cct.tools
Class XMolXYZ

java.lang.Object
  extended by cct.tools.XMolXYZ
All Implemented Interfaces:
CoordinateBuilderInterface, CoordinateParserInterface

public class XMolXYZ
extends java.lang.Object
implements CoordinateBuilderInterface, CoordinateParserInterface

Title: Computational Chemistry Tookit

Description:

Copyright: Copyright (c) 2005-2008 Dr. Vladislav Vassiliev

Company: ANU


Constructor Summary
XMolXYZ()
           
 
Method Summary
 double evaluateCompliance(java.io.BufferedReader in)
           
 void getCoordinates(MoleculeInterface mol, boolean inAngstroms, java.io.Writer writer)
           
 java.lang.String getCoordinatesAsString(MoleculeInterface molec, boolean inAngstroms)
           
 void parseCoordinates(java.io.BufferedReader in, MoleculeInterface molecule)
           
 MoleculeInterface parseXMolXYZ(java.lang.String filename, MoleculeInterface mol)
          Parses XMol XYZ files 1) The first line contains the number of atoms in the molecule.
 void saveXMolXYZ(java.lang.String filename, MoleculeInterface mol, boolean atomicSymbols, boolean inAngstroms)
           
 void saveXMolXYZ(java.io.Writer writer, MoleculeInterface mol, boolean atomicSymbols, boolean inAngstroms)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

XMolXYZ

public XMolXYZ()
Method Detail

saveXMolXYZ

public void saveXMolXYZ(java.io.Writer writer,
                        MoleculeInterface mol,
                        boolean atomicSymbols,
                        boolean inAngstroms)
                 throws java.lang.Exception
Throws:
java.lang.Exception

saveXMolXYZ

public void saveXMolXYZ(java.lang.String filename,
                        MoleculeInterface mol,
                        boolean atomicSymbols,
                        boolean inAngstroms)
                 throws java.lang.Exception
Throws:
java.lang.Exception

parseXMolXYZ

public MoleculeInterface parseXMolXYZ(java.lang.String filename,
                                      MoleculeInterface mol)
                               throws java.lang.Exception
Parses XMol XYZ files 1) The first line contains the number of atoms in the molecule. 2) The second line contains the name or title of the molecule. It can be blank if desired. 3) The rest of the file is composed of one line for each atom in the molecule. Each atom is designated by the atomic number and then the x, y, and z coordinate value. Separate each value by at least 1 space; there is no strict format for these lines.

Parameters:
filename - String
mol - MoleculeInterface
Returns:
MoleculeInterface
Throws:
java.lang.Exception

getCoordinates

public void getCoordinates(MoleculeInterface mol,
                           boolean inAngstroms,
                           java.io.Writer writer)
                    throws java.lang.Exception
Specified by:
getCoordinates in interface CoordinateBuilderInterface
Throws:
java.lang.Exception

getCoordinatesAsString

public java.lang.String getCoordinatesAsString(MoleculeInterface molec,
                                               boolean inAngstroms)
                                        throws java.lang.Exception
Specified by:
getCoordinatesAsString in interface CoordinateBuilderInterface
Throws:
java.lang.Exception

parseCoordinates

public void parseCoordinates(java.io.BufferedReader in,
                             MoleculeInterface molecule)
                      throws java.lang.Exception
Specified by:
parseCoordinates in interface CoordinateParserInterface
Throws:
java.lang.Exception

evaluateCompliance

public double evaluateCompliance(java.io.BufferedReader in)
                          throws java.lang.Exception
Specified by:
evaluateCompliance in interface CoordinateParserInterface
Throws:
java.lang.Exception