from wx import FD_CHANGE_DIR
else:
FD_CHANGE_DIR = -1
from os import sep
# relax module imports.
from graphics import WIZARD_OXYGEN_PATH
from info import print_sys_info
from lib.timing import print_time
from pipe_control.system import cd, pwd
from user_functions.data import Uf_info
uf_info = Uf_info()
from user_functions.objects import Desc_container
# The user function class.
uf_class = uf_info.add_class('system')
uf_class.title = "Class containing the OS system related functions."
uf_class.menu_text = "&system"
uf_class.gui_icon = "oxygen.actions.help-about"
# The cd user function.
uf = uf_info.add_uf('system.cd')
uf.title = "Change the current working directory to the specified path."
uf.title_short = "Change current working directory."
uf.display = True
uf.add_keyarg(name="path",
py_type="str",
arg_type="dir sel",
desc_short="path",
desc="The path to the new current working directory.",
can_be_none=False,
# #
###############################################################################
# Module docstring.
"""The spectrometer user function definitions for loading spectrometer information."""
# relax module imports.
from graphics import WIZARD_IMAGE_PATH
from pipe_control import spectrum
import pipe_control.spectrometer
from user_functions.data import Uf_info
uf_info = Uf_info()
from user_functions.objects import Desc_container
# The user function class.
uf_class = uf_info.add_class('spectrometer')
uf_class.title = "Class for manipulating spectrometer frequencies."
uf_class.menu_text = "&spectrometer"
uf_class.gui_icon = "relax.spectrometer"
# The spectrometer.frequency user function.
uf = uf_info.add_uf('spectrometer.frequency')
uf.title = "Set the spectrometer proton frequency of the experiment."
uf.title_short = "Spectrometer frequency setup."
uf.add_keyarg(
name="id",
basic_types=["str"],
desc_short="experiment ID",
desc="The experiment identification string to set the frequency of.",
wiz_element_type='combo',
wiz_combo_iter=spectrum.get_ids)
else:
FD_OPEN = -1
# relax module imports.
from graphics import WIZARD_IMAGE_PATH
from lib.frame_order.variables import MODEL_DOUBLE_ROTOR, MODEL_FREE_ROTOR, MODEL_ISO_CONE, MODEL_ISO_CONE_FREE_ROTOR, MODEL_ISO_CONE_TORSIONLESS, MODEL_PSEUDO_ELLIPSE, MODEL_PSEUDO_ELLIPSE_FREE_ROTOR, MODEL_PSEUDO_ELLIPSE_TORSIONLESS, MODEL_RIGID, MODEL_ROTOR
from specific_analyses.frame_order.optimisation import count_sobol_points
from specific_analyses.frame_order.uf import distribute, sobol_setup, pdb_model, permute_axes, pivot, quad_int, ref_domain, select_model, simulate
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.data import Uf_tables; uf_tables = Uf_tables()
from user_functions.objects import Desc_container
from user_functions.wildcards import WILDCARD_STRUCT_PDB_ALL
# The user function class.
uf_class = uf_info.add_class('frame_order')
uf_class.title = "Class containing the user functions of the Frame Order theories."
uf_class.menu_text = "&frame_order"
uf_class.gui_icon = "relax.frame_order"
# The frame_order.count_sobol_points user function.
uf = uf_info.add_uf('frame_order.count_sobol_points')
uf.title = "Count the number of Sobol' points used for the current parameter values."
uf.title_short = "Used Sobol' point count."
# Description.
uf.desc.append(Desc_container())
uf.desc[-1].add_paragraph("This allows the number of Sobol' integration points used during the Frame Order target function optimisation to be counted. This uses the current parameter values to determine how many are used for the PCS calculation compared to the total number.")
uf.backend = count_sobol_points
uf.menu_text = "&count_sobol_points"
uf.gui_icon = "oxygen.categories.applications-education"
# along with this program. If not, see <http://www.gnu.org/licenses/>. #
# #
###############################################################################
# Module docstring.
"""The align_tensor user function definitions."""
# relax module imports.
from graphics import WIZARD_IMAGE_PATH
from pipe_control import align_tensor, pipes
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.objects import Desc_container
# The user function class.
uf_class = uf_info.add_class('align_tensor')
uf_class.title = "Class for manipulating the alignment tensor."
uf_class.menu_text = "&align_tensor"
uf_class.gui_icon = "relax.align_tensor"
# The align_tensor.copy user function.
uf = uf_info.add_uf('align_tensor.copy')
uf.title = "Copy alignment tensor data."
uf.title_short = "Alignment tensor copying."
uf.add_keyarg(
name = "tensor_from",
default = None,
py_type = "str",
desc_short = "source tensor ID",
desc = "The identification string of the alignment tensor to copy the data from."
###############################################################################
# Module docstring.
"""The relax_fit user function definitions."""
# relax module imports.
from graphics import ANALYSIS_IMAGE_PATH
from lib.text.gui import i0, iinf, rx
from pipe_control import spectrum
from specific_analyses.relax_fit.uf import relax_time, select_model
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.objects import Desc_container
# The user function class.
uf_class = uf_info.add_class('relax_fit')
uf_class.title = "Class for relaxation curve fitting."
uf_class.menu_text = "&relax_fit"
uf_class.gui_icon = "relax.relax_fit"
# The relax_fit.relax_time user function.
uf = uf_info.add_uf('relax_fit.relax_time')
uf.title = "Set the relaxation delay time associated with each spectrum."
uf.title_short = "Relaxation delay time setting."
uf.add_keyarg(
name = "time",
default = 0.0,
py_type = "num",
desc_short = "relaxation time",
desc = "The time, in seconds, of the relaxation period."
# #
###############################################################################
# Module docstring.
"""The residue user function definitions."""
# relax module imports.
from graphics import WIZARD_IMAGE_PATH
from pipe_control import pipes
from pipe_control.mol_res_spin import copy_residue, create_residue, delete_residue, display_residue, get_molecule_names, get_residue_ids, id_string_doc, name_residue, number_residue
from user_functions.data import Uf_info
uf_info = Uf_info()
from user_functions.objects import Desc_container
# The user function class.
uf_class = uf_info.add_class('residue')
uf_class.title = "Class for manipulating the residue data."
uf_class.menu_text = "&residue"
uf_class.gui_icon = "relax.residue"
# The residue.copy user function.
uf = uf_info.add_uf('residue.copy')
uf.title = "Copy all data associated with a residue."
uf.title_short = "Residue copying."
uf.display = True
uf.add_keyarg(
name="pipe_from",
py_type="str",
desc_short="source pipe",
desc=
"The data pipe containing the residue from which the data will be copied. This defaults to the current data pipe.",
# Python module imports.
import dep_check
if dep_check.wx_module:
from wx import FD_OPEN
else:
FD_OPEN = -1
# relax module imports.
from graphics import WIZARD_IMAGE_PATH
from pipe_control import bruker
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.objects import Desc_container
# The user function class.
uf_class = uf_info.add_class('bruker')
uf_class.title = "Class containing the function for reading the Bruker Dynamics Center (DC) files."
uf_class.menu_text = "&bruker"
uf_class.gui_icon = "relax.bruker"
# The bruker.read user function.
uf = uf_info.add_uf('bruker.read')
uf.title = "Read a Bruker Dynamics Center (DC) relaxation data file."
uf.title_short = "Read a Bruker Dynamics Center file."
uf.add_keyarg(
name = "ri_id",
py_type = "str",
desc_short = "relaxation data ID string",
desc = "The relaxation data ID string. This must be a unique identifier."
