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)
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)
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)
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)
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)
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)
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)
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)