Author: bugman
Date: Tue Jun 19 19:44:14 2012
New Revision: 16968
URL: http://svn.gna.org/viewcvs/relax?rev=16968&view=rev
Log:
The import of old relax 1.2 results files is now operational under the
interatomic data design.
Modified:
branches/interatomic/specific_fns/model_free/results.py
Modified: branches/interatomic/specific_fns/model_free/results.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/specific_fns/model_free/results.py?rev=16968&r1=16967&r2=16968&view=diff
==============================================================================
--- branches/interatomic/specific_fns/model_free/results.py (original)
+++ branches/interatomic/specific_fns/model_free/results.py Tue Jun 19
19:44:14 2012
@@ -33,7 +33,9 @@
# relax module imports.
import generic_fns
-from generic_fns.mol_res_spin import generate_spin_id, return_spin, spin_loop
+from generic_fns import dipole_pair
+from generic_fns.interatomic import return_interatom
+from generic_fns.mol_res_spin import create_spin, generate_spin_id,
return_spin, spin_loop
from generic_fns import pipes
from relax_errors import RelaxError, RelaxInvalidDataError
@@ -147,6 +149,10 @@
res_name = spin_line[col['name']]
spin_num = None
spin_name = None
+ if search('N', spin_line[col['nucleus']]):
+ spin_name = 'N'
+ if search('C', spin_line[col['nucleus']]):
+ spin_name = 'C'
# The spin info.
else:
@@ -168,38 +174,6 @@
generic_fns.selection.sel_spin(spin_id)
else:
generic_fns.selection.desel_spin(spin_id)
-
-
- def _get_spin_id(self, spin_line, col, verbosity=1):
- """Get the spin identification string corresponding to spin_line.
-
- @param spin_line: The line of data for a single spin.
- @type spin_line: list of str
- @param col: The column indices.
- @type col: dict of int
- @keyword verbosity: A variable specifying the amount of information
to print. The higher
- the value, the greater the verbosity.
- @type verbosity: int
- """
-
- # The spin info (for relax 1.2).
- if 'num' in col:
- mol_name = None
- res_num = int(spin_line[col['num']])
- res_name = spin_line[col['name']]
- spin_num = None
- spin_name = None
-
- # The spin info.
- else:
- mol_name = spin_line[col['mol_name']]
- res_num = int(spin_line[col['res_num']])
- res_name = spin_line[col['res_name']]
- spin_num = int(spin_line[col['spin_num']])
- spin_name = spin_line[col['spin_name']]
-
- # Return the spin container.
- return generate_spin_id(mol_name, res_num, res_name, spin_num,
spin_name)
def _load_model_free_data(self, spin_line, col, data_set, spin, spin_id,
verbosity=1):
@@ -252,6 +226,9 @@
# The model type.
model_type = spin_line[col['param_set']]
+ # Get the interatomic data container.
+ interatom = return_interatom(spin_id)
+
# Values.
if data_set == 'value':
# S2.
@@ -301,12 +278,6 @@
spin.rex = float(spin_line[col['rex']]) *
self.return_conversion_factor('rex')
except ValueError:
spin.rex = None
-
- # Bond length.
- try:
- spin.r = float(spin_line[col['r']]) *
self.return_conversion_factor('r')
- except ValueError:
- spin.r = None
# CSA.
try:
@@ -338,6 +309,12 @@
else:
spin.warning = replace(spin_line[col['warn']], '_', ' ')
+ # Interatomic distances.
+ try:
+ interatom[0].r = float(spin_line[col['r']]) * 1e-10
+ except ValueError:
+ interatom[0].r = None
+
# Errors.
if data_set == 'error':
# S2.
@@ -388,18 +365,11 @@
except ValueError:
spin.rex_err = None
- # Bond length.
- try:
- spin.r_err = float(spin_line[col['r']]) *
self.return_conversion_factor('r')
- except ValueError:
- spin.r_err = None
-
# CSA.
try:
spin.csa_err = float(spin_line[col['csa']]) *
self.return_conversion_factor('csa')
except ValueError:
spin.csa_err = None
-
# Construct the simulation data structures.
if data_set == 'sim_0':
@@ -479,12 +449,6 @@
spin.rex_sim.append(float(spin_line[col['rex']]) *
self.return_conversion_factor('rex'))
except ValueError:
spin.rex_sim.append(None)
-
- # Bond length.
- try:
- spin.r_sim.append(float(spin_line[col['r']]) *
self.return_conversion_factor('r'))
- except ValueError:
- spin.r_sim.append(None)
# CSA.
try:
@@ -701,21 +665,53 @@
# The data set.
data_set = file_line[col['data_set']]
+ # The spin info (for relax 1.2).