)
from wx import FD_CHANGE_DIR
else:
FD_CHANGE_DIR = -1
from os import sep
# relax module imports.
from graphics import WIZARD_OXYGEN_PATH
from info import print_sys_info
from lib.timing import print_time
from pipe_control.system import cd, pwd
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.objects import Desc_container
# The user function class.
uf_class = uf_info.add_class('system')
uf_class.title = "Class containing the OS system related functions."
uf_class.menu_text = "&system"
uf_class.gui_icon = "oxygen.actions.help-about"
# The cd user function.
uf = uf_info.add_uf('system.cd')
uf.title = "Change the current working directory to the specified path."
uf.title_short = "Change current working directory."
uf.display = True
uf.add_keyarg(
name = "path",
py_type = "str",
arg_type = "dir sel",
desc_short = "path",
# Module docstring.
"""The pipe user function definitions."""
# relax module imports.
from graphics import WIZARD_IMAGE_PATH
from pipe_control import pipes
from specific_analyses.api import return_api
from user_functions.data import Uf_info
uf_info = Uf_info()
from user_functions.objects import Desc_container
# The hybrid API object.
hybrid_obj = return_api('hybrid')
# The user function class.
uf_class = uf_info.add_class('pipe')
uf_class.title = "Class holding the user functions for manipulating data pipes."
uf_class.menu_text = "&pipe"
uf_class.gui_icon = "relax.pipe"
# The pipe.bundle user function.
uf = uf_info.add_uf('pipe.bundle')
uf.title = "The grouping of data pipes into a bundle."
uf.title_short = "Data pipe bundling."
uf.add_keyarg(
name="bundle",
basic_types=["str"],
desc_short="pipe bundle",
desc="The pipe bundle is a special grouping or clustering of data pipes.",
wiz_element_type='combo',
wiz_combo_iter=pipes.bundle_names,
# #
###############################################################################
# Module docstring.
"""The molecule user function definitions."""
# relax module imports.
from graphics import WIZARD_IMAGE_PATH
from pipe_control import pipes
from pipe_control.mol_res_spin import ALLOWED_MOL_TYPES, copy_molecule, create_molecule, delete_molecule, display_molecule, get_molecule_ids, id_string_doc, name_molecule, type_molecule
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.objects import Desc_container
# The user function class.
uf_class = uf_info.add_class('molecule')
uf_class.title = "Class for manipulating the molecule data."
uf_class.menu_text = "&molecule"
uf_class.gui_icon = "relax.molecule"
# The molecule.copy user function.
uf = uf_info.add_uf('molecule.copy')
uf.title = "Copy all data associated with a molecule."
uf.title_short = "Molecule copying."
uf.display = True
uf.add_keyarg(
name = "pipe_from",
py_type = "str",
desc_short = "source data pipe",
desc = "The data pipe containing the molecule from which the data will be copied. This defaults to the current data pipe.",
# along with this program. If not, see <http://www.gnu.org/licenses/>. #
# #
###############################################################################
# Module docstring.
"""The state user function definitions."""
# relax module imports.
from pipe_control.state import load_state, save_state
from user_functions.data import Uf_info
uf_info = Uf_info()
from user_functions.objects import Desc_container
from user_functions.wildcards import WILDCARD_RELAX_SAVE
# The user function class.
uf_class = uf_info.add_class('state')
uf_class.title = "Class for saving or loading the program state."
uf_class.menu_text = "&state"
uf_class.gui_icon = "relax.relax"
# The state.load user function.
uf = uf_info.add_uf('state.load')
uf.title = "Load a saved program state."
uf.title_short = "Saved state loading."
uf.add_keyarg(
name="state",
default="state.bz2",
arg_type="file sel read",
desc_short="file name",
desc=
"The file name, which can be a string or a file descriptor object, of a saved program state.",
if dep_check.wx_module:
from wx import FD_OPEN
else:
FD_OPEN = -1
# relax module imports.
from graphics import WIZARD_IMAGE_PATH
from lib.physical_constants import NH_BOND_LENGTH
from pipe_control.mol_res_spin import get_spin_ids
from pipe_control import pipes, interatomic
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.objects import Desc_container
# The user function class.
uf_class = uf_info.add_class('interatom')
uf_class.title = "Class for manipulating magnetic dipole-dipole interactions."
uf_class.menu_text = "&interatom"
uf_class.gui_icon = "relax.dipole_pair"
# The interatom.copy user function.
uf = uf_info.add_uf('interatom.copy')
uf.title = "Copy all data associated with a interatomic data container."
uf.title_short = "Interatomic interaction copying."
uf.display = True
uf.add_keyarg(
name = "pipe_from",
py_type = "str",
desc_short = "source data pipe",
desc = "The data pipe containing the interatomic data container from which the data will be copied. This defaults to the current data pipe.",
FD_OPEN = -1
FD_SAVE = -1
# relax module imports.
import colour
from graphics import WIZARD_IMAGE_PATH
from pipe_control import molmol
from specific_analyses.model_free.uf import classic_style_doc
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.objects import Desc_container
from user_functions.wildcards import WILDCARD_MOLMOL_MACRO, WILDCARD_STRUCT_PDB
# The user function class.
uf_class = uf_info.add_class('molmol')
uf_class.title = "Class for interfacing with Molmol."
uf_class.menu_text = "&molmol"
uf_class.gui_icon = "relax.molmol"
# The molmol.clear_history user function.
uf = uf_info.add_uf('molmol.clear_history')
uf.title = "Clear the Molmol command history."
uf.title_short = "Clear Molmol history."""
# Description.
uf.desc.append(Desc_container())
uf.desc[-1].add_paragraph("This will clear the Molmol history from memory.")
uf.backend = molmol.molmol_obj.clear_history
uf.menu_text = "clear_&history"
uf.wizard_size = (600, 300)
import dep_check
if dep_check.wx_module:
from wx import FD_OPEN, FD_SAVE
else:
FD_OPEN = -1
FD_SAVE = -1
# relax module imports.
from graphics import WIZARD_IMAGE_PATH
from pipe_control import pipes, j_coupling
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.objects import Desc_container
# The user function class.
uf_class = uf_info.add_class('j_coupling')
uf_class.title = "Class for handling scalar couplings."
uf_class.menu_text = "&j_coupling"
uf_class.gui_icon = "relax.j_coupling"
# The j_coupling.copy user function.
uf = uf_info.add_uf('j_coupling.copy')
uf.title = "Copy J coupling data from one data pipe to another."
uf.title_short = "J coupling copying."
uf.add_keyarg(
name = "pipe_from",
py_type = "str",
desc_short = "source pipe",
desc = "The name of the pipe to copy the J coupling data from.",
wiz_element_type = 'combo',
# #
###############################################################################
# Module docstring.
"""The noe user function definitions."""
# relax module imports.
from graphics import ANALYSIS_IMAGE_PATH
from pipe_control import noesy, spectrum
from specific_analyses.noe.uf import spectrum_type
from user_functions.data import Uf_info
uf_info = Uf_info()
from user_functions.objects import Desc_container
# The user function class.
uf_class = uf_info.add_class('noe')
uf_class.title = "Class for handling steady-state NOE and NOESY data."
uf_class.menu_text = "&noe"
uf_class.gui_icon = "relax.noe"
# The noe.read_restraints user function.
uf = uf_info.add_uf('noe.read_restraints')
uf.title = "Read NOESY or ROESY restraints from a file."
uf.title_short = "Restraint reading."
uf.add_keyarg(
name="file",
arg_type="file sel read",
desc_short="file name",
desc="The name of the file containing the restraint data.",
)
uf.add_keyarg(name="dir",
# #
###############################################################################
# Module docstring.
"""The spectrometer user function definitions for loading spectrometer information."""
