/** * Procedure required by the CDOInterface. This function is only supposed to be called by the JCFL * library */ public void setObjectProperty(String objectType, String propertyType, String propertyValue) { logger.debug("objectType: " + objectType); logger.debug("propType: " + propertyType); logger.debug("property: " + propertyValue); if (objectType == null) { logger.error("Cannot add property for null object"); return; } if (propertyType == null) { logger.error("Cannot add property for null property type"); return; } if (propertyValue == null) { logger.warn("Will not add null property"); return; } if (objectType.equals("Molecule")) { if (propertyType.equals("id")) { currentMolecule.setID(propertyValue); } else if (propertyType.equals("inchi")) { currentMolecule.setProperty("iupac.nist.chemical.identifier", propertyValue); } } else if (objectType.equals("PseudoAtom")) { if (propertyType.equals("label")) { if (!(currentAtom instanceof IPseudoAtom)) { currentAtom = builder.newPseudoAtom(currentAtom); } ((IPseudoAtom) currentAtom).setLabel(propertyValue); } } else if (objectType.equals("Atom")) { if (propertyType.equals("type")) { if (propertyValue.equals("R") && !(currentAtom instanceof IPseudoAtom)) { currentAtom = builder.newPseudoAtom(currentAtom); } currentAtom.setSymbol(propertyValue); } else if (propertyType.equals("x2")) { Point2d coord = currentAtom.getPoint2d(); if (coord == null) coord = new Point2d(); coord.x = Double.parseDouble(propertyValue); currentAtom.setPoint2d(coord); } else if (propertyType.equals("y2")) { Point2d coord = currentAtom.getPoint2d(); if (coord == null) coord = new Point2d(); coord.y = Double.parseDouble(propertyValue); currentAtom.setPoint2d(coord); } else if (propertyType.equals("x3")) { Point3d coord = currentAtom.getPoint3d(); if (coord == null) coord = new Point3d(); coord.x = Double.parseDouble(propertyValue); currentAtom.setPoint3d(coord); } else if (propertyType.equals("y3")) { Point3d coord = currentAtom.getPoint3d(); if (coord == null) coord = new Point3d(); coord.y = Double.parseDouble(propertyValue); currentAtom.setPoint3d(coord); } else if (propertyType.equals("z3")) { Point3d coord = currentAtom.getPoint3d(); if (coord == null) coord = new Point3d(); coord.z = Double.parseDouble(propertyValue); currentAtom.setPoint3d(coord); } else if (propertyType.equals("xFract")) { Point3d coord = currentAtom.getFractionalPoint3d(); if (coord == null) coord = new Point3d(); coord.x = Double.parseDouble(propertyValue); currentAtom.setFractionalPoint3d(coord); } else if (propertyType.equals("yFract")) { Point3d coord = currentAtom.getFractionalPoint3d(); if (coord == null) coord = new Point3d(); coord.y = Double.parseDouble(propertyValue); currentAtom.setFractionalPoint3d(coord); } else if (propertyType.equals("zFract")) { Point3d coord = currentAtom.getFractionalPoint3d(); if (coord == null) coord = new Point3d(); coord.z = Double.parseDouble(propertyValue); currentAtom.setFractionalPoint3d(coord); } else if (propertyType.equals("formalCharge")) { currentAtom.setFormalCharge(Integer.parseInt(propertyValue)); } else if (propertyType.equals("charge") || propertyType.equals("partialCharge")) { currentAtom.setCharge(Double.parseDouble(propertyValue)); } else if (propertyType.equals("hydrogenCount")) { currentAtom.setHydrogenCount(Integer.parseInt(propertyValue)); } else if (propertyType.equals("dictRef")) { currentAtom.setProperty("org.openscience.cdk.dict", propertyValue); } else if (propertyType.equals("atomicNumber")) { currentAtom.setAtomicNumber(Integer.parseInt(propertyValue)); } else if (propertyType.equals("massNumber")) { currentAtom.setMassNumber((int) Double.parseDouble(propertyValue)); } else if (propertyType.equals("id")) { logger.debug("id: ", propertyValue); currentAtom.setID(propertyValue); atomEnumeration.put(propertyValue, numberOfAtoms); } } else if (objectType.equals("Bond")) { if (propertyType.equals("atom1")) { bond_a1 = Integer.parseInt(propertyValue); } else if (propertyType.equals("atom2")) { bond_a2 = Integer.parseInt(propertyValue); } else if (propertyType.equals("id")) { logger.debug("id: " + propertyValue); bond_id = propertyValue; } else if (propertyType.equals("order")) { try { Double order = Double.parseDouble(propertyValue); if (order == 1.0) { bond_order = IBond.Order.SINGLE; } else if (order == 2.0) { bond_order = IBond.Order.DOUBLE; } else if (order == 3.0) { bond_order = IBond.Order.TRIPLE; } else if (order == 4.0) { bond_order = IBond.Order.QUADRUPLE; } else { bond_order = IBond.Order.SINGLE; } } catch (Exception e) { logger.error("Cannot convert to double: " + propertyValue); bond_order = IBond.Order.SINGLE; } } else if (propertyType.equals("stereo")) { if (propertyValue.equals("H")) { bond_stereo = CDKConstants.STEREO_BOND_DOWN; } else if (propertyValue.equals("W")) { bond_stereo = CDKConstants.STEREO_BOND_UP; } } } logger.debug("Object property set..."); }