Author: bugman
Date: Tue Aug 3 09:00:27 2010
New Revision: 11387
URL: http://svn.gna.org/viewcvs/relax?rev=11387&view=rev
Log:
Merged revisions 11381-11385 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r11381 | bugman | 2010-07-28 11:13:46 +0200 (Wed, 28 Jul 2010) | 6 lines
Removed the docstring length check from the code validator script and
changed a printout.
The docstring length is only 100 characters in the user functions. For all
other functions, no
length is enforced.
........
r11382 | bugman | 2010-07-28 11:38:32 +0200 (Wed, 28 Jul 2010) | 3 lines
The attached proton PDB name is no longer hardcoded to 'H' in the
dauvergne_protocol auto analysis.
........
r11383 | bugman | 2010-07-29 14:18:18 +0200 (Thu, 29 Jul 2010) | 3 lines
The back-calculated alignments tensors are now being stored in the current
data pipe.
........
r11384 | bugman | 2010-07-29 16:11:51 +0200 (Thu, 29 Jul 2010) | 3 lines
The align_tensor.display() user function now prints out the generalized
degree of order (GDO) value.
........
r11385 | bugman | 2010-07-29 17:58:54 +0200 (Thu, 29 Jul 2010) | 3 lines
pipe.display() now places quotation marks around the pipe names and shows
which is the current data pipe.
........
Modified:
branches/bieri_gui/ (props changed)
branches/bieri_gui/auto_analyses/dauvergne_protocol.py
branches/bieri_gui/generic_fns/align_tensor.py
branches/bieri_gui/generic_fns/pipes.py
branches/bieri_gui/sample_scripts/full_analysis.py
branches/bieri_gui/scripts/code_validator
branches/bieri_gui/specific_fns/frame_order.py
Propchange: branches/bieri_gui/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Tue Aug 3 09:00:27 2010
@@ -1,1 +1,1 @@
-/1.3:1-11368
+/1.3:1-11386
Modified: branches/bieri_gui/auto_analyses/dauvergne_protocol.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/auto_analyses/dauvergne_protocol.py?rev=11387&r1=11386&r2=11387&view=diff
==============================================================================
--- branches/bieri_gui/auto_analyses/dauvergne_protocol.py (original)
+++ branches/bieri_gui/auto_analyses/dauvergne_protocol.py Tue Aug 3
09:00:27 2010
@@ -157,7 +157,7 @@
class dAuvergne_protocol:
- def __init__(self, save_dir=None, diff_model=None, mf_models=['m0',
'm1', 'm2', 'm3', 'm4', 'm5', 'm6', 'm7', 'm8', 'm9'],
local_tm_models=['tm0', 'tm1', 'tm2', 'tm3', 'tm4', 'tm5', 'tm6', 'tm7',
'tm8', 'tm9'], pdb_file=None, seq_args=None, het_name=None, relax_data=None,
unres=None, exclude=None, bond_length=None, csa=None, hetnuc=None,
proton='1H', grid_inc=11, min_algor='newton', mc_num=500, max_iter=None,
user_fns=None, conv_loop=True):
+ def __init__(self, save_dir=None, diff_model=None, mf_models=['m0',
'm1', 'm2', 'm3', 'm4', 'm5', 'm6', 'm7', 'm8', 'm9'],
local_tm_models=['tm0', 'tm1', 'tm2', 'tm3', 'tm4', 'tm5', 'tm6', 'tm7',
'tm8', 'tm9'], pdb_file=None, seq_args=None, het_name=None,
attached_name='H', relax_data=None, unres=None, exclude=None,
bond_length=None, csa=None, hetnuc=None, proton='1H', grid_inc=11,
min_algor='newton', mc_num=500, max_iter=None, user_fns=None, conv_loop=True):
"""Perform the full model-free analysis protocol of d'Auvergne and
Gooley, 2008b.
@keyword save_dir: The directory, where files are saved in.
@@ -174,6 +174,8 @@
@type seq_args: list of lists of [str, None or str, None
or int, None or int, None or int, None or int, None or int, None or int, None
or int, None or str]
@keyword het_name: The heteronucleus atom name
corresponding to that of the PDB file (used if the spin name is not in the
sequence data).
@type het_name: None or str
+ @keyword attached_name: The name of the proton attached to the
heteronucleus.