# relax module imports.
from graphics import WIZARD_IMAGE_PATH
from pipe_control import spectrum
import pipe_control.spectrometer
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.objects import Desc_container
# The user function class.
uf_class = uf_info.add_class('spectrometer')
uf_class.title = "Class for manipulating spectrometer frequencies."
uf_class.menu_text = "&spectrometer"
uf_class.gui_icon = "relax.spectrometer"
# The spectrometer.frequency user function.
uf = uf_info.add_uf('spectrometer.frequency')
uf.title = "Set the spectrometer proton frequency of the experiment."
uf.title_short = "Spectrometer frequency setup."
uf.add_keyarg(
name = "id",
py_type = "str",
desc_short = "experiment ID",
desc = "The experiment identification string to set the frequency of.",
wiz_element_type = 'combo',
wiz_combo_iter = spectrum.get_ids
# Python module imports.
import dep_check
if dep_check.wx_module:
from wx import FD_OPEN
else:
FD_OPEN = -1
# relax module imports.
from graphics import WIZARD_IMAGE_PATH
from pipe_control import domain, selection, spectrum
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.objects import Desc_container
# The user function class.
uf_class = uf_info.add_class("select")
uf_class.title = "Class for selecting spins."
uf_class.menu_text = "&select"
uf_class.gui_icon = "relax.spin"
# The select.all user function.
uf = uf_info.add_uf("select.all")
uf.title = "Select all spins in the current data pipe."
uf.title_short = "Selection of all spins."
uf.display = True
# Description.
uf.desc.append(Desc_container())
uf.desc[-1].add_paragraph("This will select all spins, irregardless of their current state.")
# Prompt examples.
uf.desc.append(Desc_container("Prompt examples"))
# Python module imports.
import dep_check
if dep_check.wx_module:
from wx import FD_OPEN
else:
FD_OPEN = -1
# relax module imports.
from pipe_control import dasha
from user_functions.data import Uf_info
uf_info = Uf_info()
from user_functions.objects import Desc_container
# The user function class.
uf_class = uf_info.add_class('dasha')
uf_class.title = "Class for interfacing with the program Dasha."
uf_class.menu_text = "&dasha"
# The dasha.create user function.
uf = uf_info.add_uf('dasha.create')
uf.title = "Create the Dasha script."
uf.title_short = "Script creation."
uf.add_keyarg(name="algor",
default="LM",
py_type="str",
desc_short="optimisation algorithm",
desc="The minimisation algorithm.",
wiz_element_type="combo",
wiz_combo_choices=["Levenberg-Marquardt", "Newton-Raphson"],
wiz_combo_data=["LM", "NR"],
# #
###############################################################################
# Module docstring.
"""The pipe user function definitions."""
# relax module imports.
from graphics import WIZARD_IMAGE_PATH
from pipe_control import pipes
from specific_analyses.setup import hybrid_obj
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.objects import Desc_container
# The user function class.
uf_class = uf_info.add_class('pipe')
uf_class.title = "Class holding the user functions for manipulating data pipes."
uf_class.menu_text = "&pipe"
uf_class.gui_icon = "relax.pipe"
# The pipe.bundle user function.
uf = uf_info.add_uf('pipe.bundle')
uf.title = "The grouping of data pipes into a bundle."
uf.title_short = "Data pipe bundling."
uf.add_keyarg(
name = "bundle",
py_type = "str",
desc_short = "pipe bundle",
desc = "The pipe bundle is a special grouping or clustering of data pipes.",
wiz_element_type = 'combo',
# Python module imports.
import dep_check
if dep_check.wx_module:
from wx import FD_OPEN
else:
FD_OPEN = -1
# relax module imports.
from graphics import WIZARD_IMAGE_PATH
from pipe_control import palmer
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.objects import Desc_container
# The user function class.
uf_class = uf_info.add_class('palmer')
uf_class.title = "Class for interfacing with Art Palmer's Modelfree 4."
uf_class.menu_text = "&palmer"
uf_class.gui_icon = "relax.modelfree4"
# The palmer.create user function.
uf = uf_info.add_uf('palmer.create')
uf.title = "Create the Modelfree4 input files."
uf.title_short = "Modelfree4 input file creation."
uf.add_keyarg(
name = "dir",
py_type = "str",
arg_type = "dir sel",
desc_short = "directory name",
desc = "The directory to place the files.",
import dep_check
if dep_check.wx_module:
from wx import FD_OPEN, FD_SAVE
else:
FD_OPEN = -1
FD_SAVE = -1
# relax module imports.
from graphics import WIZARD_IMAGE_PATH
from pipe_control import pipes, sequence
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.objects import Desc_container
# The user function class.
uf_class = uf_info.add_class('sequence')
uf_class.title = "Class for manipulating sequence data."
uf_class.menu_text = "&sequence"
uf_class.gui_icon = "relax.sequence"
# The sequence.attach_protons user function.
uf = uf_info.add_uf('sequence.attach_protons')
uf.title = "Attach protons to all heteronuclei."
uf.title_short = "Heteronuclei proton attachment."
# Description.
uf.desc.append(Desc_container())
uf.desc[-1].add_paragraph("This can be used to attach protons to all the heteronuclei in the current data pipe. For each proton, a spin container will be created.")
# Prompt examples.
uf.desc.append(Desc_container("Prompt examples"))
uf.desc[-1].add_paragraph("To attach protons, simply type:")
import dep_check
if dep_check.wx_module:
from wx import FD_OPEN, FD_SAVE
else:
FD_OPEN = -1
FD_SAVE = -1
# relax module imports.
from graphics import WIZARD_IMAGE_PATH
from pipe_control import pipes, sequence
from user_functions.data import Uf_info
uf_info = Uf_info()
from user_functions.objects import Desc_container
# The user function class.
uf_class = uf_info.add_class('sequence')
uf_class.title = "Class for manipulating sequence data."
uf_class.menu_text = "&sequence"
uf_class.gui_icon = "relax.sequence"
# The sequence.attach_protons user function.
uf = uf_info.add_uf('sequence.attach_protons')
uf.title = "Attach protons to all heteronuclei."
uf.title_short = "Heteronuclei proton attachment."
# Description.
uf.desc.append(Desc_container())
uf.desc[-1].add_paragraph(
"This can be used to attach protons to all the heteronuclei in the current data pipe. For each proton, a spin container will be created. This should be used when the sequence information is not being extracted from a 3D structure. Note that the proton spin containers will not possess any positional information, so for analyses which require this position or vectors from one atom to this proton, it should not be used."
)
# Prompt examples.
uf.desc.append(Desc_container("Prompt examples"))
# along with this program. If not, see <http://www.gnu.org/licenses/>. #
# #
###############################################################################
# Module docstring.
"""The diffusion_tensor user function definitions."""
# relax module imports.
from graphics import WIZARD_IMAGE_PATH
from pipe_control import diffusion_tensor, pipes
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.objects import Desc_container
# The user function class.
uf_class = uf_info.add_class('diffusion_tensor')
uf_class.title = "Class for manipulating the diffusion tensor."
uf_class.menu_text = "&diffusion_tensor"
uf_class.gui_icon = "relax.diff_tensor"
# The diffusion_tensor.copy user function.
uf = uf_info.add_uf('diffusion_tensor.copy')
uf.title = "Copy diffusion tensor data from one data pipe to another."
uf.title_short = "Diffusion tensor data copying."
uf.add_keyarg(
name = "pipe_from",
py_type = "str",
desc_short = "source data pipe",
desc = "The name of the data pipe to copy the diffusion tensor data from.",
wiz_element_type = 'combo',
if dep_check.wx_module:
from wx import FD_SAVE
else:
FD_SAVE = -1
# relax module imports.
from graphics import WIZARD_IMAGE_PATH
from specific_analyses.n_state_model import uf as n_state_model_uf
from specific_analyses.n_state_model.parameters import elim_no_prob, number_of_states, ref_domain, select_model
from user_functions.data import Uf_info
uf_info = Uf_info()
from user_functions.objects import Desc_container
from user_functions.wildcards import WILDCARD_STRUCT_PDB_ALL
# The user function class.
uf_class = uf_info.add_class('n_state_model')
uf_class.title = "Class for the N-state models."
uf_class.menu_text = "&n_state_model"
uf_class.gui_icon = "relax.n_state_model"
# The n_state_model.CoM user function.
uf = uf_info.add_uf('n_state_model.CoM')
uf.title = "The defunct centre of mass (CoM) analysis."
