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java.lang.Object jgromacs.io.IOData
public class IOData
This class contains static methods for IO of data objects
Constructor Summary | |
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IOData()
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Method Summary | |
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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 |
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equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public IOData()
Method Detail |
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public static Structure readStructureFromGRO(java.lang.String filename) throws java.io.IOException
filename
- Input file name
java.io.IOException
public static Structure readStructureFromPDB(java.lang.String filename) throws java.io.IOException
filename
- Input file name
java.io.IOException
public static Structure readStructureFromPDB(java.lang.String filename, int model) throws java.io.IOException
filename
- Input file namemodel
- model to be read
java.io.IOException
public static int howManyModelsInPDB(java.lang.String filename) throws java.io.IOException
filename
- Input file name
java.io.IOException
public static Structure[] readStructuresFromPDB(java.lang.String filename) throws java.io.IOException
filename
- Input file name
java.io.IOException
public static Structure[] readStructuresFromPDBsInDirectory(java.lang.String path) throws java.io.IOException
path
- path of directory
java.io.IOException
public static void writeStructureToGRO(java.lang.String filename, Structure structure) throws java.io.IOException
filename
- Output file namestructure
- Structure object to be written out
java.io.IOException
public static void writeStructureToPDB(java.lang.String filename, Structure structure) throws java.io.IOException
filename
- Output file namestructure
- Structure object to be written out
java.io.IOException
public static Trajectory readTrajectory(Structure structure, java.lang.String filename) throws java.io.IOException
structure
- reference structurefilename
- Input file name
java.io.IOException
public static Trajectory readDumpedTrajectory(Structure structure, java.lang.String filename) throws java.io.IOException
structure
- reference structurefilename
- Input file name
java.io.IOException
public static Sequence readSequenceFromFASTA(java.lang.String filename) throws java.io.IOException
filename
- Input file name
java.io.IOException
public static Alignment readAlignmentFromFASTA(java.lang.String filename) throws java.io.IOException
filename
- Input file name
java.io.IOException
public static void writeSequenceToFASTA(java.lang.String filename, Sequence sequence) throws java.io.IOException
filename
- Output file namesequence
- Sequence object to be written out
java.io.IOException
public static void writeAlignmentToFASTA(java.lang.String filename, Alignment alignment) throws java.io.IOException
filename
- Output file namealignment
- Alignment object to be written out
java.io.IOException
public static IndexSet readIndexSetFromNDX(java.lang.String filename) throws java.io.IOException
filename
- Input file name
java.io.IOException
public static IndexSetList readIndexSetListFromNDX(java.lang.String filename) throws java.io.IOException
filename
- Input file name
java.io.IOException
public static void writeIndexSetToNDX(java.lang.String filename, IndexSet set) throws java.io.IOException
filename
- Output file nameset
- IndexSet object to be written out
java.io.IOException
public static void writeIndexSetListToNDX(java.lang.String filename, IndexSetList indexsetlist) throws java.io.IOException
filename
- Output file nameindexsetlist
- IndexSetList object to be written out
java.io.IOException
public static java.lang.Object[] runGromacsCommand(java.lang.String command, java.lang.String[] filenames) throws java.io.IOException
command
- Gromacs command to be executedfilenames
- array of output file names to be read in
java.io.IOException
public static java.lang.Object readFromFile(java.lang.String filename) throws java.io.IOException
filename
- Input file name with correct extension
java.io.IOException
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