Author: bugman
Date: Mon Feb 23 19:59:27 2009
New Revision: 8872
URL: http://svn.gna.org/viewcvs/relax?rev=8872&view=rev
Log:
Converted the entity saveframe code from the heteronuclear NOE code.
Modified:
branches/bmrb/bmrblib/assembly_supercategory/entity.py
branches/bmrb/bmrblib/assembly_supercategory/entity_v3_1.py
branches/bmrb/specific_fns/model_free/bmrb.py
Modified: branches/bmrb/bmrblib/assembly_supercategory/entity.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/assembly_supercategory/entity.py?rev=8872&r1=8871&r2=8872&view=diff
==============================================================================
--- branches/bmrb/bmrblib/assembly_supercategory/entity.py (original)
+++ branches/bmrb/bmrblib/assembly_supercategory/entity.py Mon Feb 23
19:59:27 2009
@@ -21,9 +21,9 @@
###############################################################################
# Module docstring.
-"""The Heteronuclear NOE data saveframe category.
+"""The entity saveframe category.
-For example, see
http://www.bmrb.wisc.edu/dictionary/3.1html/SaveFramePage.html#heteronucl_NOEs.
+For example, see
http://www.bmrb.wisc.edu/dictionary/3.1html/SaveFramePage.html#entity.
"""
# relax module imports.
@@ -33,11 +33,11 @@
from pystarlib.TagTable import TagTable
-class HeteronuclNOESaveframe:
- """The Heteronuclear NOE data saveframe class."""
+class EntitySaveframe:
+ """The entity saveframe class."""
# Saveframe variables.
- label = 'NOE'
+ label = 'entity'
def __init__(self, datanodes):
@@ -50,18 +50,19 @@
# Place the data nodes into the namespace.
self.datanodes = datanodes
- # The number of relaxation data sets.
- self.r1_inc = 0
-
# Add the specific tag category objects.
self.add_tag_categories()
- def add(self, frq=None, res_nums=None, res_names=None, atom_names=None,
data=None, errors=None):
+ def add(self, frq=None, mol_name=None, mol_type='polymer',
res_nums=None, res_names=None, atom_names=None, data=None, errors=None):
"""Add relaxation data to the data nodes.
@keyword frq: The spectrometer proton frequency, in Hz.
@type frq: float
+ @keyword mol_name: The molecule name.
+ @type mol_name: str
+ @keyword mol_type: The molecule type.
+ @type mol_type: str
@keyword res_nums: The residue number list.
@type res_nums: list of int
@keyword res_names: The residue name list.
@@ -76,53 +77,44 @@
# Place the args into the namespace.
self.frq = frq
- self.res_nums = translate(res_nums)
+ self.mol_name = mol_name
+ self.mol_type = mol_type
self.res_names = translate(res_names)
self.atom_names = translate(atom_names)
self.data = translate(data)
self.errors = translate(errors)
- # Set up the R1 specific variables.
- self.r1_inc = self.r1_inc + 1
- ri_inc = self.r1_inc
-
# Initialise the save frame.
- self.frame =
SaveFrame(title='heteronuclear_'+self.label+'_list_'+`ri_inc`)
+ self.frame = SaveFrame(title=mol_name)
# Create the tag categories.
- self.heteronuclNOElist.create()
- self.heteronuclNOEexperiment.create()
- self.heteronuclNOEsoftware.create()
- self.heteronuclNOE.create()
+ self.Entity.create()
# Add the saveframe to the data nodes.
self.datanodes.append(self.frame)
def add_tag_categories(self):
- """Create the v3.1 tag categories."""
+ """Create the tag categories."""
# The tag category objects.
- self.heteronuclNOElist = HeteronuclNOEList(self)
- self.heteronuclNOEexperiment = HeteronuclNOEExperiment(self)
- self.heteronuclNOEsoftware = HeteronuclNOESoftware(self)
- self.heteronuclNOE = HeteronuclNOE(self)
+ self.entity = Entity(self)
-class HeteronuclNOEList(TagCategory):
- """Base class for the HeteronuclNOEList tag category."""
+class Entity(TagCategory):
+ """Base class for the Entity tag category."""
def create(self):
- """Create the HeteronuclNOEList tag category."""
+ """Create the Entity tag category."""
# The save frame category.
- self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.tag_names['SfCategory'])],
tagvalues=[[self.sf.label+'_relaxation']]))
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.tag_names['SfCategory'])],
tagvalues=[['entity']]))
- # Sample info.