uf.title_short = "CoM analysis."
uf.add_keyarg(name="pivot_point",
default=[0.0, 0.0, 0.0],
py_type="num_list",
dim=3,
desc_short="pivot point",
desc="The pivot point of the motions between the two domains.",
list_titles=['X coordinate', 'Y coordinate', 'Z coordinate'])
FD_OPEN = -1
# relax module imports.
from graphics import WIZARD_IMAGE_PATH
from lib.frame_order.variables import MODEL_DOUBLE_ROTOR, MODEL_FREE_ROTOR, MODEL_ISO_CONE, MODEL_ISO_CONE_FREE_ROTOR, MODEL_ISO_CONE_TORSIONLESS, MODEL_PSEUDO_ELLIPSE, MODEL_PSEUDO_ELLIPSE_FREE_ROTOR, MODEL_PSEUDO_ELLIPSE_TORSIONLESS, MODEL_RIGID, MODEL_ROTOR
from specific_analyses.frame_order.optimisation import count_sobol_points
from specific_analyses.frame_order.uf import distribute, sobol_setup, pdb_model, permute_axes, pivot, quad_int, ref_domain, select_model, simulate
from user_functions.data import Uf_info
uf_info = Uf_info()
from user_functions.data import Uf_tables
uf_tables = Uf_tables()
from user_functions.objects import Desc_container
from user_functions.wildcards import WILDCARD_STRUCT_PDB_ALL
# The user function class.
uf_class = uf_info.add_class('frame_order')
uf_class.title = "Class containing the user functions of the Frame Order theories."
uf_class.menu_text = "&frame_order"
uf_class.gui_icon = "relax.frame_order"
# The frame_order.count_sobol_points user function.
uf = uf_info.add_uf('frame_order.count_sobol_points')
uf.title = "Count the number of Sobol' points used for the current parameter values."
uf.title_short = "Used Sobol' point count."
# Description.
uf.desc.append(Desc_container())
uf.desc[-1].add_paragraph(
"This allows the number of Sobol' integration points used during the Frame Order target function optimisation to be counted. This uses the current parameter values to determine how many are used for the PCS calculation compared to the total number."
)
uf.backend = count_sobol_points
uf.menu_text = "&count_sobol_points"
from wx import FD_OPEN, FD_SAVE
else:
FD_OPEN = -1
FD_SAVE = -1
# relax module imports.
from graphics import WIZARD_IMAGE_PATH
from pipe_control import align_tensor, pipes, rdc
from pipe_control.mol_res_spin import get_spin_ids
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.objects import Desc_container
from user_functions.wildcards import WILDCARD_GRACE_ALL
# The user function class.
uf_class = uf_info.add_class('rdc')
uf_class.title = "Class for handling residual dipolar couplings."
uf_class.menu_text = "&rdc"
uf_class.gui_icon = "relax.align_tensor"
# The rdc.back_calc user function.
uf = uf_info.add_uf('rdc.back_calc')
uf.title = "Back calculate the residual dipolar couplings."
uf.title_short = "RDC back calculation."
uf.display = True
uf.add_keyarg(
name = "align_id",
py_type = "str",
desc_short = "alignment ID string",
desc = "The alignment ID string.",
# Module docstring.
"""The model_free user function definitions for model-free analysis."""
# Python module imports.
from os import sep
# relax module imports.
from graphics import ANALYSIS_IMAGE_PATH
from lib.text.gui import csa, local_tm, r, rex, s2, s2f, te, tf, ts
from specific_analyses.model_free.uf import create_model, delete, remove_tm, select_model
from user_functions.data import Uf_info
uf_info = Uf_info()
from user_functions.objects import Desc_container
# The user function class.
uf_class = uf_info.add_class('model_free')
uf_class.title = "Class for model-free analysis."
uf_class.menu_text = "&model_free"
uf_class.gui_icon = "relax.model-free"
# The model_free.create_model user function.
uf = uf_info.add_uf('model_free.create_model')
uf.title = "Create a model-free model."
uf.title_short = "Model-free model creation."
uf.display = True
uf.add_keyarg(name="model",
basic_types=["str"],
desc_short="model name",
desc="The new name of the model-free model.")
uf.add_keyarg(name="equation",
basic_types=["str"],
import dep_check
if dep_check.wx_module:
from wx import FD_SAVE
else:
FD_SAVE = -1
# relax module imports.
from graphics import WIZARD_IMAGE_PATH
from specific_analyses.n_state_model.parameters import elim_no_prob, number_of_states, ref_domain, select_model
from specific_analyses.setup import n_state_model_obj
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.objects import Desc_container
# The user function class.
uf_class = uf_info.add_class('n_state_model')
uf_class.title = "Class for the N-state models."
uf_class.menu_text = "&n_state_model"
uf_class.gui_icon = "relax.n_state_model"
# The n_state_model.CoM user function.
uf = uf_info.add_uf('n_state_model.CoM')
uf.title = "The defunct centre of mass (CoM) analysis."
uf.title_short = "CoM analysis."
uf.add_keyarg(
name = "pivot_point",
default = [0.0, 0.0, 0.0],
py_type = "num_list",
dim = 3,
desc_short = "pivot point",
else:
FD_OPEN = -1
FD_SAVE = -1
# relax module imports.
import colour
from graphics import WIZARD_IMAGE_PATH
from pipe_control import pymol_control
from specific_analyses.model_free.uf import classic_style_doc
from user_functions.data import Uf_info
uf_info = Uf_info()
from user_functions.objects import Desc_container
from user_functions.wildcards import WILDCARD_PYMOL_MACRO, WILDCARD_STRUCT_PDB_ALL
# The user function class.
uf_class = uf_info.add_class('pymol')
uf_class.title = "Class for interfacing with PyMOL."
uf_class.menu_text = "&pymol"
uf_class.gui_icon = "relax.pymol_icon"
# The pymol.cartoon user function.
uf = uf_info.add_uf('pymol.cartoon')
uf.title = "Apply the PyMOL cartoon style and colour by secondary structure."
uf.title_short = "PyMOL cartoon style application."
# Description.
uf.desc.append(Desc_container())
uf.desc[-1].add_paragraph(
"This applies the PyMOL cartoon style which is equivalent to hiding everything and clicking on show cartoon. It also colours the cartoon with red helices, yellow strands, and green loops. The following commands are executed:"
)
uf.desc[-1].add_list_element("cmd.hide('everything', file)")
uf.desc[-1].add_list_element("cmd.show('cartoon', file)")
"""The chemical_shift user function definitions."""
# Python module imports.
from os import sep
# relax module imports.
from graphics import WIZARD_IMAGE_PATH
from pipe_control import chemical_shift
from user_functions.data import Uf_info
uf_info = Uf_info()
from user_functions.objects import Desc_container
from user_functions.wildcards import WILDCARD_SPECTRUM_PEAKLIST
# The user function class.
uf_class = uf_info.add_class('chemical_shift')
uf_class.title = "Class for handling chemical shifts."
uf_class.menu_text = "&chemical_shift"
uf_class.gui_icon = "relax.chemical_shift"
# The chemical_shift.read user function.
uf = uf_info.add_uf('chemical_shift.read')
uf.title = "Read chemical shifts from a file."
uf.title_short = "Chemical shift reading."
uf.add_keyarg(
name="file",
arg_type="file sel read",
desc_short="file name",
desc=
"The name of the peak list of generic formatted file containing the chemical shifts.",
wiz_filesel_wildcard=WILDCARD_SPECTRUM_PEAKLIST,
# Module docstring.
"""The error_analysis user function definitions."""
