Ejemplo n.º 1
0
def write(param=None, file=None, dir=None, scaling=1.0, return_value=None, return_data_desc=None, comment=None, bc=False, force=False):
    """Write data to a file.

    @keyword param:             The name of the parameter to write to file.
    @type param:                str
    @keyword file:              The file to write the data to.
    @type file:                 str
    @keyword dir:               The name of the directory to place the file into (defaults to the current directory).
    @type dir:                  str
    @keyword scaling:           The value to scale the parameter by.
    @type scaling:              float
    @keyword return_value:      An optional function which if supplied will override the default value returning function.
    @type return_value:         None or func
    @keyword return_data_desc:  An optional function which if supplied will override the default parameter description returning function.
    @type return_data_desc:     None or func
    @keyword comment:           Text which will be added to the start of the file as comments.  All lines will be prefixed by '# '.
    @type comment:              str
    @keyword bc:                A flag which if True will cause the back calculated values to be written.
    @type bc:                   bool
    @keyword force:             A flag which if True will cause any pre-existing file to be overwritten.
    @type force:                bool
    """

    # Test if the current pipe exists.
    check_pipe()

    # Test if the sequence data is loaded.
    if not exists_mol_res_spin_data():
        raise RelaxNoSequenceError

    # Open the file for writing.
    file_path = get_file_path(file, dir)
    file = open_write_file(file, dir, force)

    # Write the data.
    write_data(param=param, file=file, scaling=scaling, return_value=return_value, return_data_desc=return_data_desc, comment=comment, bc=bc)

    # Close the file.
    file.close()

    # Add the file to the results file list.
    add_result_file(type='text', label='Text', file=file_path)
Ejemplo n.º 2
0
def write(param=None, file=None, dir=None, scaling=1.0, return_value=None, return_data_desc=None, comment=None, bc=False, force=False):
    """Write data to a file.

    @keyword param:             The name of the parameter to write to file.
    @type param:                str
    @keyword file:              The file to write the data to.
    @type file:                 str
    @keyword dir:               The name of the directory to place the file into (defaults to the current directory).
    @type dir:                  str
    @keyword scaling:           The value to scale the parameter by.
    @type scaling:              float
    @keyword return_value:      An optional function which if supplied will override the default value returning function.
    @type return_value:         None or func
    @keyword return_data_desc:  An optional function which if supplied will override the default parameter description returning function.
    @type return_data_desc:     None or func
    @keyword comment:           Text which will be added to the start of the file as comments.  All lines will be prefixed by '# '.
    @type comment:              str
    @keyword bc:                A flag which if True will cause the back calculated values to be written.
    @type bc:                   bool
    @keyword force:             A flag which if True will cause any pre-existing file to be overwritten.
    @type force:                bool
    """

    # Test if the current pipe exists.
    check_pipe()

    # Test if the sequence data is loaded.
    if not exists_mol_res_spin_data():
        raise RelaxNoSequenceError

    # Open the file for writing.
    file_path = get_file_path(file, dir)
    file = open_write_file(file, dir, force)

    # Write the data.
    write_data(param=param, file=file, scaling=scaling, return_value=return_value, return_data_desc=return_data_desc, comment=comment, bc=bc)

    # Close the file.
    file.close()

    # Add the file to the results file list.
    add_result_file(type='text', label='Text', file=file_path)
Ejemplo n.º 3
0
def macro_write(data_type=None,
                style="classic",
                colour_start_name=None,
                colour_start_rgb=None,
                colour_end_name=None,
                colour_end_rgb=None,
                colour_list=None,
                file=None,
                dir=None,
                force=False):
    """Create a Molmol macro.