- self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.tag_names['SampleConditionListLabel'])],
tagvalues=[['$conditions_1']]))
+ # The entity name.
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.tag_names['Name'])],
tagvalues=[[self.mol_name]]))
- # NMR info.
- self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.tag_names['SpectrometerFrequency1H'])],
tagvalues=[[str(self.sf.frq/1e6)]]))
+ # The entity type.
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.tag_names['Type'])],
tagvalues=[[self.mol_type]]))
def tag_setup(self, tag_category_label=None, sep=None):
@@ -139,93 +131,5 @@
# Tag names for the relaxation data.
self.tag_names['SfCategory'] = 'Saveframe_category'
- self.tag_names['SampleConditionListLabel'] =
'Sample_conditions_label'
- self.tag_names['SpectrometerFrequency1H'] =
'Spectrometer_frequency_1H'
-
-
-class HeteronuclNOEExperiment(TagCategory):
- """Base class for the HeteronuclNOEExperiment tag category."""
-
- def create(self):
- """Create the HeteronuclNOEExperiment tag category."""
-
- # Sample info.
- self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.tag_names['SampleLabel'])],
tagvalues=[['$sample_1']]))
-
-
- def tag_setup(self, tag_category_label=None, sep=None):
- """Replacement method for setting up the tag names.
-
- @keyword tag_category_label: The tag name prefix specific for the
tag category.
- @type tag_category_label: None or str
- @keyword sep: The string separating the tag name
prefix and suffix.
- @type sep: str
- """
-
- # Execute the base class tag_setup() method.
- TagCategory.tag_setup(self, tag_category_label=tag_category_label,
sep=sep)
-
- # Tag names for the relaxation data.
- self.tag_names['SampleLabel'] = 'Sample_label'
-
-
-class HeteronuclNOESoftware(TagCategory):
- """Base class for the HeteronuclNOESoftware tag category."""
-
- def create(self):
- """Create the HeteronuclNOESoftware tag category."""
-
-
-class HeteronuclNOE(TagCategory):
- """Base class for the HeteronuclNOE tag category."""
-
- def create(self):
- """Create the HeteronuclNOE tag category."""
-
- # The relaxation tag names.
- tag_names = []
- missing = []
- for key in ['SeqID', 'CompID', 'AtomID', 'Val', 'ValErr']:
- if not self.tag_names.has_key(key):
- missing.append(key)
- else:
- tag_names.append(self.create_tag_label(self.tag_names[key]))
-
- # The tag values.
- tag_values = []
- if 'SeqID' not in missing:
- tag_values.append(self.sf.res_nums)
- if 'CompID' not in missing:
- tag_values.append(self.sf.res_names)
- if 'AtomID' not in missing:
- tag_values.append(self.sf.atom_names)
- if 'Val' not in missing:
- tag_values.append(self.sf.data)
- if 'ValErr' not in missing:
- tag_values.append(self.sf.errors)
-
- # Add the data.
- table = TagTable(tagnames=tag_names, tagvalues=tag_values)
-
- # Add the tagtable to the save frame.
- self.sf.frame.tagtables.append(table)
-
-
- def tag_setup(self, tag_category_label=None, sep=None):
- """Replacement method for setting up the tag names.
-
- @keyword tag_category_label: The tag name prefix specific for the
tag category.
- @type tag_category_label: None or str
- @keyword sep: The string separating the tag name
prefix and suffix.
- @type sep: str
- """
-
- # Execute the base class tag_setup() method.
- TagCategory.tag_setup(self, tag_category_label=tag_category_label,
sep=sep)
-
- # Tag names for the relaxation data.
- self.tag_names['SeqID'] = 'Residue_seq_code'
- self.tag_names['CompID'] = 'Residue_label'
- self.tag_names['AtomID'] = 'Atom_name'
- self.tag_names['Val'] = self.sf.label+'_value'
- self.tag_names['ValErr'] = self.sf.label+'_value_error'
+ self.tag_names['Name'] = 'Name'
+ self.tag_names['Type'] = 'Type'
Modified: branches/bmrb/bmrblib/assembly_supercategory/entity_v3_1.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/assembly_supercategory/entity_v3_1.py?rev=8872&r1=8871&r2=8872&view=diff
==============================================================================
--- branches/bmrb/bmrblib/assembly_supercategory/entity_v3_1.py (original)
+++ branches/bmrb/bmrblib/assembly_supercategory/entity_v3_1.py Mon Feb 23
19:59:27 2009
@@ -21,66 +21,31 @@
###############################################################################
# Module docstring.
-"""The v3.1 Heteronuclear NOE data saveframe category.
