Author: bugman
Date: Thu Mar 3 10:44:30 2011
New Revision: 12757
URL: http://svn.gna.org/viewcvs/relax?rev=12757&view=rev
Log:
Updated all of the Dasha module for the new relax data ID string design.
Modified:
branches/relax_data/generic_fns/dasha.py
Modified: branches/relax_data/generic_fns/dasha.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_data/generic_fns/dasha.py?rev=12757&r1=12756&r2=12757&view=diff
==============================================================================
--- branches/relax_data/generic_fns/dasha.py (original)
+++ branches/relax_data/generic_fns/dasha.py Thu Mar 3 10:44:30 2011
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2005-2009 Edward d'Auvergne
#
+# Copyright (C) 2005-2011 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -30,7 +30,7 @@
import sys
# relax module imports.
-from generic_fns import angles, diffusion_tensor, pipes, value
+from generic_fns import angles, diffusion_tensor, pipes, relax_data, value
from generic_fns.mol_res_spin import exists_mol_res_spin_data,
first_residue_num, last_residue_num, residue_loop, spin_loop
from relax_errors import RelaxDirError, RelaxError, RelaxFileError,
RelaxNoPdbError, RelaxNoSequenceError, RelaxNoTensorError
from relax_io import mkdir_nofail, open_write_file, test_binary
@@ -52,23 +52,22 @@
# Loop over the sequence.
for spin in spin_loop():
# Relaxation data must exist!
- if not hasattr(spin, 'relax_data'):
+ if not hasattr(spin, 'ri_data'):
spin.select = False
# Require 3 or more relaxation data points.
- elif len(spin.relax_data) < 3:
+ elif len(spin.ri_data) < 3:
spin.select = False
# Require at least as many data points as params to prevent
over-fitting.
- elif hasattr(spin, 'params') and spin.params and len(spin.params) >
len(spin.relax_data):
+ elif hasattr(spin, 'params') and spin.params and len(spin.params) >
len(spin.ri_data):
spin.select = False
def create(algor='LM', dir=None, force=False):
"""Create the Dasha script file 'dasha_script' for controlling the
program.
- @keyword algor: The optimisation algorithm to use. This can be the
Levenberg-Marquardt
- algorithm 'LM' or the Newton-Raphson algorithm 'NR'.
+ @keyword algor: The optimisation algorithm to use. This can be the
Levenberg-Marquardt algorithm 'LM' or the Newton-Raphson algorithm 'NR'.
@type algor: str
@keyword dir: The optional directory to place the script into.
@type dir: str or None
@@ -96,7 +95,7 @@
# Test the optimisation algorithm.
if algor not in ['LM', 'NR']:
- raise RelaxError("The Dasha optimisation algorithm " + repr(algor) +
" is unknown, it should either be 'LM' or 'NR'.")
+ raise RelaxError("The Dasha optimisation algorithm '%s' is unknown,
it should either be 'LM' or 'NR'." % algor)
# Multiple spins per residue not allowed.
for residue in residue_loop():
@@ -112,20 +111,6 @@
dir = pipes.cdp_name()
mkdir_nofail(dir, verbosity=0)
- # Number of field strengths and values.
- num_frq = 0
- frq = []
- for spin in spin_loop():
- if hasattr(spin, 'num_frq'):
- if spin.num_frq > num_frq:
- # Number of field strengths.
- num_frq = spin.num_frq
-
- # Field strength values.
- for val in spin.frq:
- if val not in frq:
- frq.append(val)
-
# Calculate the angle alpha of the XH vector in the spheroid diffusion
frame.
if cdp.diff_tensor.type == 'spheroid':
angles.spheroid_frame()
@@ -147,17 +132,16 @@
@type file: file object
@param model_type: The model-free model type.
@type model_type: str
- @param algor: The optimisation algorithm to use. This can be the
Levenberg-Marquardt
- algorithm 'LM' or the Newton-Raphson algorithm 'NR'.
