ffe.parsers
Class MMFilter

java.lang.Object
  ffe.parsers.MMFilter

public final class MMFilter

extends java.lang.Object

The MMFilter Class is used to parse and store molecular mechanics data from TINKER Keyword (*.KEY) and Parameter (*.PRM) files.

Field Summary

static java.util.Hashtable	aalookup A Hashtable of Amino Acid Name Strings, stored by three-letter abreviations
java.util.Hashtable	angle Hashtable of MMTerm objects stored by concatenation of Keys
java.util.Hashtable	atom A Hashtable of MMAtom objects
java.util.Hashtable	atomlookup
java.util.Hashtable	bond Hashtable of MMTerm objects stored by concatenation of Keys
java.util.Hashtable	dihedral Hashtable of MMTerm objects stored by concatenation of Keys
java.util.Hashtable	improper Hashtable of MMTerm objects stored by concatenation of Keys

Constructor Summary

MMFilter()
The default Constructor intialized the HashTables, then attempts to parse a Force Field Data File.

Method Summary

void	destroy()
java.lang.String	getForceField()
MMAtom	getMMAtom(int prm_num) Return a Force Field Atom type specified by prm_num
MMAtom	getMMAtom(java.lang.String res, java.lang.String pdb_symbol) Find and returns a Force Field Atom type for the corresponding pdb symbol specified by the Residue name (res) and PDB Symbol (pdb_symbol).
boolean	parse()
void	setForceField(java.io.File key, java.lang.String param)
void	setForceFieldFile(java.io.File ff)
void	setForceFieldLookup(java.lang.String ff)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

atom

public java.util.Hashtable atom

A Hashtable of MMAtom objects

bond

public java.util.Hashtable bond

Hashtable of MMTerm objects stored by concatenation of Keys

angle

public java.util.Hashtable angle

Hashtable of MMTerm objects stored by concatenation of Keys

improper

public java.util.Hashtable improper

Hashtable of MMTerm objects stored by concatenation of Keys

dihedral

public java.util.Hashtable dihedral

Hashtable of MMTerm objects stored by concatenation of Keys

atomlookup

public java.util.Hashtable atomlookup

aalookup

public static final java.util.Hashtable aalookup

A Hashtable of Amino Acid Name Strings, stored by three-letter abreviations

Constructor Detail

MMFilter

public MMFilter()

The default Constructor intialized the HashTables, then attempts to parse a Force Field Data File.

Method Detail

getMMAtom

public MMAtom getMMAtom(java.lang.String res,
                        java.lang.String pdb_symbol)

Find and returns a Force Field Atom type for the corresponding pdb symbol specified by the Residue name (res) and PDB Symbol (pdb_symbol).

getMMAtom

public MMAtom getMMAtom(int prm_num)

Return a Force Field Atom type specified by prm_num

parse

public boolean parse()

setForceField

public void setForceField(java.io.File key,
                          java.lang.String param)

setForceFieldLookup

public void setForceFieldLookup(java.lang.String ff)

setForceFieldFile

public void setForceFieldFile(java.io.File ff)

getForceField

public java.lang.String getForceField()

destroy

public void destroy()