    @keyword data_type:         The data type to map to the structure.
    @type data_type:            str
    @keyword style:             The style of the macro.
    @type style:                str
    @keyword colour_start_name: The name of the starting colour of the linear gradient.
    @type colour_start_name:    str
    @keyword colour_start_rgb:  The RGB array starting colour of the linear gradient.
    @type colour_start_rgb:     RBG colour array (len 3 with vals from 0 to 1)
    @keyword colour_end_name:   The name of the ending colour of the linear gradient.
    @type colour_end_name:      str
    @keyword colour_end_rgb:    The RGB array ending colour of the linear gradient.
    @type colour_end_rgb:       RBG colour array (len 3 with vals from 0 to 1)
    @keyword colour_list:       The colour list to search for the colour names.  Can be either 'molmol' or 'x11'.
    @type colour_list:          str or None
    @keyword file:              The name of the macro file to create.
    @type file:                 str
    @keyword dir:               The name of the directory to place the macro file into.
    @type dir:                  str
    @keyword force:             Flag which if set to True will cause any pre-existing file to be overwritten.
    @type force:                bool
    """

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

    # Test if sequence data exists.
    if not exists_mol_res_spin_data():
        raise RelaxNoSequenceError

    # Check the arguments.
    if colour_start_name != None and colour_start_rgb != None:
        raise RelaxError(
            "The starting colour name and RGB colour array cannot both be supplied."
        )
    if colour_end_name != None and colour_end_rgb != None:
        raise RelaxError(
            "The ending colour name and RGB colour array cannot both be supplied."
        )

    # Merge the colour args.
    if colour_start_name != None:
        colour_start = colour_start_name
    else:
        colour_start = colour_start_rgb
    if colour_end_name != None:
        colour_end = colour_end_name
    else:
        colour_end = colour_end_rgb

    # Create the macro.
    commands = create_macro(data_type=data_type,
                            style=style,
                            colour_start=colour_start,
                            colour_end=colour_end,
                            colour_list=colour_list)

    # File name.
    if file == None:
        file = data_type + '.mac'

    # Open the file for writing.
    file_path = get_file_path(file, dir)
    file = open_write_file(file, dir, force)

    # Loop over the commands and write them.
    for command in commands:
        file.write(command + "\n")

    # Close the file.
    file.close()

    # Add the file to the results file list.
    add_result_file(type='molmol', label='Molmol', file=file_path)
Ejemplo n.º 4
0
def write(file=None, dir=None, version='3.1', force=False):
    """Create a BMRB NMR-STAR formatted file.

    @keyword file:      The name of the file to create or a file object.
    @type file:         str or file object
    @keyword dir:       The optional directory to place the file into.  If set to 'pipe_name', then it will be placed in a directory with the same name as the current data pipe.
    @type dir:          str or None
    @keyword version:   The NMR-STAR version to create.  This can be either '2.1', '3.0', or '3.1'.
    @type version:      str
    @keyword force:     A flag which if True will allow a currently existing file to be overwritten.
    @type force:        bool
    """

    # Test if bmrblib is installed.
    if not dep_check.bmrblib_module:
        raise RelaxNoModuleInstallError('BMRB library', 'bmrblib')

    # Test if the current data pipe exists.
    pipe_name = cdp_name()
    if not pipe_name:
        raise RelaxNoPipeError

    # Check the file name.
    if file == None:
        raise RelaxError("The file name must be specified.")

    # A file object.
    if isinstance(file, str):
        # The special data pipe name directory.
        if dir == 'pipe_name':
            dir = pipe_name

        # Get the full file path.
        file = get_file_path(file, dir)

        # Fail if the file already exists and the force flag is False.
        if access(file, F_OK) and not force:
            raise RelaxFileOverwriteError(file, 'force flag')

        # Print out.
        print("Opening the file '%s' for writing." % file)

        # Create the directories.
        mkdir_nofail(dir, verbosity=0)

    # Get the info box.
    info = Info_box()

    # Add the relax citations.
    for id, key in zip(['relax_ref1', 'relax_ref2'],
                       ['dAuvergneGooley08a', 'dAuvergneGooley08b']):
        # Alias the bib entry.
        bib = info.bib[key]

        # Add.
        exp_info.citation(cite_id=id,
                          authors=bib.author2,
                          doi=bib.doi,
                          pubmed_id=bib.pubmed_id,
                          full_citation=bib.cite_short(doi=False, url=False),
                          title=bib.title,
                          status=bib.status,
                          type=bib.type,
                          journal_abbrev=bib.journal,
                          journal_full=bib.journal_full,
                          volume=bib.volume,
                          issue=bib.number,
                          page_first=bib.page_first,
                          page_last=bib.page_last,
                          year=bib.year)

