def save_state():
"""Save the program state, for debugging purposes."""
# relax data store singleton import. Must be done here!
try:
from data_store import Relax_data_store
ds = Relax_data_store()
# Ok, this is not relax so don't do anything!
except ImportError:
return
# Append the date and time to the save file.
now = time.localtime()
file_name = "relax_state_%i%02i%02i_%02i%02i%02i" % (
now[0], now[1], now[2], now[3], now[4], now[5])
# Open the file for writing.
if bz2:
sys.stderr.write(
"\nStoring the relax state in the file '%s.bz2'.\n\n" % file_name)
file = BZ2File(file_name + '.bz2', 'w')
else:
sys.stderr.write("\nStoring the relax state in the file '%s'.\n\n" %
file_name)
file = open(file_name, 'w')
# Pickle the data class and write it to file
pickle.dump(ds, file, 1)
# Close the file.
file.close()
# Script for testing the reading and writing of BMRB files.
# Python module imports.
from os import sep
# relax module imports.
from data_store import Relax_data_store; ds = Relax_data_store()
from status import Status; status = Status()
# Missing temp file (allow this script to run outside of the system test framework).
state_file = 'devnull'
if not hasattr(ds, 'tmpfile'):
stand_alone = True
ds.tmpfile = 'temp_bmrb'
ds.version = '3.1'
state_file = 'temp_bmrb_state'
# Create the data pipe.
self._execute_uf(uf_name='pipe.create', pipe_name='results', pipe_type='mf')
# Read the results.
self._execute_uf(uf_name='results.read', file='final_results_trunc_1.3_v2', dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'OMP')
# Speed these tests up a bit.
self._execute_uf(uf_name='residue.delete', res_id=':15-200')
# Play with the data.
self._execute_uf(uf_name='deselect.all')
self._execute_uf(uf_name='select.spin', spin_id=':9@N')
self._execute_uf(uf_name='select.spin', spin_id=':10@N')
# 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/>. #
# #
###############################################################################
# Python module imports.
from os import getcwd, sep
# relax module imports.
from data_store import Relax_data_store
ds = Relax_data_store()
#########################################
#### Setup
# The pipe names.
if not (hasattr(ds, 'pipe_name') and hasattr(ds, 'pipe_bundle')
and hasattr(ds, 'pipe_type')):
# Set pipe name, bundle and type.
ds.pipe_name = 'base pipe'
ds.pipe_bundle = 'relax_disp'
ds.pipe_type = 'relax_disp'
# The data path
if not hasattr(ds, 'data_path'):
ds.data_path = getcwd()
# Script for checking the free rotor pseudo-ellipse frame order model.
# Python module imports.
from numpy import array, float64
from os import sep
# relax module imports.
from data_store import Relax_data_store; ds = Relax_data_store()
from lib.geometry.rotations import R_to_euler_zyz
from status import Status; status = Status()
def get_angle(index, incs=None, deg=False):
"""Return the angle corresponding to the incrementation index."""
# The angle of one increment.
inc_angle = pi / incs
# The angle of the increment.
angle = inc_angle * (index+1)
# Return.
if deg:
return angle / (2*pi) * 360
else:
return angle
# Init.
INC = 18
EIG_FRAME = array([[ 2, -1, 2],
"""Script for optimising the 'MQ NS 2-site' model.
This performs the analysis of:
Remco Sprangers, Anna Gribun, Peter M. Hwang, Walid A. Houry, and Lewis E. Kay (2005) Quantitative NMR spectroscopy of supramolecular complexes: Dynamic side pores in ClpP are important for product release, PNAS, 102 (46), 16678-16683. (doi: http://dx.doi.org/10.1073/pnas.0507370102)
"""
# Python module imports.
from os import sep
# relax module imports.
from auto_analyses.relax_disp import Relax_disp
from data_store import Relax_data_store; ds = Relax_data_store()
from status import Status; status = Status()
# Analysis variables.
#####################
# The dispersion models.
if not hasattr(ds, 'models'):
ds.models = ['R2eff', 'No Rex', 'NS MMQ 2-site']
# The grid search size (the number of increments per dimension).
GRID_INC = 4
# The number of Monte Carlo simulations to be used for error analysis at the end of the analysis.
MC_NUM = 3
# The temporary directory, if needed.
if not hasattr(ds, 'tmpdir'):
# Script for model-free analysis using the program 'Modelfree4'.
# Python module imports.
from os import sep
# relax module imports.
from data_store import Relax_data_store; ds = Relax_data_store()
from status import Status; status = Status()
# Missing temp directory (allow this script to run outside of the system test framework).
if not hasattr(ds, 'tmpdir'):
ds.tmpdir = 'temp_script'
# Path of the relaxation data.
DATA_PATH = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'OMP'
def exec_stage_1(pipes):
"""Stage 1 function.
Initial model-free minimisation.
"""
# Loop over the data pipes.
for name in pipes:
# Create the data pipe.
print("\n\n# " + name + " #")
pipe.create(name, 'mf')
# Copy the sequence.
# Script for checking the parametric restriction of the free rotor pseudo-ellipse to the free rotor isotropic cone frame order model.
# Python module imports.
from numpy import array, cross, float64, zeros
from numpy.linalg import norm
from os import sep
# relax module imports.
from data_store import Relax_data_store; ds = Relax_data_store()
from lib.geometry.rotations import R_to_euler_zyz
from status import Status; status = Status()
def get_angle(index, incs=None, deg=False):
"""Return the angle corresponding to the incrementation index."""
# The angle of one increment.
inc_angle = pi / incs
# The angle of the increment.
angle = inc_angle * (index+1)
# Return.
if deg:
return angle / (2*pi) * 360
else:
return angle
# Init.
INC = 18
# 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.
"""Script for CPMG relaxation dispersion curve fitting using Dr. Flemming Hansen's data from http://dx.doi.org/10.1021/jp074793o."""
