def cartoon():
    """Apply the PyMOL cartoon style and colour by secondary structure."""

    # Test if the current data pipe exists.
    pipes.test()

    # Test for the structure.
    if not hasattr(cdp, 'structure'):
        raise RelaxNoPdbError

    # Loop over the PDB files.
    open_files = []
    for model in cdp.structure.structural_data:
        for mol in model.mol:
            # Identifier.
            pdb_file = mol.file_name
            if mol.file_path:
                pdb_file = mol.file_path + sep + pdb_file
            id = file_root(pdb_file)

            # Already loaded.
            if pdb_file in open_files:
                continue

            # Add to the open file list.
            open_files.append(pdb_file)

            # Hide everything.
            pymol_obj.exec_cmd("cmd.hide('everything'," + repr(id) + ")")

            # Show the cartoon style.
            pymol_obj.exec_cmd("cmd.show('cartoon'," + repr(id) + ")")

            # Colour by secondary structure.
            pymol_obj.exec_cmd("util.cbss(" + repr(id) + ", 'red', 'yellow', 'green')")
Beispiel #2
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def cartoon():
    """Apply the PyMOL cartoon style and colour by secondary structure."""

    # Test if the current data pipe exists.
    check_pipe()

    # Test for the structure.
    if not hasattr(cdp, 'structure'):
        raise RelaxNoPdbError

    # Loop over the PDB files.
    open_files = []
    for model in cdp.structure.structural_data:
        for mol in model.mol:
            # Identifier.
            pdb_file = mol.file_name
            if mol.file_path:
                pdb_file = mol.file_path + sep + pdb_file
            id = file_root(pdb_file)

            # Already loaded.
            if pdb_file in open_files:
                continue

            # Add to the open file list.
            open_files.append(pdb_file)

            # Hide everything.
            pymol_obj.exec_cmd("cmd.hide('everything'," + repr(id) + ")")

            # Show the cartoon style.
            pymol_obj.exec_cmd("cmd.show('cartoon'," + repr(id) + ")")

            # Colour by secondary structure.
            pymol_obj.exec_cmd("util.cbss(" + repr(id) + ", 'red', 'yellow', 'green')")
Beispiel #3
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def show_apod_rmsd_to_file(file_name=None, dir=None, path_to_command='showApod', outdir=None, force=False):
    """Extract showApod 'Noise Std Dev' from showApod, and write to file with same filename and ending '.rmsd'

    @keyword file:              The filename of the NMRPipe fourier transformed file.
    @type file:                 str
    @keyword dir:               The directory where the file is located.
    @type dir:                  str
    @keyword path_to_command:   If showApod not in PATH, then specify absolute path as: /path/to/showApod
    @type path_to_command:      str
    @keyword outdir:            The directory where to write the file.  If 'None', then write in same directory.
    @type outdir:               str
    @param force:               Boolean argument which if True causes the file to be overwritten if it already exists.
    @type force:                bool
    @return:                    Write the 'Noise Std Dev' from showApod to a file with same file filename, with ending '.rmsd'.  This will be a file path.
    @rtype:                     str
    """

    # Call extract function.
    apod_rmsd = show_apod_rmsd(file_name=file_name, dir=dir, path_to_command=path_to_command)

    # Get the filename striped of extension details.
    file_name_root = file_root(file_name)

    # Define extension.
    extension = ".rmsd"

    # Define file name for writing.
    file_name_out = file_name_root + extension

    # Define folder to write to.
    if outdir == None:
        write_outdir = dir
    else:
        write_outdir = outdir

    # Open file for writing,
    wfile, wfile_path = open_write_file(file_name=file_name_out, dir=write_outdir, force=force, verbosity=1, return_path=True)

    # Write to file.
    out_write_data = [['%s'%apod_rmsd]]

    # Write data
    write_data(out=wfile, headings=None, data=out_write_data, sep=None)

    # Close file.
    wfile.close()

    # Return path to file.
    return wfile_path
Beispiel #4
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def show_apod_rmsd_to_file(file_name=None, dir=None, path_to_command='showApod', outdir=None, force=False):
    """Extract showApod 'Noise Std Dev' from showApod, and write to file with same filename and ending '.rmsd'