# Python module imports.
from os import sep
# relax module imports.
from graphics import ANALYSIS_IMAGE_PATH
from pipe_control.error_analysis import covariance_matrix
from user_functions.data import Uf_info
uf_info = Uf_info()
from user_functions.objects import Desc_container
# The user function class.
uf_class = uf_info.add_class('error_analysis')
uf_class.title = "Class for relaxation curve fitting."
uf_class.menu_text = "&error_analysis"
# The error_analysis.covariance_matrix user function.
uf = uf_info.add_uf('error_analysis.covariance_matrix')
uf.title = "Parameter error estimation via the covariance matrix."
uf.title_short = "Covariance matrix parameter error estimation."
uf.add_keyarg(
name="epsrel",
basic_types=["float"],
default=0.0,
desc_short="parameter to remove linear-dependent columns.",
desc=
"The parameter to remove linear-dependent columns when J is rank deficient.",
can_be_none=False)
FD_OPEN = -1
# relax module imports.
from graphics import WIZARD_IMAGE_PATH
from lib.software.opendx.execute import run
from pipe_control import diffusion_tensor
from pipe_control.opendx import map
from prompt.doc_string import regexp_doc
from specific_analyses.model_free import Model_free
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.data import Uf_tables; uf_tables = Uf_tables()
from user_functions.objects import Desc_container
# The user function class.
uf_class = uf_info.add_class("dx")
uf_class.title = "Class for interfacing with OpenDX."
uf_class.menu_text = "&dx"
uf_class.gui_icon = "relax.opendx"
# The dx.execute user function.
uf = uf_info.add_uf("dx.execute")
uf.title = "Execute an OpenDX program."
uf.title_short = "OpenDX execution."
uf.add_keyarg(
name = "file_prefix",
default = "map",
py_type = "str",
desc_short = "file name",
desc = "The file name prefix. For example if file is set to 'temp', then the OpenDX program temp.net will be loaded."
# Module docstring.
"""The error_analysis user function definitions."""
# Python module imports.
from os import sep
# relax module imports.
from graphics import ANALYSIS_IMAGE_PATH
from pipe_control.error_analysis import covariance_matrix
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.objects import Desc_container
# The user function class.
uf_class = uf_info.add_class('error_analysis')
uf_class.title = "Class for relaxation curve fitting."
uf_class.menu_text = "&error_analysis"
# The error_analysis.covariance_matrix user function.
uf = uf_info.add_uf('error_analysis.covariance_matrix')
uf.title = "Parameter error estimation via the covariance matrix."
uf.title_short = "Covariance matrix parameter error estimation."
uf.add_keyarg(
name = "epsrel",
py_type = "float",
default = 0.0,
desc_short = "parameter to remove linear-dependent columns.",
desc = "The parameter to remove linear-dependent columns when J is rank deficient.",
can_be_none = False
###############################################################################
# Module docstring.
"""The minimisation user function definitions."""
# relax module imports.
from graphics import WIZARD_IMAGE_PATH
from pipe_control import minimise
from user_functions.data import Uf_info, Uf_tables
uf_info = Uf_info()
uf_tables = Uf_tables()
from user_functions.objects import Desc_container
# The user function class.
uf_class = uf_info.add_class('minimise')
uf_class.title = "Class for setting parameter values."
uf_class.menu_text = "&minimise"
uf_class.gui_icon = "relax.rosenbrock"
# The minimise.calculate user function.
uf = uf_info.add_uf('minimise.calculate')
uf.title = "Calculate the model parameters or the current target function value."
uf.title_short = "Model parameter or target function value calculation."
uf.display = True
uf.add_keyarg(
name="verbosity",
default=1,
basic_types=["int"],
desc_short="verbosity level",
desc=
if dep_check.wx_module:
from wx import FD_OPEN
else:
FD_OPEN = -1
# relax module imports.
from graphics import WIZARD_IMAGE_PATH
from pipe_control import spectrum
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.data import Uf_tables; uf_tables = Uf_tables()
from user_functions.objects import Desc_container
from user_functions.wildcards import WILDCARD_SPECTRUM_PEAKLIST
# The user function class.
uf_class = uf_info.add_class('spectrum')
uf_class.title = "Class for supporting the input of spectral data."
uf_class.menu_text = "&spectrum"
uf_class.gui_icon = "relax.fid"
# The spectrum.baseplane_rmsd user function.
uf = uf_info.add_uf('spectrum.baseplane_rmsd')
uf.title = "Set the baseplane RMSD of a given spin in a spectrum for error analysis."
uf.title_short = "Baseplane RMSD setting."
uf.add_keyarg(
name = "error",
default = 0.0,
py_type = "num",
desc_short = "error",
desc = "The baseplane RMSD error value."
jw_mapping_params = Jw_mapping_params()
from specific_analyses.model_free.parameter_object import Model_free_params
model_free_params = Model_free_params()
from specific_analyses.noe.parameter_object import Noe_params
noe_params = Noe_params()
from specific_analyses.relax_disp.parameter_object import Relax_disp_params
relax_disp_params = Relax_disp_params()
from specific_analyses.relax_fit.parameter_object import Relax_fit_params
relax_fit_params = Relax_fit_params()
from user_functions.data import Uf_info
uf_info = Uf_info()
from user_functions.objects import Desc_container
from user_functions.wildcards import WILDCARD_GRACE_ALL
# The user function class.
uf_class = uf_info.add_class('grace')
uf_class.title = "Class for interfacing with Grace."
uf_class.menu_text = "&grace"
uf_class.gui_icon = "relax.grace_icon"
# The grace.view user function.
uf = uf_info.add_uf('grace.view')
uf.title = "Visualise the file within Grace."
uf.title_short = "Grace execution."
uf.add_keyarg(
name="file",
arg_type="file sel read",
desc_short="file name",
desc="The name of the file.",
wiz_filesel_wildcard=WILDCARD_GRACE_ALL,
)
# along with this program. If not, see <http://www.gnu.org/licenses/>. #
# #
###############################################################################
# Module docstring.
"""The align_tensor user function definitions."""
# relax module imports.
from graphics import WIZARD_IMAGE_PATH
from pipe_control import align_tensor, pipes
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.objects import Desc_container
# The user function class.
uf_class = uf_info.add_class('align_tensor')
uf_class.title = "Class for manipulating the alignment tensor."
uf_class.menu_text = "&align_tensor"
uf_class.gui_icon = "relax.align_tensor"
# The align_tensor.copy user function.
uf = uf_info.add_uf('align_tensor.copy')
uf.title = "Copy alignment tensor data."
uf.title_short = "Alignment tensor copying."
uf.add_keyarg(
name = "tensor_from",
default = None,
py_type = "str",
desc_short = "source tensor ID",
desc = "The identification string of the alignment tensor to copy the data from.",
import dep_check
if dep_check.wx_module:
from wx import FD_OPEN, FD_SAVE
else:
FD_OPEN = -1
FD_SAVE = -1
# relax module imports.
from graphics import WIZARD_IMAGE_PATH
from pipe_control import bmrb, exp_info, pipes
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.objects import Desc_container
# The user function class.
uf_class = uf_info.add_class('bmrb')
uf_class.title = "Class for interfacing with the BMRB (http://www.bmrb.wisc.edu/)."
uf_class.menu_text = "&bmrb"
uf_class.gui_icon = "relax.bmrb"
# The bmrb.citation user function.
uf = uf_info.add_uf('bmrb.citation')
uf.title = "Specify a citation to be added the BMRB data file."
uf.title_short = "Add a citation."
uf.add_keyarg(
name = "cite_id",
py_type = "str",
desc_short = "citation ID",
desc = "The citation ID string."