    # Add the relax software package.
    exp_info.software(name=exp_info.SOFTWARE['relax'].name,
                      version=version_full(),
                      vendor_name=exp_info.SOFTWARE['relax'].authors,
                      url=exp_info.SOFTWARE['relax'].url,
                      cite_ids=['relax_ref1', 'relax_ref2'],
                      tasks=exp_info.SOFTWARE['relax'].tasks)

    # Execute the specific BMRB writing code.
    api = return_api(pipe_name=pipe_name)
    api.bmrb_write(file, version=version)

    # Add the file to the results file list.
    if isinstance(file, str):
        add_result_file(type='text', label='BMRB', file=file)
Ejemplo n.º 5
0
def write(file=None, dir=None, version='3.1', force=False):
    """Create a BMRB NMR-STAR formatted file.

    @keyword file:      The name of the file to create or a file object.
    @type file:         str or file object
    @keyword dir:       The optional directory to place the file into.  If set to 'pipe_name', then it will be placed in a directory with the same name as the current data pipe.
    @type dir:          str or None
    @keyword version:   The NMR-STAR version to create.  This can be either '2.1', '3.0', or '3.1'.
    @type version:      str
    @keyword force:     A flag which if True will allow a currently existing file to be overwritten.
    @type force:        bool
    """

    # Test if bmrblib is installed.
    if not dep_check.bmrblib_module:
        raise RelaxNoModuleInstallError('BMRB library', 'bmrblib')

    # Test if the current data pipe exists.
    pipe_name = cdp_name()
    if not pipe_name:
        raise RelaxNoPipeError

    # Check the file name.
    if file == None:
        raise RelaxError("The file name must be specified.")

    # A file object.
    if isinstance(file, str):
        # The special data pipe name directory.
        if dir == 'pipe_name':
            dir = pipe_name

        # Get the full file path.
        file = get_file_path(file, dir)

        # Fail if the file already exists and the force flag is False.
        if access(file, F_OK) and not force:
            raise RelaxFileOverwriteError(file, 'force flag')

        # Print out.
        print("Opening the file '%s' for writing." % file)

        # Create the directories.
        mkdir_nofail(dir, verbosity=0)

    # Specific results writing function.
    write_function = specific_analyses.setup.get_specific_fn('bmrb_write', ds[pipe_name].pipe_type)

    # Get the info box.
    info = Info_box()

    # Add the relax citations.
    for id, key in zip(['relax_ref1', 'relax_ref2'], ['dAuvergneGooley08a', 'dAuvergneGooley08b']):
        # Alias the bib entry.
        bib = info.bib[key]

        # Add.
        exp_info.citation(cite_id=id, authors=bib.author2, doi=bib.doi, pubmed_id=bib.pubmed_id, full_citation=bib.cite_short(doi=False, url=False), title=bib.title, status=bib.status, type=bib.type, journal_abbrev=bib.journal, journal_full=bib.journal_full, volume=bib.volume, issue=bib.number, page_first=bib.page_first, page_last=bib.page_last, year=bib.year)

    # Add the relax software package.
    exp_info.software(name=exp_info.SOFTWARE['relax'].name, version=version_full(), vendor_name=exp_info.SOFTWARE['relax'].authors, url=exp_info.SOFTWARE['relax'].url, cite_ids=['relax_ref1', 'relax_ref2'], tasks=exp_info.SOFTWARE['relax'].tasks)

    # Execute the specific BMRB writing code.
    write_function(file, version=version)

    # Add the file to the results file list.
    if isinstance(file, str):
        add_result_file(type='text', label='BMRB', file=file)
Ejemplo n.º 6
0
def macro_write(data_type=None, style="classic", colour_start_name=None, colour_start_rgb=None, colour_end_name=None, colour_end_rgb=None, colour_list=None, file=None, dir=None, force=False):
    """Create a PyMOL macro file.

