Author: bugman
Date: Mon Oct 26 19:57:48 2009
New Revision: 9793
URL: http://svn.gna.org/viewcvs/relax?rev=9793&view=rev
Log:
Merged revisions 9709,9747 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r9709 | bugman | 2009-10-09 20:06:21 +0200 (Fri, 09 Oct 2009) | 3 lines
Comment fix.
........
r9747 | bugman | 2009-10-12 16:00:39 +0200 (Mon, 12 Oct 2009) | 3 lines
__linear_ave() is no longer a private function.
........
Modified:
branches/bmrb/ (props changed)
branches/bmrb/data/pipe_container.py
branches/bmrb/generic_fns/mol_res_spin.py
Propchange: branches/bmrb/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Mon Oct 26 19:57:48 2009
@@ -1,1 +1,1 @@
-/1.3:1-9706
+/1.3:1-9792
Modified: branches/bmrb/data/pipe_container.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/data/pipe_container.py?rev=9793&r1=9792&r2=9793&view=diff
==============================================================================
--- branches/bmrb/data/pipe_container.py (original)
+++ branches/bmrb/data/pipe_container.py Mon Oct 26 19:57:48 2009
@@ -144,7 +144,7 @@
# Get the alignment tensor data nodes and, if they exist, fill the
contents.
align_tensor_nodes = relax_node.getElementsByTagName('align_tensors')
if align_tensor_nodes:
- # Create the diffusion tensor object.
+ # Create the alignment tensor object.
self.align_tensors = AlignTensorList()
# Fill its contents.
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=9793&r1=9792&r2=9793&view=diff
==============================================================================
--- branches/bmrb/generic_fns/mol_res_spin.py (original)
+++ branches/bmrb/generic_fns/mol_res_spin.py Mon Oct 26 19:57:48 2009
@@ -491,36 +491,6 @@
-def __linear_ave(positions):
- """Perform linear averaging of the atomic positions.
-
- @param positions: The atomic positions. The first index is that of
the positions to be
- averaged over. The second index is over the
different models. The last
- index is over the x, y, and z coordinates.
- @type positions: list of lists of numpy float arrays
- @return: The averaged positions as a list of vectors.
- @rtype: list of numpy float arrays
- """
-
- # Loop over the multiple models.
- ave = []
- for model_index in range(len(positions[0])):
- # Append an empty vector.
- ave.append(array([0.0, 0.0, 0.0]))
-
- # Loop over the x, y, and z coordinates.
- for coord_index in range(3):
- # Loop over the atomic positions.
- for atom_index in range(len(positions)):
- ave[model_index][coord_index] =
ave[model_index][coord_index] +
positions[atom_index][model_index][coord_index]
-
- # Average.
- ave[model_index][coord_index] = ave[model_index][coord_index] /
len(positions)
-
- # Return the averaged positions.
- return ave
-
-
def bmrb_read(star):
"""Generate the molecule and residue spin containers from the entity
saveframe records.
@@ -1006,7 +976,7 @@
spin.averaging = averaging
spin.members = members
if averaging == 'linear':
- spin.pos = __linear_ave(positions)
+ spin.pos = linear_ave(positions)
def create_spin(spin_num=None, spin_name=None, res_num=None, res_name=None,
mol_name=None):
@@ -1564,6 +1534,36 @@
# Yield the molecule data container.
yield mol
+
+
+def linear_ave(positions):
+ """Perform linear averaging of the atomic positions.
+
+ @param positions: The atomic positions. The first index is that of
the positions to be
+ averaged over. The second index is over the
different models. The last
+ index is over the x, y, and z coordinates.
+ @type positions: list of lists of numpy float arrays
+ @return: The averaged positions as a list of vectors.
+ @rtype: list of numpy float arrays
+ """
+
+ # Loop over the multiple models.
+ ave = []
+ for model_index in range(len(positions[0])):
+ # Append an empty vector.
+ ave.append(array([0.0, 0.0, 0.0]))
+
+ # Loop over the x, y, and z coordinates.
+ for coord_index in range(3):
+ # Loop over the atomic positions.
+ for atom_index in range(len(positions)):
+ ave[model_index][coord_index] =
ave[model_index][coord_index] +
positions[atom_index][model_index][coord_index]
+
+ # Average.
+ ave[model_index][coord_index] = ave[model_index][coord_index] /
len(positions)
+
+ # Return the averaged positions.
+ return ave
def name_molecule(mol_id, name=None, force=False):
r9793 - in /branches/bmrb: ./ data/pipe_container.py generic_fns/mol_res_spin.py