cct.modelling
Class MolecularFileFormats

java.lang.Object
  extended by 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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extension_ADF_Output

public static final java.lang.String extension_ADF_Output
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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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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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extension_Geom

public static final java.lang.String extension_Geom
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extension_VRML

public static final java.lang.String extension_VRML
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extension_Mol2

public static final java.lang.String extension_Mol2
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extension_CCT

public static final java.lang.String extension_CCT
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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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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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allFormats

public static final java.lang.String allFormats
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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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triposMol2

public static final java.lang.String triposMol2
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cctFileFormat

public static final java.lang.String cctFileFormat
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xmolXYZFileFormat

public static final java.lang.String xmolXYZFileFormat
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mdlMolfileFormat

public static final java.lang.String mdlMolfileFormat
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gromacsGROFormat

public static final java.lang.String gromacsGROFormat
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amberPrmtopFormat

public static final java.lang.String amberPrmtopFormat
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amberPrepFormat

public static final java.lang.String amberPrepFormat
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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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format_SIESTA_Input

public static final int format_SIESTA_Input
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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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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()