# Python module imports.
from os import sep
# relax module imports.
from auto_analyses.relax_disp import Relax_disp
from data_store import Relax_data_store; ds = Relax_data_store()
from lib.dispersion.variables import MODEL_NOREX, MODEL_R2EFF
from status import Status; status = Status()
# The dispersion models.
MODELS = [MODEL_R2EFF, MODEL_NOREX]
if hasattr(ds, 'models'):
MODELS = ds.models
# The temporary directory, if needed.
if not hasattr(ds, 'tmpdir'):
ds.tmpdir = 'temp'
# The numeric flag.
if not hasattr(ds, 'numeric_only'):
# #
# 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.
"""Optimise the R1rho on-resonance synthetic data using the DPL94 model."""
# Python module imports.
from os import sep
# relax module imports.
from auto_analyses.relax_disp import Relax_disp
from data_store import Relax_data_store
ds = Relax_data_store()
from status import Status
status = Status()
# Analysis variables.
#####################
# The dispersion models.
if not hasattr(ds, 'models'):
ds.models = ['R2eff', 'TP02']
# The grid search size (the number of increments per dimension).
GRID_INC = 4
# The number of Monte Carlo simulations to be used for error analysis at the end of the analysis.
MC_NUM = 3
# 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.
"""Script for testing the loading of phthalic acid NOEs from a generically formatted file."""
# Python module imports.
from os import sep
# relax module imports.
from data_store import Relax_data_store; ds = Relax_data_store()
from status import Status; status = Status()
# Add a date pipe if one doesn't already exist.
if not len(ds):
self._execute_uf(uf_name='pipe.create', pipe_name='test', pipe_type='N-state')
# NOE restraint file.
if not hasattr(ds, 'file_name'):
ds.file_name = 'phthalic_acid'
# Path of the relaxation data.
DATA_PATH = status.install_path + sep+'test_suite'+sep+'shared_data'+sep
# Pseudo-atoms.
# Script for relaxation curve fitting.
# Python module imports.
from os import sep
# relax module imports.
from data_store import Relax_data_store; ds = Relax_data_store()
from status import Status; status = Status()
# Missing intensity type (allow this script to run outside of the system test framework).
if not hasattr(ds, 'int_type'):
ds.int_type = 'height'
# Create the data pipe.
pipe.create('rx', 'relax_fit')
# The path to the data files.
data_path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'curve_fitting'+sep+'inversion_recovery'
# Load the sequence.
sequence.read('Ap4Aase.seq', dir=status.install_path + sep+'test_suite'+sep+'shared_data', res_num_col=1, res_name_col=2)
# Name the spins so they can be matched to the assignments.
spin.name(name='N')
# Spectrum names.
names = [
'T1_inv-recov_200_ms',
'T1_inv-recov_450_ms',
# 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/>. #
# #
###############################################################################
# Python module imports.
from os import getcwd, sep
import re
# relax module imports.
from auto_analyses.relax_disp import Relax_disp
from data_store import Relax_data_store; ds = Relax_data_store()
from lib.dispersion.variables import MODEL_R2EFF
#########################################
#### Setup
# The data path
if not hasattr(ds, 'data_path'):
ds.data_path = getcwd()
# The models to analyse.
if not hasattr(ds, 'models'):
ds.models = [MODEL_R2EFF]
# The number of increments per parameter, to split up the search interval in grid search.
if not hasattr(ds, 'grid_inc'):
# relax script for regenerating the 'basic_single_pipe.bz2' saved state. This is for when the saved
# state becomes incompatible with relax.
# The relax data store.
from data_store import Relax_data_store; ds = Relax_data_store()
# Add a data pipe to the data store.
ds.add(pipe_name='orig', pipe_type='mf')
# Add a single object to the 'orig' data pipe.
ds['orig'].x = 1
# Add a single object to the storage object.
ds.y = 'Hello'
# Save the state.
state.save('basic_single_pipe', force=True)
"""Script for testing diffusion tensor optimisation."""
# Python module imports.
from numpy import array, float64
from os import sep
# relax module imports.
from data_store import Relax_data_store; ds = Relax_data_store()
from status import Status; status = Status()
# Stand alone operation.
if not hasattr(ds, 'diff_type'):
ds.diff_type = 'spheroid'
# A data pipe.
pipe.create('diff_opt', 'mf')
# Path of the files.
path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'diffusion_tensor'+sep+ds.diff_type
# Load the sequence.
sequence.read('NOE.500.out', dir=path, res_num_col=1)
# Load a PDB file.
structure.read_pdb('uniform.pdb', dir=path)
# Set the spin names.
spin.name(name='N')
# Load the relaxation data.
# 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.
"""Script for testing diffusion tensor optimisation."""
# Python module imports.
from os import sep
# relax module imports.
from data_store import Relax_data_store
ds = Relax_data_store()
from status import Status
status = Status()
# The frequency list.
FRQ = [500, 600, 700, 800]
# Stand alone operation.
if not hasattr(ds, 'diff_type'):
ds.diff_type = 'ellipsoid'
if not hasattr(ds, 'diff_dir'):
ds.diff_dir = 'ellipsoid'
# A data pipe.
pipe.create('back_calc', 'mf')
# 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/>. #
# #
###############################################################################
# Python module imports.
from os import getcwd, sep
# relax module imports.
from auto_analyses.relax_disp import Relax_disp
from data_store import Relax_data_store
ds = Relax_data_store()
from lib.dispersion.variables import MODEL_NOREX_R1RHO_FIT_R1, MODEL_DPL94_FIT_R1, MODEL_TP02_FIT_R1, MODEL_TAP03_FIT_R1, MODEL_MP05_FIT_R1
#########################################
#### Setup
# The pipe names.
if not (hasattr(ds, 'pipe_name') and hasattr(ds, 'pipe_bundle')
and hasattr(ds, 'pipe_type')):
# Set pipe name, bundle and type.
ds.pipe_name = 'base pipe'
ds.pipe_bundle = 'relax_disp'
ds.pipe_type = 'relax_disp'
# The data path
if not hasattr(ds, 'data_path'):
ds.data_path = getcwd()
"""Script for testing out the N-state model alignment tensor optimisation using pyrotarctic anhydride.
