Author: bugman
Date: Sat Oct 11 21:09:54 2008
New Revision: 7601
URL: http://svn.gna.org/viewcvs/relax?rev=7601&view=rev
Log:
Converted the create_script() function to the new design.
Modified:
1.3/generic_fns/dasha.py
Modified: 1.3/generic_fns/dasha.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/dasha.py?rev=7601&r1=7600&r2=7601&view=diff
==============================================================================
--- 1.3/generic_fns/dasha.py (original)
+++ 1.3/generic_fns/dasha.py Sat Oct 11 21:09:54 2008
@@ -32,8 +32,8 @@
# relax module imports.
from data import Relax_data_store; ds = Relax_data_store()
-from generic_fns import angles, pipes
-from generic_fns.mol_res_spin import exists_mol_res_spin_data, spin_loop
+from generic_fns import angles, diffusion_tensor, pipes
+from generic_fns.mol_res_spin import exists_mol_res_spin_data, residue_loop,
spin_loop
from relax_errors import RelaxDirError, RelaxError, RelaxFileError,
RelaxNoPdbError, RelaxNoSequenceError, RelaxNoTensorError, RelaxNucleusError
from relax_io import mkdir_nofail, open_write_file, test_binary
from specific_fns.setup import model_free_obj
@@ -105,12 +105,24 @@
# The 'dasha_script' file.
script = open_write_file(file_name='dasha_script', dir=dir, force=force)
- create_script(script)
+ create_script(script, model_type, algor)
script.close()
-def create_script(file):
- """Create the Dasha script file."""
+def create_script(file, model_type, algor):
+ """Create the Dasha script file.
+
+ @param file: The opened file descriptor.
+ @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'.
+ @type algor: str
+ """
+
+ # Get the current data pipe.
+ cdp = pipes.get_pipe()
# Delete all data.
file.write('# Delete all data.\n')
@@ -118,10 +130,20 @@
# Nucleus type.
file.write('\n# Nucleus type.\n')
- nucleus = self.relax.generic.nuclei.find_nucleus()
- if nucleus == 'N':
+ nucleus = None
+ for spin in spin_loop():
+ # Can only handle one spin type.
+ if nucleus and spin.heteronuc_type != nucleus:
+ raise RelaxError, "The nuclei '%s' and '%s' do not match, relax
can only handle one nucleus type in Dasha." % (nucleus, spin.heteronuc_type)
+
+ # Set the nucleus.
+ if not nucleus:
+ nucleus = spin.heteronuc_type
+
+ # Convert the name and write it.
+ if nucleus == '15N':
nucleus = 'N15'
- elif nucleus == 'C':
+ elif nucleus == '13C':
nucleus = 'C13'
else:
raise RelaxError, 'Cannot handle the nucleus type ' + `nucleus` + '
within Dasha.'
@@ -129,38 +151,38 @@
# Number of frequencies.
file.write('\n# Number of frequencies.\n')
- file.write('set n_freq ' + `ds.num_frq[self.run]` + '\n')
+ file.write('set n_freq ' + `cdp.num_frq` + '\n')
# Frequency values.
file.write('\n# Frequency values.\n')
- for i in xrange(ds.num_frq[self.run]):
- file.write('set H1_freq ' + `ds.frq[self.run][i] / 1e6` + ' ' +
`i+1` + '\n')
+ for i in xrange(cdp.num_frq):
+ file.write('set H1_freq ' + `cdp.frq[i] / 1e6` + ' ' + `i+1` + '\n')
# Set the diffusion tensor.
file.write('\n# Set the diffusion tensor.\n')
if model_type != 'local_tm':
# Sphere.
- if ds.diff[self.run].type == 'sphere':
- file.write('set tr ' + `ds.diff[self.run].tm / 1e-9` + '\n')
+ if cdp.diff_tensor.type == 'sphere':
+ file.write('set tr ' + `cdp.diff_tensor.tm / 1e-9` + '\n')
