Author: bugman
Date: Fri Oct 9 13:10:03 2009
New Revision: 9689
URL: http://svn.gna.org/viewcvs/relax?rev=9689&view=rev
Log:
A number of changes to create the infrastructure for v3.0 and lower of the
NMR-STAR dictionary format.
Modified:
branches/bmrb/bmrblib/kinetics/relaxation.py
branches/bmrb/bmrblib/nmr_star_dict.py
branches/bmrb/specific_fns/model_free/bmrb.py
branches/bmrb/test_suite/system_tests/scripts/bmrb_rw.py
Modified: branches/bmrb/bmrblib/kinetics/relaxation.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/kinetics/relaxation.py?rev=9689&r1=9688&r2=9689&view=diff
==============================================================================
--- branches/bmrb/bmrblib/kinetics/relaxation.py (original)
+++ branches/bmrb/bmrblib/kinetics/relaxation.py Fri Oct 9 13:10:03 2009
@@ -50,6 +50,36 @@
self.heteronucl_T2_relaxation = HeteronuclT2Saveframe(datanodes)
+ def add(self, data_type=None, frq=None, res_nums=None, res_names=None,
atom_names=None, isotope=None, data=None, errors=None):
+ """Add relaxation data to the data nodes.
+
+ @keyword data_type: The relaxation data type (one of 'NOE',
'R1', or 'R2').
+ @type data_type: str
+ @keyword frq: The spectrometer proton frequency, in Hz.
+ @type frq: float
+ @keyword res_nums: The residue number list.
+ @type res_nums: list of int
+ @keyword res_names: The residue name list.
+ @type res_names: list of str
+ @keyword atom_names: The atom name list.
+ @type atom_names: list of str
+ @keyword isotope: The isotope type list, ie 15 for '15N'.
+ @type isotope: list of int
+ @keyword data: The relaxation data.
+ @type data: list of float
+ @keyword errors: The errors associated with the relaxation
data.
+ @type errors: list of float
+ """
+
+ # Pack specific the data.
+ if data_type == 'R1':
+ self.heteronucl_T1_relaxation.add(frq=frq, res_nums=res_nums,
res_names=res_names, atom_names=atom_names, isotope=isotope, data=data,
errors=errors)
+ elif data_type == 'R2':
+ self.heteronucl_T2_relaxation.add(frq=frq, res_nums=res_nums,
res_names=res_names, atom_names=atom_names, isotope=isotope, data=data,
errors=errors)
+ elif data_type == 'NOE':
+ self.heteronucl_NOEs.add(frq=frq, res_nums=res_nums,
res_names=res_names, atom_names=atom_names, isotope=isotope, data=data,
errors=errors)
+
+
def loop(self):
"""Generator method for looping over and returning all relaxation
data."""
@@ -97,36 +127,6 @@
self.heteronucl_NOEs = HeteronuclNOESaveframe_v3_1(datanodes)
self.heteronucl_T1_relaxation = HeteronuclT1Saveframe_v3_1(datanodes)
self.heteronucl_T2_relaxation = HeteronuclT2Saveframe_v3_1(datanodes)
-
-
- def add(self, data_type=None, frq=None, res_nums=None, res_names=None,
atom_names=None, isotope=None, data=None, errors=None):
- """Add relaxation data to the data nodes.
-
- @keyword data_type: The relaxation data type (one of 'NOE',
'R1', or 'R2').
- @type data_type: str
- @keyword frq: The spectrometer proton frequency, in Hz.
- @type frq: float
- @keyword res_nums: The residue number list.
- @type res_nums: list of int
- @keyword res_names: The residue name list.
- @type res_names: list of str
- @keyword atom_names: The atom name list.
- @type atom_names: list of str
- @keyword isotope: The isotope type list, ie 15 for '15N'.
- @type isotope: list of int
- @keyword data: The relaxation data.
- @type data: list of float
- @keyword errors: The errors associated with the relaxation
data.
