Package jgromacs.io

Class IOData


  • public class IOData
    extends java.lang.Object
    This class contains static methods for IO of data objects
    • 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