+ @param algor: The optimisation algorithm to use. This can be the
Levenberg-Marquardt algorithm 'LM' or the Newton-Raphson algorithm 'NR'.
@type algor: str
"""
# Delete all data.
- file.write('# Delete all data.\n')
- file.write('del 1 10000\n')
+ file.write("# Delete all data.\n")
+ file.write("del 1 10000\n")
# Nucleus type.
- file.write('\n# Nucleus type.\n')
+ file.write("\n# Nucleus type.\n")
nucleus = None
for spin in spin_loop():
# Can only handle one spin type.
@@ -174,31 +158,30 @@
elif nucleus == '13C':
nucleus = 'C13'
else:
- raise RelaxError('Cannot handle the nucleus type ' + repr(nucleus) +
' within Dasha.')
- file.write('set nucl ' + nucleus + '\n')
+ raise RelaxError("Cannot handle the nucleus type '%s' within Dasha."
% nucleus)
+ file.write("set nucl %s\n" % nucleus)
# Number of frequencies.
- file.write('\n# Number of frequencies.\n')
- file.write('set n_freq ' + repr(cdp.num_frq) + '\n')
+ file.write("\n# Number of frequencies.\n")
+ file.write("set n_freq %s\n" % relax_data.num_frq())
# Frequency values.
- file.write('\n# Frequency values.\n')
- frqs = []
- for ri_id in cdp.ri_ids:
- if not cdp.frq[ri_id] in frqs:
- frqs.append(cdp.frq[ri_id])
- file.write('set H1_freq ' + repr(cdp.frq[ri_id] / 1e6) + ' ' +
repr(i+1) + '\n')
+ file.write("\n# Frequency values.\n")
+ count = 1
+ for frq in relax_data.frq_loop():
+ file.write("set H1_freq %s %s\n" % (frq / 1e6, count))
+ count += 1
# Set the diffusion tensor.
- file.write('\n# Set the diffusion tensor.\n')
+ file.write("\n# Set the diffusion tensor.\n")
if model_type != 'local_tm':
# Sphere.
if cdp.diff_tensor.type == 'sphere':
- file.write('set tr ' + repr(cdp.diff_tensor.tm / 1e-9) + '\n')
+ file.write("set tr %s\n" % (cdp.diff_tensor.tm / 1e-9))
# Spheroid.
elif cdp.diff_tensor.type == 'spheroid':
- file.write('set tr ' + repr(cdp.diff_tensor.tm / 1e-9) + '\n')
+ file.write('set tr %s\n' % (cdp.diff_tensor.tm / 1e-9))
# Ellipsoid.
elif cdp.diff_tensor.type == 'ellipsoid':
@@ -206,24 +189,24 @@
Dx, Dy, Dz = diffusion_tensor.return_eigenvalues()
# Geometric parameters.
- file.write('set tr ' + repr(cdp.diff_tensor.tm / 1e-9) + '\n')
- file.write('set D1/D3 ' + repr(Dx / Dz) + '\n')
- file.write('set D2/D3 ' + repr(Dy / Dz) + '\n')
+ file.write("set tr %s\n" % (cdp.diff_tensor.tm / 1e-9))
+ file.write("set D1/D3 %s\n" % (Dx / Dz))
+ file.write("set D2/D3 %s\n" % (Dy / Dz))
# Orientational parameters.
- file.write('set alfa ' + repr(cdp.diff_tensor.alpha / (2.0 * pi)
* 360.0) + '\n')
- file.write('set betta ' + repr(cdp.diff_tensor.beta / (2.0 * pi)
* 360.0) + '\n')
- file.write('set gamma ' + repr(cdp.diff_tensor.gamma / (2.0 *
pi) * 360.0) + '\n')
+ file.write("set alfa %s\n" % (cdp.diff_tensor.alpha / (2.0 * pi)
* 360.0))
+ file.write("set betta %s\n" % (cdp.diff_tensor.beta / (2.0 * pi)
* 360.0))
+ file.write("set gamma %s\n" % (cdp.diff_tensor.gamma / (2.0 *
pi) * 360.0))