This is for testing both the optimisation of long range RDCs (2J and 3J) to pseudo-atoms and for testing the absolute T and absolute J data type.
"""
# Python module imports.
from os import sep
# relax imports.
from data_store import Relax_data_store; ds = Relax_data_store()
from status import Status; status = Status()
# Setup for stand-alone operation.
if not hasattr(ds, 'abs_data'):
ds.abs_data = 'mix'
# Path of the files.
str_path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures'
data_path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'align_data'+sep+'pyrotartaric_anhydride'
# Create the data pipe.
self._execute_uf(uf_name='pipe.create', pipe_name='pyrotartaric anhydride', pipe_type='N-state')
# Load the structure.
self._execute_uf(uf_name='structure.read_pdb', file='pyrotartaric_anhydride.pdb', dir=str_path)
# Set up the 13C and 1H spins information.
self._execute_uf(uf_name='structure.load_spins', spin_id='@C*', ave_pos=False)
self._execute_uf(uf_name='structure.load_spins', spin_id='@H*', ave_pos=False)
"""Script for testing diffusion tensor optimisation."""
# Python module imports.
from os import sep
# relax module imports.
from data_store import Relax_data_store; ds = Relax_data_store()
from status import Status; status = Status()
# The frequency list.
FRQ = [500, 600, 700, 800]
# Stand alone operation.
if not hasattr(ds, 'diff_type'):
ds.diff_type = 'ellipsoid'
# A data pipe.
pipe.create('back_calc', 'mf')
# Path of the files.
path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'diffusion_tensor'+sep+ds.diff_type
# Load the sequence.
sequence.read('NOE.500.out', dir=path, res_num_col=1)
# Load the original relaxation data.
for i in range(len(FRQ)):
relax_data.read(ri_id='R1_%i'%FRQ[i], ri_type='R1', frq=FRQ[i]*1e6, file='R1.%s.out'%str(int(FRQ[i])), dir=path, res_num_col=1, data_col=2, error_col=3)
relax_data.read(ri_id='R2_%i'%FRQ[i], ri_type='R2', frq=FRQ[i]*1e6, file='R2.%s.out'%str(int(FRQ[i])), dir=path, res_num_col=1, data_col=2, error_col=3)
relax_data.read(ri_id='NOE_%i'%FRQ[i], ri_type='NOE', frq=FRQ[i]*1e6, file='NOE.%s.out'%str(int(FRQ[i])), dir=path, res_num_col=1, data_col=2, error_col=3)
# Script for CPMG relaxation dispersion curve fitting using Dr. Flemming Hansen's data from http://dx.doi.org/10.1021/jp074793o.
# Python module imports.
from os import sep
# relax module imports.
from auto_analyses.relax_disp import Relax_disp
from data_store import Relax_data_store; ds = Relax_data_store()
from status import Status; status = Status()
# The dispersion models.
MODELS = ['LM63']
if hasattr(ds, 'models'):
MODELS = ds.models
# The temporary directory, if needed.
if not hasattr(ds, 'tmpdir'):
ds.tmpdir = 'temp'
# The numeric flag.
if not hasattr(ds, 'numeric_only'):
ds.numeric_only = False
# The grid search size (the number of increments per dimension).
GRID_INC = 6
# The number of Monte Carlo simulations to be used for error analysis at the end of the analysis.
MC_NUM = 3
# along with this program. If not, see <http://www.gnu.org/licenses/>. # # # ############################################################################### # Module docstring. """Script for catching bug #20464, the failure due to missing relaxation data (https://web.archive.org/web/https://gna.org/bugs/?20464).""" # Python module imports. from os import sep from tempfile import mkdtemp # relax module imports. from auto_analyses.dauvergne_protocol import dAuvergne_protocol from data_store import Relax_data_store ds = Relax_data_store() from status import Status status = Status() # Analysis variables. ##################### # The diffusion model. DIFF_MODEL = 'final' # The model-free models. Do not change these unless absolutely necessary, the protocol is likely to fail if these are changed. MF_MODELS = ['m0', 'm1', 'm2', 'm3', 'm4', 'm5', 'm6', 'm7', 'm9'] LOCAL_TM_MODELS = ['tm0', 'tm1', 'tm2', 'tm3', 'tm4', 'tm5', 'tm9'] # The grid search size (the number of increments per dimension).
and build the C module with:
gcc -o target_functions/c_chi2.os -c -I/data/python/pydebug/include/python2.7/ -fPIC target_functions/c_chi2.c
gcc -o target_functions/exponential.os -c -I/data/python/pydebug/include/python2.7/ -fPIC target_functions/exponential.c
gcc -o target_functions/relax_fit.os -c -I/data/python/pydebug/include/python2.7/ -fPIC target_functions/relax_fit.c
gcc -o target_functions/relax_fit.so -shared target_functions/c_chi2.os target_functions/exponential.os target_functions/relax_fit.os
"""
# Python module imports.
from os import sep
import sys
# relax module imports.
from data_store import Relax_data_store; ds = Relax_data_store()
from status import Status; status = Status()
# Missing intensity type (allow this script to run outside of the system test framework).
if not hasattr(ds, 'int_type'):
ds.int_type = 'height'
# Missing temporary directory.
if not hasattr(ds, 'tmpdir'):
ds.tmpdir = 'temp'
# Create the data pipe.
pipe.create('rx', 'relax_fit')
# The path to the data files.
# 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. """Optimise the R1rho on-resonance synthetic data using the M61 model.""" # Python module imports. from os import sep # relax module imports. from auto_analyses.relax_disp import Relax_disp from data_store import Relax_data_store ds = Relax_data_store() from status import Status status = Status() # Analysis variables. ##################### # The dispersion models. MODELS = ['R2eff', 'No Rex', 'M61'] # The grid search size (the number of increments per dimension). GRID_INC = None # The number of Monte Carlo simulations to be used for error analysis at the end of the analysis. MC_NUM = 3
# 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/>. #
# #
###############################################################################
"""Script for relaxation curve fitting."""
