jgromacs.io

Class IOData

java.lang.Object

jgromacs.io.IOData

public class IOData
extends java.lang.Object

This class contains static methods for IO of data objects

Constructor Summary

Constructors

Constructor and Description
IOData()

Method Summary

Methods

Modifier and Type	Method and Description
static int	howManyModelsInPDB(java.lang.String filename) Returns the number of models in the given PDB file
static Alignment	readAlignmentFromFASTA(java.lang.String filename) Reads an alignment from the given FASTA file
static Trajectory	readDumpedTrajectory(Structure structure, java.lang.String filename) Reads a trajectory from the given dumped XTC or TRR file
static java.lang.Object	readFromFile(java.lang.String filename) Reads a JGromacs object (Structure, IndexSetList, Trajectory or Sequence) from a file automatically identifying the type of the file
static IndexSet	readIndexSetFromNDX(java.lang.String filename) Reads an index set from the given NDX file
static IndexSetList	readIndexSetListFromNDX(java.lang.String filename) Reads an index set list from the given NDX file
static Sequence	readSequenceFromFASTA(java.lang.String filename) Reads a sequence from the given FASTA file
static Structure	readStructureFromGRO(java.lang.String filename) Reads structure from the given GRO file
static Structure	readStructureFromPDB(java.lang.String filename) Reads structure from the given PDB file
static Structure	readStructureFromPDB(java.lang.String filename, int model) Reads the given model from the given PDB file
static Structure[]	readStructuresFromPDB(java.lang.String filename) Reads an ensemble of structures from the given PDB file
static Structure[]	readStructuresFromPDBsInDirectory(java.lang.String path) Reads an ensemble of structures from PDB files in the given directory
static Trajectory	readTrajectory(Structure structure, java.lang.String filename) Reads a trajectory from the given XTC or TRR file
static java.lang.Object[]	runGromacsCommand(java.lang.String command, java.lang.String[] filenames) Executes Gromacs commands from within the Java code and reads the listed output files back into JGromacs objects.
static void	writeAlignmentToFASTA(java.lang.String filename, Alignment alignment) Writes an alignment to the given FASTA file
static void	writeIndexSetListToNDX(java.lang.String filename, IndexSetList indexsetlist) Writes an index set list to the given NDX file
static void	writeIndexSetToNDX(java.lang.String filename, IndexSet set) Writes an index set to the given NDX file
static void	writeSequenceToFASTA(java.lang.String filename, Sequence sequence) Writes a sequence to the given FASTA file
static void	writeStructureToGRO(java.lang.String filename, Structure structure) Writes a structure to the given GRO file
static void	writeStructureToPDB(java.lang.String filename, Structure structure) Writes a structure to the given PDB file

Methods inherited from class java.lang.Object

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

Constructor Detail

IOData

public IOData()

Method Detail

readStructureFromGRO

public static Structure readStructureFromGRO(java.lang.String filename)
                                      throws java.io.IOException

Reads structure from the given GRO file

Parameters:

filename - Input file name

Returns:

structure as a Structure object

Throws:

java.io.IOException

readStructureFromPDB

public static Structure readStructureFromPDB(java.lang.String filename)
                                      throws java.io.IOException

Reads structure from the given PDB file

Parameters:

filename - Input file name

Returns:

structure as a Structure object

Throws:

java.io.IOException

readStructureFromPDB

public static Structure readStructureFromPDB(java.lang.String filename,
                             int model)
                                      throws java.io.IOException

Reads the given model from the given PDB file

Parameters:

filename - Input file name

model - model to be read

Returns:

structure as a Structure object

Throws:

java.io.IOException

howManyModelsInPDB

public static int howManyModelsInPDB(java.lang.String filename)
                              throws java.io.IOException

Returns the number of models in the given PDB file

Parameters:

filename - Input file name

Returns:

number of models

Throws:

java.io.IOException

readStructuresFromPDB

public static Structure[] readStructuresFromPDB(java.lang.String filename)
                                         throws java.io.IOException

Reads an ensemble of structures from the given PDB file

Parameters:

filename - Input file name

Returns:

ensemble of structures as a Structure[] object

Throws:

java.io.IOException

readStructuresFromPDBsInDirectory

public static Structure[] readStructuresFromPDBsInDirectory(java.lang.String path)
                                                     throws java.io.IOException

Reads an ensemble of structures from PDB files in the given directory

Parameters:

path - path of directory

Returns:

ensemble of structures as a Structure[] object

Throws:

java.io.IOException

writeStructureToGRO

public static void writeStructureToGRO(java.lang.String filename,
                       Structure structure)
                                throws java.io.IOException

