r27282 - /trunk/user_functions/structure.py -- January 23, 2015 - 09:40

Author: bugman
Date: Fri Jan 23 09:40:55 2015
New Revision: 27282

URL: http://svn.gna.org/viewcvs/relax?rev=27282&view=rev
Log:
Added the sequence alignment arguments to the structure.align user function 
front end.

This includes the 'matrix', 'gap_open_penalty', 'gap_extend_penalty', 
'end_gap_open_penalty', and
'end_gap_extend_penalty' arguments.  The 'algorithm' argument has not been 
added to save room, as
there is only one choice of 'NW70'.  A paragraph has been added to the user 
function description to
explain the sequence alignment part of the user function.


Modified:
    trunk/user_functions/structure.py

Modified: trunk/user_functions/structure.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/user_functions/structure.py?rev=27282&r1=27281&r2=27282&view=diff
==============================================================================
--- trunk/user_functions/structure.py   (original)
+++ trunk/user_functions/structure.py   Fri Jan 23 09:40:55 2015
@@ -213,6 +213,48 @@
     wiz_read_only = True
 )
 uf.add_keyarg(
+    name = "matrix",
+    default = "BLOSUM62",
+    py_type = "str",
+    desc_short = "substitution matrix",
+    desc = "The substitution matrix to use in the pairwise sequence 
alignment algorithm.",
+    wiz_element_type = "combo",
+    wiz_combo_choices = ["BLOSUM62", "PAM250", "NUC 4.4"],
+    wiz_read_only = True
+)
+uf.add_keyarg(
+    name = "gap_open_penalty",
+    default = 10.0,
+    py_type = "float",
+    desc_short = "gap opening penalty",
+    desc = "The penalty for introducing gaps, as a positive number.",
+    can_be_none = False
+)
+uf.add_keyarg(
+    name = "gap_extend_penalty",
+    default = 1.0,
+    py_type = "float",
+    desc_short = "gap extension penalty",
+    desc = "The penalty for extending a gap, as a positive number.",
+    can_be_none = False
+)
+uf.add_keyarg(
+    name = "end_gap_open_penalty",
+    default = None,
+    py_type = "float",
+    desc_short = "end gap opening penalty",
+    desc = "The optional penalty for opening a gap at the end of a 
sequence.",
+    can_be_none = True
+)
+uf.add_keyarg(
+    name = "end_gap_extend_penalty",
+    default = None,
+    py_type = "float",
+    desc_short = "end gap extension penalty",
+    desc = "The optional penalty for extending a gap at the end of a 
sequence.",
+    can_be_none = True
+)
+uf.add_keyarg(
     name = "centre_type",
     py_type = "str",
     default = "centroid",
@@ -237,6 +279,7 @@
 uf.desc[-1].add_paragraph(paragraph_multi_struct)
 uf.desc[-1].add_paragraph(paragraph_atom_id)
 uf.desc[-1].add_paragraph(paragraph_displace_id)
+uf.desc[-1].add_paragraph("To find common atoms between diverse structures, 
a sequence alignment is performed between the molecules.  This will be a 
pairwise alignment of each structure to the first.  The Needleman-Wunsch 
algorithm (NW70), modified to use the logic of the EMBOSS software for 
handling gap opening and extension penalties, as well as end penalties, will 
be used.  The substitution matrix can be one of BLOSUM62 or PAM250 for 
proteins, or NUC 4.4 for DNA/RNA.")
 uf.desc[-1].add_paragraph("By supplying the position of the centroid, an 
alternative position than the standard rigid body centre is used as the focal 
point of the superimposition.  The allows, for example, the superimposition 
about a pivot point.")
 # Prompt examples.
 uf.desc.append(Desc_container("Prompt examples"))
@@ -254,7 +297,7 @@
 uf.backend = pipe_control.structure.main.align
 uf.menu_text = "&align"
 uf.wizard_apply_button = False
-uf.wizard_height_desc = 370
+uf.wizard_height_desc = 250
 uf.wizard_size = (1000, 750)
 uf.wizard_image = WIZARD_IMAGE_PATH + 'structure' + sep + '2JK4.png'