# Reading the relaxation data.
- file.write('\n# Reading the relaxation data.\n')
- file.write('echo Reading the relaxation data.\n')
+ file.write("\n# Reading the relaxation data.\n")
+ file.write("echo Reading the relaxation data.\n")
noe_index = 1
r1_index = 1
r2_index = 1
- for i in xrange(cdp.num_ri):
+ for ri_id in cdp.ri_ids:
# NOE.
- if cdp.ri_labels[i] == 'NOE':
+ if cdp.ri_type[ri_id] == 'NOE':
# Data set number.
number = noe_index
@@ -234,7 +217,7 @@
noe_index = noe_index + 1
# R1.
- elif cdp.ri_labels[i] == 'R1':
+ elif cdp.ri_type[ri_id] == 'R1':
# Data set number.
number = r1_index
@@ -245,7 +228,7 @@
r1_index = r1_index + 1
# R2.
- elif cdp.ri_labels[i] == 'R2':
+ elif cdp.ri_type[ri_id] == 'R2':
# Data set number.
number = r2_index
@@ -257,9 +240,9 @@
# Set the data type.
if number == 1:
- file.write('\nread < ' + data_type + '\n')
+ file.write("\nread < %s\n" % data_type)
else:
- file.write('\nread < ' + data_type + ' ' + repr(number) + '\n')
+ file.write("\nread < %s %s\n" % (data_type, number))
# The relaxation data.
for residue in residue_loop():
@@ -271,15 +254,15 @@
continue
# Skip and deselect spins for which relaxation data is missing.
- if len(spin.relax_data) != cdp.num_ri:
+ if len(spin.ri_data) != len(cdp.ri_ids):
spin.select = False
continue
# Data and errors.
- file.write(repr(residue.num) + ' ' + repr(spin.relax_data[i]) +
' ' + repr(spin.relax_error[i]) + '\n')
+ file.write("%s %s %s\n" % (residue.num, spin.ri_data[ri_id],
spin.ri_data_err[ri_id]))
# Terminate the reading.
- file.write('exit\n')
+ file.write("exit\n")
# Individual residue optimisation.
if model_type == 'mf':
@@ -293,24 +276,24 @@
continue
# Comment.
- file.write('\n\n\n# Residue ' + repr(residue.num) + '\n\n')
+ file.write("\n\n\n# Residue %s\n\n" % residue.num)
# Echo.
- file.write('echo Optimisation of residue ' + repr(residue.num) +
'\n')
+ file.write("echo Optimisation of residue %s\n" % residue.num)
# Select the spin.
- file.write('\n# Select the residue.\n')
- file.write('set cres ' + repr(residue.num) + '\n')
+ file.write("\n# Select the residue.\n")
+ file.write("set cres %s\n" % residue.num)
# The angle alpha of the XH vector in the spheroid diffusion
frame.
if cdp.diff_tensor.type == 'spheroid':
- file.write('set teta ' + repr(spin.alpha) + '\n')
+ file.write("set teta %s\n" % spin.alpha)
# The angles theta and phi of the XH vector in the ellipsoid
diffusion frame.
elif cdp.diff_tensor.type == 'ellipsoid':
- file.write('\n# Setting the spherical angles of the XH
vector in the ellipsoid diffusion frame.\n')
- file.write('set teta ' + repr(spin.theta) + '\n')
- file.write('set fi ' + repr(spin.phi) + '\n')
+ file.write("\n# Setting the spherical angles of the XH
vector in the ellipsoid diffusion frame.\n")
+ file.write("set teta %s\n" % spin.theta)
+ file.write("set fi %s\n" % spin.phi)
# The 'jmode'.
if 'ts' in spin.params:
