Author: bugman
Date: Thu Oct 8 18:05:53 2009
New Revision: 9666
URL: http://svn.gna.org/viewcvs/relax?rev=9666&view=rev
Log:
Added better versioning support to be able to switch to NMR-STAR v3.2 in the
future.
This will be easier for completing the general relaxation saveframe without
breakage.
Added:
branches/bmrb/bmrblib/nmr_star_dict_v3_2.py
- copied, changed from r9658,
branches/bmrb/bmrblib/nmr_star_dict_v3_1.py
Modified:
branches/bmrb/generic_fns/bmrb.py
branches/bmrb/generic_fns/mol_res_spin.py
branches/bmrb/generic_fns/relax_data.py
branches/bmrb/specific_fns/model_free/bmrb.py
Copied: branches/bmrb/bmrblib/nmr_star_dict_v3_2.py (from r9658,
branches/bmrb/bmrblib/nmr_star_dict_v3_1.py)
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/nmr_star_dict_v3_2.py?p2=branches/bmrb/bmrblib/nmr_star_dict_v3_2.py&p1=branches/bmrb/bmrblib/nmr_star_dict_v3_1.py&r1=9658&r2=9666&rev=9666&view=diff
==============================================================================
--- branches/bmrb/bmrblib/nmr_star_dict_v3_1.py (original)
+++ branches/bmrb/bmrblib/nmr_star_dict_v3_2.py Thu Oct 8 18:05:53 2009
@@ -21,22 +21,22 @@
###############################################################################
# Module docstring.
-"""The NMR-STAR dictionary API for version 3.1.
+"""The NMR-STAR dictionary API for version 3.2.
-The v3.1 NMR-STAR dictionary is documented at
-http://www.bmrb.wisc.edu/dictionary/3.1html/SuperGroupPage.html.
+The v3.2 NMR-STAR dictionary is documented at
+http://www.bmrb.wisc.edu/dictionary/3.2html/SuperGroupPage.html.
"""
# relax module imports.
from bmrblib.assembly_supercategory.entity_v3_1 import EntitySaveframe_v3_1
-from bmrblib.kinetics.relaxation import Relaxation_v3_1
+from bmrblib.kinetics.relaxation import Relaxation_v3_2
from bmrblib.NMR_parameters.chem_shift_anisotropy_v3_1 import
ChemShiftAnisotropySaveframe_v3_1
from bmrblib.thermodynamics.order_parameters_v3_1 import
OrderParameterSaveframe_v3_1
from bmrblib.nmr_star_dict import NMR_STAR
-class NMR_STAR_v3_1(NMR_STAR):
- """The v3.1 NMR-STAR dictionary."""
+class NMR_STAR_v3_2(NMR_STAR):
+ """The v3.2 NMR-STAR dictionary."""
# Class extension string.
ext = ''
Modified: branches/bmrb/generic_fns/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/bmrb.py?rev=9666&r1=9665&r2=9666&view=diff
==============================================================================
--- branches/bmrb/generic_fns/bmrb.py (original)
+++ branches/bmrb/generic_fns/bmrb.py Thu Oct 8 18:05:53 2009
@@ -100,4 +100,4 @@
mkdir_nofail(directory, verbosity=0)
# Execute the specific BMRB writing code.
- write_function(file_path)
+ write_function(file_path, version='3.1')
Modified: branches/bmrb/generic_fns/mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/mol_res_spin.py?rev=9666&r1=9665&r2=9666&view=diff
==============================================================================
--- branches/bmrb/generic_fns/mol_res_spin.py (original)
+++ branches/bmrb/generic_fns/mol_res_spin.py Thu Oct 8 18:05:53 2009
@@ -535,11 +535,13 @@
create_residue(res_nums[i], res_names[i], mol_name=mol_name)
-def bmrb_write_entity(star):
+def bmrb_write_entity(star, version=None):
"""Generate the entity saveframe records for the NMR-STAR dictionary
object.
- @param star: The NMR-STAR dictionary object.
- @type star: NMR_STAR instance
+ @param star: The NMR-STAR dictionary object.
+ @type star: NMR_STAR instance
+ @keyword version: The BMRB NMR-STAR dictionary format to output to.
+ @type version: str
"""
# Can't handle multiple molecules yet.
Modified: branches/bmrb/generic_fns/relax_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/relax_data.py?rev=9666&r1=9665&r2=9666&view=diff
==============================================================================
--- branches/bmrb/generic_fns/relax_data.py (original)
+++ branches/bmrb/generic_fns/relax_data.py Thu Oct 8 18:05:53 2009
@@ -228,11 +228,13 @@
-def bmrb_write(star):
+def bmrb_write(star, version='3.1'):
"""Generate the relaxation data saveframes for the NMR-STAR dictionary
object.
- @param star: The NMR-STAR dictionary object.
- @type star: NMR_STAR instance
+ @param star: The NMR-STAR dictionary object.
+ @type star: NMR_STAR instance
+ @keyword version: The BMRB NMR-STAR dictionary format to output to.