    @keyword file:              The filename of the NMRPipe fourier transformed file.
    @type file:                 str
    @keyword dir:               The directory where the file is located.
    @type dir:                  str
    @keyword path_to_command:   If showApod not in PATH, then specify absolute path as: /path/to/showApod
    @type path_to_command:      str
    @keyword outdir:            The directory where to write the file.  If 'None', then write in same directory.
    @type outdir:               str
    @param force:               Boolean argument which if True causes the file to be overwritten if it already exists.
    @type force:                bool
    @return:                    Write the 'Noise Std Dev' from showApod to a file with same file filename, with ending '.rmsd'.  This will be a file path.
    @rtype:                     str
    """

    # Call extract function.
    apod_rmsd = show_apod_rmsd(file_name=file_name, dir=dir, path_to_command=path_to_command)

    # Get the filename striped of extension details.
    file_name_root = file_root(file_name)

    # Define extension.
    extension = ".rmsd"

    # Define file name for writing.
    file_name_out = file_name_root + extension

    # Define folder to write to.
    if outdir == None:
        write_outdir = dir
    else:
        write_outdir = outdir

    # Open file for writing,
    wfile, wfile_path = open_write_file(file_name=file_name_out, dir=write_outdir, force=force, verbosity=1, return_path=True)

    # Write to file.
    out_write_data = [['%s'%apod_rmsd]]

    # Write data
    write_data(out=wfile, headings=None, data=out_write_data, sep=None)

    # Close file.
    wfile.close()

    # Return path to file.
    return wfile_path
    def setUp(self):
        """Set up for all the internal relax structural object unit tests."""

        # The path to a PDB file.
        self.test_pdb_path = status.install_path+sep+'test_suite'+sep+'shared_data'+sep+'structures'+sep+'Ap4Aase_res1-12.pdb'
        expanded = path.split(self.test_pdb_path)
        self.test_pdb_dir = expanded[0]
        self.test_pdb_file_name = expanded[1]
        self.test_pdb_root = file_root(self.test_pdb_path)

        # Instantiate the structural data object.
        self.data = Internal()

        # Instantiate a MolContainer object.
        self.mol_cont = MolContainer()
Beispiel #6
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def frame_order_geometric(root=None, path=None):
    """Display the frame order geometric object.

    @keyword root:  The file root of the PDB file containing the frame order geometric object.
    @type root:     str
    """

    # Find all PDB files.
    pdb_files = find_pdb_files(path=path, file_root=root)
    pdb_files += find_pdb_files(path=path, file_root=root+'_A')
    pdb_files += find_pdb_files(path=path, file_root=root+'_B')
    pdb_files += find_pdb_files(path=path, file_root=root+'_sim')
    pdb_files += find_pdb_files(path=path, file_root=root+'_sim_A')
    pdb_files += find_pdb_files(path=path, file_root=root+'_sim_B')

    # Read in the PDB files.
    for file in pdb_files:
        # Read in the PDB file.
        pymol_obj.exec_cmd("load " + file)

        # The object ID.
        id = file_root(file)

        # First hide everything.
        pymol_obj.exec_cmd("select %s" % id)
        pymol_obj.exec_cmd("hide ('sele')")
        pymol_obj.exec_cmd("cmd.delete('sele')")

        # Set up the titles.
        represent_titles(id=id)

        # Set up the pivot points.
        represent_pivots(id=id)

        # Set up the rotor objects.
        represent_rotor_object(id=id)

        # Set up the cone axis.
        represent_cone_axis(id=id)

        # Set up the cone object.
        represent_cone_object(id=id)

    # Disable the MC simulation representation - the user can find this out for themselves.
    pymol_obj.exec_cmd("disable %s_sim" % root)
    pymol_obj.exec_cmd("disable %s_sim_A" % root)
    pymol_obj.exec_cmd("disable %s_sim_B" % root)
Beispiel #7
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def frame_order_geometric(root=None, path=None):
    """Display the frame order geometric object.

    @keyword root:  The file root of the PDB file containing the frame order geometric object.
    @type root:     str
    """

    # Find all PDB files.
    pdb_files = find_pdb_files(path=path, file_root=root)
    pdb_files += find_pdb_files(path=path, file_root=root + '_A')
    pdb_files += find_pdb_files(path=path, file_root=root + '_B')
    pdb_files += find_pdb_files(path=path, file_root=root + '_sim')
    pdb_files += find_pdb_files(path=path, file_root=root + '_sim_A')
    pdb_files += find_pdb_files(path=path, file_root=root + '_sim_B')

    # Read in the PDB files.
    for file in pdb_files:
        # Read in the PDB file.
        pymol_obj.exec_cmd("load " + file)