)
uf.add_keyarg(
import dep_check
if dep_check.wx_module:
from wx import FD_OPEN
else:
FD_OPEN = -1
# relax module imports.
from graphics import ANALYSIS_IMAGE_PATH
from pipe_control import noesy, spectrum
from specific_analyses.noe.uf import spectrum_type
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.objects import Desc_container
# The user function class.
uf_class = uf_info.add_class('noe')
uf_class.title = "Class for handling steady-state NOE and NOESY data."
uf_class.menu_text = "&noe"
uf_class.gui_icon = "relax.noe"
# The noe.read_restraints user function.
uf = uf_info.add_uf('noe.read_restraints')
uf.title = "Read NOESY or ROESY restraints from a file."
uf.title_short = "Restraint reading."
uf.add_keyarg(
name = "file",
py_type = "str",
arg_type = "file sel",
desc_short = "file name",
desc = "The name of the file containing the restraint data.",
if dep_check.wx_module:
from wx import FD_OPEN
else:
FD_OPEN = -1
# relax module imports.
from graphics import WIZARD_IMAGE_PATH
from pipe_control import bruker
from user_functions.data import Uf_info
uf_info = Uf_info()
from user_functions.objects import Desc_container
# The user function class.
uf_class = uf_info.add_class("bruker")
uf_class.title = "Class containing the function for reading the Bruker Dynamics Center (DC) files."
uf_class.menu_text = "&bruker"
uf_class.gui_icon = "relax.bruker"
# The bruker.read user function.
uf = uf_info.add_uf("bruker.read")
uf.title = "Read a Bruker Dynamics Center (DC) relaxation data file."
uf.title_short = "Read a Bruker Dynamics Center file."
uf.add_keyarg(
name="ri_id",
py_type="str",
desc_short="relaxation data ID string",
desc="The relaxation data ID string. This must be a unique identifier.",
)
# along with this program. If not, see <http://www.gnu.org/licenses/>. #
# #
###############################################################################
# Module docstring.
"""The jw_mapping user function definitions for Reduced Spectral Density Mapping."""
# relax module imports.
from pipe_control import spectrometer
from specific_analyses.setup import jw_mapping_obj
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.objects import Desc_container
# The user function class.
uf_class = uf_info.add_class('jw_mapping')
uf_class.title = "Class containing functions specific to reduced spectral density mapping."
uf_class.menu_text = "&jw_mapping"
uf_class.gui_icon = "relax.jw_mapping"
# The jw_mapping.set_frq user function.
uf = uf_info.add_uf('jw_mapping.set_frq')
uf.title = "Select which relaxation data to use in the J(w) mapping by NMR spectrometer frequency."
uf.title_short = "Spectrometer selection."
uf.add_keyarg(
name = "frq",
py_type = "float",
desc_short = "spectrometer frequency in Hz",
desc = "The spectrometer frequency in Hz. This must match the currently loaded data to the last decimal point. See the 'sfrq' parameter in the Varian procpar file or the 'SFO1' parameter in the Bruker acqus file.",
wiz_element_type = 'combo',
###############################################################################
# Module docstring.
"""The statistics user function definitions."""
# relax module imports.
from graphics import WIZARD_IMAGE_PATH
from pipe_control.statistics import aic, model_statistics
from user_functions.data import Uf_info
uf_info = Uf_info()
from user_functions.objects import Desc_container
# The user function class.
uf_class = uf_info.add_class("statistics")
uf_class.title = "Class containing the statistics related functions."
uf_class.menu_text = "&statistics"
uf_class.gui_icon = "oxygen.actions.office-chart-pie"
# The statistics.aic user function.
uf = uf_info.add_uf("statistics.aic")
uf.title = "Calculate and store Akaike's Information Criterion (AIC) for each model."
uf.title_short = "Calculate AIC values."
# Description.
uf.desc.append(Desc_container())
uf.desc[-1].add_paragraph(
"This will perform a calculation to obtain the chi-squared statistic for the current parameter values for each model, count the number of parameters per model and calculate Akaike's Information Criterion (AIC) using the formula AIC = chi2 + 2k. The AIC values, chi-squared values, and number of parameters will be stored in the appropriate location for the model in the relax data store."
)
uf.backend = aic
from pipe_control import pipes, value
from specific_analyses.consistency_tests.parameter_object import Consistency_tests_params; consistency_test_params = Consistency_tests_params()
from specific_analyses.frame_order.parameter_object import Frame_order_params; frame_order_params = Frame_order_params()
from specific_analyses.jw_mapping.parameter_object import Jw_mapping_params; jw_mapping_params = Jw_mapping_params()
from specific_analyses.model_free.parameter_object import Model_free_params; model_free_params = Model_free_params()
from specific_analyses.n_state_model.parameter_object import N_state_params; n_state_params = N_state_params()
from specific_analyses.noe.parameter_object import Noe_params; noe_params = Noe_params()
from specific_analyses.relax_disp.parameter_object import Relax_disp_params; relax_disp_params = Relax_disp_params()
from specific_analyses.relax_fit.parameter_object import Relax_fit_params; relax_fit_params = Relax_fit_params()
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.data import Uf_tables; uf_tables = Uf_tables()
from user_functions.objects import Desc_container
# The user function class.
uf_class = uf_info.add_class('value')
uf_class.title = "Class for setting parameter values."
uf_class.menu_text = "&value"
uf_class.gui_icon = "relax.value"
# The value.copy user function.
uf = uf_info.add_uf('value.copy')
uf.title = "Copy parameters from one data pipe to another."
uf.title_short = "Value copying."
uf.add_keyarg(
name = "pipe_from",
basic_types = ["str"],
desc_short = "source data pipe",
desc = "The name of the pipe to copy from.",
wiz_element_type = 'combo',
# #
###############################################################################
# Module docstring.
"""The consistency_tests user function definitions."""
# relax module imports.
from graphics import ANALYSIS_IMAGE_PATH
from pipe_control import spectrometer
from specific_analyses.consistency_tests.uf import set_frq
from user_functions.data import Uf_info
uf_info = Uf_info()
from user_functions.objects import Desc_container
# The user function class.
uf_class = uf_info.add_class('consistency_tests')
uf_class.title = "Class containing functions specific to consistency tests for datasets from different fields."
uf_class.menu_text = "&consistency_tests"
uf_class.gui_icon = "relax.consistency_testing"
# The consistency_tests.set_frq user function.
uf = uf_info.add_uf('consistency_tests.set_frq')
uf.title = "Select which relaxation data to use in the consistency tests by NMR spectrometer frequency."
uf.title_short = "Spectrometer selection."
uf.add_keyarg(
name="frq",
py_type="float",
desc_short="spectrometer frequency in Hz",
desc=
"The spectrometer frequency in Hz. This must match the currently loaded data to the last decimal point. See the 'sfrq' parameter in the Varian procpar file or the 'SFO1' parameter in the Bruker acqus file.",
wiz_element_type='combo',
# #
###############################################################################
# Module docstring.
"""The consistency_tests user function definitions."""
# relax module imports.
from graphics import ANALYSIS_IMAGE_PATH
from pipe_control import spectrometer
from specific_analyses.setup import consistency_tests_obj
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.objects import Desc_container
# The user function class.
uf_class = uf_info.add_class('consistency_tests')
uf_class.title = "Class containing functions specific to consistency tests for datasets from different fields."
uf_class.menu_text = "&consistency_tests"
uf_class.gui_icon = "relax.consistency_testing"
# The consistency_tests.set_frq user function.
uf = uf_info.add_uf('consistency_tests.set_frq')
uf.title = "Select which relaxation data to use in the consistency tests by NMR spectrometer frequency."
uf.title_short = "Spectrometer selection."
uf.add_keyarg(
name = "frq",
py_type = "float",
desc_short = "spectrometer frequency in Hz",
desc = "The spectrometer frequency in Hz. This must match the currently loaded data to the last decimal point. See the 'sfrq' parameter in the Varian procpar file or the 'SFO1' parameter in the Bruker acqus file.",
wiz_element_type = 'combo',
if dep_check.wx_module:
from wx import FD_OPEN
else:
FD_OPEN = -1
from os import sep
# relax module imports.
from graphics import WIZARD_IMAGE_PATH
from pipe_control import chemical_shift
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.objects import Desc_container
from user_functions.wildcards import WILDCARD_SPECTRUM_PEAKLIST
# The user function class.
uf_class = uf_info.add_class('chemical_shift')
uf_class.title = "Class for handling chemical shifts."
uf_class.menu_text = "&chemical_shift"
uf_class.gui_icon = "relax.chemical_shift"
# The chemical_shift.read user function.
uf = uf_info.add_uf('chemical_shift.read')
uf.title = "Read chemical shifts from a file."
uf.title_short = "Chemical shift reading."
uf.add_keyarg(
name = "file",
py_type = "str",
arg_type = "file sel",
desc_short = "file name",
desc = "The name of the peak list of generic formatted file containing the chemical shifts.",
###############################################################################
# Module docstring.
"""The relax_fit user function definitions."""
