# Module docstring.
"""Module for selecting and deselecting spins."""
# Python module imports
from warnings import warn
# relax module imports.
from lib.errors import RelaxError, RelaxNoDomainError, RelaxNoSequenceError
from lib.io import read_spin_data
from lib.selection import Selection, spin_id_to_data_list
from lib.warnings import RelaxNoSpinWarning
from pipe_control import pipes
from pipe_control.interatomic import interatomic_loop
from pipe_control.mol_res_spin import exists_mol_res_spin_data, generate_spin_id_unique, return_spin, spin_loop
from user_functions.data import Uf_tables; uf_tables = Uf_tables()
from user_functions.objects import Desc_container
boolean_doc = Desc_container("Boolean operators")
boolean_doc.add_paragraph("The boolean operator can be used to change how spin systems or interatomic data containers are selected. The allowed values are: 'OR', 'NOR', 'AND', 'NAND', 'XOR', 'XNOR'. The following table details how the selections will occur for the different boolean operators.")
table = uf_tables.add_table(label="table: bool operators", caption="Boolean operators and their effects on selections")
table.add_headings(["Spin system or interatomic data container", "1", "2", "3", "4", "5", "6", "7", "8", "9"])
table.add_row(["Original selection", "0", "1", "1", "1", "1", "0", "1", "0", "1"])
table.add_row(["New selection", "0", "1", "1", "1", "1", "1", "0", "0", "0"])
table.add_row(["OR", "0", "1", "1", "1", "1", "1", "1", "0", "1"])
table.add_row(["NOR", "1", "0", "0", "0", "0", "0", "0", "1", "0"])
table.add_row(["AND", "0", "1", "1", "1", "1", "0", "0", "0", "0"])
table.add_row(["NAND", "1", "0", "0", "0", "0", "1", "1", "1", "1"])
table.add_row(["XOR", "0", "0", "0", "0", "0", "1", "1", "0", "1"])
table.add_row(["XNOR", "1", "1", "1", "1", "1", "0", "0", "1", "0"])
# 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 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())
# Module docstring.
"""The spectrum user function definitions."""
# Python module imports.
from os import sep
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 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."
# Python module imports.
from os import sep
# relax module imports.
from graphics import WIZARD_IMAGE_PATH
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(
"""The model-free analysis user functions."""
# Python module imports.
from re import match
# relax module imports.
from lib.errors import RelaxError, RelaxFuncSetupError, RelaxNoSequenceError, RelaxTensorError
from pipe_control import pipes
from pipe_control.mol_res_spin import exists_mol_res_spin_data, spin_loop
from pipe_control.pipes import check_pipe
import specific_analyses
from specific_analyses.model_free.api import Model_free
from specific_analyses.model_free.model import model_map
from user_functions.data import Uf_tables
uf_tables = Uf_tables()
from user_functions.objects import Desc_container
# The API object.
api_model_free = Model_free()
# Classic style documentation.
classic_style_doc = Desc_container("Model-free classic style")
classic_style_doc.add_paragraph("Creator: Edward d'Auvergne")
classic_style_doc.add_paragraph('Argument string: "classic"')
classic_style_doc.add_paragraph(
"Description: The classic style draws the backbone of a protein in a cylindrical bond style. Rather than colouring the amino acids to which the NH bond belongs, the three covalent bonds of the peptide bond from Ca to Ca in which the NH bond is located are coloured. Deselected residues are shown as black lines."
)
classic_style_doc.add_paragraph("Supported data types:")
table = uf_tables.add_table(
# Module docstring.
"""The model-free analysis user functions."""
# Python module imports.
from re import match
# relax module imports.
from lib.errors import RelaxError, RelaxFuncSetupError, RelaxNoSequenceError, RelaxTensorError
from pipe_control import pipes
from pipe_control.mol_res_spin import exists_mol_res_spin_data, spin_loop
from pipe_control.pipes import check_pipe
import specific_analyses
from specific_analyses.model_free.api import Model_free
from specific_analyses.model_free.model import model_map
from user_functions.data import Uf_tables
uf_tables = Uf_tables()
from user_functions.objects import Desc_container
# The API object.
api_model_free = Model_free()
# Classic style documentation.
classic_style_doc = Desc_container("Model-free classic style")
classic_style_doc.add_paragraph("Creator: Edward d'Auvergne")
classic_style_doc.add_paragraph("Argument string: \"classic\"")
classic_style_doc.add_paragraph(
"Description: The classic style draws the backbone of a protein in a cylindrical bond style. Rather than colouring the amino acids to which the NH bond belongs, the three covalent bonds of the peptide bond from Ca to Ca in which the NH bond is located are coloured. Deselected residues are shown as black lines."
)
classic_style_doc.add_paragraph("Supported data types:")
table = uf_tables.add_table(
label="table: model-free macro classic style",
# #
# 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 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",
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(
###############################################################################
# Module docstring.
"""Module for model minimisation/optimisation."""