        # The object ID.
        id = file_root(file)

        # First hide everything.
        pymol_obj.exec_cmd("select %s" % id)
        pymol_obj.exec_cmd("hide ('sele')")
        pymol_obj.exec_cmd("cmd.delete('sele')")

        # Set up the titles.
        represent_titles(id=id)

        # Set up the pivot points.
        represent_pivots(id=id)

        # Set up the rotor objects.
        represent_rotor_object(id=id)

        # Set up the cone axis.
        represent_cone_axis(id=id)

        # Set up the cone object.
        represent_cone_object(id=id)

    # Disable the MC simulation representation - the user can find this out for themselves.
    pymol_obj.exec_cmd("disable %s_sim" % root)
    pymol_obj.exec_cmd("disable %s_sim_A" % root)
    pymol_obj.exec_cmd("disable %s_sim_B" % root)
Beispiel #8
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def cone_pdb(file=None):
    """Display the cone geometric object.

    @keyword file:  The name of the file containing the cone geometric object.
    @type file:     str
    """

    # Read in the cone PDB file.
    pymol_obj.exec_cmd("load " + file)

    # The object ID.
    id = file_root(file)

    # The cone axes.
    represent_cone_axis(id=id)

    # The cone object.
    represent_cone_object(id=id)
Beispiel #9
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def cone_pdb(file=None):
    """Display the cone geometric object.

    @keyword file:  The name of the file containing the cone geometric object.
    @type file:     str
    """

    # Read in the cone PDB file.
    pymol_obj.exec_cmd("load " + file)

    # The object ID.
    id = file_root(file)

    # The cone axes.
    represent_cone_axis(id=id)

    # The cone object.
    represent_cone_object(id=id)
Beispiel #10
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def frame_order_ave_pos(root=None, path=None):
    """Display the PDB structure for the frame order average domain position.

    @keyword root:  The file root of the PDB file containing the frame order average structure.
    @type root:     str
    """

    # Find all PDB files.
    pdb_files = find_pdb_files(path=path, file_root=root)
    pdb_files += find_pdb_files(path=path, file_root=root+'_sim')

    # Read in the PDB files.
    for file in pdb_files:
        pymol_obj.exec_cmd("load " + file)

        # The object ID.
        id = file_root(file)

    # Disable the MC simulation representation - the user can find this out for themselves.
    pymol_obj.exec_cmd("disable %s_sim" % root)
Beispiel #11
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def frame_order_ave_pos(root=None, path=None):
    """Display the PDB structure for the frame order average domain position.

    @keyword root:  The file root of the PDB file containing the frame order average structure.
    @type root:     str
    """

    # Find all PDB files.
    pdb_files = find_pdb_files(path=path, file_root=root)
    pdb_files += find_pdb_files(path=path, file_root=root + '_sim')

    # Read in the PDB files.
    for file in pdb_files:
        pymol_obj.exec_cmd("load " + file)

        # The object ID.
        id = file_root(file)

    # Disable the MC simulation representation - the user can find this out for themselves.
    pymol_obj.exec_cmd("disable %s_sim" % root)
Beispiel #12
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def vector_dist(file=None):
    """Display the XH bond vector distribution.

    @keyword file:   The vector distribution PDB file.
    @type file:     str
    """

    # Test if the current data pipe exists.
    check_pipe()

    # The file root.
    id = file_root(file)

    # Read in the vector distribution PDB file.
    pymol_obj.exec_cmd("load " + file)

    # Create a surface.
    ###################

    # Select the vector distribution.
    pymol_obj.exec_cmd("cmd.show('surface', " + repr(id) + ")")
def vector_dist(file=None):
    """Display the XH bond vector distribution.

    @keyword file:   The vector distribution PDB file.
    @type file:     str
    """

    # Test if the current data pipe exists.
    pipes.test()

    # The file root.
    id = file_root(file)

    # Read in the vector distribution PDB file.
    pymol_obj.exec_cmd("load " + file)


    # Create a surface.
    ###################

    # Select the vector distribution.
    pymol_obj.exec_cmd("cmd.show('surface', " + repr(id) + ")")
Beispiel #14
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def correlation_matrix(matrix=None, labels=None, file=None, dir=None, force=False):
    """Gnuplot plotting function for representing correlation matrices.