+"""The v3.1 entity saveframe category.
-See
http://www.bmrb.wisc.edu/dictionary/3.1html/SaveFramePage.html#heteronucl_NOEs.
+See http://www.bmrb.wisc.edu/dictionary/3.1html/SaveFramePage.html#entity.
"""
# relax module imports.
-from bmrblib.kinetics.heteronucl_NOEs import HeteronuclNOESaveframe,
HeteronuclNOEList, HeteronuclNOEExperiment, HeteronuclNOESoftware,
HeteronuclNOE
+from bmrblib.assembly_supercategory.entity import EntitySaveframe, Entity
-class HeteronuclNOESaveframe_v3_1(HeteronuclNOESaveframe):
- """The v3.1 Heteronuclear NOE data saveframe class."""
+class EntitySaveframe_v3_1(EntitySaveframe):
+ """The v3.1 entity saveframe class."""
def add_tag_categories(self):
"""Create the v3.1 tag categories."""
# The tag category objects.
- self.heteronuclNOElist = HeteronuclNOEList_v3_1(self)
- self.heteronuclNOEexperiment = HeteronuclNOEExperiment_v3_1(self)
- self.heteronuclNOEsoftware = HeteronuclNOESoftware_v3_1(self)
- self.heteronuclNOE = HeteronuclNOE_v3_1(self)
+ self.entity = Entity_v3_1(self)
-class HeteronuclNOEList_v3_1(HeteronuclNOEList):
- """v3.1 HeteronuclNOEList tag category."""
+class Entity_v3_1(Entity):
+ """v3.1 Entity tag category."""
def tag_setup(self, tag_category_label=None, sep=None):
# Execute the base class tag_setup() method.
- HeteronuclNOEList.tag_setup(self,
tag_category_label='Heteronucl_NOE_list', sep=sep)
+ Entity.tag_setup(self, tag_category_label='Entity', sep=sep)
# Tag names for the relaxation data.
self.tag_names['SfCategory'] = 'Sf_category'
- self.tag_names['SampleConditionListLabel'] =
'Sample_condition_list_label'
-
-
-class HeteronuclNOEExperiment_v3_1(HeteronuclNOEExperiment):
- """v3.1 HeteronuclNOEExperiment tag category."""
-
- def tag_setup(self, tag_category_label=None, sep=None):
- # Execute the base class tag_setup() method.
- HeteronuclNOEExperiment.tag_setup(self,
tag_category_label='Heteronucl_NOE_experiment', sep=sep)
-
-
-class HeteronuclNOESoftware_v3_1(HeteronuclNOESoftware):
- """v3.1 HeteronuclNOESoftware tag category."""
-
- def tag_setup(self, tag_category_label=None, sep=None):
- # Execute the base class tag_setup() method.
- HeteronuclNOESoftware.tag_setup(self,
tag_category_label='Heteronucl_NOE_software', sep=sep)
-
-
-class HeteronuclNOE_v3_1(HeteronuclNOE):
- """v3.1 HeteronuclNOE tag category."""
-
- def tag_setup(self, tag_category_label=None, sep=None):
- # Execute the base class tag_setup() method.
- HeteronuclNOE.tag_setup(self, tag_category_label='Heteronucl_NOE',
sep=sep)
-
- # Tag names for the relaxation data.
- self.tag_names['SeqID'] = 'Seq_ID'
- self.tag_names['CompID'] = 'Comp_ID'
- self.tag_names['AtomID'] = 'Atom_ID'
- self.tag_names['Val'] = 'Val'
- self.tag_names['ValErr'] = 'Val_err'
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=8872&r1=8871&r2=8872&view=diff
==============================================================================
--- branches/bmrb/specific_fns/model_free/bmrb.py (original)
+++ branches/bmrb/specific_fns/model_free/bmrb.py Mon Feb 23 19:59:27 2009
@@ -57,6 +57,7 @@
cdp = get_pipe()
# Initialise the spin specific data lists.
+ mol_name_list = []
res_num_list = []
res_name_list = []
atom_name_list = []
@@ -72,7 +73,7 @@
if not spin.select:
continue
- # The residue/spin info.
+ # The molecule/R1residue/spin info.
res_num_list.append(str(res_num))
res_name_list.append(str(res_name))
atom_name_list.append(str(spin.name))
r8872 - in /branches/bmrb: bmrblib/assembly_supercategory/ specific_fns/model_free/