    @keyword data_type:         The data type to map to the structure.
    @type data_type:            str
    @keyword style:             The style of the macro.
    @type style:                str
    @keyword colour_start_name: The name of the starting colour of the linear gradient.
    @type colour_start_name:    str
    @keyword colour_start_rgb:  The RGB array starting colour of the linear gradient.
    @type colour_start_rgb:     RBG colour array (len 3 with vals from 0 to 1)
    @keyword colour_end_name:   The name of the ending colour of the linear gradient.
    @type colour_end_name:      str
    @keyword colour_end_rgb:    The RGB array ending colour of the linear gradient.
    @type colour_end_rgb:       RBG colour array (len 3 with vals from 0 to 1)
    @keyword colour_list:       The colour list to search for the colour names.  Can be either 'molmol' or 'x11'.
    @type colour_list:          str or None
    @keyword file:              The name of the macro file to create.
    @type file:                 str
    @keyword dir:               The name of the directory to place the macro file into.
    @type dir:                  str
    @keyword force:             Flag which if set to True will cause any pre-existing file to be overwritten.
    @type force:                bool
    """

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

    # Test if sequence data exists.
    if not exists_mol_res_spin_data():
        raise RelaxNoSequenceError

    # Check the arguments.
    if colour_start_name != None and colour_start_rgb != None:
        raise RelaxError("The starting colour name and RGB colour array cannot both be supplied.")
    if colour_end_name != None and colour_end_rgb != None:
        raise RelaxError("The ending colour name and RGB colour array cannot both be supplied.")

    # Merge the colour args.
    if colour_start_name != None:
        colour_start = colour_start_name
    else:
        colour_start = colour_start_rgb
    if colour_end_name != None:
        colour_end = colour_end_name
    else:
        colour_end = colour_end_rgb

    # Create the macro.
    commands = create_macro(data_type=data_type, style=style, colour_start=colour_start, colour_end=colour_end, colour_list=colour_list)

    # File name.
    if file == None:
        file = data_type + '.pml'

    # Open the file for writing.
    file_path = get_file_path(file, dir)
    file = open_write_file(file, dir, force)

    # Loop over the commands and write them.
    for command in commands:
        file.write(command + "\n")

    # Close the file.
    file.close()

    # Add the file to the results file list.
    add_result_file(type='pymol', label='PyMOL', file=file_path)
Ejemplo n.º 7
0
def write_xy(format='grace', x_data_type='res_num', y_data_type=None, spin_id=None, plot_data='value', norm_type='first', file=None, dir=None, force=False, norm=True):
    """Writing data to a file.

    @keyword format:        The specific backend to use.  The currently support backends are 'grace'.
    @type format:           str
    @keyword x_data_type:   The category of the X-axis data.
    @type x_data_type:      str
    @keyword y_data_type:   The category of the Y-axis data.
    @type y_data_type:      str
    @keyword spin_id:       The spin identification string.
    @type spin_id:          str
    @keyword plot_data:     The type of the plotted data, one of 'value', 'error', or 'sim'.
    @type plot_data:        str
    @keyword norm_type:     The point to normalise to 1.  This can be 'first' or 'last'.
    @type norm_type:        str
    @keyword file:          The name of the Grace file to create.
    @type file:             str
    @keyword dir:           The optional directory to place the file into.
    @type dir:              str
    @param force:           Boolean argument which if True causes the file to be overwritten if it already exists.
    @type force:            bool
    @keyword norm:          The normalisation flag which if set to True will cause all graphs to be normalised to a starting value of 1.
    @type norm:             bool
    """

    # Checks.
    check_pipe()
    check_mol_res_spin_data()

    # Test if the plot_data argument is one of 'value', 'error', or 'sim'.
    if plot_data not in ['value', 'error', 'sim']:
        raise RelaxError("The plot data argument " + repr(plot_data) + " must be set to either 'value', 'error', 'sim'.")

    # Test if the simulations exist.
    if plot_data == 'sim' and not hasattr(cdp, 'sim_number'):
        raise RelaxNoSimError

    # Open the file for writing.
    file_path = get_file_path(file, dir)
    file = open_write_file(file, dir, force)

    # Get the data.
    data, set_names, graph_type = assemble_data(spin_id, x_data_name=x_data_type, y_data_name=y_data_type, plot_data=plot_data)

    # Convert the graph type.
    if graph_type == 'X,Y':
        graph_type = 'xy'
    elif graph_type == 'X,Y,dX':
        graph_type = 'xydx'
    elif graph_type == 'X,Y,dY':
        graph_type = 'xydy'
    elif graph_type == 'X,Y,dX,dY':
        graph_type = 'xydxdy'

