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')")
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')")
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 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()
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)
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)
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)
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)
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)
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)
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) + ")")
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)
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)