# Python module imports.
from os import sep
# relax module imports.
from data_store import Relax_data_store; ds = Relax_data_store()
from status import Status; status = Status()
# Missing temporary directory.
if not hasattr(ds, 'tmpdir'):
ds.tmpdir = 'temp'
# Create the 'rx' data pipe.
pipe.create('rx', 'relax_fit')
# The path to the data files.
data_path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'curve_fitting'+sep+'saturation_recovery'
# Load the sequence.
spin.create(spin_name='H', res_name='G', res_num=17)
# #
# 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/>. #
# #
###############################################################################
# Python module imports.
from os import getcwd, sep
# relax module imports.
from data_store import Relax_data_store; ds = Relax_data_store()
#########################################
#### Setup
# The pipe names.
if not (hasattr(ds, 'pipe_name') and hasattr(ds, 'pipe_bundle') and hasattr(ds, 'pipe_type')):
# Set pipe name, bundle and type.
ds.pipe_name = 'base pipe'
ds.pipe_bundle = 'relax_disp'
ds.pipe_type = 'relax_disp'
# The data path
if not hasattr(ds, 'data_path'):
ds.data_path = getcwd()
#########################################
# Module docstring.
"""Script for testing translation and rotation in the frame order analyses.
This script should be run from the directory where it is found with the commands:
$ ../../../../relax full_analysis.py
"""
# Python module imports.
from numpy import array, float64
from os import sep
# relax module imports.
from data_store import Relax_data_store
ds = Relax_data_store()
from status import Status
status = Status()
# The data path.
PATH = status.install_path + sep + 'test_suite' + sep + 'shared_data' + sep + 'frame_order' + sep + 'displacements'
# Create the data pipe.
self._execute_uf(uf_name='pipe.create',
pipe_name='rigid test',
pipe_type='frame order')
# Read the structures.
self._execute_uf(uf_name='structure.read_pdb',
file='displaced.pdb',
dir=PATH,
###############################################################################
# Module docstring.
"""Script for optimising the 'MQ NS 2-site' model.
This performs the analysis of:
Remco Sprangers, Anna Gribun, Peter M. Hwang, Walid A. Houry, and Lewis E. Kay (2005) Quantitative NMR spectroscopy of supramolecular complexes: Dynamic side pores in ClpP are important for product release, PNAS, 102 (46), 16678-16683. (doi: http://dx.doi.org/10.1073/pnas.0507370102)
"""
# Python module imports.
from os import sep
# relax module imports.
from auto_analyses.relax_disp import Relax_disp
from data_store import Relax_data_store; ds = Relax_data_store()
from status import Status; status = Status()
# Analysis variables.
#####################
# The dispersion models.
if not hasattr(ds, 'models'):
ds.models = ['R2eff', 'No Rex', 'NS MMQ 2-site']
# The grid search size (the number of increments per dimension).
GRID_INC = 4
# The number of Monte Carlo simulations to be used for error analysis at the end of the analysis.
MC_NUM = 3
# 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/>. #
# #
###############################################################################
# Python module imports.
from os import sep
# relax imports.
from data_store import Relax_data_store
ds = Relax_data_store()
from status import Status
status = Status()
# Missing temp directory (allow this script to run outside of the system test framework).
if not hasattr(ds, 'tmpdir'):
ds.tmpdir = 'temp_script'
# Create a data pipe.
pipe.create('pca test', 'N-state')
# Load the structures.
path = status.install_path + sep + 'test_suite' + sep + 'shared_data' + sep + 'structures' + sep + 'pca'
structure.read_pdb('distribution.pdb',
dir=path,
read_mol=1,
# 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.
"""Script for determining populations for lactose conformations using RDCs and PCSs."""
# Python module imports.
from os import sep
# relax imports.
from data_store import Relax_data_store
ds = Relax_data_store()
from specific_analyses.api import return_api
from status import Status
status = Status()
# Path of the files.
str_path = status.install_path + sep + 'test_suite' + sep + 'shared_data' + sep + 'structures' + sep + 'lactose'
data_path = status.install_path + sep + 'test_suite' + sep + 'shared_data' + sep + 'align_data'
# Create the data pipe.
self._execute_uf('lactose', 'N-state', uf_name='pipe.create')
# The population model for free operation of this script.
if not hasattr(ds, 'model'):
ds.model = 'population'
# 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. """Script for performing a very minimal model-free analysis using the OMP relaxation data.""" # Python module imports. from os import sep # relax module imports. from data_store import Relax_data_store ds = Relax_data_store() from status import Status status = Status() # Path of the relaxation data. DATA_PATH = status.install_path + sep + 'test_suite' + sep + 'shared_data' + sep + 'model_free' + sep + 'OMP' # Mini subset of local tm and model-free data pipes. LOCAL_TM_MODELS = ['tm0', 'tm1', 'tm2'] MF_MODELS = ['m0', 'm1', 'm2'] # The bond length, CSA values, heteronucleus type, and proton type. BOND_LENGTH = 1.02 * 1e-10 CSA = -172 * 1e-6 HETNUC = '15N' PROTON = '1H'
# along with this program. If not, see <http://www.gnu.org/licenses/>. #
# #
###############################################################################
# Module docstring.
"""Script for testing out the N-state model alignment tensor optimisation using pyrotarctic anhydride.
This is for testing both the optimisation of long range RDCs (2J and 3J) to pseudo-atoms and for testing the absolute T and absolute J data type.
"""
# Python module imports.
from os import sep
# relax imports.
from data_store import Relax_data_store
ds = Relax_data_store()
from status import Status
status = Status()
# Setup for stand-alone operation.
if not hasattr(ds, 'abs_data'):
ds.abs_data = 'mix'
# Path of the files.
str_path = status.install_path + sep + 'test_suite' + sep + 'shared_data' + sep + 'structures'
data_path = status.install_path + sep + 'test_suite' + sep + 'shared_data' + sep + 'align_data' + sep + 'pyrotartaric_anhydride'
# Create the data pipe.
self._execute_uf(uf_name='pipe.create',
pipe_name='pyrotartaric anhydride',
pipe_type='N-state')
# 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.
"""Script for testing the fitting of the paramagnetic centre of the PCSs."""