@@ -339,58 +322,58 @@
sym = False
# Set the jmode.
- file.write('\n# Set the jmode.\n')
- file.write('set def jmode ' + repr(jmode))
+ file.write("\n# Set the jmode.\n")
+ file.write("set def jmode %s" % jmode)
if exch:
- file.write(' exch')
+ file.write(" exch")
if anis:
- file.write(' anis')
+ file.write(" anis")
if sym:
- file.write(' sym')
- file.write('\n')
+ file.write(" sym")
+ file.write("\n")
# Parameter default values.
- file.write('\n# Parameter default values.\n')
- file.write('reset jmode ' + repr(residue.num) + '\n')
+ file.write("\n# Parameter default values.\n")
+ file.write("reset jmode %s\n" % residue.num)
# Bond length.
- file.write('\n# Bond length.\n')
- file.write('set r_hx ' + repr(spin.r / 1e-10) + '\n')
+ file.write("\n# Bond length.\n")
+ file.write("set r_hx %s\n" % (spin.r / 1e-10))
# CSA value.
- file.write('\n# CSA value.\n')
- file.write('set csa ' + repr(spin.csa / 1e-6) + '\n')
+ file.write("\n# CSA value.\n")
+ file.write("set csa %s\n" % (spin.csa / 1e-6))
# Fix the tf parameter if it isn't in the model.
if not 'tf' in spin.params and jmode == 3:
- file.write('\n# Fix the tf parameter.\n')
- file.write('fix tf 0\n')
+ file.write("\n# Fix the tf parameter.\n")
+ file.write("fix tf 0\n")
# Optimisation of all residues.
- file.write('\n\n\n# Optimisation of all residues.\n')
+ file.write("\n\n\n# Optimisation of all residues.\n")
if algor == 'LM':
- file.write('lmin ' + repr(first_residue_num()) + ' ' +
repr(last_residue_num()))
+ file.write("lmin %s %s" % (first_residue_num(),
last_residue_num()))
elif algor == 'NR':
- file.write('min ' + repr(first_residue_num()) + ' ' +
repr(last_residue_num()))
+ file.write("min %s %s" % (first_residue_num(),
last_residue_num()))
# Show the results.
- file.write('\n# Show the results.\n')
- file.write('echo\n')
- file.write('show all\n')
+ file.write("\n# Show the results.\n")
+ file.write("echo\n")
+ file.write("show all\n")
# Write the results.
- file.write('\n# Write the results.\n')
- file.write('write S2.out S\n')
- file.write('write S2f.out Sf\n')
- file.write('write S2s.out Ss\n')
- file.write('write te.out te\n')
- file.write('write tf.out tf\n')
- file.write('write ts.out ts\n')
- file.write('write Rex.out rex\n')
- file.write('write chi2.out F\n')
+ file.write("\n# Write the results.\n")
+ file.write("write S2.out S\n")
+ file.write("write S2f.out Sf\n")
+ file.write("write S2s.out Ss\n")
+ file.write("write te.out te\n")
+ file.write("write tf.out tf\n")
+ file.write("write ts.out ts\n")
+ file.write("write Rex.out rex\n")
+ file.write("write chi2.out F\n")
else:
- raise RelaxError('Optimisation of the parameter set ' +
repr(model_type) + ' currently not supported.')
+ raise RelaxError("Optimisation of the parameter set '%s' currently
not supported." % model_type)
def execute(dir, force, binary):
@@ -398,8 +381,7 @@
@param dir: The optional directory where the script is located.
@type dir: str or None
- @param force: A flag which if True will cause any pre-existing files
to be overwritten by
- Dasha.
+ @param force: A flag which if True will cause any pre-existing files
to be overwritten by Dasha.
@type force: bool
@param binary: The name of the Dasha binary file. This can include the
path to the binary.
@type binary: str
@@ -457,7 +439,7 @@
chdir(orig_dir)
# Print some blank lines (aesthetics)
- sys.stdout.write('\n\n')
+ sys.stdout.write("\n\n")
def extract(dir):
r12757 - /branches/relax_data/generic_fns/dasha.py