io.mol2
Class InMol2

java.lang.Object
  io.mol2.InMol2

public class InMol2

extends java.lang.Object

Created on Feb 22, 2005 see www.tripos.com/data/support/mol2.pdf for format specification. Class to read and parse the Tripos MOL2 format.

Author:

mika kastenholz, ulf boerjesson

Field Summary

(package private) java.util.ArrayList	Atomblock
(package private) java.util.ArrayList	Bondblock
(package private) java.lang.String	fileName
(package private) java.lang.String	line
static java.util.HashMap	sybylToG96IAC

Constructor Summary

InMol2()

InMol2(java.lang.String fileName)

Method Summary

Particles	parseParticles() Parses atom information from mol2 file into a Particles object, which are then returned.
SimSystem	parseSystem() Parses system information from mol2 file into a SimSystem object, which are then returned.
void	readMol2fromfile() Method readMol2fromfile() reads a single mol2 file and stores any encountered \@ATOM or @BOND block.

Methods inherited from class java.lang.Object

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

Field Detail

sybylToG96IAC

public static final java.util.HashMap sybylToG96IAC

Atomblock

java.util.ArrayList Atomblock

Bondblock

java.util.ArrayList Bondblock

fileName

java.lang.String fileName

line

java.lang.String line

Constructor Detail

InMol2

public InMol2()
       throws java.io.IOException

InMol2

public InMol2(java.lang.String fileName)
       throws java.io.IOException

Method Detail

readMol2fromfile

public void readMol2fromfile()
                      throws java.io.IOException

Method readMol2fromfile() reads a single mol2 file and stores any encountered \@ATOM or @BOND block.

Throws:

java.io.IOException

parseParticles

public Particles parseParticles()

Parses atom information from mol2 file into a Particles object, which are then returned.

Returns:

Particles particles

parseSystem

public SimSystem parseSystem()

Parses system information from mol2 file into a SimSystem object, which are then returned.

Returns:

SimSystem system