Author: bugman
Date: Fri Jan 23 17:49:29 2015
New Revision: 27293
URL: http://svn.gna.org/viewcvs/relax?rev=27293&view=rev
Log:
Modified the gap penalty arguments for the structure.align user function.
These now must always be supplied, as None is not handled by the backend
lib.sequence_alignment.needleman_wunsch module. The previous defaults of None
are now set to 0.0.
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=27293&r1=27292&r2=27293&view=diff
==============================================================================
--- trunk/user_functions/structure.py (original)
+++ trunk/user_functions/structure.py Fri Jan 23 17:49:29 2015
@@ -227,32 +227,28 @@
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
+ desc = "The penalty for introducing gaps, as a positive number."
)
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
+ desc = "The penalty for extending a gap, as a positive number."
)
uf.add_keyarg(
name = "end_gap_open_penalty",
- default = None,
+ default = 0.0,
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
+ desc = "The optional penalty for opening a gap at the end of a sequence."
)
uf.add_keyarg(
name = "end_gap_extend_penalty",
- default = None,
+ default = 0.0,
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
+ desc = "The optional penalty for extending a gap at the end of a sequence."
)
uf.add_keyarg(
name = "centre_type",
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