# Spheroid.
- elif ds.diff[self.run].type == 'spheroid':
- file.write('set tr ' + `ds.diff[self.run].tm / 1e-9` + '\n')
+ elif cdp.diff_tensor.type == 'spheroid':
+ file.write('set tr ' + `cdp.diff_tensor.tm / 1e-9` + '\n')
# Ellipsoid.
- elif ds.diff[self.run].type == 'ellipsoid':
+ elif cdp.diff_tensor.type == 'ellipsoid':
# Get the eigenvales.
- Dx, Dy, Dz =
self.relax.generic.diffusion_tensor.return_eigenvalues(self.run)
+ Dx, Dy, Dz = diffusion_tensor.return_eigenvalues()
# Geometric parameters.
- file.write('set tr ' + `ds.diff[self.run].tm / 1e-9` + '\n')
+ file.write('set tr ' + `cdp.diff_tensor.tm / 1e-9` + '\n')
file.write('set D1/D3 ' + `Dx / Dz` + '\n')
file.write('set D2/D3 ' + `Dy / Dz` + '\n')
# Orientational parameters.
- file.write('set alfa ' + `ds.diff[self.run].alpha / (2.0 * pi) *
360.0` + '\n')
- file.write('set betta ' + `ds.diff[self.run].beta / (2.0 * pi) *
360.0` + '\n')
- file.write('set gamma ' + `ds.diff[self.run].gamma / (2.0 * pi)
* 360.0` + '\n')
+ file.write('set alfa ' + `cdp.diff_tensor.alpha / (2.0 * pi) *
360.0` + '\n')
+ file.write('set betta ' + `cdp.diff_tensor.beta / (2.0 * pi) *
360.0` + '\n')
+ file.write('set gamma ' + `cdp.diff_tensor.gamma / (2.0 * pi) *
360.0` + '\n')
# Reading the relaxation data.
file.write('\n# Reading the relaxation data.\n')
@@ -168,9 +190,9 @@
noe_index = 1
r1_index = 1
r2_index = 1
- for i in xrange(ds.num_ri[self.run]):
+ for i in xrange(cdp.num_ri):
# NOE.
- if ds.ri_labels[self.run][i] == 'NOE':
+ if cdp.ri_labels[i] == 'NOE':
# Data set number.
number = noe_index
@@ -181,7 +203,7 @@
noe_index = noe_index + 1
# R1.
- elif ds.ri_labels[self.run][i] == 'R1':
+ elif cdp.ri_labels[i] == 'R1':
# Data set number.
number = r1_index
@@ -192,7 +214,7 @@
r1_index = r1_index + 1
# R2.
- elif ds.ri_labels[self.run][i] == 'R2':
+ elif cdp.ri_labels[i] == 'R2':
# Data set number.
number = r2_index
@@ -209,16 +231,18 @@
file.write('\nread < ' + data_type + ' ' + `number` + '\n')
# The relaxation data.
- for j in xrange(len(ds.res[self.run])):
- # Reassign the data.
- data = ds.res[self.run][j]
-
- # Skip deselected residues.
- if not data.select:
+ for spin in spin_loop():
+ # Skip deselected spins.
+ if not spin.select:
continue
+ # Skip and deselect spins for which relaxation data is missing.
+ if len(spin.relax_data) != cdp.num_ri:
+ spin.select = False
+ continue
+
# Data and errors.
- file.write(`data.num` + ' ' + `data.relax_data[i]` + ' ' +
`data.relax_error[i]` + '\n')
+ file.write(`spin.num` + ' ' + `spin.relax_data[i]` + ' ' +
`spin.relax_error[i]` + '\n')
# Terminate the reading.
file.write('exit\n')
@@ -226,59 +250,63 @@
# Individual residue optimisation.
if model_type == 'mf':
# Loop over the residues.
- for i in xrange(len(ds.res[self.run])):
- # Reassign the data.
- data = ds.res[self.run][i]
-
- # Skip deselected residues.
- if not data.select:
+ for residue in residue_loop():
+ # Test the number of spins.