- @type errors: list of float
- """
-
- # Pack specific the data.
- if data_type == 'R1':
- self.heteronucl_T1_relaxation.add(frq=frq, res_nums=res_nums,
res_names=res_names, atom_names=atom_names, isotope=isotope, data=data,
errors=errors)
- elif data_type == 'R2':
- self.heteronucl_T2_relaxation.add(frq=frq, res_nums=res_nums,
res_names=res_names, atom_names=atom_names, isotope=isotope, data=data,
errors=errors)
- elif data_type == 'NOE':
- self.heteronucl_NOEs.add(frq=frq, res_nums=res_nums,
res_names=res_names, atom_names=atom_names, isotope=isotope, data=data,
errors=errors)
class Relaxation_v3_2(Relaxation_v3_1):
Modified: branches/bmrb/bmrblib/nmr_star_dict.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/nmr_star_dict.py?rev=9689&r1=9688&r2=9689&view=diff
==============================================================================
--- branches/bmrb/bmrblib/nmr_star_dict.py (original)
+++ branches/bmrb/bmrblib/nmr_star_dict.py Fri Oct 9 13:10:03 2009
@@ -29,6 +29,7 @@
# relax module imports.
from bmrblib.assembly_supercategory.entity import EntitySaveframe
+from bmrblib.kinetics.relaxation import Relaxation
from bmrblib.NMR_parameters.chem_shift_anisotropy import ChemShiftAnisotropy
from bmrblib.thermodynamics.order_parameters import OrderParameterSaveframe
from pystarlib.File import File
Modified: branches/bmrb/specific_fns/model_free/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/specific_fns/model_free/bmrb.py?rev=9689&r1=9688&r2=9689&view=diff
==============================================================================
--- branches/bmrb/specific_fns/model_free/bmrb.py (original)
+++ branches/bmrb/specific_fns/model_free/bmrb.py Fri Oct 9 13:10:03 2009
@@ -25,6 +25,7 @@
import string
# relax module imports.
+from bmrblib.nmr_star_dict import NMR_STAR
from bmrblib.nmr_star_dict_v3_1 import NMR_STAR_v3_1
from bmrblib.nmr_star_dict_v3_2 import NMR_STAR_v3_2
from generic_fns import mol_res_spin, pipes, relax_data
@@ -46,6 +47,8 @@
star = NMR_STAR_v3_2('relax_model_free_results', file_path)
elif version == '3.1':
star = NMR_STAR_v3_1('relax_model_free_results', file_path)
+ else:
+ star = NMR_STAR('relax_model_free_results', file_path)
# Read the contents of the STAR formatted file.
star.read()
@@ -74,6 +77,8 @@
star = NMR_STAR_v3_2('relax_model_free_results', file_path)
elif version == '3.1':
star = NMR_STAR_v3_1('relax_model_free_results', file_path)
+ else:
+ star = NMR_STAR('relax_model_free_results', file_path)
# Generate the entity saveframe.
mol_res_spin.bmrb_write_entity(star)
Modified: branches/bmrb/test_suite/system_tests/scripts/bmrb_rw.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/test_suite/system_tests/scripts/bmrb_rw.py?rev=9689&r1=9688&r2=9689&view=diff
==============================================================================
--- branches/bmrb/test_suite/system_tests/scripts/bmrb_rw.py (original)
+++ branches/bmrb/test_suite/system_tests/scripts/bmrb_rw.py Fri Oct 9
13:10:03 2009
@@ -10,7 +10,7 @@
# Missing temp file (allow this script to run outside of the system test
framework).
if not hasattr(ds, 'tmpfile'):
ds.tmpfile = 'temp_bmrb'
- ds.version = '3.2'
+ ds.version = '3.0'
# Create the data pipe.
pipe.create(pipe_name='results', pipe_type='mf')
r9689 - in /branches/bmrb: bmrblib/ bmrblib/kinetics/ specific_fns/model_free/ test_suite/system_tests/scripts/