOW, "Which IChemObjectBuilder should be used?", "DefaultChemObjectBuilder")); }
private void initIOSettings() { cmlIds = addSetting(new BooleanIOSetting("CMLIDs", IOSetting.Importance.LOW, "Should the output use CML identifiers?", "true")); namespacedOutput = addSetting(new BooleanIOSetting("NamespacedOutput", IOSetting.Importance.LOW, "Should the output use namespaced output?", "true")); namespacePrefix = addSetting(new StringIOSetting("NamespacePrefix", IOSetting.Importance.LOW, "What should the namespace prefix be? [empty is no prefix]", "")); schemaInstanceOutput = addSetting(new BooleanIOSetting("SchemaInstance", IOSetting.Importance.LOW, "Should the output use the Schema-Instance attribute?", "false")); instanceLocation = addSetting(new StringIOSetting("InstanceLocation", IOSetting.Importance.LOW, "Where is the schema found?", "")); indent = addSetting(new BooleanIOSetting("Indenting", IOSetting.Importance.LOW, "Should the output be indented?", "true")); xmlDeclaration = addSetting(new BooleanIOSetting("XMLDeclaration", IOSetting.Importance.LOW, "Should the output contain an XML declaration?", "true")); }
private void initIOSettings() { cmlIds = addSetting(new BooleanIOSetting("CMLIDs", IOSetting.Importance.LOW, "Should the output use CML identifiers?", "true")); namespacedOutput = addSetting(new BooleanIOSetting("NamespacedOutput", IOSetting.Importance.LOW, "Should the output use namespaced output?", "true")); namespacePrefix = addSetting(new StringIOSetting("NamespacePrefix", IOSetting.Importance.LOW, "What should the namespace prefix be? [empty is no prefix]", "")); schemaInstanceOutput = addSetting(new BooleanIOSetting("SchemaInstance", IOSetting.Importance.LOW, "Should the output use the Schema-Instance attribute?", "false")); instanceLocation = addSetting(new StringIOSetting("InstanceLocation", IOSetting.Importance.LOW, "Where is the schema found?", "")); indent = addSetting(new BooleanIOSetting("Indenting", IOSetting.Importance.LOW, "Should the output be indented?", "true")); xmlDeclaration = addSetting(new BooleanIOSetting("XMLDeclaration", IOSetting.Importance.LOW, "Should the output contain an XML declaration?", "true")); }
private void initIOSettings() { optimize = addSetting(new BooleanIOSetting("Optimize", IOSetting.Importance.MEDIUM, "Should the structure be optimized?", "true")); mopacCommands = addSetting(new StringIOSetting("Commands", IOSetting.Importance.LOW, "What Mopac commands should be used (overwrites other choices)?", "PM3 NOINTER NOMM BONDS MULLIK PRECISE")); }
private void initIOSettings() { optimize = addSetting(new BooleanIOSetting("Optimize", IOSetting.Importance.MEDIUM, "Should the structure be optimized?", "true")); mopacCommands = addSetting(new StringIOSetting("Commands", IOSetting.Importance.LOW, "What Mopac commands should be used (overwrites other choices)?", "PM3 NOINTER NOMM BONDS MULLIK PRECISE")); }
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()); }