# Python module imports.
from os import sep
# relax module imports.
from data_store import Relax_data_store
ds = Relax_data_store()
from status import Status
status = Status()
# Path of the alignment data and structure.
DATA_PATH = status.install_path + sep + 'test_suite' + sep + 'shared_data' + sep + 'align_data' + sep + 'CaM'
STRUCT_PATH = status.install_path + sep + 'test_suite' + sep + 'shared_data' + sep + 'structures'
# Create the data pipe.
self._execute_uf(uf_name='pipe.create',
pipe_name='para_centre',
pipe_type='N-state')
# Set the mode, if not specified by the system test.
if not hasattr(ds, 'mode'):
ds.mode = 'all'
# relax script for regenerating the 'peak_heights_T2_ncyc1.bz2' saved state. This is necessary when
# the saved state becomes incompatible with relax during development.
# Python module imports.
from os import sep
# The relax data store.
from data_store import Relax_data_store; ds = Relax_data_store()
from status import Status; status = Status()
# Add a data pipe to the data store.
ds.add(pipe_name='rx', pipe_type='relax_fit')
# Load the Lupin Ap4Aase sequence.
sequence.read(file="Ap4Aase.seq", dir=status.install_path + sep+'test_suite'+sep+'shared_data', res_num_col=1, res_name_col=2)
# Name the spins so they can be matched to the assignments.
spin.name(name='N')
# Read the peak heights.
spectrum.read_intensities(file="T2_ncyc1_ave.list", dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'curve_fitting', spectrum_id='0.0176')
# Save the state.
state.save('basic_heights_T2_ncyc1', force=True)
"""Script for testing the fitting an alignment tensor to RDCs or PCSs."""
# Python module imports.
from os import sep
# relax module imports.
from data_store import Relax_data_store; ds = Relax_data_store()
from status import Status; status = Status()
# Path of the alignment data and structure.
DATA_PATH = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'align_data'+sep+'CaM'
STRUCT_PATH = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures'
# Create the data pipe.
self._execute_uf('rdc', 'N-state', uf_name='pipe.create')
# Set the mode, if not specified by the system test.
if not hasattr(ds, 'mode'):
ds.mode = 'all'
# The data to use.
if hasattr(ds, 'rand') and ds.rand:
rdc_file = 'synth_rdc_rand'
pcs_file = 'synth_pcs_rand'
else:
rdc_file = 'synth_rdc'
pcs_file = 'synth_pcs'
# Load the CaM structure.
self._execute_uf(uf_name='structure.read_pdb', file='bax_C_1J7P_N_H_Ca', dir=STRUCT_PATH)
# 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/>. # # # ############################################################################### # Script for calculating synthetics CPMG data. # Python module imports. from math import sqrt # relax module imports. from lib.io import open_write_file from data_store import Relax_data_store; ds = Relax_data_store() from pipe_control.mol_res_spin import return_spin from specific_analyses.relax_disp.data import generate_r20_key, loop_exp_frq, loop_offset_point from specific_analyses.relax_disp import optimisation from status import Status; status = Status() # The variables already defined in relax. from lib.dispersion.variables import EXP_TYPE_CPMG_SQ, MODEL_PARAMS # Analytical from lib.dispersion.variables import MODEL_CR72, MODEL_IT99, MODEL_TSMFK01, MODEL_B14 # Analytical full from lib.dispersion.variables import MODEL_CR72_FULL, MODEL_B14_FULL # NS : Numerical Solution from lib.dispersion.variables import MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_EXPANDED # NS full from lib.dispersion.variables import MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_STAR_FULL
# 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. """Script for calculating R2eff values.""" # Python module imports. from os import sep # relax module imports. from auto_analyses.relax_disp import Relax_disp from data_store import Relax_data_store; ds = Relax_data_store() from status import Status; status = Status() # Analysis variables. ##################### # The dispersion models. MODELS = ['R2eff'] # The grid search size (the number of increments per dimension). GRID_INC = 5 # The number of Monte Carlo simulations to be used for the error analyses. MC_NUM = 3
"""Script for testing diffusion tensor optimisation."""
# Python module imports.
from numpy import array, float64
from os import sep
# relax module imports.
from data_store import Relax_data_store; ds = Relax_data_store()
from status import Status; status = Status()
# Stand alone operation.
if not hasattr(ds, 'diff_type'):
ds.diff_type = 'spheroid'
if not hasattr(ds, 'diff_dir'):
ds.diff_dir = ds.diff_type
# A data pipe.
pipe.create('diff_opt', 'mf')
# Path of the files.
path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'diffusion_tensor'+sep+ds.diff_dir
# Load the sequence.
sequence.read('NOE.500.out', dir=path, res_num_col=1)
# Load a PDB file.
structure.read_pdb('uniform.pdb', dir=path)
# Set the spin names.
spin.name(name='N')
# #
# 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/>. #
# #
###############################################################################
# Python module imports.
from os import sep
# relax imports.
from data_store import Relax_data_store; ds = Relax_data_store()
from status import Status; status = Status()
# Missing temp directory (allow this script to run outside of the system test framework).
if not hasattr(ds, 'tmpdir'):
ds.tmpdir = 'temp_script'
# Create a data pipe.
pipe.create('pca test', 'N-state')
# Load the structures.
path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures'+sep+'pca'
structure.read_pdb('distribution.pdb', dir=path, read_mol=1, set_mol_name='CaM A')
structure.read_pdb('distribution.pdb', dir=path, read_mol=4, set_mol_name='CaM A', merge=True)
# Script for determining populations for lactose conformations using RDCs and PCSs.
# Python module imports.
from os import sep
# relax imports.
from data_store import Relax_data_store; ds = Relax_data_store()
from specific_analyses.setup import n_state_model_obj
from status import Status; status = Status()
# Path of the files.
str_path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures'+sep+'lactose'
data_path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'align_data'
# Create the data pipe.
self._execute_uf('lactose', 'N-state', uf_name='pipe.create')
# The population model for free operation of this script.
if not hasattr(ds, 'model'):
ds.model = 'population'
