cct.modelling
Class MolecularFileFormats

java.lang.Object
  cct.modelling.MolecularFileFormats

public class MolecularFileFormats
extends java.lang.Object

Title: Picking

Description:

Copyright: Copyright (c) 2005

Company:

Field Summary

static java.lang.String	adfInput
static java.lang.String	adfOutput
static java.lang.String	allFormats
static java.lang.String	allMolecularExtensions
static java.lang.String	allMolecularFormats
static java.lang.String	amberCoordFormat
static java.lang.String	amberLibFormat
static java.lang.String	amberMdcrdFormat
static java.lang.String	amberPrepFormat
static java.lang.String	amberPrmtopFormat
static java.lang.String	cctFileFormat
static java.util.LinkedHashMap<CHEMISTRY_FILE_FORMAT,java.lang.String>	commonReadFormatDescription
static java.util.LinkedHashMap<CHEMISTRY_FILE_FORMAT,java.lang.String>	commonReadFormats
static java.lang.String	extension_ADF_Input
static java.lang.String	extension_ADF_Output
static java.lang.String	extension_All_Formats
static java.lang.String	extension_Ambercrd
static java.lang.String	extension_AmberLib
static java.lang.String	extension_AmberTraj
static java.lang.String	extension_CCT
static java.lang.String	extension_G03_Cube
static java.lang.String	extension_G03_FormCheckpoint
static java.lang.String	extension_G03_Fragment
static java.lang.String	extension_G03_GJF
static java.lang.String	extension_G03_Output
static java.lang.String	extension_G03_Trajectory
static java.lang.String	extension_GAMESS_Input
static java.lang.String	extension_GAMESS_Output
static java.lang.String	extension_Geom
static java.lang.String	extension_GRO
static java.lang.String	extension_GULP_Input
static java.lang.String	extension_GULP_Trajectory
static java.lang.String	extension_MDL_Molfile
static java.lang.String	extension_Mol2
static java.lang.String	extension_MOPAC_Input
static java.lang.String	extension_MOPAC_Log
static java.lang.String	extension_MOPAC_Output
static java.lang.String	extension_PDB
static java.lang.String	extension_Povray
static java.lang.String	extension_Prep
static java.lang.String	extension_Prmtop
static java.lang.String	extension_QChem_Input
static java.lang.String	extension_QChem_Output
static java.lang.String	extension_SIESTA_Input
static java.lang.String	extension_VASP_POSCAR
static java.lang.String	extension_VASP_Vasprun
static java.lang.String	extension_VRML
static java.lang.String	extension_XMol_XYZ
static int	format_ADF_Input
static int	format_ADF_Output
static int	format_AmberCrd
static int	format_G03_FormCheckpoint
static int	format_G03_Trajectory
static int	format_GAMESS_Input
static int	format_GAMESS_Output
static int	format_GRO
static int	format_GULP_Input
static int	format_GULP_Trajectory
static int	format_MDL_Molfile
static int	format_MOPAC_Input
static int	format_MOPAC_Log
static int	format_MOPAC_Output
static int	format_Povray
static int	format_Prmtop
static int	format_QChem_Input
static int	format_QChem_Output
static int	format_SIESTA_Input
static int	format_VASP_Poscar
static int	format_VASP_Vasprun
static int	format_XMol_XYZ
static int	formatCCT
static int	formatG03_Cube
static int	formatG03_Fragment
static int	formatG03_GJF
static int	formatG03_Output
static int	formatPDB
static int	formatTripos_Mol2
static int	formatUnknown
static java.lang.String	gamessInput
static java.lang.String	gamessOutput
static java.lang.String	gaussian03Cube
static java.lang.String	gaussian03GJF
static java.lang.String	gaussian03Output
static java.lang.String	gaussianFormCheckpoint
static java.lang.String	gaussianFragment
static java.lang.String	gaussianTrajectory
static java.lang.String	geomFormat
static java.lang.String	gromacsGROFormat
static java.lang.String	gulpInputFormat
static java.lang.String	gulpTrajectoryFormat
static java.lang.String	mdlMolfileFormat
static java.lang.String	mopacInput
static java.lang.String	mopacLog
static java.lang.String	mopacOutput
static java.lang.String	pdbFile
static java.lang.String	povrayFormat
static java.lang.String	qchemFormat
static java.lang.String	qchemOutputFormat
static java.util.LinkedHashMap	readFormats
(package private) static java.util.LinkedHashMap	readFormatsTypes
static java.util.LinkedHashMap<CHEMISTRY_FILE_FORMAT,java.lang.String>	remoteReadFormatDescription
static java.util.LinkedHashMap<CHEMISTRY_FILE_FORMAT,java.lang.String>	remoteReadFormats
(package private) static java.util.LinkedHashMap	saveFormats
static java.lang.String	siestaInputFormat
protected static java.util.LinkedHashMap<TRAJECTORY_FILE_FORMAT,java.lang.String>	trajectoryReadFormatDescription
protected static java.util.LinkedHashMap<TRAJECTORY_FILE_FORMAT,java.lang.String>	trajectoryReadFormats
static java.lang.String	triposMol2
(package private) static java.util.LinkedHashMap	updateCoordFormats
static java.lang.String	vaspPoscarFormat
static java.lang.String	vaspVasprunFormat
static java.lang.String	vrmlFormat
static java.lang.String	xmolXYZFileFormat