# relax module imports.
from graphics import ANALYSIS_IMAGE_PATH
from lib.text.gui import i0, iinf, rx
from pipe_control import spectrum
from specific_analyses.relax_fit.uf import relax_time, select_model
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.objects import Desc_container
# The user function class.
uf_class = uf_info.add_class('relax_fit')
uf_class.title = "Class for relaxation curve fitting."
uf_class.menu_text = "&relax_fit"
uf_class.gui_icon = "relax.relax_fit"
# The relax_fit.relax_time user function.
uf = uf_info.add_uf('relax_fit.relax_time')
uf.title = "Set the relaxation delay time associated with each spectrum."
uf.title_short = "Relaxation delay time setting."
uf.add_keyarg(
name = "time",
default = 0.0,
py_type = "num",
desc_short = "relaxation time",
desc = "The time, in seconds, of the relaxation period."
# along with this program. If not, see <http://www.gnu.org/licenses/>. #
# #
###############################################################################
# Module docstring.
"""The minimisation user function definitions."""
# relax module imports.
from graphics import WIZARD_IMAGE_PATH
from pipe_control import minimise
from user_functions.data import Uf_info, Uf_tables; uf_info = Uf_info(); uf_tables = Uf_tables()
from user_functions.objects import Desc_container
# The user function class.
uf_class = uf_info.add_class('minimise')
uf_class.title = "Class for setting parameter values."
uf_class.menu_text = "&minimise"
uf_class.gui_icon = "relax.rosenbrock"
# The minimise.calculate user function.
uf = uf_info.add_uf('minimise.calculate')
uf.title = "Calculate the model parameters or the current target function value."
uf.title_short = "Model parameter or target function value calculation."
uf.display = True
uf.add_keyarg(
name = "verbosity",
default = 1,
py_type = "int",
desc_short = "verbosity level",
# You should have received a copy of the GNU General Public License #
# along with this program. If not, see <http://www.gnu.org/licenses/>. #
# #
###############################################################################
# Module docstring.
"""The angles user function definitions."""
# relax module imports.
from pipe_control import angles
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.objects import Desc_container
# The user function class.
uf_class = uf_info.add_class('angles')
uf_class.title = "Class containing the function for calculating XH bond angles."
uf_class.menu_text = "&angles"
# The angles.diff_frame user function.
uf = uf_info.add_uf('angles.diff_frame')
uf.title = "Calculate the angles defining the XH bond vector within the diffusion frame."
uf.title_short = "Diffusion frame XH vector angle calculation."
# Description.
uf.desc.append(Desc_container())
uf.desc[-1].add_paragraph("If the diffusion tensor is isotropic, then nothing will be done.")
uf.desc[-1].add_paragraph("If the diffusion tensor is axially symmetric, then the angle alpha will be calculated for each XH bond vector.")
uf.desc[-1].add_paragraph("If the diffusion tensor is asymmetric, then the three angles will be calculated.")
uf.backend = angles.angle_diff_frame
uf.menu_text = "&diff_frame"
uf.wizard_size = (800, 400)
# #
###############################################################################
# Module docstring.
"""The diffusion_tensor user function definitions."""
# relax module imports.
from graphics import WIZARD_IMAGE_PATH
from pipe_control import diffusion_tensor, pipes
from user_functions.data import Uf_info
uf_info = Uf_info()
from user_functions.objects import Desc_container
# The user function class.
uf_class = uf_info.add_class('diffusion_tensor')
uf_class.title = "Class for manipulating the diffusion tensor."
uf_class.menu_text = "&diffusion_tensor"
uf_class.gui_icon = "relax.diff_tensor"
# The diffusion_tensor.copy user function.
uf = uf_info.add_uf('diffusion_tensor.copy')
uf.title = "Copy diffusion tensor data from one data pipe to another."
uf.title_short = "Diffusion tensor data copying."
uf.add_keyarg(
name="pipe_from",
py_type="str",
desc_short="source data pipe",
desc="The name of the data pipe to copy the diffusion tensor data from.",
wiz_element_type='combo',
wiz_combo_iter=pipes.pipe_names,
# along with this program. If not, see <http://www.gnu.org/licenses/>. #
# #
###############################################################################
# Module docstring.
"""The select user function definitions."""
# relax module imports.
from graphics import WIZARD_IMAGE_PATH
from pipe_control import domain, selection, spectrum
from user_functions.data import Uf_info
uf_info = Uf_info()
from user_functions.objects import Desc_container
# The user function class.
uf_class = uf_info.add_class("select")
uf_class.title = "Class for selecting spins."
uf_class.menu_text = "&select"
uf_class.gui_icon = "relax.spin"
# The select.all user function.
uf = uf_info.add_uf("select.all")
uf.title = "Select all spins in the current data pipe."
uf.title_short = "Selection of all spins."
uf.display = True
# Description.
uf.desc.append(Desc_container())
uf.desc[-1].add_paragraph(
"This will select all spins, irregardless of their current state.")
# Prompt examples.
uf.desc.append(Desc_container("Prompt examples"))
from wx import FD_OPEN, FD_SAVE
else:
FD_OPEN = -1
FD_SAVE = -1
# relax module imports.
from graphics import WIZARD_IMAGE_PATH
from pipe_control import align_tensor, pcs, pipes
from pipe_control.mol_res_spin import get_spin_ids
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.objects import Desc_container
from user_functions.wildcards import WILDCARD_GRACE_ALL
# The user function class.
uf_class = uf_info.add_class('pcs')
uf_class.title = "Class for handling pseudo-contact shifts."
uf_class.menu_text = "&pcs"
uf_class.gui_icon = "relax.align_tensor"
# The pcs.back_calc user function.
uf = uf_info.add_uf('pcs.back_calc')
uf.title = "Back calculate the pseudo-contact shifts."
uf.title_short = "PCS back calculation."
uf.display = True
uf.add_keyarg(
name = "align_id",
py_type = "str",
desc_short = "alignment ID string",
desc = "The alignment ID string.",
)
monte_carlo_desc.add_prompt(
"relax> monte_carlo.setup(number=500) # Step 3."
)
monte_carlo_desc.add_prompt(
"relax> monte_carlo.create_data(method='back_calc') # Step 4."
)
monte_carlo_desc.add_prompt(
"relax> minimise.calculate() # Step 6."
)
monte_carlo_desc.add_prompt(
"relax> monte_carlo.error_analysis() # Step 8."
)
# The user function class.
uf_class = uf_info.add_class('monte_carlo')
uf_class.title = "Class containing the functions for Monte Carlo and related simulations."
uf_class.menu_text = "&monte_carlo"
uf_class.gui_icon = "oxygen.actions.roll-relax-blue"
# The monte_carlo.create_data user function.
uf = uf_info.add_uf('monte_carlo.create_data')
uf.title = "Create the Monte Carlo simulation data."
uf.title_short = "Data creation."
uf.add_keyarg(name="method",
default="back_calc",
basic_types=["str"],
desc_short="method",
desc="The simulation method.",
wiz_element_type="combo",
wiz_combo_choices=["Monte Carlo", "Bootstrapping"],
# #
###############################################################################
# Module docstring.
"""The statistics user function definitions."""
