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'
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