コード例 #1
0
  private IChemFile readChemFile() throws CDKException {
    IChemSequence seq = file.getBuilder().newChemSequence();
    IChemModel model = file.getBuilder().newChemModel();
    IMoleculeSet containerSet = file.getBuilder().newMoleculeSet();
    IMolecule container = file.getBuilder().newMolecule();

    int lineNumber = 0;

    try {
      String line = input.readLine();
      while (input.ready() && line != null) {
        logger.debug((lineNumber++) + ": ", line);
        String command = null;
        if (isCommand(line)) {
          command = getCommand(line);
          int lineCount = getContentLinesCount(line);
          if ("ATOMS".equals(command)) {
            processAtomsBlock(lineCount, container);
          } else if ("BONDS".equals(command)) {
            processBondsBlock(lineCount, container);
          } else if ("IDENT".equals(command)) {
            processIdentBlock(lineCount, container);
          } else if ("NAME".equals(command)) {
            processNameBlock(lineCount, container);
          } else {
            // skip lines
            logger.warn("Dropping block: ", command);
            for (int i = 0; i < lineCount; i++) input.readLine();
          }
        } else {
          logger.warn("Unexpected content at line: ", lineNumber);
        }
        line = input.readLine();
      }
      containerSet.addAtomContainer(container);
      model.setMoleculeSet(containerSet);
      seq.addChemModel(model);
      file.addChemSequence(seq);
    } catch (Exception exception) {
      String message = "Error while parsing CTX file: " + exception.getMessage();
      logger.error(message);
      logger.debug(exception);
      throw new CDKException(message, exception);
    }
    return file;
  }
コード例 #2
0
  /**
   * 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...");
  }