    # No data, so close the empty file and exit.
    if not len(data) or not len(data[0]) or not len(data[0][0]):
        warn(RelaxWarning("No data could be found, creating an empty file."))
        file.close()
        return

    # Get the axis information.
    data_type = [x_data_type, y_data_type]
    seq_type, axis_labels = axis_setup(data_type=data_type, norm=norm)

    # Write the header.
    write_xy_header(format=format, file=file, data_type=data_type, seq_type=seq_type, sets=[len(data[0])], set_names=[set_names], axis_labels=[axis_labels], norm=[norm])

    # Write the data.
    write_xy_data(format=format, data=data, file=file, graph_type=graph_type, norm_type=norm_type, norm=[norm])

    # Close the file.
    file.close()

    # Add the file to the results file list.
    label = None
    if format == 'grace':
        label = 'Grace'
    add_result_file(type=format, label='Grace', file=file_path)
Ejemplo n.º 8
0
def write_xy(format='grace', x_data_type='res_num', y_data_type=None, spin_id=None, plot_data='value', norm_type='first', file=None, dir=None, force=False, norm=True):
    """Writing data to a file.

    @keyword format:        The specific backend to use.  The currently support backends are 'grace'.
    @type format:           str
    @keyword x_data_type:   The category of the X-axis data.
    @type x_data_type:      str
    @keyword y_data_type:   The category of the Y-axis data.
    @type y_data_type:      str
    @keyword spin_id:       The spin identification string.
    @type spin_id:          str
    @keyword plot_data:     The type of the plotted data, one of 'value', 'error', or 'sim'.
    @type plot_data:        str
    @keyword norm_type:     The point to normalise to 1.  This can be 'first' or 'last'.
    @type norm_type:        str
    @keyword file:          The name of the Grace file to create.
    @type file:             str
    @keyword dir:           The optional directory to place the file into.
    @type dir:              str
    @param force:           Boolean argument which if True causes the file to be overwritten if it already exists.
    @type force:            bool
    @keyword norm:          The normalisation flag which if set to True will cause all graphs to be normalised to a starting value of 1.
    @type norm:             bool
    """

    # Checks.
    check_pipe()
    check_mol_res_spin_data()

    # Test if the plot_data argument is one of 'value', 'error', or 'sim'.
    if plot_data not in ['value', 'error', 'sim']:
        raise RelaxError("The plot data argument " + repr(plot_data) + " must be set to either 'value', 'error', 'sim'.")

    # Test if the simulations exist.
    if plot_data == 'sim' and not hasattr(cdp, 'sim_number'):
        raise RelaxNoSimError

    # Open the file for writing.
    file_path = get_file_path(file, dir)
    file = open_write_file(file, dir, force)

    # Get the data.
    data, set_names, graph_type = assemble_data(spin_id, x_data_name=x_data_type, y_data_name=y_data_type, plot_data=plot_data)

    # Convert the graph type.
    if graph_type == 'X,Y':
        graph_type = 'xy'
    elif graph_type == 'X,Y,dX':
        graph_type = 'xydx'
    elif graph_type == 'X,Y,dY':
        graph_type = 'xydy'
    elif graph_type == 'X,Y,dX,dY':
        graph_type = 'xydxdy'

    # No data, so close the empty file and exit.
    if not len(data) or not len(data[0]) or not len(data[0][0]):
        warn(RelaxWarning("No data could be found, creating an empty file."))
        file.close()
        return

    # Get the axis information.
    data_type = [x_data_type, y_data_type]
    seq_type, axis_labels = axis_setup(data_type=data_type, norm=norm)

    # Write the header.
    write_xy_header(format=format, file=file, data_type=data_type, seq_type=seq_type, sets=[len(data[0])], set_names=[set_names], axis_labels=[axis_labels], norm=[norm])

    # Write the data.
    write_xy_data(format=format, data=data, file=file, graph_type=graph_type, norm_type=norm_type, norm=[norm])

    # Close the file.
    file.close()

    # Add the file to the results file list.
    label = None
    if format == 'grace':
        label = 'Grace'
    add_result_file(type=format, label='Grace', file=file_path)