Author: bugman
Date: Tue Oct 29 12:13:02 2013
New Revision: 21304
URL: http://svn.gna.org/viewcvs/relax?rev=21304&view=rev
Log:
Implemented the relax_disp.r2eff_read user function.
Bot the frontend and backend have been implemented and are functional.
Modified:
branches/relax_disp/specific_analyses/relax_disp/disp_data.py
branches/relax_disp/user_functions/relax_disp.py
Modified: branches/relax_disp/specific_analyses/relax_disp/disp_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/disp_data.py?rev=21304&r1=21303&r2=21304&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/disp_data.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/disp_data.py Tue Oct 29
12:13:02 2013
@@ -39,14 +39,15 @@
# relax module imports.
from lib.errors import RelaxError, RelaxNoSpectraError, RelaxSpinTypeError
-from lib.io import get_file_path, open_write_file
+from lib.io import get_file_path, open_write_file, read_spin_data
from lib.physical_constants import g1H, return_gyromagnetic_ratio
from lib.software.grace import write_xy_data, write_xy_header,
script_grace2images
from pipe_control import pipes
-from pipe_control.mol_res_spin import exists_mol_res_spin_data, return_spin,
spin_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.result_files import add_result_file
from pipe_control.selection import desel_spin
-from pipe_control.spectrum import check_spectrum_id
+from pipe_control.spectrum import add_spectrum_id, check_spectrum_id
+from pipe_control.spectrometer import set_frequency
from specific_analyses.relax_disp.checks import check_exp_type,
check_mixed_curve_types
from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG,
EXP_TYPE_DESC_CPMG, EXP_TYPE_DESC_DQ_CPMG, EXP_TYPE_DESC_R1RHO,
EXP_TYPE_DESC_MQ_CPMG, EXP_TYPE_DESC_MQ_R1RHO, EXP_TYPE_DESC_ZQ_CPMG,
EXP_TYPE_DQ_CPMG, EXP_TYPE_LIST, EXP_TYPE_LIST_CPMG, EXP_TYPE_LIST_R1RHO,
EXP_TYPE_MQ_CPMG, EXP_TYPE_MQ_R1RHO, EXP_TYPE_R1RHO, EXP_TYPE_ZQ_CPMG
from stat import S_IRWXU, S_IRGRP, S_IROTH
@@ -1042,6 +1043,113 @@
add_result_file(type='grace', label='Grace', file=file_path)
+def r2eff_read(file=None, dir=None, exp_type=None, frq=None, disp_frq=None,
spin_id_col=None, mol_name_col=None, res_num_col=None, res_name_col=None,
spin_num_col=None, spin_name_col=None, data_col=None, error_col=None,
sep=None):
+ """Read R2eff/R1rho values directly from a file whereby each row
corresponds to a different spin.
+
+ @keyword file: The name of the file to open.
+ @type file: str
+ @keyword dir: The directory containing the file (defaults to
the current directory if None).
+ @type dir: str or None
+ @keyword exp_type: The relaxation dispersion experiment type.
+ @type exp_type: str
+ @keyword frq: The spectrometer frequency in Hertz.
+ @type frq: float
+ @keyword disp_frq: For CPMG-type data, the frequency of the CPMG
pulse train. For R1rho-type data, the spin-lock field strength (nu1). The
units must be Hertz.
+ @type disp_frq: float
+ @keyword spin_id_col: The column containing the spin ID strings. If
supplied, the mol_name_col, res_name_col, res_num_col, spin_name_col, and
spin_num_col arguments must be none.
+ @type spin_id_col: int or None
+ @keyword mol_name_col: The column containing the molecule name
information. If supplied, spin_id_col must be None.
+ @type mol_name_col: int or None
+ @keyword res_name_col: The column containing the residue name
information. If supplied, spin_id_col must be None.
+ @type res_name_col: int or None
+ @keyword res_num_col: The column containing the residue number
information. If supplied, spin_id_col must be None.
+ @type res_num_col: int or None
+ @keyword spin_name_col: The column containing the spin name information.
If supplied, spin_id_col must be None.
+ @type spin_name_col: int or None
+ @keyword spin_num_col: The column containing the spin number
information. If supplied, spin_id_col must be None.
+ @type spin_num_col: int or None
+ @keyword data_col: The column containing the RDC data in Hz.
+ @type data_col: int or None
+ @keyword error_col: The column containing the RDC errors.
+ @type error_col: int or None
+ @keyword sep: The column separator which, if None, defaults to
whitespace.
+ @type sep: str or None
+ """
+
+ # Data checks.
