Author: bugman
Date: Wed Jul 11 15:31:08 2012
New Revision: 17229
URL: http://svn.gna.org/viewcvs/relax?rev=17229&view=rev
Log:
Shifted some of the sample scripts into the analysis specific sub-directories.
Added:
trunk/sample_scripts/model_free/generate_ri.py
- copied unchanged from r17228, trunk/sample_scripts/generate_ri.py
trunk/sample_scripts/n_state_model/stereochem_analysis.py
- copied unchanged from r17228,
trunk/sample_scripts/stereochem_analysis.py
Removed:
trunk/sample_scripts/generate_ri.py
trunk/sample_scripts/stereochem_analysis.py
Removed: trunk/sample_scripts/generate_ri.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/sample_scripts/generate_ri.py?rev=17228&view=auto
==============================================================================
--- trunk/sample_scripts/generate_ri.py (original)
+++ trunk/sample_scripts/generate_ri.py (removed)
@@ -1,120 +1,0 @@
-###############################################################################
-#
#
-# Copyright (C) 2004-2012 Edward d'Auvergne
#
-#
#
-# This file is part of the program relax (http://www.nmr-relax.com).
#
-#
#
-# This program is free software: you can redistribute it and/or modify
#
-# it under the terms of the GNU General Public License as published by
#
-# the Free Software Foundation, either version 3 of the License, or
#
-# (at your option) any later version.
#
-#
#
-# 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/>.
#
-#
#
-###############################################################################
-
-"""Script for back-calculating the relaxation data."""
-
-# relax module imports.
-from generic_fns.mol_res_spin import spin_loop
-
-
-def back_calc():
- """Function for back calculating the relaxation data."""
-
- relax_data.back_calc(ri_id='NOE_600', ri_type='NOE', frq=600e6)
- relax_data.back_calc(ri_id='R1_600', ri_type='R1', frq=600e6)
- relax_data.back_calc(ri_id='R2_600', ri_type='R2', frq=600e6)
- relax_data.back_calc(ri_id='NOE_500', ri_type='NOE', frq=500e6)
- relax_data.back_calc(ri_id='R1_500', ri_type='R1', frq=500e6)
- relax_data.back_calc(ri_id='R2_500', ri_type='R2', frq=500e6)
-
-
-def errors():
- """Function for generating relaxation data errors."""
-
- # Loop over the sequence.
- for spin in spin_loop():
- # Loop over the relaxation data.
- for ri_id in cdp.ri_ids:
- # No data.
- if spin.ri_data_bc[ri_id] == None:
- continue
-
- # Set up the error relaxation data structure if needed.
- if not hasattr(spin, 'ri_data_err'):
- spin.ri_data_err = {}
-
- # 600 MHz NOE.
- if ri_id == 'NOE_600':
- spin.ri_data_err[ri_id] = 0.04
-
- # 500 MHz NOE.
- elif ri_id == 'NOE_500':
- spin.ri_data_err[ri_id] = 0.05
-
- # All other data.
- else:
- spin.ri_data_err[ri_id] = spin.ri_data_bc[ri_id] * 0.02
-
-
-def write():
- """Function for writing the relaxation data to file."""
-
- relax_data.write(ri_id='NOE_600', file='noe.600.out', force=True)
- relax_data.write(ri_id='R1_600', file='r1.600.out', force=True)
- relax_data.write(ri_id='R2_600', file='r2.600.out', force=True)
- relax_data.write(ri_id='NOE_500', file='noe.500.out', force=True)
- relax_data.write(ri_id='R1_500', file='r1.500.out', force=True)
- relax_data.write(ri_id='R2_500', file='r2.500.out', force=True)
-
-
-# Create the data pipe.
-pipe.create('test', 'mf')
-
-# Load a PDB file.
-structure.read_pdb('example.pdb')
-
-# Load the spins from the structure.
-structure.load_spins(spin_id='@N')
-structure.load_spins(spin_id='@H')
-
-# Define the magnetic dipole-dipole relaxation interaction.
-dipole_pair.define(spin_id1='@N', spin_id2='@H', direct_bond=True)
-dipole_pair.set_dist(spin_id1='@N', spin_id2='@H', ave_dist=1.02 * 1e-10)
-dipole_pair.unit_vectors()
-
-# Define the CSA relaxation interaction.
-value.set(val=-172e-6, param='csa')
-
-# Set the diffusion tensor in the PDB frame (Dxx, Dyy, Dzz, Dxy, Dxz, Dyz).
-diffusion_tensor.init((1.340e7, 1.516e7, 1.691e7, 0.000e7, 0.000e7,
0.000e7), param_types=3)
-
-# Set the spin information.
-spin.isotope('15N', spin_id='@N')
-spin.isotope('1H', spin_id='@H')
-
-# Set the required values.
-value.set(val=0.8, param='s2')
-value.set(val=20e-12, param='te')
-
-# Select model-free model m2.
-model_free.select_model(model='m2')
-
-# Back calculate the relaxation data (using the function defined in this
script).
-back_calc()
-
-# Generate the errors (using the function defined in this script).
-errors()
-
-# Write the data (using the function defined in this script).
-write()
-
-# Write the relaxation data to file.