+ if 'num' in col:
+ mol_name = None
+ res_num = int(file_line[col['num']])
+ res_name = file_line[col['name']]
+ spin_num = None
+ spin_name = None
+ if search('N', file_line[col['nucleus']]):
+ spin_name = 'N'
+ if search('C', file_line[col['nucleus']]):
+ spin_name = 'C'
+
+ # The spin info.
+ else:
+ mol_name = file_line[col['mol_name']]
+ res_num = int(file_line[col['res_num']])
+ res_name = file_line[col['res_name']]
+ spin_num = int(file_line[col['spin_num']])
+ spin_name = file_line[col['spin_name']]
+
+ # Create the spin ID.
+ spin_id = generate_spin_id(mol_name, res_num, res_name,
spin_num, spin_name)
+
# Get the spin container.
- spin_id = self._get_spin_id(file_line, col, verbosity)
spin = return_spin(spin_id)
+
+ # Create a new spin container for the proton, then set up a
dipole interaction between the two spins.
+ if data_set == 'value':
+ h_spin = create_spin(mol_name=mol_name, res_num=res_num,
res_name=res_name, spin_name='H')
+ spin_id2 = generate_spin_id(mol_name=mol_name,
res_num=res_num, res_name=res_name, spin_name='H')
+ dipole_pair.define(spin_id, spin_id2, verbose=False)
# Backwards compatibility for the reading of the results file
from versions 1.2.0 to 1.2.9.
if len(file_line) == 4:
continue
- # Set the heteronucleus and proton types (absent from the 1.2
results file).
+ # Set the nuclear isotope types and spin names (absent from the
1.2 results file).
if data_set == 'value':
if file_line[col['nucleus']] != 'None':
if search('N', file_line[col['nucleus']]):
spin.isotope = '15N'
+ if spin.name == None:
+ spin.name = 'N'
elif search('C', file_line[col['nucleus']]):
spin.isotope = '13C'
+ if spin.name == None:
+ spin.name = 'C'
# Simulation number.
if data_set != 'value' and data_set != 'error':
@@ -734,6 +730,7 @@
# Selected simulations.
all_select_sim[-1].append(bool(file_line[col['select']]))
+ all_select_sim[-1].append(None)
# Initial printout for the simulation.
if verbosity:
@@ -768,7 +765,7 @@
# XH vector, heteronucleus, and proton.
if data_set == 'value':
- self._set_xh_vect(file_line, col, spin, spin_id=spin_id,
verbosity=verbosity)
+ self._set_xh_vect(file_line, col, spin, spin_id1=spin_id,
spin_id2=spin_id2, verbosity=verbosity)
# Relaxation data.
self._load_relax_data(file_line, col, data_set, spin, verbosity)
@@ -1080,7 +1077,7 @@
generic_fns.diffusion_tensor.init(params=diff_params,
angle_units='rad', spheroid_type=spheroid_type)
- def _set_xh_vect(self, spin_line, col, spin, spin_id=None, verbosity=1):
+ def _set_xh_vect(self, spin_line, col, spin, spin_id1=None,
spin_id2=None, verbosity=1):
"""Set the XH unit vector and the attached proton name.
@param spin_line: The line of data for a single spin.
@@ -1089,19 +1086,18 @@
@type col: dict of int
@param spin: The spin container.
@type spin: SpinContainer instance
- @keyword spin_id: The spin ID string.
- @type spin_id: str
+ @keyword spin_id1: The ID string of the first spin.
+ @type spin_id1: str
+ @keyword spin_id2: The ID string of the second spin.
+ @type spin_id2: str
@keyword verbosity: A variable specifying the amount of information
to print. The higher the value, the greater the verbosity.
@type verbosity: int
"""
- # First create a proton spin container.
- h_spin = create_spin(mol_name=spin_line[col['mol_name']],
res_num=spin_line[col['res_num']], res_name=spin_line[col['res_name']],
spin_name='H')
- h_id = generate_spin_id(mol_name=spin_line[col['mol_name']],
res_num=spin_line[col['res_num']], res_name=spin_line[col['res_name']],
spin_name='H')
-
- # Then set up a dipole interaction between the two.
- dipole_pair.define(spin_id, h_id)
- interatom = return_interatom(spin_id1=spin_i1, spin_id2=h_id)
+ # Get the interatomic data container.
+ interatom = return_interatom(spin_id1=spin_id1, spin_id2=spin_id2)
+ if len(interatom) != 1:
+ raise RelaxError("Only one interatomic interaction is allowed.")
# The vector.
vector = eval(spin_line[col['xh_vect']])
@@ -1113,7 +1109,7 @@
raise RelaxError("The XH unit vector " +
spin_line[col['xh_vect']] + " is invalid.")
# Set the vector.
- interatom.vector = vector
+ interatom[0].vector = vector
# The attached proton name.
spin.attached_proton = spin_line[col['pdb_proton']]
r16968 - /branches/interatomic/specific_fns/model_free/results.py