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")); }
/** * Convenience method to set the option for writing aromatic bond types. * * @param val the value. */ public void setWriteAromaticBondTypes(boolean val) { try { writeAromaticBondTypes.setSetting(Boolean.toString(val)); } catch (CDKException e) { // ignored can't happen since we are statically typed here } }
private int getNumberOfDimensions(IAtomContainer mol) { for (IAtom atom : mol.atoms()) { if (atom.getPoint3d() != null && !forceWriteAs2DCoords.isSet()) return 3; else if (atom.getPoint2d() != null) return 2; } return 0; }
private void customizeJob() { fireIOSettingQuestion(optimize); try { if (optimize.isSet()) { mopacCommands.setSetting("PM3 NOINTER NOMM BONDS MULLIK PRECISE"); } else { mopacCommands.setSetting("PM3 NOINTER NOMM BONDS MULLIK XYZ 1SCF"); } } catch (CDKException exception) { throw new IllegalArgumentException(exception); } fireIOSettingQuestion(mopacCommands); }
private int getNumberOfDimensions(IAtomContainer mol) { for (IAtom atom : mol.atoms()) { if (atom.getPoint3d() != null && !forceWriteAs2DCoords.isSet()) { return 3; } else if (atom.getPoint2d() != null) { return 2; } } return 0; }
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")); }
/** * Convenience method to set the option for writing aromatic bond types. * * @param val the value. */ public void setWriteAromaticBondTypes(boolean val) { try { writeAromaticBondTypes.setSetting(Boolean.toString(val)); } catch (CDKException e) { // ignored can't happen since we are statically typed here } }
private void customizeJob() { fireIOSettingQuestion(optimize); try { if (optimize.isSet()) { mopacCommands.setSetting("PM3 NOINTER NOMM BONDS MULLIK PRECISE"); } else { mopacCommands.setSetting("PM3 NOINTER NOMM BONDS MULLIK XYZ 1SCF"); } } catch (CDKException exception) { throw new IllegalArgumentException(exception); } fireIOSettingQuestion(mopacCommands); }
private void initIOSettings() { readOptimizedStructureOnly = addSetting(new BooleanIOSetting("ReadOptimizedStructureOnly", IOSetting.Importance.LOW, "Should I only read the optimized structure from a geometry optimization?", "false")); }
public void setAlwaysV3000(boolean val) { try { paramWriteV3000.setSetting(Boolean.toString(val)); } catch (CDKException e) { // ignored, no type unsafety throw new InternalError(e.getMessage()); } }
private void writeAtom(IAtom atom) throws Exception { if (atom instanceof IPseudoAtom) { writer.write(" IPseudoAtom " + atom.getID() + " = builder.newInstance(IPseudoAtom.class);"); writer.write('\n'); writer.write(" atom.setLabel(\"" + ((IPseudoAtom) atom).getLabel() + "\");"); writer.write('\n'); } else { writer.write(" IAtom " + atom.getID() + " = builder.newInstance(IAtom.class,\"" + atom.getSymbol() + "\");"); writer.write('\n'); } if (atom.getFormalCharge() != null) { writer.write(" " + atom.getID() + ".setFormalCharge(" + atom.getFormalCharge() + ");"); writer.write('\n'); } if (write2DCoordinates.isSet() && atom.getPoint2d() != null) { Point2d p2d = atom.getPoint2d(); writer.write(" " + atom.getID() + ".setPoint2d(new Point2d(" + p2d.x + ", " + p2d.y + "));"); writer.write('\n'); } if (write3DCoordinates.isSet() && atom.getPoint3d() != null) { Point3d p3d = atom.getPoint3d(); writer.write(" " + atom.getID() + ".setPoint3d(new Point3d(" + p3d.x + ", " + p3d.y + ", " + p3d.z + "));"); writer.write('\n'); } }
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 customizeJob() { fireIOSettingQuestion(cmlIds); fireIOSettingQuestion(namespacedOutput); if (namespacedOutput.isSet()) { fireIOSettingQuestion(namespacePrefix); } fireIOSettingQuestion(schemaInstanceOutput); if (schemaInstanceOutput.isSet()) { fireIOSettingQuestion(instanceLocation); } fireIOSettingQuestion(indent); fireIOSettingQuestion(xmlDeclaration); }
private void initIOSettings() { forceReadAs3DCoords = new BooleanIOSetting("ForceReadAs3DCoordinates", IOSetting.Importance.LOW, "Should coordinates always be read as 3D?", "false"); addSetting(forceReadAs3DCoords); }
private void initIOSettings() { useAromaticityFlag = addSetting(new BooleanIOSetting("UseAromaticity", IOSetting.Importance.LOW, "Should aromaticity information be stored in the SMILES?", "false")); }
private void writeAtom(IAtom atom) throws Exception { if (atom instanceof IPseudoAtom) { writer.write(" IPseudoAtom " + atom.getID() + " = builder.newInstance(IPseudoAtom.class);"); writer.write('\n'); writer.write(" atom.setLabel(\"" + ((IPseudoAtom) atom).getLabel() + "\");"); writer.write('\n'); } else { writer.write(" IAtom " + atom.getID() + " = builder.newInstance(IAtom.class,\"" + atom.getSymbol() + "\");"); writer.write('\n'); } if (atom.getFormalCharge() != null) { writer.write(" " + atom.getID() + ".setFormalCharge(" + atom.getFormalCharge() + ");"); writer.write('\n'); } if (write2DCoordinates.isSet() && atom.getPoint2d() != null) { Point2d p2d = atom.getPoint2d(); writer.write(" " + atom.getID() + ".setPoint2d(new Point2d(" + p2d.x + ", " + p2d.y + "));"); writer.write('\n'); } if (write3DCoordinates.isSet() && atom.getPoint3d() != null) { Point3d p3d = atom.getPoint3d(); writer.write(" " + atom.getID() + ".setPoint3d(new Point3d(" + p3d.x + ", " + p3d.y + ", " + p3d.z + "));"); writer.write('\n'); } }
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 customizeJob() { fireIOSettingQuestion(cmlIds); fireIOSettingQuestion(namespacedOutput); if (namespacedOutput.isSet()) { fireIOSettingQuestion(namespacePrefix); } fireIOSettingQuestion(schemaInstanceOutput); if (schemaInstanceOutput.isSet()) { fireIOSettingQuestion(instanceLocation); } fireIOSettingQuestion(indent); fireIOSettingQuestion(xmlDeclaration); }
private void initIOSettings() { readOptimizedStructureOnly = addSetting(new BooleanIOSetting("ReadOptimizedStructureOnly", IOSetting.Importance.LOW, "Should I only read the optimized structure from a geometry optimization?", "false")); }