io.g96.in
Class InTopoG96

java.lang.Object
  io.g96.in.InTopoG96

public class InTopoG96

extends java.lang.Object

The InTopoG96 class reads in a GROMOS96 topology file.

Version:

0.2, August 2005

Author:

Vincent Kraeutler, Mika Kastenholz

Nested Class Summary

class

InTopoG96.Topology A collection of stuff to hold data read from the topology file.

Constructor Summary

InTopoG96()

Method Summary

static int[]	determineMolecules(Particles atoms, Bonds bonds) Fast method for determining molecule bounds.
static int[]	determineMoleculesFloyd(Particles atoms, Bonds bonds) slow (N^3) but accurate molecule bounds method.
static int[]	getBoundaryAtoms(int[] molecule) Find the last atom of each molecule.
static Angles	parseAngleBlock(java.util.ArrayList block, java.util.Hashtable angleTypes)
static void	parseAtomTypeNameBlock(java.util.ArrayList block, InteractionParameters intpara)
static java.util.Hashtable	parseBondAngleTypeBlock(java.util.ArrayList block)
static Bonds	parseBondBlock(java.util.ArrayList block, java.util.Hashtable bondTypes)
static java.util.Hashtable	parseBondTypeBlock(java.util.ArrayList block)
static Dihedrals	parseDihedralBlock(java.util.ArrayList block, java.util.Hashtable dihedralType)
static java.util.Hashtable	parseDihedralTypeBlock(java.util.ArrayList block)
static java.util.ArrayList	parseExclusionLine(java.lang.String[] words, int offset, java.util.ArrayList exclusionList) Parse the remaining exclusions from an array of Strings.
static java.util.Hashtable	parseImpDihedralTypeBlock(java.util.ArrayList block)
static ImproperDihedrals	parseImproperBlock(java.util.ArrayList block, java.util.Hashtable impDihedralTypes)
static LJTypeHashMap	parseLJBlock(java.util.ArrayList block)
static java.util.ArrayList	parseResNameBlock(java.util.ArrayList block)
static Particles	parseSoluteAtomBlock(java.util.ArrayList block, java.util.ArrayList residueNames, SimSystem sys)
static G96SolventTopology	parseSolventAtomBlock(java.util.ArrayList block)
static Bonds	parseSolventConstraintBlock(java.util.ArrayList block)
static void	parseTopPhysConBlock(java.util.ArrayList block, SimSystem sys)
static void	parseTopVersionBlock(java.util.ArrayList block, InteractionParameters intpara)
static InTopoG96.Topology	readTopology(java.lang.String topologyFileName)

Methods inherited from class java.lang.Object

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

Constructor Detail

InTopoG96

public InTopoG96()

Method Detail

readTopology

public static InTopoG96.Topology readTopology(java.lang.String topologyFileName)
                                       throws java.io.IOException

Parameters:

topologyFileName -

Returns:

the topology

Throws:

java.io.IOException

parseSolventConstraintBlock

public static Bonds parseSolventConstraintBlock(java.util.ArrayList block)

Parameters:

block -

Returns:

the constraints

parseSolventAtomBlock

public static G96SolventTopology parseSolventAtomBlock(java.util.ArrayList block)

Parameters:

block -

Returns:

the solvent topology

parseLJBlock

public static LJTypeHashMap parseLJBlock(java.util.ArrayList block)

Parameters:

block -

Returns:

the LJTypes

parseDihedralTypeBlock

public static java.util.Hashtable parseDihedralTypeBlock(java.util.ArrayList block)

Parameters:

block -

Returns:

the dihedral types

parseImpDihedralTypeBlock

public static java.util.Hashtable parseImpDihedralTypeBlock(java.util.ArrayList block)

Parameters:

block -

Returns:

the ImpDihedralTypes

parseBondAngleTypeBlock

public static java.util.Hashtable parseBondAngleTypeBlock(java.util.ArrayList block)

Parameters:

block -

Returns:

the angle types

parseBondTypeBlock

public static java.util.Hashtable parseBondTypeBlock(java.util.ArrayList block)

Parameters:

block -

Returns:

the bond types

parseSoluteAtomBlock

public static Particles parseSoluteAtomBlock(java.util.ArrayList block,
                                             java.util.ArrayList residueNames,
                                             SimSystem sys)

Parameters:

block -

Returns:

the particles (contents of SOLUTEATOM block)

parseExclusionLine

public static java.util.ArrayList parseExclusionLine(java.lang.String[] words,
                                                     int offset,
                                                     java.util.ArrayList exclusionList)

Parse the remaining exclusions from an array of Strings.

Parameters:

words -

offset -

exclusionList -

Returns:

the (remaining) exclusions

parseResNameBlock

public static java.util.ArrayList parseResNameBlock(java.util.ArrayList block)

Parameters:

block -

Returns:

the residue names

parseAtomTypeNameBlock

public static void parseAtomTypeNameBlock(java.util.ArrayList block,
                                          InteractionParameters intpara)

Parameters:

block -

intpara -

parseTopVersionBlock

public static void parseTopVersionBlock(java.util.ArrayList block,
                                        InteractionParameters intpara)

Parameters:

block - the lines of the block

intpara - add the topology version to this

parseTopPhysConBlock

public static void parseTopPhysConBlock(java.util.ArrayList block,
                                        SimSystem sys)

Parameters:

block -

sys -

parseBondBlock

public static Bonds parseBondBlock(java.util.ArrayList block,
                                   java.util.Hashtable bondTypes)

Parameters:

block - ArrayList containing the Bond block

bondTypes -

Returns:

Bonds the parsed Bonds object

parseAngleBlock

public static Angles parseAngleBlock(java.util.ArrayList block,
                                     java.util.Hashtable angleTypes)

Parameters:

block - the block to be parsed

angleTypes - available angleTypes

Returns:

angles

parseImproperBlock

public static ImproperDihedrals parseImproperBlock(java.util.ArrayList block,
                                                   java.util.Hashtable impDihedralTypes)

Parameters:

block -

impDihedralTypes -

Returns:

the improper dihedrals

parseDihedralBlock

public static Dihedrals parseDihedralBlock(java.util.ArrayList block,
                                           java.util.Hashtable dihedralType)

Parameters:

block -

dihedralType -

Returns:

the dihedrals

determineMolecules

public static int[] determineMolecules(Particles atoms,
                                       Bonds bonds)

Fast method for determining molecule bounds. Scales N * M, where N is the number of bonds and M is the number of molecules. Assumes that

• the indices all atoms belonging to one molecule are contiguous.
• bond.I[bb] < bond.J[bb] for all bb.

Molecule determination is performed via inspection of each bond in turn and incremental construction of the molecules.

Parameters:

atoms -

bonds -

Returns:

the index of the last atom of each molecule

See Also:

determineMoleculesFloyd(core.Particles, forcefield.Bonds)

determineMoleculesFloyd

public static int[] determineMoleculesFloyd(Particles atoms,
                                            Bonds bonds)

slow (N^3) but accurate molecule bounds method. works via explicit graph analysis of the connectivity matrix.

Parameters:

atoms -

bonds -

Returns:

the index of the last atom of each molecule

See Also:

determineMolecules(core.Particles, forcefield.Bonds)

getBoundaryAtoms

public static int[] getBoundaryAtoms(int[] molecule)

Find the last atom of each molecule.

Parameters:

molecule -

Returns:

the boundary atoms