cct.gromacs
Class Gromacs

java.lang.Object
  extended by cct.gromacs.Gromacs

public class Gromacs
extends java.lang.Object

Title:

Description:

Copyright: Copyright (c) 2006

Company: ANU


Field Summary
(package private) static java.lang.String DefaultGromacsAtomMapFile
           
(package private) static java.util.HashMap GromacsAtomMap
           
(package private) static java.util.HashMap GromacsElements
           
 
Method Summary
static int getChemicalElement(java.lang.String residue, java.lang.String atom_name)
           
static java.lang.String getGromacsAtomType(java.lang.String residue_name, java.lang.String atom_name)
           
static int guessElement(java.lang.String atom_name)
           
static java.util.HashMap readGromacsAtomMap(java.lang.String filename)
          Reads gromacs atom map
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

GromacsElements

static java.util.HashMap GromacsElements

GromacsAtomMap

static java.util.HashMap GromacsAtomMap

DefaultGromacsAtomMapFile

static final java.lang.String DefaultGromacsAtomMapFile
See Also:
Constant Field Values
Method Detail

getChemicalElement

public static int getChemicalElement(java.lang.String residue,
                                     java.lang.String atom_name)

guessElement

public static int guessElement(java.lang.String atom_name)

getGromacsAtomType

public static java.lang.String getGromacsAtomType(java.lang.String residue_name,
                                                  java.lang.String atom_name)

readGromacsAtomMap

public static java.util.HashMap readGromacsAtomMap(java.lang.String filename)
                                            throws java.lang.Exception
Reads gromacs atom map

Parameters:
filename - String
Returns:
HashMap contains HashMaps of residues (map.put(String residue_name, HashMap residue)) where each residue HashMap contains gromacs atom map residue.put(String atom_name, String gromacs_atom_type)
Throws:
java.lang.Exception