    @keyword matrix:    The correlation matrix.  This must be a square matrix.
    @type matrix:       numpy rank-2 array.
    @keyword labels:    The labels for each element of the matrix.  The same label is assumed for each [i, i] pair in the matrix.
    @type labels:       list of str
    @keyword file:      The name of the file to create.
    @type file:         str
    @keyword dir:       The directory where the PDB file will be placed.  If set to None, then the file will be placed in the current directory.
    @type dir:          str or None
    """

    # The dimensions.
    n = len(matrix)

    # Generate the text file for loading into gnuplot.
    text.correlation_matrix(matrix=matrix, labels=labels, file=file, dir=dir, force=force)

    # The script file name with the extension swapped.
    file_name = swap_extension(file=file, ext='gnu')

    # Open the script file for writing.
    output = open_write_file(file_name, dir=dir, force=force)

    # Gnuplot script setup. 
    output.write("#!/usr/bin/env gnuplot\n\n")


    # Set up the terminal type and make the plot square.
    output.write("# Set up the terminal type and make the plot square.\n")
    output.write("set terminal postscript eps size 10,10 enhanced color font 'Helvetica,20' linewidth 0.1\n")
    output.write("set size square\n")

    # The colour map.
    output.write("\n# Blue-red colour map.\n")
    output.write("set palette model RGB\n")
    output.write("set palette defined\n")

    # The labels.
    if labels != None:
        output.write("\n# Labels.\n")
        for axis in ['x', 'y']:
            output.write("set %stics out " % axis)
            if axis == 'x':
                output.write("rotate ")
            output.write("font \",8\" (")
            for i in range(n):
                if i != 0:
                    output.write(", ")
                output.write("\"%s\" %s" % (format_enhanced(labels[i]), i))
            output.write(")\n")

    # Output to EPS.
    output.write("\n# Output to EPS.\n")
    output.write("set output \"%s.eps\"\n" % file_root(file))

    # Load and show the text data.
    output.write("\n# Load and show the text data\n")
    output.write("plot \"%s\" matrix with image\n" % file)

    # Close the file.
    output.close()

    # Make the script executable.
    chmod(get_file_path(file_name=file_name, dir=dir), S_IRWXU|S_IRGRP|S_IROTH)
Beispiel #15
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def correlation_matrix(matrix=None,
                       labels=None,
                       file=None,
                       dir=None,
                       force=False):
    """Gnuplot plotting function for representing correlation matrices.

    @keyword matrix:    The correlation matrix.  This must be a square matrix.
    @type matrix:       numpy rank-2 array.
    @keyword labels:    The labels for each element of the matrix.  The same label is assumed for each [i, i] pair in the matrix.
    @type labels:       list of str
    @keyword file:      The name of the file to create.
    @type file:         str
    @keyword dir:       The directory where the PDB file will be placed.  If set to None, then the file will be placed in the current directory.
    @type dir:          str or None
    """

    # The dimensions.
    n = len(matrix)

    # Generate the text file for loading into gnuplot.
    text.correlation_matrix(matrix=matrix,
                            labels=labels,
                            file=file,
                            dir=dir,
                            force=force)

    # The script file name with the extension swapped.
    file_name = swap_extension(file=file, ext='gnu')

    # Open the script file for writing.
    output = open_write_file(file_name, dir=dir, force=force)

    # Gnuplot script setup.
    output.write("#!/usr/bin/env gnuplot\n\n")

    # Set up the terminal type and make the plot square.
    output.write("# Set up the terminal type and make the plot square.\n")
    output.write(
        "set terminal postscript eps size 10,10 enhanced color font 'Helvetica,20' linewidth 0.1\n"
    )
    output.write("set size square\n")

    # The colour map.
    output.write("\n# Blue-red colour map.\n")
    output.write("set palette model RGB\n")
    output.write("set palette defined\n")

    # The labels.
    if labels != None:
        output.write("\n# Labels.\n")
        for axis in ['x', 'y']:
            output.write("set %stics out " % axis)
            if axis == 'x':
                output.write("rotate ")
            output.write("font \",8\" (")
            for i in range(n):
                if i != 0:
                    output.write(", ")
                output.write("\"%s\" %s" % (format_enhanced(labels[i]), i))
            output.write(")\n")

    # Output to EPS.
    output.write("\n# Output to EPS.\n")
    output.write("set output \"%s.eps\"\n" % file_root(file))

    # Load and show the text data.
    output.write("\n# Load and show the text data\n")
    output.write("plot \"%s\" matrix with image\n" % file)

    # Close the file.
    output.close()

    # Make the script executable.
    chmod(get_file_path(file_name=file_name, dir=dir),
          S_IRWXU | S_IRGRP | S_IROTH)