Author: bugman
Date: Fri Jan 23 09:42:22 2015
New Revision: 27283

URL: http://svn.gna.org/viewcvs/relax?rev=27283&view=rev
Log:
Added the sequence alignment arguments to the back end of the structure.align 
user function.

This is to allow the code in trunk to be functional before the sequence 
alignment before
superimposition has been implemented.


Modified:
    trunk/pipe_control/structure/main.py

Modified: trunk/pipe_control/structure/main.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/structure/main.py?rev=27283&r1=27282&r2=27283&view=diff
==============================================================================
--- trunk/pipe_control/structure/main.py        (original)
+++ trunk/pipe_control/structure/main.py        Fri Jan 23 09:42:22 2015
@@ -108,25 +108,37 @@
     print("Created the empty model number %s." % model_num)
 
 
-def align(pipes=None, models=None, molecules=None, atom_id=None, 
displace_id=None, method='fit to mean', centre_type="centroid", centroid=None):
+def align(pipes=None, models=None, molecules=None, atom_id=None, 
displace_id=None, method='fit to mean', algorithm='NW70', matrix='BLOSUM62', 
gap_open_penalty=1.0, gap_extend_penalty=1.0, end_gap_open_penalty=0.0, 
end_gap_extend_penalty=0.0, centre_type="centroid", centroid=None):
     """Superimpose a set of related, but not identical structures.
 
-    @keyword pipes:         The data pipes to include in the alignment and 
superimposition.
-    @type pipes:            None or list of str
-    @keyword models:        The list of models to for each data pipe 
superimpose.  The number of elements must match the pipes argument.  If set to 
None, then all models will be used.
-    @type models:           list of lists of int or None
-    @keyword molecules:     The molecule names to include in the alignment and 
superimposition.  The number of elements must match the pipes argument.
-    @type molecules:        None or list of str
-    @keyword atom_id:       The molecule, residue, and atom identifier string. 
 This matches the spin ID string format.
-    @type atom_id:          str or None
-    @keyword displace_id:   The atom ID string for restricting the 
displacement to a subset of all atoms.  If not set, then all atoms will be 
translated and rotated.  This can be a list of atom IDs with each element 
corresponding to one of the structures.
-    @type displace_id:      None, str, or list of str
-    @keyword method:        The superimposition method.  It must be one of 
'fit to mean' or 'fit to first'.
-    @type method:           str
-    @keyword centre_type:   The type of centre to superimpose over.  This can 
either be the standard centroid superimposition or the CoM could be used 
instead.
-    @type centre_type:      str
-    @keyword centroid:      An alternative position of the centroid to allow 
for different superpositions, for example of pivot point motions.
-    @type centroid:         list of float or numpy rank-1, 3D array
+    @keyword pipes:                     The data pipes to include in the 
alignment and superimposition.
+    @type pipes:                        None or list of str
+    @keyword models:                    The list of models to for each data 
pipe superimpose.  The number of elements must match the pipes argument.  If 
set to None, then all models will be used.
+    @type models:                       list of lists of int or None
+    @keyword molecules:                 The molecule names to include in the 
alignment and superimposition.  The number of elements must match the pipes 
argument.
+    @type molecules:                    None or list of str
+    @keyword atom_id:                   The molecule, residue, and atom 
identifier string.  This matches the spin ID string format.
+    @type atom_id:                      str or None
+    @keyword displace_id:               The atom ID string for restricting the 
displacement to a subset of all atoms.  If not set, then all atoms will be 
translated and rotated.  This can be a list of atom IDs with each element 
corresponding to one of the structures.
+    @type displace_id:                  None, str, or list of str
+    @keyword method:                    The superimposition method.  It must 
be one of 'fit to mean' or 'fit to first'.
+    @type method:                       str
+    @keyword algorithm:                 The pairwise sequence alignment 
algorithm to use.
+    @type algorithm:                    str
+    @keyword matrix:                    The substitution matrix to use.
+    @type matrix:                       str
+    @keyword gap_open_penalty:          The penalty for introducing gaps, as a 
positive number.
+    @type gap_open_penalty:             float
+    @keyword gap_extend_penalty:        The penalty for extending a gap, as a 
positive number.
+    @type gap_extend_penalty:           float
+    @keyword end_gap_open_penalty:      The optional penalty for opening a gap 
at the end of a sequence.
+    @type end_gap_open_penalty:         float
+    @keyword end_gap_extend_penalty:    The optional penalty for extending a 
gap at the end of a sequence.
+    @type end_gap_extend_penalty:       float
+    @keyword centre_type:               The type of centre to superimpose 
over.  This can either be the standard centroid superimposition or the CoM 
could be used instead.
+    @type centre_type:                  str
+    @keyword centroid:                  An alternative position of the 
centroid to allow for different superpositions, for example of pivot point 
motions.
+    @type centroid:                     list of float or numpy rank-1, 3D array
     """
 
     # Check the method.


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