+ if len(residue.spin) > 1:
+ raise RelaxError, "More than one spin per residue is not
supported."
+
+ # Alias the spin.
+ spin = residue.spin[0]
+
+ # Skip deselected spins.
+ if not spin.select:
continue
# Comment.
- file.write('\n\n\n# Residue ' + `data.num` + '\n\n')
+ file.write('\n\n\n# Residue ' + `residue.num` + '\n\n')
# Echo.
- file.write('echo Optimisation of residue ' + `data.num` + '\n')
-
- # Select the residue.
+ file.write('echo Optimisation of residue ' + `residue.num` +
'\n')
+
+ # Select the spin.
file.write('\n# Select the residue.\n')
- file.write('set cres ' + `data.num` + '\n')
+ file.write('set cres ' + `residue.num` + '\n')
# The angle alpha of the XH vector in the spheroid diffusion
frame.
- if ds.diff[self.run].type == 'spheroid':
- file.write('set teta ' + `data.alpha` + '\n')
+ if cdp.diff_tensor.type == 'spheroid':
+ file.write('set teta ' + `spin.alpha` + '\n')
# The angles theta and phi of the XH vector in the ellipsoid
diffusion frame.
- elif ds.diff[self.run].type == 'ellipsoid':
+ 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 ' + `data.theta` + '\n')
- file.write('set fi ' + `data.phi` + '\n')
+ file.write('set teta ' + `spin.theta` + '\n')
+ file.write('set fi ' + `spin.phi` + '\n')
# The 'jmode'.
- if 'ts' in data.params:
+ if 'ts' in spin.params:
jmode = 3
- elif 'te' in data.params:
+ elif 'te' in spin.params:
jmode = 2
- elif 'S2' in data.params:
+ elif 'S2' in spin.params:
jmode = 1
# Chemical exchange.
- if 'Rex' in data.params:
- exch = 1
+ if 'Rex' in spin.params:
+ exch = True
else:
- exch = 0
+ exch = False
# Anisotropic diffusion.
- if ds.diff[self.run].type == 'sphere':
- anis = 0
+ if cdp.diff_tensor.type == 'sphere':
+ anis = False
else:
- anis = 1
+ anis = True
# Axial symmetry.
- if ds.diff[self.run].type == 'spheroid':
- sym = 1
+ if cdp.diff_tensor.type == 'spheroid':
+ sym = True
else:
- sym = 0
+ sym = False
# Set the jmode.
file.write('\n# Set the jmode.\n')
@@ -293,27 +321,27 @@
# Parameter default values.
file.write('\n# Parameter default values.\n')
- file.write('reset jmode ' + `data.num` + '\n')
+ file.write('reset jmode ' + `residue.num` + '\n')
# Bond length.
file.write('\n# Bond length.\n')
- file.write('set r_hx ' + `data.r / 1e-10` + '\n')
+ file.write('set r_hx ' + `spin.r / 1e-10` + '\n')
# CSA value.
file.write('\n# CSA value.\n')
- file.write('set csa ' + `data.csa / 1e-6` + '\n')
+ file.write('set csa ' + `spin.csa / 1e-6` + '\n')
# Fix the tf parameter if it isn't in the model.
- if not 'tf' in data.params and jmode == 3:
+ if not 'tf' in spin.params and jmode == 3:
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')
- if self.algor == 'LM':
- file.write('lmin ' + `ds.res[self.run][0].num` + ' ' +
`ds.res[self.run][-1].num`)
- elif self.algor == 'NR':
- file.write('min ' + `ds.res[self.run][0].num` + ' ' +
`ds.res[self.run][-1].num`)
+ if algor == 'LM':
+ file.write('lmin ' + `first_residue_num()` + ' ' +
`last_residue_num()`)
+ elif algor == 'NR':
+ file.write('min ' + `first_residue_num()` + ' ' +
`last_residue_num()`)
# Show the results.
file.write('\n# Show the results.\n')
r7601 - /1.3/generic_fns/dasha.py