+ @type version: str
"""
# Get the current data pipe.
@@ -294,13 +296,21 @@
# Add the relaxation data.
for i in range(cdp.num_ri):
- star.relaxation.add(operator_pair=operator_pair[i],
frq=cdp.frq[cdp.remap_table[i]], res_nums=res_num_list,
res_names=res_name_list, atom_names=atom_name_list, isotope=isotope_list,
data=relax_data_list[i], errors=relax_error_list[i])
- #if cdp.ri_labels[i] == 'R1':
- #
star.heteronucl_T1_relaxation.add(frq=cdp.frq[cdp.remap_table[i]],
res_nums=res_num_list, res_names=res_name_list, atom_names=atom_name_list,
isotope=isotope_list, data=relax_data_list[i], errors=relax_error_list[i])
- #elif cdp.ri_labels[i] == 'R2':
- #
star.heteronucl_T2_relaxation.add(frq=cdp.frq[cdp.remap_table[i]],
res_nums=res_num_list, res_names=res_name_list, atom_names=atom_name_list,
isotope=isotope_list, data=relax_data_list[i], errors=relax_error_list[i])
- #elif cdp.ri_labels[i] == 'NOE':
- # star.heteronucl_NOEs.add(frq=cdp.frq[cdp.remap_table[i]],
res_nums=res_num_list, res_names=res_name_list, atom_names=atom_name_list,
isotope=isotope_list, data=relax_data_list[i], errors=relax_error_list[i])
+ # The general relaxation saveframe versions.
+ if version in ['3.2']:
+ if cdp.ri_labels[i] in ['R1', 'R2']:
+ star.relaxation.add(operator_pair=operator_pair[i],
frq=cdp.frq[cdp.remap_table[i]], res_nums=res_num_list,
res_names=res_name_list, atom_names=atom_name_list, isotope=isotope_list,
data=relax_data_list[i], errors=relax_error_list[i])
+ elif cdp.ri_labels[i] == 'NOE':
+ star.heteronucl_NOEs.add(frq=cdp.frq[cdp.remap_table[i]],
res_nums=res_num_list, res_names=res_name_list, atom_names=atom_name_list,
isotope=isotope_list, data=relax_data_list[i], errors=relax_error_list[i])
+
+ # Older versions.
+ if version in ['3.0', '3.1']:
+ if cdp.ri_labels[i] == 'R1':
+
star.heteronucl_T1_relaxation.add(frq=cdp.frq[cdp.remap_table[i]],
res_nums=res_num_list, res_names=res_name_list, atom_names=atom_name_list,
isotope=isotope_list, data=relax_data_list[i], errors=relax_error_list[i])
+ elif cdp.ri_labels[i] == 'R2':
+
star.heteronucl_T2_relaxation.add(frq=cdp.frq[cdp.remap_table[i]],
res_nums=res_num_list, res_names=res_name_list, atom_names=atom_name_list,
isotope=isotope_list, data=relax_data_list[i], errors=relax_error_list[i])
+ elif cdp.ri_labels[i] == 'NOE':
+ star.heteronucl_NOEs.add(frq=cdp.frq[cdp.remap_table[i]],
res_nums=res_num_list, res_names=res_name_list, atom_names=atom_name_list,
isotope=isotope_list, data=relax_data_list[i], errors=relax_error_list[i])
def copy(pipe_from=None, pipe_to=None, ri_label=None, frq_label=None):
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=9666&r1=9665&r2=9666&view=diff
==============================================================================
--- branches/bmrb/specific_fns/model_free/bmrb.py (original)
+++ branches/bmrb/specific_fns/model_free/bmrb.py Thu Oct 8 18:05:53 2009
@@ -26,6 +26,7 @@
# relax module imports.
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
from generic_fns.mol_res_spin import spin_loop
@@ -33,7 +34,7 @@
class Bmrb:
"""Class containing methods related to BMRB STAR file reading and
writing."""
- def bmrb_read(self, file_path):
+ def bmrb_read(self, file_path, version='3.1'):
"""Read the model-free results from a BMRB NMR-STAR v3.1 formatted
file.
@param file_path: The full file path.
@@ -41,7 +42,10 @@
"""
# Initialise the NMR-STAR data object.
- star = NMR_STAR_v3_1('relax_model_free_results', file_path)
+ if version == '3.2':
+ 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)
# Read the contents of the STAR formatted file.
star.read()
@@ -53,24 +57,29 @@
relax_data.bmrb_read(star)
- def bmrb_write(self, file_path):
+ def bmrb_write(self, file_path, version=None):
"""Write the model-free results to a BMRB NMR-STAR v3.1 formatted
file.
@param file_path: The full file path.
@type file_path: str
+ @keyword version: The BMRB NMR-STAR dictionary format to output to.
+ @type version: str
"""
# Alias the current data pipe.
cdp = pipes.get_pipe()
# Initialise the NMR-STAR data object.
- star = NMR_STAR_v3_1('relax_model_free_results', file_path)
+ if version == '3.2':
+ 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)
# Generate the entity saveframe.
- mol_res_spin.bmrb_write_entity(star)
+ mol_res_spin.bmrb_write_entity(star, version=version)
# Generate the relaxation data saveframes.
- relax_data.bmrb_write(star)
+ relax_data.bmrb_write(star, version=version)
# Rex frq.
rex_frq = cdp.frq[0]
r9666 - in /branches/bmrb: bmrblib/ generic_fns/ specific_fns/model_free/