cct.gromacs
Class Gromacs

java.lang.Object
  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