Constructor Summary

MolecularFileFormats()

Method Summary

static FileFilterImpl[]	formTrajectoryFileFilters()
static java.util.LinkedHashMap<java.lang.String,TRAJECTORY_FILE_FORMAT>	formTrajectoryFileRef()
static java.util.LinkedHashMap	getReadCoordFormats()
static int	getReadFileType(java.lang.String description)
static java.util.LinkedHashMap	getSaveCoordFormats()
static java.util.LinkedHashMap<TRAJECTORY_FILE_FORMAT,java.lang.String>	getTrajectoryReadFormatDescription()
static java.util.LinkedHashMap<TRAJECTORY_FILE_FORMAT,java.lang.String>	getTrajectoryReadFormats()
static java.util.LinkedHashMap	getUpdateCoordFormats()
static int	guessMolecularFileFormat(java.lang.String fileName, java.lang.String Ext) Currently very simple implementation for guessing molecular file format based on file extension

Methods inherited from class java.lang.Object

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

Field Detail

extension_All_Formats

public static final java.lang.String extension_All_Formats

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Constant Field Values

extension_ADF_Input

public static final java.lang.String extension_ADF_Input

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Constant Field Values

extension_ADF_Output

public static final java.lang.String extension_ADF_Output

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Constant Field Values

extension_G03_GJF

public static final java.lang.String extension_G03_GJF

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extension_G03_Output

public static final java.lang.String extension_G03_Output

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extension_G03_Cube

public static final java.lang.String extension_G03_Cube

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extension_G03_Fragment

public static final java.lang.String extension_G03_Fragment

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extension_G03_Trajectory

public static final java.lang.String extension_G03_Trajectory

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extension_G03_FormCheckpoint

