Author: bugman
Date: Mon Feb 16 10:08:49 2015
New Revision: 27646
URL: http://svn.gna.org/viewcvs/relax?rev=27646&view=rev
Log:
Introduced the max_rotations argument into the frame_order.distribute user
function.
This is used to prevent the user function from running forever. This happens
whenever a cone
opening angle or torsion angle is zero, and hence the random sampling of the
rotational space will
never find rotations within the motional distribution.
Modified:
branches/frame_order_cleanup/lib/frame_order/simulation.py
branches/frame_order_cleanup/specific_analyses/frame_order/uf.py
branches/frame_order_cleanup/user_functions/frame_order.py
Modified: branches/frame_order_cleanup/lib/frame_order/simulation.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/frame_order/simulation.py?rev=27646&r1=27645&r2=27646&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/frame_order/simulation.py (original)
+++ branches/frame_order_cleanup/lib/frame_order/simulation.py Mon Feb 16
10:08:49 2015
@@ -211,7 +211,7 @@
structure.write_pdb(file=file)
-def uniform_distribution(file=None, model=None, structure=None, parameters={},
eigenframe=None, pivot=None, atom_id=None, total=1000):
+def uniform_distribution(file=None, model=None, structure=None, parameters={},
eigenframe=None, pivot=None, atom_id=None, total=1000, max_rotations=100000):
"""Uniform distribution of the frame order motions.
@keyword file: The opened and writable file object to place the
PDB models of the distribution into.
@@ -230,6 +230,8 @@
@type atom_id: None or str
@keyword total: The total number of states in the distribution.
@type total: int
+ @keyword max_rotations: The maximum number of rotations to generate the
distribution from. This prevents an execution for an infinite amount of time
when a frame order amplitude parameter is close to zero so that the subset of
all rotations within the distribution is close to zero.
+ @type max_rotations: int
"""
# Check the structural object.
@@ -287,9 +289,13 @@
# Distribution.
current_state = 1
+ num = -1
while True:
+ # The total number of rotations.
+ num += 1
+
# End.
- if current_state == total:
+ if current_state == total or num >= max_rotations:
break
# Loop over each state, or motional mode.
Modified: branches/frame_order_cleanup/specific_analyses/frame_order/uf.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/frame_order/uf.py?rev=27646&r1=27645&r2=27646&view=diff
==============================================================================
--- branches/frame_order_cleanup/specific_analyses/frame_order/uf.py
(original)
+++ branches/frame_order_cleanup/specific_analyses/frame_order/uf.py Mon Feb
16 10:08:49 2015
@@ -47,19 +47,21 @@
from specific_analyses.frame_order.parameters import assemble_param_vector,
update_model
-def distribute(file="distribution.pdb.bz2", dir=None, total=1000, model=1,
force=True):
+def distribute(file="distribution.pdb.bz2", dir=None, total=1000,
max_rotations=100000, model=1, force=True):
"""Create a uniform distribution of structures for the frame order motions.
- @keyword file: The PDB file for storing the frame order motional
distribution. The compression is determined automatically by the file
extensions '*.pdb', '*.pdb.gz', and '*.pdb.bz2'.
- @type file: str
- @keyword dir: The directory name to place the file into.
- @type dir: str or None
- @keyword total: The total number of states/model/structures in the
distribution.
- @type total: int
- @keyword model: Only one model from an analysed ensemble of structures
can be used for the distribution, as the corresponding PDB file consists of one
model per state.
- @type model: int
- @keyword force: A flag which, if set to True, will overwrite the any
pre-existing file.
- @type force: bool
+ @keyword file: The PDB file for storing the frame order motional
distribution. The compression is determined automatically by the file
extensions '*.pdb', '*.pdb.gz', and '*.pdb.bz2'.
+ @type file: str
+ @keyword dir: The directory name to place the file into.
+ @type dir: str or None
+ @keyword total: The total number of states/model/structures in the
distribution.
+ @type total: int
+ @keyword max_rotations: The maximum number of rotations to generate the
distribution from. This prevents an execution for an infinite amount of time
when a frame order amplitude parameter is close to zero so that the subset of
all rotations within the distribution is close to zero.
+ @type max_rotations: int
+ @keyword model: Only one model from an analysed ensemble of
structures can be used for the distribution, as the corresponding PDB file
consists of one model per state.
+ @type model: int
+ @keyword force: A flag which, if set to True, will overwrite the
any pre-existing file.
+ @type force: bool
"""
# Printout.
@@ -108,7 +110,7 @@
frame = generate_axis_system()
# Create the distribution.
- uniform_distribution(file=file, model=cdp.model, structure=structure,
parameters=params, eigenframe=frame, pivot=pivot, atom_id=domain_moving(),
total=total)
+ uniform_distribution(file=file, model=cdp.model, structure=structure,
parameters=params, eigenframe=frame, pivot=pivot, atom_id=domain_moving(),
total=total, max_rotations=max_rotations)
# Close the file.
file.close()
Modified: branches/frame_order_cleanup/user_functions/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/user_functions/frame_order.py?rev=27646&r1=27645&r2=27646&view=diff
==============================================================================
--- branches/frame_order_cleanup/user_functions/frame_order.py (original)
+++ branches/frame_order_cleanup/user_functions/frame_order.py Mon Feb 16
10:08:49 2015
@@ -93,6 +93,16 @@
py_type = "int",
desc_short = "total number of structures",
desc = "The total number of structures to include in the uniform
distribution.",
+ wiz_element_type = "spin"
+)
+uf.add_keyarg(
+ name = "max_rotations",
+ default = 1000000,
+ min = 1,
+ max = 100000000,
+ py_type = "int",
+ desc_short = "maximum number of rotations",
+ desc = "The maximum number of rotations to generate the distribution from.
This prevents the user function from executing for an infinite amount of time.
This occurs whenever a frame order amplitude parameter (cone opening angle or
torsion angle) is zero so that the subset of all rotations within the motional
distribution is also zero.",
wiz_element_type = "spin"
)
uf.add_keyarg(
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