Author: bugman
Date: Thu Mar 5 15:07:18 2009
New Revision: 8907
URL: http://svn.gna.org/viewcvs/relax?rev=8907&view=rev
Log:
The Entity saveframes are now being read and the sequence info recreated.
Modified:
branches/bmrb/bmrblib/assembly_supercategory/entity.py
branches/bmrb/generic_fns/mol_res_spin.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=8907&r1=8906&r2=8907&view=diff
==============================================================================
--- branches/bmrb/bmrblib/assembly_supercategory/entity.py (original)
+++ branches/bmrb/bmrblib/assembly_supercategory/entity.py Thu Mar 5
15:07:18 2009
@@ -101,6 +101,40 @@
self.entity_comp_index = EntityCompIndex(self)
+ def loop(self):
+ """Loop over the entity saveframes, yielding the entity info.
+
+ @return: The entity information consisting of the molecule name,
molecule type, residue
+ numbers, and residue names.
+ @rtype: tuple of str, str, list of int, list of str
+ """
+
+ # Loop over all datanodes.
+ for datanode in self.datanodes:
+ # Find the Entity saveframes via the SfCategory tag index.
+ found = False
+ for index in range(len(datanode.tagtables[0].tagnames)):
+ # First match the tag names.
+ if datanode.tagtables[0].tagnames[index] ==
self.entity.create_tag_label(self.entity.tag_names['SfCategory']):
+ # Then the tag value.
+ if datanode.tagtables[0].tagvalues[index][0] == 'entity':
+ found = True
+ break
+
+ # Skip the datanode.
+ if not found:
+ continue
+
+ # Get entity info.
+ mol_name, mol_type = self.entity.read(datanode.tagtables[0])
+
+ # Get the EntityCompIndex info.
+ res_nums, res_names =
self.entity_comp_index.read(datanode.tagtables[1])
+
+ # Yield the data.
+ yield mol_name, mol_type, res_nums, res_names
+
+
class Entity(TagCategory):
"""Base class for the Entity tag category."""
@@ -118,6 +152,23 @@
# The entity type.
self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.tag_names['Type'])],
tagvalues=[[self.sf.mol_type]]))
+
+
+ def read(self, tagtable):
+ """Extract the Entity tag category info.
+
+ @param tagtable: The Entity tagtable.
+ @type tagtable: Tagtable instance
+ @return: The entity name and type.
+ @rtype: tuple of str, str
+ """
+
+ # The entity info.
+ mol_name =
tagtable.tagvalues[tagtable.tagnames.index(self.create_tag_label(self.tag_names['Name']))][0]
+ mol_type =
tagtable.tagvalues[tagtable.tagnames.index(self.create_tag_label(self.tag_names['Type']))][0]
+
+ # Return the data.
+ return mol_name, mol_type
def tag_setup(self, tag_category_label=None, sep=None):
@@ -170,6 +221,27 @@
self.sf.frame.tagtables.append(table)
+ def read(self, tagtable):
+ """Extract the EntityCompIndex tag category info.
+
+ @param tagtable: The Entity tagtable.
+ @type tagtable: Tagtable instance
+ @return: The residue numbers and names.
+ @rtype: tuple of list of int, list of str
+ """
+
+ # The entity info.
+ res_nums =
tagtable.tagvalues[tagtable.tagnames.index(self.create_tag_label(self.tag_names['EntityCompIndexID']))]
+ res_names =
tagtable.tagvalues[tagtable.tagnames.index(self.create_tag_label(self.tag_names['CompID']))]
+
+ # Convert the residue numbers to ints.
+ for i in range(len(res_nums)):
+ res_nums[i] = int(res_nums[i])
+
+ # Return the data.
+ return res_nums, res_names
+
+
def tag_setup(self, tag_category_label=None, sep=None):
"""Replacement method for setting up the tag names.
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=8907&r1=8906&r2=8907&view=diff
==============================================================================
--- branches/bmrb/generic_fns/mol_res_spin.py (original)
+++ branches/bmrb/generic_fns/mol_res_spin.py Thu Mar 5 15:07:18 2009
@@ -488,6 +488,23 @@
# Create the union.
self._union = (select_obj0, select_obj1)
+
+
+def bmrb_read(star):
+ """Generate the molecule and residue spin containers from the entity
saveframe records.
+
+ @param star: The NMR-STAR dictionary object.
+ @type star: NMR_STAR instance
+ """
+
+ # Get the entities.
+ for mol_name, mol_type, res_nums, res_names in star.entity.loop():
+ # Add the molecule.
+ create_molecule(mol_name)
+
+ # Add the residues.
+ for i in range(len(res_nums)):
+ create_residue(res_nums[i], res_names[i], mol_id='#'+mol_name)
def bmrb_write_entity(star):
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=8907&r1=8906&r2=8907&view=diff
==============================================================================
--- branches/bmrb/specific_fns/model_free/bmrb.py (original)
+++ branches/bmrb/specific_fns/model_free/bmrb.py Thu Mar 5 15:07:18 2009
@@ -42,6 +42,9 @@
# Read the contents of the STAR formatted file.
star.read()
+ # Generate the molecule and residue containers.
+ mol_res_spin.bmrb_read(star)
+
def bmrb_write(self, file_path):
"""Write the model-free results to a BMRB NMR-STAR v3.1 formatted
file.
r8907 - in /branches/bmrb: bmrblib/assembly_supercategory/entity.py generic_fns/mol_res_spin.py specific_fns/model_free/bmrb.py