private void processAtomsBlock(int lineCount, IAtomContainer container) throws IOException {
   for (int i = 0; i < lineCount; i++) {
     String line = input.readLine();
     int atomicNumber = Integer.parseInt(line.substring(7, 10).trim());
     IAtom atom = container.getBuilder().newAtom();
     atom.setAtomicNumber(atomicNumber);
     atom.setSymbol(Symbols.byAtomicNumber[atomicNumber]);
     container.addAtom(atom);
   }
 }
Beispiel #2
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 private void fixHydrogenIsotopes(IAtomContainer molecule, IsotopeFactory isotopeFactory) {
   for (IAtom atom : AtomContainerManipulator.getAtomArray(molecule)) {
     if (atom instanceof IPseudoAtom) {
       IPseudoAtom pseudo = (IPseudoAtom) atom;
       if ("D".equals(pseudo.getLabel())) {
         IAtom newAtom = molecule.getBuilder().newInstance(IAtom.class, atom);
         newAtom.setSymbol("H");
         newAtom.setAtomicNumber(1);
         isotopeFactory.configure(newAtom, isotopeFactory.getIsotope("H", 2));
         AtomContainerManipulator.replaceAtomByAtom(molecule, atom, newAtom);
       } else if ("T".equals(pseudo.getLabel())) {
         IAtom newAtom = molecule.getBuilder().newInstance(IAtom.class, atom);
         newAtom.setSymbol("H");
         newAtom.setAtomicNumber(1);
         isotopeFactory.configure(newAtom, isotopeFactory.getIsotope("H", 3));
         AtomContainerManipulator.replaceAtomByAtom(molecule, atom, newAtom);
       }
     }
   }
 }
  /**
   * 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...");
  }