# Load the structures.
NUM_STR = 4
for i in range(NUM_STR):
self._execute_uf(uf_name='structure.read_pdb', file='lactose_MCMM4_S1_'+repr(i+1), dir=str_path, set_model_num=i+1, set_mol_name='lactose_MCMM4_S1')
# Set up the 13C and 1H spins information.
self._execute_uf(uf_name='structure.load_spins', spin_id=':UNK@C*', ave_pos=False)
self._execute_uf(uf_name='structure.load_spins', spin_id=':UNK@H*', ave_pos=False)
self._execute_uf(uf_name='spin.isotope', isotope='13C', spin_id='@C*')
# Module docstring. """Script for performing a full relaxation dispersion analysis using CPMG-type data. This uses Dr. Flemming Hansen's data from http://dx.doi.org/10.1021/jp074793o. This is here to test the ./sample_scripts/relax_disp/cpmg_analysis.py sample script. The differences between the two files should be minimal. """ # Python module imports. from os import sep # relax module imports. from auto_analyses.relax_disp import Relax_disp from data_store import Relax_data_store ds = Relax_data_store() from status import Status status = Status() # Analysis variables. ##################### # The dispersion models. MODELS = ['R2eff'] # The grid search size (the number of increments per dimension). GRID_INC = 3 # The number of Monte Carlo simulations to be used for error analysis at the end of the analysis. MC_NUM = 3
# Script for catching bug #20464, the failure due to missing relaxation data (https://gna.org/bugs/?20464). # Python module imports. from os import sep from tempfile import mkdtemp # relax module imports. from auto_analyses.dauvergne_protocol import dAuvergne_protocol from data_store import Relax_data_store; ds = Relax_data_store() from status import Status; status = Status() # Analysis variables. ##################### # The diffusion model. DIFF_MODEL = 'final' # The model-free models. Do not change these unless absolutely necessary, the protocol is likely to fail if these are changed. MF_MODELS = ['m0', 'm1', 'm2', 'm3', 'm4', 'm5', 'm6', 'm7', 'm9'] LOCAL_TM_MODELS = ['tm0', 'tm1', 'tm2', 'tm3', 'tm4', 'tm5', 'tm9'] # The grid search size (the number of increments per dimension). GRID_INC = 4 # The optimisation technique. MIN_ALGOR = 'newton' # The number of Monte Carlo simulations to be used for error analysis at the end of the analysis. MC_NUM = 3
# # # 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. """Script for catching bug #20464, the failure due to missing relaxation data (https://web.archive.org/web/https://gna.org/bugs/?20464).""" # Python module imports. from os import sep from tempfile import mkdtemp # relax module imports. from auto_analyses.dauvergne_protocol import dAuvergne_protocol from data_store import Relax_data_store; ds = Relax_data_store() from status import Status; status = Status() # The diffusion model. DIFF_MODEL = 'local_tm' # The model-free models. Do not change these unless absolutely necessary, the protocol is likely to fail if these are changed. MF_MODELS = ['m0', 'm1', 'm2', 'm3', 'm4', 'm5', 'm6', 'm7', 'm8', 'm9'] LOCAL_TM_MODELS = ['tm0', 'tm4', 'tm9'] # The grid search size (the number of increments per dimension). GRID_INC = 3 # The optimisation technique. MIN_ALGOR = 'newton'
# 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/>. # # # ############################################################################### # Script for calculating synthetics CPMG data. # Python module imports. from math import sqrt # relax module imports. from lib.io import open_write_file from data_store import Relax_data_store; ds = Relax_data_store() from pipe_control.mol_res_spin import return_spin from specific_analyses.relax_disp.data import generate_r20_key, loop_exp_frq, loop_offset_point from specific_analyses.relax_disp import optimisation from status import Status; status = Status() # The variables already defined in relax. from lib.dispersion.variables import EXP_TYPE_CPMG_SQ, MODEL_PARAMS # Analytical from lib.dispersion.variables import MODEL_CR72, MODEL_IT99, MODEL_TSMFK01, MODEL_B14 # Analytical full from lib.dispersion.variables import MODEL_CR72_FULL, MODEL_B14_FULL # NS : Numerical Solution from lib.dispersion.variables import MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_EXPANDED # NS full from lib.dispersion.variables import MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_STAR_FULL
# 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.
"""Script for testing the reading and writing of BMRB files."""
# Python module imports.
from os import sep
# relax module imports.
from data_store import Relax_data_store
ds = Relax_data_store()
from status import Status
status = Status()
# Missing temp file (allow this script to run outside of the system test framework).
state_file = 'devnull'
if not hasattr(ds, 'tmpfile'):
stand_alone = True
ds.tmpfile = 'temp_bmrb'
ds.version = '3.1'
state_file = 'temp_bmrb_state'
# Create the data pipe.
self._execute_uf(uf_name='pipe.create', pipe_name='results', pipe_type='mf')
# Read the results.
"""Script for testing diffusion tensor optimisation."""
# Python module imports.
from os import sep
# relax module imports.
from data_store import Relax_data_store; ds = Relax_data_store()
from status import Status; status = Status()
# The frequency list.
FRQ = [500, 600, 700, 800]
# Stand alone operation.
if not hasattr(ds, 'diff_type'):
ds.diff_type = 'ellipsoid'
if not hasattr(ds, 'diff_dir'):
ds.diff_dir = 'ellipsoid'
# A data pipe.
pipe.create('back_calc', 'mf')
# Path of the files.
path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'diffusion_tensor'+sep+ds.diff_dir
# Load the sequence.
sequence.read('NOE.500.out', dir=path, res_num_col=1)
# Load the original relaxation data.
for i in range(len(FRQ)):
relax_data.read(ri_id='R1_%i'%FRQ[i], ri_type='R1', frq=FRQ[i]*1e6, file='R1.%s.out'%str(int(FRQ[i])), dir=path, res_num_col=1, data_col=2, error_col=3)
# Optimise the R1rho on-resonance synthetic data using the M61 model.
# Python module imports.
from os import sep
# relax module imports.
from auto_analyses.relax_disp import Relax_disp
from data_store import Relax_data_store; ds = Relax_data_store()
from status import Status; status = Status()
# Analysis variables.
#####################
# The dispersion models.
MODELS = ['R2eff', 'No Rex', 'M61']
# The grid search size (the number of increments per dimension).
GRID_INC = 5
# The number of Monte Carlo simulations to be used for error analysis at the end of the analysis.
MC_NUM = 3
# Fixed relaxation time period flag.
if not hasattr(ds, 'fixed'):
ds.fixed = True
# Set up the data pipe.
#######################
# #
# 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.
"""Script for relaxation curve fitting."""