Writes a structure to the given GRO file

Parameters:

filename - Output file name

structure - Structure object to be written out

Throws:

java.io.IOException

writeStructureToPDB

public static void writeStructureToPDB(java.lang.String filename,
                       Structure structure)
                                throws java.io.IOException

Writes a structure to the given PDB file

Parameters:

filename - Output file name

structure - Structure object to be written out

Throws:

java.io.IOException

readTrajectory

public static Trajectory readTrajectory(Structure structure,
                        java.lang.String filename)
                                 throws java.io.IOException

Reads a trajectory from the given XTC or TRR file

Parameters:

structure - reference structure

filename - Input file name

Returns:

trajectory as a Trajectory object

Throws:

java.io.IOException

readDumpedTrajectory

public static Trajectory readDumpedTrajectory(Structure structure,
                              java.lang.String filename)
                                       throws java.io.IOException

Reads a trajectory from the given dumped XTC or TRR file

Parameters:

structure - reference structure

filename - Input file name

Returns:

trajectory as a Trajectory object

Throws:

java.io.IOException

readSequenceFromFASTA

public static Sequence readSequenceFromFASTA(java.lang.String filename)
                                      throws java.io.IOException

Reads a sequence from the given FASTA file

Parameters:

filename - Input file name

Returns:

sequence as a Sequence object

Throws:

java.io.IOException

readAlignmentFromFASTA

public static Alignment readAlignmentFromFASTA(java.lang.String filename)
                                        throws java.io.IOException

Reads an alignment from the given FASTA file

Parameters:

filename - Input file name

Returns:

alignment as an Alignment object

Throws:

java.io.IOException

writeSequenceToFASTA

public static void writeSequenceToFASTA(java.lang.String filename,
                        Sequence sequence)
                                 throws java.io.IOException

Writes a sequence to the given FASTA file

Parameters:

filename - Output file name

sequence - Sequence object to be written out

Throws:

java.io.IOException

writeAlignmentToFASTA

public static void writeAlignmentToFASTA(java.lang.String filename,
                         Alignment alignment)
                                  throws java.io.IOException

Writes an alignment to the given FASTA file

Parameters:

filename - Output file name

alignment - Alignment object to be written out

Throws:

java.io.IOException

readIndexSetFromNDX

public static IndexSet readIndexSetFromNDX(java.lang.String filename)
                                    throws java.io.IOException

Reads an index set from the given NDX file

Parameters:

filename - Input file name

Returns:

index set as an IndexSet object

Throws:

java.io.IOException

readIndexSetListFromNDX

public static IndexSetList readIndexSetListFromNDX(java.lang.String filename)
                                            throws java.io.IOException

Reads an index set list from the given NDX file

Parameters:

filename - Input file name

Returns:

index set list as an IndexSetList object

Throws:

java.io.IOException

writeIndexSetToNDX

public static void writeIndexSetToNDX(java.lang.String filename,
                      IndexSet set)
                               throws java.io.IOException

Writes an index set to the given NDX file

Parameters:

filename - Output file name

set - IndexSet object to be written out

Throws:

java.io.IOException

writeIndexSetListToNDX

public static void writeIndexSetListToNDX(java.lang.String filename,
                          IndexSetList indexsetlist)
                                   throws java.io.IOException

Writes an index set list to the given NDX file

Parameters:

filename - Output file name

indexsetlist - IndexSetList object to be written out

Throws:

java.io.IOException

runGromacsCommand

public static java.lang.Object[] runGromacsCommand(java.lang.String command,
                                   java.lang.String[] filenames)
                                            throws java.io.IOException

Executes Gromacs commands from within the Java code and reads the listed output files back into JGromacs objects. (Note that the method can be used to execute not only Gromacs commands.) The commands are run in the Unix shell (sh), so for example shell pipes (>,>>,<,|) can also be used in the command line. The first element of the returned array is the standard output and next elements are the JGromacs objects read in.

Parameters:

command - Gromacs command to be executed

filenames - array of output file names to be read in

Returns:

array of JGromacs objects read from the files

Throws:

java.io.IOException

readFromFile

public static java.lang.Object readFromFile(java.lang.String filename)
                                     throws java.io.IOException

Reads a JGromacs object (Structure, IndexSetList, Trajectory or Sequence) from a file automatically identifying the type of the file

Parameters:

filename - Input file name with correct extension

Returns:

JGromacs object

Throws:

java.io.IOException