public static final java.lang.String extension_G03_FormCheckpoint

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extension_GAMESS_Input

public static final java.lang.String extension_GAMESS_Input

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Constant Field Values

extension_GAMESS_Output

public static final java.lang.String extension_GAMESS_Output

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extension_MOPAC_Input

public static final java.lang.String extension_MOPAC_Input

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extension_MOPAC_Output

public static final java.lang.String extension_MOPAC_Output

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extension_MOPAC_Log

public static final java.lang.String extension_MOPAC_Log

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extension_PDB

public static final java.lang.String extension_PDB

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Constant Field Values

extension_Geom

public static final java.lang.String extension_Geom

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Constant Field Values

extension_VRML

public static final java.lang.String extension_VRML

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Constant Field Values

extension_Mol2

public static final java.lang.String extension_Mol2

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Constant Field Values

extension_CCT

public static final java.lang.String extension_CCT

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Constant Field Values

extension_XMol_XYZ

public static final java.lang.String extension_XMol_XYZ

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extension_MDL_Molfile

public static final java.lang.String extension_MDL_Molfile

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extension_GRO

public static final java.lang.String extension_GRO

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extension_Prmtop

public static final java.lang.String extension_Prmtop

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extension_Prep

public static final java.lang.String extension_Prep

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extension_AmberLib

public static final java.lang.String extension_AmberLib

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extension_Ambercrd

public static final java.lang.String extension_Ambercrd

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extension_AmberTraj

public static final java.lang.String extension_AmberTraj

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extension_Povray

public static final java.lang.String extension_Povray

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Constant Field Values

extension_VASP_POSCAR

public static final java.lang.String extension_VASP_POSCAR

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extension_VASP_Vasprun

public static final java.lang.String extension_VASP_Vasprun

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extension_QChem_Input

public static final java.lang.String extension_QChem_Input

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extension_QChem_Output

public static final java.lang.String extension_QChem_Output

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extension_GULP_Input

public static final java.lang.String extension_GULP_Input

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extension_GULP_Trajectory

public static final java.lang.String extension_GULP_Trajectory

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extension_SIESTA_Input

public static final java.lang.String extension_SIESTA_Input

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Constant Field Values

allFormats

public static final java.lang.String allFormats

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Constant Field Values

adfInput

public static final java.lang.String adfInput

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adfOutput

public static final java.lang.String adfOutput

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gaussian03GJF

public static final java.lang.String gaussian03GJF

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gaussian03Output

public static final java.lang.String gaussian03Output

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gaussian03Cube

public static final java.lang.String gaussian03Cube

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gaussianFragment

public static final java.lang.String gaussianFragment

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gaussianTrajectory

public static final java.lang.String gaussianTrajectory

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gaussianFormCheckpoint

public static final java.lang.String gaussianFormCheckpoint

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gamessInput

public static final java.lang.String gamessInput

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gamessOutput

public static final java.lang.String gamessOutput

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geomFormat

public static final java.lang.String geomFormat

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vrmlFormat

public static final java.lang.String vrmlFormat

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mopacInput

public static final java.lang.String mopacInput

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mopacLog

public static final java.lang.String mopacLog

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mopacOutput

public static final java.lang.String mopacOutput

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pdbFile

public static final java.lang.String pdbFile

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Constant Field Values

triposMol2

public static final java.lang.String triposMol2

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Constant Field Values

cctFileFormat

public static final java.lang.String cctFileFormat

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Constant Field Values

xmolXYZFileFormat

public static final java.lang.String xmolXYZFileFormat

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Constant Field Values

mdlMolfileFormat

public static final java.lang.String mdlMolfileFormat

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Constant Field Values

gromacsGROFormat

public static final java.lang.String gromacsGROFormat

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Constant Field Values

amberPrmtopFormat

public static final java.lang.String amberPrmtopFormat

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Constant Field Values

amberPrepFormat

public static final java.lang.String amberPrepFormat

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Constant Field Values

amberLibFormat

public static final java.lang.String amberLibFormat

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amberCoordFormat

public static final java.lang.String amberCoordFormat

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amberMdcrdFormat

public static final java.lang.String amberMdcrdFormat

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povrayFormat

