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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