Python Uf_info.add_class方法代码示例

# 需要导入模块: from user_functions.data import Uf_info [as 别名]
# 或者: from user_functions.data.Uf_info import add_class [as 别名]
    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)

# 需要导入模块: from user_functions.data import Uf_info [as 别名]
# 或者: from user_functions.data.Uf_info import add_class [as 别名]
###############################################################################

# 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."

# 需要导入模块: from user_functions.data import Uf_info [as 别名]
# 或者: from user_functions.data.Uf_info import add_class [as 别名]
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"

# 需要导入模块: from user_functions.data import Uf_info [as 别名]
# 或者: from user_functions.data.Uf_info import add_class [as 别名]
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:")

# 需要导入模块: from user_functions.data import Uf_info [as 别名]
# 或者: from user_functions.data.Uf_info import add_class [as 别名]
#                                                                             #
###############################################################################

# 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',

# 需要导入模块: from user_functions.data import Uf_info [as 别名]
# 或者: from user_functions.data.Uf_info import add_class [as 别名]
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."

# 需要导入模块: from user_functions.data import Uf_info [as 别名]
# 或者: from user_functions.data.Uf_info import add_class [as 别名]
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.",

# 需要导入模块: from user_functions.data import Uf_info [as 别名]
# 或者: from user_functions.data.Uf_info import add_class [as 别名]
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",

# 需要导入模块: from user_functions.data import Uf_info [as 别名]
# 或者: from user_functions.data.Uf_info import add_class [as 别名]
    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."

# 需要导入模块: from user_functions.data import Uf_info [as 别名]
# 或者: from user_functions.data.Uf_info import add_class [as 别名]
#                                                                             #
###############################################################################

# 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

# 需要导入模块: from user_functions.data import Uf_info [as 别名]
# 或者: from user_functions.data.Uf_info import add_class [as 别名]
# 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.",

# 需要导入模块: from user_functions.data import Uf_info [as 别名]
# 或者: from user_functions.data.Uf_info import add_class [as 别名]
    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",

# 需要导入模块: from user_functions.data import Uf_info [as 别名]
# 或者: from user_functions.data.Uf_info import add_class [as 别名]
#                                                                             #
###############################################################################

# 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.",

# 需要导入模块: from user_functions.data import Uf_info [as 别名]
# 或者: from user_functions.data.Uf_info import add_class [as 别名]
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.",

# 需要导入模块: from user_functions.data import Uf_info [as 别名]
# 或者: from user_functions.data.Uf_info import add_class [as 别名]
# 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