public static final java.lang.String povrayFormat

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vaspPoscarFormat

public static final java.lang.String vaspPoscarFormat

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vaspVasprunFormat

public static final java.lang.String vaspVasprunFormat

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qchemFormat

public static final java.lang.String qchemFormat

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qchemOutputFormat

public static final java.lang.String qchemOutputFormat

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gulpInputFormat

public static final java.lang.String gulpInputFormat

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gulpTrajectoryFormat

public static final java.lang.String gulpTrajectoryFormat

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siestaInputFormat

public static final java.lang.String siestaInputFormat

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formatUnknown

public static final int formatUnknown

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formatG03_GJF

public static final int formatG03_GJF

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formatG03_Output

public static final int formatG03_Output

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formatPDB

public static final int formatPDB

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formatTripos_Mol2

public static final int formatTripos_Mol2

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formatCCT

public static final int formatCCT

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formatG03_Fragment

public static final int formatG03_Fragment

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format_XMol_XYZ

public static final int format_XMol_XYZ

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format_MDL_Molfile

public static final int format_MDL_Molfile

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format_GRO

public static final int format_GRO

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format_Prmtop

public static final int format_Prmtop

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format_AmberCrd

public static final int format_AmberCrd

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format_GAMESS_Input

public static final int format_GAMESS_Input

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formatG03_Cube

public static final int formatG03_Cube

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format_GAMESS_Output

public static final int format_GAMESS_Output

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format_MOPAC_Log

public static final int format_MOPAC_Log

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format_MOPAC_Output

public static final int format_MOPAC_Output

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format_Povray

public static final int format_Povray

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format_VASP_Poscar

public static final int format_VASP_Poscar

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format_QChem_Input

public static final int format_QChem_Input

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format_QChem_Output

public static final int format_QChem_Output

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format_MOPAC_Input

public static final int format_MOPAC_Input

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format_ADF_Input

public static final int format_ADF_Input

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format_G03_Trajectory

public static final int format_G03_Trajectory

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format_GULP_Input

public static final int format_GULP_Input

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format_GULP_Trajectory

public static final int format_GULP_Trajectory

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format_VASP_Vasprun

public static final int format_VASP_Vasprun

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format_ADF_Output

public static final int format_ADF_Output

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Constant Field Values

format_SIESTA_Input

public static final int format_SIESTA_Input

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Constant Field Values

format_G03_FormCheckpoint

public static final int format_G03_FormCheckpoint

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Constant Field Values

readFormats

public static final java.util.LinkedHashMap readFormats

remoteReadFormats

public static final java.util.LinkedHashMap<CHEMISTRY_FILE_FORMAT,java.lang.String> remoteReadFormats

commonReadFormats

public static final java.util.LinkedHashMap<CHEMISTRY_FILE_FORMAT,java.lang.String> commonReadFormats

remoteReadFormatDescription

public static final java.util.LinkedHashMap<CHEMISTRY_FILE_FORMAT,java.lang.String> remoteReadFormatDescription

commonReadFormatDescription

public static final java.util.LinkedHashMap<CHEMISTRY_FILE_FORMAT,java.lang.String> commonReadFormatDescription

readFormatsTypes

static final java.util.LinkedHashMap readFormatsTypes

saveFormats

static final java.util.LinkedHashMap saveFormats

updateCoordFormats

static final java.util.LinkedHashMap updateCoordFormats

trajectoryReadFormats

protected static final java.util.LinkedHashMap<TRAJECTORY_FILE_FORMAT,java.lang.String> trajectoryReadFormats

trajectoryReadFormatDescription

protected static final java.util.LinkedHashMap<TRAJECTORY_FILE_FORMAT,java.lang.String> trajectoryReadFormatDescription

allMolecularFormats

public static final java.lang.String allMolecularFormats

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Constant Field Values

allMolecularExtensions

public static final java.lang.String allMolecularExtensions

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Constant Field Values

Constructor Detail

MolecularFileFormats

public MolecularFileFormats()

Method Detail

guessMolecularFileFormat

public static int guessMolecularFileFormat(java.lang.String fileName,
                                           java.lang.String Ext)

Currently very simple implementation for guessing molecular file format based on file extension

Parameters:

fileName - String

Ext - String

Returns:

int

getUpdateCoordFormats

public static java.util.LinkedHashMap getUpdateCoordFormats()

getReadCoordFormats

public static java.util.LinkedHashMap getReadCoordFormats()

getSaveCoordFormats

public static java.util.LinkedHashMap getSaveCoordFormats()

getReadFileType

public static int getReadFileType(java.lang.String description)

getTrajectoryReadFormats

public static java.util.LinkedHashMap<TRAJECTORY_FILE_FORMAT,java.lang.String> getTrajectoryReadFormats()

getTrajectoryReadFormatDescription

public static java.util.LinkedHashMap<TRAJECTORY_FILE_FORMAT,java.lang.String> getTrajectoryReadFormatDescription()

formTrajectoryFileFilters

public static FileFilterImpl[] formTrajectoryFileFilters()

formTrajectoryFileRef

public static java.util.LinkedHashMap<java.lang.String,TRAJECTORY_FILE_FORMAT> formTrajectoryFileRef()