# Python module imports.
from os import sep
# relax module imports.
from auto_analyses.relax_fit import Relax_fit
from data_store import Relax_data_store
ds = Relax_data_store()
from status import Status
status = Status()
# Missing temporary directory.
if not hasattr(ds, 'tmpdir'):
ds.tmpdir = 'temp'
# The path to the data files.
DATA_PATH = status.install_path + sep + 'test_suite' + sep + 'shared_data' + sep + 'curve_fitting' + sep + 'bug_23244_Iinf_graph'
# Create the 'test' data pipe.
pipe.create(pipe_name='test', bundle='R1 analysis', pipe_type='relax_fit')
# Set up the sequence.
spin.create(res_num=51, spin_name='CG2')
# Script for checking the free rotor frame order model. # Python module imports. from numpy import array, float64 from os import sep # relax module imports. from data_store import Relax_data_store; ds = Relax_data_store() from lib.geometry.coord_transform import cartesian_to_spherical from status import Status; status = Status() # Generate 3 orthogonal vectors. vect_z = array([2, 1, 3], float64) r, theta, phi = cartesian_to_spherical(vect_z) # Load the tensors. self._execute_uf(uf_name='script', file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'tensors'+sep+'free_rotor_axis2_1_3_rot_tensors.py') # Data init. cdp.ave_pos_beta = 0.5 cdp.ave_pos_gamma = 0.2 cdp.axis_theta = theta cdp.axis_phi = phi # Select the Frame Order model. self._execute_uf(uf_name='frame_order.select_model', model='free rotor') # Set the reference domain. self._execute_uf(uf_name='frame_order.ref_domain', ref='full')
# 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. """relax script for regenerating the 'peak_heights_T2_ncyc1.bz2' saved state. This is necessary when the saved state becomes incompatible with relax during development. """ # Python module imports. from os import sep # The relax data store. from data_store import Relax_data_store; ds = Relax_data_store() from status import Status; status = Status() # Add a data pipe to the data store. ds.add(pipe_name='rx', pipe_type='relax_fit') # Load the Lupin Ap4Aase sequence. sequence.read(file="Ap4Aase.seq", dir=status.install_path + sep+'test_suite'+sep+'shared_data', res_num_col=1, res_name_col=2) # Name the spins so they can be matched to the assignments. spin.name(name='N') # Read the peak heights. spectrum.read_intensities(file="T2_ncyc1_ave.list", dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'curve_fitting', spectrum_id='0.0176')
# 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/>. #
# #
###############################################################################
# Python module imports.
from os import getcwd, sep
import re
# relax module imports.
from auto_analyses.relax_disp import Relax_disp
from data_store import Relax_data_store
ds = Relax_data_store()
from lib.dispersion.variables import MODEL_R2EFF
#########################################
#### Setup
# The data path
if not hasattr(ds, 'data_path'):
ds.data_path = getcwd()
# The models to analyse.
if not hasattr(ds, 'models'):
ds.models = [MODEL_R2EFF]
# The number of increments per parameter, to split up the search interval in grid search.
if not hasattr(ds, 'grid_inc'):
ds.grid_inc = 21
# # ############################################################################### """Script for testing translation and rotation in the frame order analyses. This script should be run from the directory where it is found with the commands: $ ../../../../relax full_analysis.py """ # Python module imports. from numpy import array, float64 from os import sep # relax module imports. from data_store import Relax_data_store; ds = Relax_data_store() from status import Status; status = Status() # The data path. PATH = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'frame_order'+sep+'displacements' # Create the data pipe. self._execute_uf(uf_name='pipe.create', pipe_name='rigid test', pipe_type='frame order') # Read the structures. self._execute_uf(uf_name='structure.read_pdb', file='displaced.pdb', dir=PATH, set_mol_name='fancy_mol') # Set up the 15N and 1H spins. self._execute_uf(uf_name='structure.load_spins')
# Optimise the R1rho on-resonance synthetic data using the DPL94 model.
# Python module imports.
from os import sep
# relax module imports.
from auto_analyses.relax_disp import Relax_disp
from data_store import Relax_data_store; ds = Relax_data_store()
from status import Status; status = Status()
# Analysis variables.
#####################
# The dispersion models.
if not hasattr(ds, 'models'):
ds.models = ['R2eff', 'TP02']
# The grid search size (the number of increments per dimension).
GRID_INC = 4
# The number of Monte Carlo simulations to be used for error analysis at the end of the analysis.
MC_NUM = 1
# Set up the data pipe.
#######################
# The results directory.
if not hasattr(ds, 'tmpdir'):
# 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.
"""Script for relaxation curve fitting."""
# Python module imports.
from os import sep
# relax module imports.
from data_store import Relax_data_store
ds = Relax_data_store()
from status import Status
status = Status()
# Missing intensity type (allow this script to run outside of the system test framework).
if not hasattr(ds, 'int_type'):
ds.int_type = 'height'
# Missing temporary directory.
if not hasattr(ds, 'tmpdir'):
ds.tmpdir = 'temp'
# Create the data pipe.
pipe.create('rx', 'relax_fit')
# The path to the data files.
# 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/>. #
# #
###############################################################################
# Python module imports.
from math import pi
from os import sep
from tempfile import mkdtemp
# relax module imports.
from data_store import Relax_data_store; ds = Relax_data_store()
import dep_check
from pipe_control.interatomic import interatomic_loop
from pipe_control.mol_res_spin import spin_loop
from lib.io import test_binary
from status import Status; status = Status()
from test_suite.system_tests.base_classes import SystemTestCase
class Dasha(SystemTestCase):
"""Class for testing various aspects specific to model-free analysis using the program 'Dasha'."""
def __init__(self, methodName='runTest'):
"""Skip the tests if the subprocess module is not available (Python 2.3 and earlier).