# Python module imports.
from re import search
# relax module imports.
from lib.errors import RelaxError
from multi import Processor_box
from pipe_control.mol_res_spin import return_spin, spin_loop
from pipe_control import pipes
import specific_analyses
from status import Status; status = Status()
from user_functions.data import Uf_tables; uf_tables = Uf_tables()
from user_functions.objects import Desc_container
def calc(verbosity=1):
"""Function for calculating the function value.
@param verbosity: The amount of information to print. The higher the value, the greater
the verbosity.
@type verbosity: int
"""
# Test if the current data pipe exists.
pipes.test()
# Specific calculate function setup.
# 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 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(
# Module docstring.
"""Module for selecting and deselecting spins."""
# Python module imports
import sys
from warnings import warn
# relax module imports.
from lib.errors import RelaxError, RelaxNoDomainError, RelaxNoSequenceError
from lib.selection import Selection, spin_id_to_data_list
from lib.sequence import read_spin_data, write_spin_data
from lib.warnings import RelaxNoSpinWarning
from pipe_control.interatomic import interatomic_loop
from pipe_control.mol_res_spin import check_mol_res_spin_data, exists_mol_res_spin_data, generate_spin_id_unique, return_spin, spin_loop
from pipe_control.pipes import check_pipe
from user_functions.data import Uf_tables; uf_tables = Uf_tables()
from user_functions.objects import Desc_container
boolean_doc = Desc_container("Boolean operators")
boolean_doc.add_paragraph("The boolean operator can be used to change how spin systems or interatomic data containers are selected. The allowed values are: 'OR', 'NOR', 'AND', 'NAND', 'XOR', 'XNOR'. The following table details how the selections will occur for the different boolean operators.")
table = uf_tables.add_table(label="table: bool operators", caption="Boolean operators and their effects on selections")
table.add_headings(["Spin system or interatomic data container", "1", "2", "3", "4", "5", "6", "7", "8", "9"])
table.add_row(["Original selection", "0", "1", "1", "1", "1", "0", "1", "0", "1"])
table.add_row(["New selection", "0", "1", "1", "1", "1", "1", "0", "0", "0"])
table.add_row(["OR", "0", "1", "1", "1", "1", "1", "1", "0", "1"])
table.add_row(["NOR", "1", "0", "0", "0", "0", "0", "0", "1", "0"])
table.add_row(["AND", "0", "1", "1", "1", "1", "0", "0", "0", "0"])
table.add_row(["NAND", "1", "0", "0", "0", "0", "1", "1", "1", "1"])
table.add_row(["XOR", "0", "0", "0", "0", "0", "1", "1", "0", "1"])
table.add_row(["XNOR", "1", "1", "1", "1", "1", "0", "0", "1", "0"])
from gui.fonts import font
from gui.input_elements.bool import Selector_bool
from gui.input_elements.dir import Selector_dir
from gui.input_elements.file import Selector_file, Selector_file_multiple
from gui.input_elements.sequence import Sequence
from gui.input_elements.sequence_2D import Sequence_2D
from gui.input_elements.spin_id import Spin_id
from gui.input_elements.value import Value
from gui.interpreter import Interpreter; interpreter = Interpreter()
from gui.misc import format_table
from gui.wizards.wiz_objects import Wiz_page, Wiz_window
from lib.errors import AllRelaxErrors, RelaxError
from lib.text.string import strip_lead
from status import Status; status = Status()
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.data import Uf_tables; uf_tables = Uf_tables()
def build_uf_menus(parent=None, menubar=None):
"""Auto-generate the user function sub-menu.
@keyword parent: The parent window to bind the events to.
@type parent: wx instance
@keyword menubar: The menubar to attach the user function menus to.
@type menubar: wx.MenuBar instance
@return: The menu ID.
@rtype: int
"""
# The user function menus.
menu1 = wx.Menu()
# Module docstring.
"""The spectrum user function definitions."""
# Python module imports.
from os import sep
# 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,
# Module docstring.
"""The parameter list object base class for the specific analyses.
This provides a uniform interface for defining and handling parameters - either optimised or fixed - of the specific analyses.
"""
# Python module imports.
from math import pi
from re import search
from types import FunctionType, MethodType
# relax module imports.
from lib.errors import RelaxError
from user_functions.data import Uf_tables
uf_tables = Uf_tables()
from user_functions.objects import Desc_container
def da_lower(incs=None, model_info=None):
"""Determine the lower grid bound for the Da diffusion parameter.
@keyword incs: The number of grid search increments.
@type incs: int
@keyword model_info: The model information from model_loop().
@type model_info: unknown
@return: The lower grid search bound for the Da diffusion parameter.
@rtype: float
"""
# Return the lower bound.
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License for more details. #
# #
# 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 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
"""The frame_order user function definitions."""
# 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 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."
# Module docstring.
"""The spectrum user function definitions."""
# Python module imports.
from os import sep
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 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."
