Author: bugman
Date: Fri Mar 16 07:56:02 2007
New Revision: 3206
URL: http://svn.gna.org/viewcvs/relax?rev=3206&view=rev
Log:
Created the 'generic_fns.residue.copy()' function.
Two unit tests for this function have been added.
Modified:
1.3/docs/data_model_redesign
1.3/generic_fns/residue.py
Modified: 1.3/docs/data_model_redesign
URL:
http://svn.gna.org/viewcvs/relax/1.3/docs/data_model_redesign?rev=3206&r1=3205&r2=3206&view=diff
==============================================================================
--- 1.3/docs/data_model_redesign (original)
+++ 1.3/docs/data_model_redesign Fri Mar 16 07:56:02 2007
@@ -69,6 +69,7 @@
The molecule.add() user function should be used to create all the residue
and spin structures for that molecule from a loaded structure. This can be
done through an API to allow users to code their own PDB readers (which could
in future be incorporated into relax). For more information see Gary
Thompson's post at
https://mail.gna.org/public/relax-devel/2007-01/msg00014.html (Message-ID:
<f001463a0701071417w6bd7927cp8fdd052e698575ec@xxxxxxxxxxxxxx>). The user
function should also allow for the creation of an empty molecule data
container to allow for analyses whereby no structure is needed (relaxation
curve-fitting, NOE calculation, model-free analysis with isotropic diffusion,
etc.). The sequence user function class can then be used to load the
sequence (or spin.read()).
11. Create the 'residue' user function class:
+ residue.copy()
residue.create() # This is currently named 'sequence.add()'.
residue.delete()
residue.merge()
Modified: 1.3/generic_fns/residue.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/residue.py?rev=3206&r1=3205&r2=3206&view=diff
==============================================================================
--- 1.3/generic_fns/residue.py (original)
+++ 1.3/generic_fns/residue.py Fri Mar 16 07:56:02 2007
@@ -30,6 +30,65 @@
+def copy(res_num_from=None, res_name_from=None, res_num_to=None,
res_name_to=None):
+ """Copy the contents of the residue structure from one residue to a new
residue.
+
+ For copying to be successful, the res_num_from and res_name_from must
match an existant residue.
+ The res_name_from and res_name_to arguments need not be supplied. The
new residue number must
+ be unique.
+
+ @param res_num_from: The residue number identifying the structure to
copy the data from.
+ This argument must be supplied.
+ @type res_num_from: int
+ @param res_name_from: The residue name identifying the structure to
copy the data from. This
+ argument is optional.
+ @type res_name_from: str
+ @param res_num_to: The residue number identifying the structure to
copy the data to. This
+ argument must be supplied.
+ @type res_num_to: int
+ @param res_name_to: The residue name identifying the structure to
copy the data to. This
+ argument is optional but if supplied will rename the copied residue.
+ @type res_name_to: str
+ """
+
+ # Alias the current data pipe.
+ cdp = relax_data_store[relax_data_store.current_pipe]
+
+ # Test if the residue number already exists.
+ for i in xrange(len(cdp.mol[0].res)):
+ if cdp.mol[0].res[i].num == res_num_to:
+ raise RelaxError, "The residue number '" + `res_num_to` + "'
already exists in the sequence."
+
+ # Find the index corresponding to the residue number and name.
+ index = None
+ for i in xrange(len(cdp.mol[0].res)):
+ # Residue number match.
+ if cdp.mol[0].res[i].num == res_num_from:
+ # Residue name match (if required).
+ if res_name_from:
+ if cdp.mol[0].res[i].name == res_name_from:
+ index = i
+ else:
+ index = i
+
+ # No residue to copy data from.
+ if index == None:
+ if res_name_from:
+ raise RelaxError, "The residue '" + `res_num_from` + " " +
res_name_from + "' does not exist."
+ else:
+ raise RelaxError, "The residue number '" + `res_num_from` + "'
does not exist."
+
+ # Copy the data.
+ cdp.mol[0].res.append(cdp.mol[0].res[index].__clone__())
+
+ # Change the new residue number.
+ cdp.mol[0].res[-1].num = res_num_to
+
+ # Change the new residue name.
+ if res_name_to:
+ cdp.mol[0].res[-1].name = res_name_to
+
+
def create(res_num=None, res_name=None):
"""Function for adding a residue into the relax data store."""
@@ -60,39 +119,6 @@
"""Class containing functions specific to amino-acid sequence."""
self.relax = relax
-
-
- def copy(self, run1=None, run2=None):
- """Function for copying the sequence from run1 to run2."""
-
- # Test if run1 exists.
- if not run1 in relax_data_store.run_names:
- raise RelaxNoRunError, run1
-
- # Test if run2 exists.
- if not run2 in relax_data_store.run_names:
- raise RelaxNoRunError, run2
-
- # Test if the sequence data for run1 is loaded.
- if not relax_data_store.res.has_key(run1):
- raise RelaxNoSequenceError, run1
-
- # Test if the sequence data already exists.
- if relax_data_store.res.has_key(run2):
- raise RelaxSequenceError, run2
-
- # Add run2 to 'relax_data_store.res'.
- relax_data_store.res.add_list(run2)
-
- # Copy the data.
- for i in xrange(len(relax_data_store.res[run1])):
- # Append a data container to run2.
- relax_data_store.res[run2].add_item()
-
- # Insert the data.
- relax_data_store.res[run2][i].num =
relax_data_store.res[run1][i].num
- relax_data_store.res[run2][i].name =
relax_data_store.res[run1][i].name
- relax_data_store.res[run2][i].select =
relax_data_store.res[run1][i].select
def data_names(self):
r3206 - in /1.3: docs/data_model_redesign generic_fns/residue.py