@keyword methodName: The name of the test.
# 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.
"""relax script for regenerating the 'basic_single_pipe.bz2' saved state.
This is for when the saved state becomes incompatible with relax.
"""
# The relax data store.
from data_store import Relax_data_store
ds = Relax_data_store()
# Add a data pipe to the data store.
ds.add(pipe_name='orig', pipe_type='mf')
# Add a single object to the 'orig' data pipe.
ds['orig'].x = 1
# Add a single object to the storage object.
ds.y = 'Hello'
# Save the state.
state.save('basic_single_pipe', force=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/>. #
# #
###############################################################################
# Python module imports.
from os import getcwd, sep
# relax module imports.
from auto_analyses.relax_disp import Relax_disp
from data_store import Relax_data_store; ds = Relax_data_store()
from lib.dispersion.variables import MODEL_NOREX_R1RHO_FIT_R1, MODEL_DPL94_FIT_R1, MODEL_TP02_FIT_R1, MODEL_TAP03_FIT_R1, MODEL_MP05_FIT_R1
from pipe_control.mol_res_spin import spin_loop
#########################################
#### Setup
# The pipe names.
if not (hasattr(ds, 'pipe_name') and hasattr(ds, 'pipe_bundle') and hasattr(ds, 'pipe_type') and hasattr(ds, 'pipe_bundle_cluster')):
# Set pipe name, bundle and type.
ds.pipe_name = 'base pipe'
ds.pipe_bundle = 'relax_disp'
ds.pipe_type = 'relax_disp'
ds.pipe_bundle_cluster = 'cluster'
# The data path
if not hasattr(ds, 'data_path'):
"""Script for testing the loading of phthalic acid NOEs from a generically formatted file."""
# Python module imports.
from os import sep
# relax module imports.
from data_store import Relax_data_store; ds = Relax_data_store()
from status import Status; status = Status()
# Add a date pipe if one doesn't already exist.
if not ds.keys():
self._execute_uf(uf_name='pipe.create', pipe_name='test', pipe_type='N-state')
# NOE restraint file.
if not hasattr(ds, 'file_name'):
ds.file_name = 'phthalic_acid'
# Path of the relaxation data.
DATA_PATH = status.install_path + sep+'test_suite'+sep+'shared_data'+sep
# Pseudo-atoms.
PSEUDO = [
['Q7', ['@H16', '@H17', '@H18']],
['Q9', ['@H20', '@H21', '@H22']],
['Q10', ['@H23', '@H24', '@H25']]
]
# Read the structure.
self._execute_uf(uf_name='structure.read_pdb', file='gromacs.pdb', dir=DATA_PATH+sep+'structures'+sep+'phthalic_acid')
# #
# 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.
"""Script for CPMG relaxation dispersion curve fitting using Dr. Flemming Hansen's data from http://dx.doi.org/10.1021/jp074793o."""
# Python module imports.
from os import sep
# relax module imports.
from auto_analyses.relax_disp import Relax_disp
from data_store import Relax_data_store
ds = Relax_data_store()
from status import Status
status = Status()
# The dispersion models.
MODELS = ['LM63']
if hasattr(ds, 'models'):
MODELS = ds.models
# The temporary directory, if needed.
if not hasattr(ds, 'tmpdir'):
ds.tmpdir = 'temp'
# The numeric flag.
if not hasattr(ds, 'numeric_only'):
ds.numeric_only = False
# Script for exponential curve-fitting to synthetic R1rho dispersion data.
# Python module imports.
from os import sep
# relax module imports.
from auto_analyses.relax_disp import Relax_disp
from data_store import Relax_data_store; ds = Relax_data_store()
from status import Status; status = Status()
# Analysis variables.
#####################
# The dispersion models.
MODELS = ['R2eff']
# The grid search size (the number of increments per dimension).
GRID_INC = 3
# The number of Monte Carlo simulations to be used for error analysis at the end of the analysis.
MC_NUM = 3
# Set up the data pipe.
#######################
# The results directory.
if not hasattr(ds, 'tmpdir'):
ds.tmpdir = None
# 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.
"""Script for testing the fitting an alignment tensor to RDCs or PCSs."""
# Python module imports.
from os import sep
# relax module imports.
from data_store import Relax_data_store; ds = Relax_data_store()
from status import Status; status = Status()
# Path of the alignment data and structure.
DATA_PATH = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'align_data'+sep+'CaM'
STRUCT_PATH = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures'
# Create the data pipe.
self._execute_uf('rdc', 'N-state', uf_name='pipe.create')
# Set the mode, if not specified by the system test.
if not hasattr(ds, 'mode'):
ds.mode = 'all'
# The data to use.
"""Script for testing the loading of phthalic acid NOEs from a generically formatted file."""
# Python module imports.
from os import sep
# relax module imports.
from data_store import Relax_data_store; ds = Relax_data_store()
from status import Status; status = Status()
# Add a date pipe if one doesn't already exist.
if not len(ds):
self._execute_uf(uf_name='pipe.create', pipe_name='test', pipe_type='N-state')
# NOE restraint file.
if not hasattr(ds, 'file_name'):
ds.file_name = 'phthalic_acid'
# Path of the relaxation data.
DATA_PATH = status.install_path + sep+'test_suite'+sep+'shared_data'+sep
# Pseudo-atoms.
PSEUDO = [
['Q7', ['@H16', '@H17', '@H18']],
['Q9', ['@H20', '@H21', '@H22']],
['Q10', ['@H23', '@H24', '@H25']]
]
# Read the structure.
self._execute_uf(uf_name='structure.read_pdb', file='gromacs.pdb', dir=DATA_PATH+sep+'structures'+sep+'phthalic_acid')