+ pipes.test()
+ check_mol_res_spin_data()
+
+ # Create a key for the global data (the pseudo-spectrum ID).
+ spectrum_id = "%s_%s" % (frq, disp_frq)
+ print("Using the pseudo-spectrum ID of '%s'." % spectrum_id)
+
+ # Loop over the data.
+ data_flag = False
+ for data in read_spin_data(file=file, dir=dir, spin_id_col=spin_id_col,
mol_name_col=mol_name_col, res_num_col=res_num_col,
res_name_col=res_name_col, spin_num_col=spin_num_col,
spin_name_col=spin_name_col, data_col=data_col, error_col=error_col, sep=sep):
+ # Unpack.
+ if data_col and error_col:
+ mol_name, res_num, res_name, spin_num, spin_name, value, error =
data
+ elif data_col:
+ mol_name, res_num, res_name, spin_num, spin_name, value = data
+ error = None
+ else:
+ mol_name, res_num, res_name, spin_num, spin_name, error = data
+ value = None
+
+ # Test the error value (cannot be 0.0).
+ if error == 0.0:
+ raise RelaxError("An invalid error value of zero has been
encountered.")
+
+ # Get the corresponding spin container.
+ id = generate_spin_id_unique(mol_name=mol_name, res_num=res_num,
res_name=res_name, spin_num=spin_num, spin_name=spin_name)
+ spin = return_spin(id)
+ if spin == None:
+ warn(RelaxNoSpinWarning(id))
+ continue
+
+ # The dispersion point key.
+ point_key = return_param_key_from_data(frq=frq, point=disp_frq)
+
+ # Store the R2eff data.
+ if data_col:
+ # Initialise if necessary.
+ if not hasattr(spin, 'r2eff'):
+ spin.r2eff = {}
+
+ # Store.
+ spin.r2eff[point_key] = value
+
+ # Store the R2eff error.
+ if error_col:
+ # Initialise if necessary.
+ if not hasattr(spin, 'r2eff_err'):
+ spin.r2eff_err = {}
+
+ # Store.
+ spin.r2eff_err[point_key] = error
+
+ # Data added.
+ data_flag = True
+
+ # Update the global structures.
+ if data_flag:
+ # Store the spectrum ID.
+ add_spectrum_id(spectrum_id)
+
+ # Set the spectrometer frequency information.
+ set_frequency(id=spectrum_id, frq=frq)
+
+ # Set the experiment type.
+ set_exp_type(spectrum_id=spectrum_id, exp_type=exp_type)
+
+ # Set the dispersion point frequency.
+ if exp_type in EXP_TYPE_LIST_CPMG:
+ cpmg_frq(spectrum_id=spectrum_id, cpmg_frq=disp_frq)
+ else:
+ spin_lock_field(spectrum_id=spectrum_id, field=disp_frq)
+
+
def randomise_R1(spin=None, ri_id=None, N=None):
"""Randomise the R1 data for the given spin for use in the Monte Carlo
simulations.
Modified: branches/relax_disp/user_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/user_functions/relax_disp.py?rev=21304&r1=21303&r2=21304&view=diff
==============================================================================
--- branches/relax_disp/user_functions/relax_disp.py (original)
+++ branches/relax_disp/user_functions/relax_disp.py Tue Oct 29 12:13:02 2013
@@ -38,7 +38,7 @@
from pipe_control.mol_res_spin import get_spin_ids
from specific_analyses.relax_disp.catia import catia_execute, catia_input
from specific_analyses.relax_disp.cpmgfit import cpmgfit_execute,
cpmgfit_input
-from specific_analyses.relax_disp.disp_data import cpmg_frq, insignificance,
plot_disp_curves, plot_exp_curves, relax_time, set_exp_type, spin_lock_field,
spin_lock_offset
+from specific_analyses.relax_disp.disp_data import cpmg_frq, insignificance,
plot_disp_curves, plot_exp_curves, r2eff_read, relax_time, set_exp_type,
spin_lock_field, spin_lock_offset
from specific_analyses.relax_disp.nessy import nessy_input
from specific_analyses.relax_disp.parameters import copy
from specific_analyses.relax_disp.sherekhan import sherekhan_input
@@ -516,6 +516,144 @@
uf.gui_icon = "oxygen.actions.document-save"
uf.wizard_size = (800, 600)
uf.wizard_image = WIZARD_IMAGE_PATH + 'grace.png'
+
+
+# The relax_disp.r2eff_read user function.
+uf = uf_info.add_uf('relax_disp.r2eff_read')
+uf.title = "Read R2eff/R1rho values and errors from a file."
