Python data.Uf_info类代码示例

def initialise():
    """Initialise all of the user function definitions by importing then validating them."""

    # Import all the modules to set up the data.
    import user_functions.align_tensor
    import user_functions.angles
    import user_functions.bmrb
    import user_functions.bruker
    import user_functions.chemical_shift
    import user_functions.consistency_tests
    import user_functions.dasha
    import user_functions.deselect
    import user_functions.diffusion_tensor
    import user_functions.domain
    import user_functions.dx
    import user_functions.eliminate
    import user_functions.fix
    import user_functions.frame_order
    import user_functions.grace
    import user_functions.interatom
    import user_functions.j_coupling
    import user_functions.jw_mapping
    import user_functions.minimisation
    import user_functions.model_free
    import user_functions.model_selection
    import user_functions.molecule
    import user_functions.molmol
    import user_functions.monte_carlo
    import user_functions.n_state_model
    import user_functions.noe
    import user_functions.palmer
    import user_functions.paramag
    import user_functions.pcs
    import user_functions.pipe
    import user_functions.pymol_control
    import user_functions.rdc
    import user_functions.relax_data
    import user_functions.relax_disp
    import user_functions.relax_fit
    import user_functions.residue
    import user_functions.reset
    import user_functions.results
    import user_functions.script
    import user_functions.select
    import user_functions.sequence
    import user_functions.spectrometer
    import user_functions.spectrum
    import user_functions.spin
    import user_functions.state
    import user_functions.structure
    import user_functions.sys_info
    import user_functions.value
    import user_functions.vmd

    # Import the data structure.
    from user_functions.data import Uf_info; uf_info = Uf_info()

    # Check the validity of the data.
    uf_info.validate()

# 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 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",

# Module docstring.
"""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."

# 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 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(

# 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 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(

# Module docstring.
"""The sequence user function definitions."""

# Python module imports.
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.

# Module docstring.
"""The noe 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 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(

# 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."

# This program is distributed in the hope that it will be useful,             #
# 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 sys_info user function definitions."""

# relax module imports.
from info import print_sys_info
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.objects import Desc_container


# The sys_info user function.
uf = uf_info.add_uf('sys_info')
uf.title = "Display all system information relating to this version of relax."
uf.title_short = "Display system information."
uf.display = True
# Description.
uf.desc.append(Desc_container())
uf.desc[-1].add_paragraph("This will display all of the relax, Python, python package and hardware information currently being used by relax.  This is useful for seeing if all packages are up to date and if the correct software versions are being used.  It is also very useful information for reporting relax bugs.")
uf.backend = print_sys_info
uf.menu_text = "s&ys_info"
uf.gui_icon = "oxygen.actions.help-about"
uf.wizard_size = (700, 400)

# 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."

# Module docstring.
"""The n_state_model user function definitions."""

# Python module imports.
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(

# 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 eliminate user function definitions for removing failed models."""

# relax module imports.
from graphics import WIZARD_IMAGE_PATH
from pipe_control import eliminate
from specific_analyses.model_free import Model_free
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.objects import Desc_container


# The eliminate user function.
uf = uf_info.add_uf('eliminate')
uf.title = "Elimination or rejection of models."
uf.title_short = "Model elimination."
uf.display = True
uf.add_keyarg(
    name = "function",
    py_type = "func",
    arg_type = "func",
    desc_short = "function",
    desc = "An optional user supplied function for model elimination.",
    can_be_none = True

# This program is distributed in the hope that it will be useful,             #
# 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 domain user function definitions."""

# relax module imports.
from pipe_control import domain
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.objects import Desc_container


# The domain user function.
uf = uf_info.add_uf('domain')
uf.title = "Definition of structural domains."
uf.title_short = "Domain definition."
uf.add_keyarg(
    name = "id",
    py_type = "str",
    desc_short = "domain ID string",
    desc = "The ID string used to identify molecular domains.",
)
uf.add_keyarg(
    name = "spin_id",

# 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 model_selection user function definitions."""

# relax module imports.
from graphics import WIZARD_IMAGE_PATH
from pipe_control import model_selection, pipes
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.objects import Desc_container


# The model_selection user function.
uf = uf_info.add_uf('model_selection')
uf.title = "Select the best model from a set of optimised models."
uf.title_short = "Model selection."
uf.display = True
uf.add_keyarg(
    name = "method",
    default = "AIC",
    py_type = "str",
    desc_short = "model selection method",
    desc = "The model selection technique (see below).",
    wiz_element_type = 'combo',

###############################################################################

# Module docstring.
"""The palmer user function definitions for controlling the Modelfree4 software."""

# 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(