-results.write()
Removed: trunk/sample_scripts/stereochem_analysis.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/sample_scripts/stereochem_analysis.py?rev=17228&view=auto
==============================================================================
--- trunk/sample_scripts/stereochem_analysis.py (original)
+++ trunk/sample_scripts/stereochem_analysis.py (removed)
@@ -1,141 +1,0 @@
-###############################################################################
-#
#
-# Copyright (C) 2010-2012 Edward d'Auvergne
#
-#
#
-# This file is part of the program relax (http://www.nmr-relax.com).
#
-#
#
-# This program is free software: you can redistribute it and/or modify
#
-# it under the terms of the GNU General Public License as published by
#
-# the Free Software Foundation, either version 3 of the License, or
#
-# (at your option) any later version.
#
-#
#
-# 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/>.
#
-#
#
-###############################################################################
-
-"""Script for the determination of relative stereochemistry.
-
-The analysis is preformed by using multiple ensembles of structures,
randomly sampled from a given
-set of structures. The discrimination is performed by comparing the sets of
ensembles using NOE
-violations and RDC Q-factors.
-
-This script is split into multiple stages:
-
- 1. The random sampling of the snapshots to generate the N ensembles
(NUM_ENS, usually 10,000 to
- 100,000) of M members (NUM_MODELS, usually ~10). The original snapshot
files are expected to be
- named the SNAPSHOT_DIR + CONFIG + a number from SNAPSHOT_MIN to
SNAPSHOT_MAX + ".pdb", e.g.
- "snapshots/R647.pdb". The ensembles will be placed into the "ensembles"
directory.
-
- 2. The NOE violation analysis.
-
- 3. The superimposition of ensembles. For each ensemble, Molmol is used
for superimposition
- using the fit to first algorithm. The superimposed ensembles will be
placed into the
- "ensembles_superimposed" directory. This stage is not necessary for the
NOE analysis.
-
- 4. The RDC Q-factor analysis.
-
- 5. Generation of Grace graphs.
-
- 6. Final ordering of ensembles using the combined RDC and NOE
Q-factors, whereby the NOE
- Q-factor is defined as::
-
- Q^2 = U / sum(NOE_i^2),
-
- where U is the quadratic flat bottom well potential - the NOE violation
in Angstrom^2. The
- denominator is the sum of all squared NOEs - this must be given as the
value of NOE_NORM. The
- combined Q is given by::
-
- Q_total^2 = Q_NOE^2 + Q_RDC^2.
-"""
-
-# relax module imports.
-from auto_analyses.stereochem_analysis import Stereochem_analysis
-
-
-# Stage of analysis (see the docstring above for the options).
-STAGE = 1
-
-# Number of ensembles.
-NUM_ENS = 100000
-
-# Ensemble size.
-NUM_MODELS = 10
-
-# Configurations.
-CONFIGS = ["R", "S"]
-
-# Snapshot directories (corresponding to CONFIGS).
-SNAPSHOT_DIR = ["snapshots", "snapshots"]
-
-# Min and max number of the snapshots (corresponding to CONFIGS).
-SNAPSHOT_MIN = [0, 0]
-SNAPSHOT_MAX = [76, 71]
-
-# Pseudo-atoms.
-PSEUDO = [
-["Q7", ["@H16", "@H17", "@H18"]],
-["Q9", ["@H20", "@H21", "@H22"]],
-["Q10", ["@H23", "@H24", "@H25"]]
-]
-
-# NOE info.
-NOE_FILE = "noes"
-NOE_NORM = 50 * 4**2 # The NOE normalisation factor (sum of all NOEs
squared).
-
-# RDC file info.
-RDC_NAME = "PAN"
-RDC_FILE = "pan_rdcs"
-RDC_SPIN_ID1_COL = 1
-RDC_SPIN_ID2_COL = 2
-RDC_DATA_COL = 2
-RDC_ERROR_COL = None
-
-# Bond length.
-BOND_LENGTH = 1.117 * 1e-10
-
-# Log file output (only for certain stages).
-LOG = True
-
-# Number of buckets for the distribution plots.
-BUCKET_NUM = 200
-
-# Distribution plot limits.
-LOWER_LIM_NOE = 0.0
-UPPER_LIM_NOE = 600.0
-LOWER_LIM_RDC = 0.0
-UPPER_LIM_RDC = 1.0
-
-
-# Set up and code execution.
-analysis = Stereochem_analysis(
- stage=STAGE,
- num_ens=NUM_ENS,
- num_models=NUM_MODELS,
- configs=CONFIGS,
- snapshot_dir=SNAPSHOT_DIR,
- snapshot_min=SNAPSHOT_MIN,
- snapshot_max=SNAPSHOT_MAX,
- pseudo=PSEUDO,
- noe_file=NOE_FILE,
- noe_norm=NOE_NORM,
- rdc_name=RDC_NAME,
- rdc_file=RDC_FILE,
- rdc_spin_id1_col=RDC_SPIN_ID1_COL,
- rdc_spin_id2_col=RDC_SPIN_ID2_COL,
- rdc_data_col=RDC_DATA_COL,
- rdc_error_col=RDC_ERROR_COL,
- bond_length=BOND_LENGTH,
- log=LOG,
- bucket_num=BUCKET_NUM,
- lower_lim_noe=LOWER_LIM_NOE,
- upper_lim_noe=UPPER_LIM_NOE,
- lower_lim_rdc=LOWER_LIM_RDC,
- upper_lim_rdc=UPPER_LIM_RDC
-)
-analysis.run()
r17229 - in /trunk/sample_scripts: ./ model_free/ n_state_model/