# relax module imports.
from graphics import WIZARD_IMAGE_PATH
from pipe_control.statistics import aic, model_statistics
from user_functions.data import Uf_info
uf_info = Uf_info()
from user_functions.objects import Desc_container
# The user function class.
uf_class = uf_info.add_class('statistics')
uf_class.title = "Class containing the statistics related functions."
uf_class.menu_text = "&statistics"
uf_class.gui_icon = "oxygen.actions.office-chart-pie"
# The statistics.aic user function.
uf = uf_info.add_uf('statistics.aic')
uf.title = "Calculate and store Akaike's Information Criterion (AIC) for each model."
uf.title_short = "Calculate AIC values."
# Description.
uf.desc.append(Desc_container())
uf.desc[-1].add_paragraph(
"This will perform a calculation to obtain the chi-squared statistic for the current parameter values for each model, count the number of parameters per model and calculate Akaike's Information Criterion (AIC) using the formula AIC = chi2 + 2k. The AIC values, chi-squared values, and number of parameters will be stored in the appropriate location for the model in the relax data store."
)
uf.backend = aic
uf.menu_text = "&aic"
"""The interatom user function definitions."""
# Python module imports.
from os import sep
# relax module imports.
from graphics import WIZARD_IMAGE_PATH
from lib.physical_constants import NH_BOND_LENGTH
from pipe_control.mol_res_spin import get_spin_ids
from pipe_control import pipes, interatomic
from user_functions.data import Uf_info
uf_info = Uf_info()
from user_functions.objects import Desc_container
# The user function class.
uf_class = uf_info.add_class('interatom')
uf_class.title = "Class for manipulating magnetic dipole-dipole interactions."
uf_class.menu_text = "&interatom"
uf_class.gui_icon = "relax.dipole_pair"
# The interatom.copy user function.
uf = uf_info.add_uf('interatom.copy')
uf.title = "Copy all data associated with a interatomic data container."
uf.title_short = "Interatomic interaction copying."
uf.display = True
uf.add_keyarg(
name="pipe_from",
basic_types=["str"],
desc_short="source data pipe",
desc=
"The data pipe containing the interatomic data container from which the data will be copied. This defaults to the current data pipe.",
import dep_check
if dep_check.wx_module:
from wx import FD_OPEN, FD_SAVE
else:
FD_OPEN = -1
FD_SAVE = -1
# relax module imports.
from graphics import WIZARD_IMAGE_PATH
from pipe_control import pipes, relax_data
from user_functions.data import Uf_info
uf_info = Uf_info()
from user_functions.objects import Desc_container
# The user function class.
uf_class = uf_info.add_class('relax_data')
uf_class.title = "Class for manipulating R1, R2, NOE, or R2eff relaxation data."
uf_class.menu_text = "&relax_data"
uf_class.gui_icon = "relax.fid"
# The relax_data.back_calc user function.
uf = uf_info.add_uf('relax_data.back_calc')
uf.title = "Back calculate the relaxation data at the given frequency."
uf.title_short = "Relaxation data back calculation."
uf.add_keyarg(name="ri_id",
py_type="str",
desc_short="relaxation ID string",
desc="The relaxation data ID string.",
can_be_none=True)
uf.add_keyarg(name="ri_type",
py_type="str",
# Python module imports.
from os import sep
# relax module imports.
import colour
from graphics import WIZARD_IMAGE_PATH
from pipe_control import molmol
from specific_analyses.model_free.uf import classic_style_doc
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.objects import Desc_container
from user_functions.wildcards import WILDCARD_MOLMOL_MACRO, WILDCARD_STRUCT_PDB
# The user function class.
uf_class = uf_info.add_class('molmol')
uf_class.title = "Class for interfacing with Molmol."
uf_class.menu_text = "&molmol"
uf_class.gui_icon = "relax.molmol"
# The molmol.clear_history user function.
uf = uf_info.add_uf('molmol.clear_history')
uf.title = "Clear the Molmol command history."
uf.title_short = "Clear Molmol history."""
# Description.
uf.desc.append(Desc_container())
uf.desc[-1].add_paragraph("This will clear the Molmol history from memory.")
uf.backend = molmol.molmol_obj.clear_history
uf.menu_text = "clear_&history"
uf.wizard_size = (600, 300)
# relax module imports.
from graphics import WIZARD_IMAGE_PATH
from pipe_control import grace, minimise
from prompt.doc_string import regexp_doc
from specific_analyses.consistency_tests import Consistency_tests
from specific_analyses.jw_mapping import Jw_mapping
from specific_analyses.model_free import Model_free
from specific_analyses.noe import Noe
from specific_analyses.relax_disp.api import Relax_disp
from specific_analyses.relax_fit import Relax_fit
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.objects import Desc_container
# The user function class.
uf_class = uf_info.add_class('grace')
uf_class.title = "Class for interfacing with Grace."
uf_class.menu_text = "&grace"
uf_class.gui_icon = "relax.grace_icon"
# The grace.view user function.
uf = uf_info.add_uf('grace.view')
uf.title = "Visualise the file within Grace."
uf.title_short = "Grace execution."
uf.add_keyarg(
name = "file",
py_type = "str",
arg_type = "file sel",
desc_short = "file name",
desc = "The name of the file.",
monte_carlo_desc.add_prompt("relax> monte_carlo.setup(number=500) # Step 3.")
monte_carlo_desc.add_prompt("relax> monte_carlo.create_data(method='back_calc') # Step 4.")
monte_carlo_desc.add_prompt("relax> monte_carlo.initial_values() # Step 5.")
monte_carlo_desc.add_prompt("relax> minimise.execute('newton') # Step 6.")
monte_carlo_desc.add_prompt("relax> eliminate() # Step 7.")
monte_carlo_desc.add_prompt("relax> monte_carlo.error_analysis() # Step 8.")
monte_carlo_desc.add_paragraph("An example for reduced spectral density mapping is:")
monte_carlo_desc.add_prompt("relax> minimise.calculate() # Step 2.")
monte_carlo_desc.add_prompt("relax> monte_carlo.setup(number=500) # Step 3.")
monte_carlo_desc.add_prompt("relax> monte_carlo.create_data(method='back_calc') # Step 4.")
monte_carlo_desc.add_prompt("relax> minimise.calculate() # Step 6.")
monte_carlo_desc.add_prompt("relax> monte_carlo.error_analysis() # Step 8.")
# The user function class.
uf_class = uf_info.add_class('monte_carlo')
uf_class.title = "Class containing the functions for Monte Carlo and related simulations."
uf_class.menu_text = "&monte_carlo"
uf_class.gui_icon = "oxygen.actions.roll-relax-blue"
# The monte_carlo.create_data user function.
uf = uf_info.add_uf('monte_carlo.create_data')
uf.title = "Create the Monte Carlo simulation data."
uf.title_short = "Data creation."
uf.add_keyarg(
name = "method",
default = "back_calc",
py_type = "str",
desc_short = "method",
desc = "The simulation method.",
# #
###############################################################################
# Module docstring.
"""The spin user function definitions."""
# relax module imports.
from graphics import WIZARD_IMAGE_PATH
from pipe_control import pipes
from pipe_control.mol_res_spin import copy_spin, create_pseudo_spin, create_spin, delete_spin, display_spin, get_molecule_names, get_residue_ids, get_residue_names, get_residue_nums, get_spin_ids, id_string_doc, name_spin, number_spin, set_spin_element, set_spin_isotope
from user_functions.data import Uf_info
uf_info = Uf_info()
from user_functions.objects import Desc_container
# The user function class.
uf_class = uf_info.add_class('spin')
uf_class.title = "Class for manipulating the spin data."
uf_class.menu_text = "&spin"
uf_class.gui_icon = "relax.spin"
# The spin.copy user function.
uf = uf_info.add_uf('spin.copy')
uf.title = "Copy all data associated with a spin."
uf.title_short = "Spin copying."
uf.display = True
uf.add_keyarg(
name="pipe_from",
basic_types=["str"],
desc_short="source data pipe",
desc=
"The data pipe containing the spin from which the data will be copied. This defaults to the current data pipe.",