+uf.title_short = "R2eff/R1rho value reading."
+uf.add_keyarg(
+ name = "file",
+ py_type = "str",
+ arg_type = "file sel",
+ desc_short = "file name",
+ desc = "The name of the file.",
+ wiz_filesel_style = FD_SAVE
+)
+uf.add_keyarg(
+ name = "dir",
+ py_type = "str",
+ arg_type = "dir",
+ desc_short = "directory name",
+ desc = "The directory name.",
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "exp_type",
+ default = "CPMG",
+ py_type = "str",
+ desc_short = "experiment type",
+ desc = "The type of relaxation dispersion experiment performed.",
+ wiz_element_type = "combo",
+ wiz_combo_choices = [
+ "Single quantum (SQ) CPMG-type data",
+ "Zero quantum (ZQ) CPMG-type data",
+ "Double quantum (DQ) CPMG-type data",
+ "Multiple quantum (MQ) CPMG-type data",
+ "%s-type data" % r1rho
+ ],
+ wiz_combo_data = [
+ EXP_TYPE_CPMG,
+ EXP_TYPE_ZQ_CPMG,
+ EXP_TYPE_DQ_CPMG,
+ EXP_TYPE_MQ_CPMG,
+ EXP_TYPE_R1RHO
+ ],
+ wiz_read_only = True
+)
+uf.add_keyarg(
+ name = "frq",
+ py_type = "num",
+ desc_short = "spectrometer frequency",
+ desc = "The spectrometer frequency in Hertz. See the 'sfrq' parameter
in the Varian procpar file or the 'SFO1' parameter in the Bruker acqus file."
+)
+uf.add_keyarg(
+ name = "disp_frq",
+ py_type = "num",
+ desc_short = "CPMG frequency or spin-lock field strength (Hz)",
+ desc = "For CPMG-type data, the frequency of the CPMG pulse train. For
R1rho-type data, the spin-lock field strength nu1. The units must be Hertz",
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "spin_id_col",
+ py_type = "int",
+ arg_type = "free format",
+ desc_short = "spin ID string column",
+ desc = "The spin ID string column used by the generic file format (an
alternative to the mol, res, and spin name and number columns).",
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "mol_name_col",
+ py_type = "int",
+ arg_type = "free format",
+ desc_short = "molecule name column",
+ desc = "The molecule name column used by the generic file format
(alternative to the spin ID column).",
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "res_num_col",
+ py_type = "int",
+ arg_type = "free format",
+ desc_short = "residue number column",
+ desc = "The residue number column used by the generic file format
(alternative to the spin ID column).",
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "res_name_col",
+ py_type = "int",
+ arg_type = "free format",
+ desc_short = "residue name column",
+ desc = "The residue name column used by the generic file format
(alternative to the spin ID column).",
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "spin_num_col",
+ py_type = "int",
+ arg_type = "free format",
+ desc_short = "spin number column",
+ desc = "The spin number column used by the generic file format
(alternative to the spin ID column).",
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "spin_name_col",
+ py_type = "int",
+ arg_type = "free format",
+ desc_short = "spin name column",
+ desc = "The spin name column used by the generic file format
(alternative to the spin ID column).",
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "data_col",
+ py_type = "int",
+ arg_type = "free format",
+ desc_short = "data column",
+ desc = "The RDC data column.",
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "error_col",
+ py_type = "int",
+ arg_type = "free format",
+ desc_short = "error column",
+ desc = "The experimental error column.",
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "sep",
+ py_type = "str",
+ arg_type = "free format",
+ desc_short = "column separator",
+ desc = "The column separator used by the generic format (the default is
white space).",
+ can_be_none = True
+)
+# Description.
+uf.desc.append(Desc_container())
+uf.desc[-1].add_paragraph("This will read R2eff/R1rho data directly from a
file. The format of this text file must be that each row corresponds to a
unique spin system and that there is one file per dispersion point (i.e. per
CPMG frequency nu_CPMG or per spin-lock field strength n1). The file must be
in columnar format and information to identify the spin must be in columns of
the file.")
+uf.backend = r2eff_read
+uf.menu_text = "&r2eff_read"
+uf.gui_icon = "oxygen.actions.document-open"
+uf.wizard_size = (900, 600)
+uf.wizard_image = ANALYSIS_IMAGE_PATH + 'relax_disp_200x200.png'
# The relax_disp.relax_time user function.
r21304 - in /branches/relax_disp: specific_analyses/relax_disp/disp_data.py user_functions/relax_disp.py