+ @type attached_name: str
@keyword relax_data: The relaxation data (data type,
frequency label, frequency, file name, dir, mol_name_col, res_num_col,
res_name_col, spin_num_col, spin_name_col, data_col, error_col, sep). These
are the arguments to the relax_data.read() user function, please see the
documentation for that function for more information.
@type relax_data: list of lists of [str, str, float, str,
None or str, None or int, None or int, None or int, None or int, None or int,
None or int, None or int, None or str]
@keyword unres: The file containing the list of
unresolved spins to exclude from the analysis (set this to None if no spin is
to be excluded).
@@ -209,6 +211,7 @@
self.pdb_file = pdb_file
self.seq_args = seq_args
self.het_name = het_name
+ self.attached_name = attached_name
self.relax_data = relax_data
self.unres = unres
self.exclude = exclude
@@ -319,7 +322,7 @@
# Load the PDB file and calculate the unit vectors
parallel to the XH bond.
if self.pdb_file:
self.interpreter.structure.read_pdb(self.pdb_file)
- self.interpreter.structure.vectors(attached='H')
+
self.interpreter.structure.vectors(attached=self.attached_name)
# Add an arbitrary diffusion tensor which will be
optimised.
if self.diff_model == 'sphere':
@@ -494,6 +497,8 @@
# Atom name.
if not isinstance(self.het_name, str):
raise RelaxError("The het_name heteronucleus atom name user
variable '%s' must be a string." % self.het_name)
+ if not isinstance(self.attached_name, str):
+ raise RelaxError("The attached_name proton atom name user
variable '%s' must be a string." % self.attached_name)
# Relaxation data.
if not isinstance(self.relax_data, list):
@@ -809,7 +814,7 @@
# Load the PDB file and calculate the unit vectors parallel to
the XH bond.
if not local_tm and self.pdb_file:
self.interpreter.structure.read_pdb(self.pdb_file)
- self.interpreter.structure.vectors(attached='H')
+
self.interpreter.structure.vectors(attached=self.attached_name)
# Load the relaxation data.
for data in self.relax_data:
Modified: branches/bieri_gui/generic_fns/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/generic_fns/align_tensor.py?rev=11387&r1=11386&r2=11387&view=diff
==============================================================================
--- branches/bieri_gui/generic_fns/align_tensor.py (original)
+++ branches/bieri_gui/generic_fns/align_tensor.py Tue Aug 3 09:00:27 2010
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2003-2009 Edward d'Auvergne
#
+# Copyright (C) 2003-2010 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -25,8 +25,9 @@
# Python module imports.
from copy import deepcopy
-from math import pi
+from math import pi, sqrt
from numpy import arccos, dot, float64, linalg, zeros
+from numpy.linalg import norm
from re import search
import sys
@@ -417,6 +418,10 @@
title = "# Geometric description."
print("\n\n" + title + '\n' + '#'*len(title) + '\n')
+ # The GDO.
+ print("# Generalized degree of order (GDO).")
+ print("GDO = %-25.12e\n" % gdo(data.A))
+
# Anisotropy.
print("# Alignment tensor axial component (Aa = 3/2 * Azz, where Aii
are the eigenvalues).")
print("Aa = %-25.12e\n" % data.Aa)
@@ -525,6 +530,22 @@
elif cdp.align_tensors.beta_sim[sim_index] <= cdp.align_tensors.beta
- pi/2.0:
cdp.align_tensors.alpha_sim[sim_index] = pi -
cdp.align_tensors.alpha_sim[sim_index]
cdp.align_tensors.beta_sim[sim_index] =
cdp.align_tensors.beta_sim[sim_index] + pi
+
+
+def gdo(A):
+ """Calculate the generalized degree of order (GDO) for the given
alignment tensor.
+
+ @param A: The alignment tensor.
+ @type A: rank-2, 3D numpy array
+ @return: The GDO value.
+ @rtype: float
+ """
+
+ # The matrix norm.
+ gdo = sqrt(3.0/2.0) * norm(A)
+
+ # Return the GDO.
+ return gdo
def get_tensor_index(tensor, pipe=None):
Modified: branches/bieri_gui/generic_fns/pipes.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/generic_fns/pipes.py?rev=11387&r1=11386&r2=11387&view=diff
==============================================================================
--- branches/bieri_gui/generic_fns/pipes.py (original)
+++ branches/bieri_gui/generic_fns/pipes.py Tue Aug 3 09:00:27 2010
@@ -138,11 +138,17 @@
"""Print the details of all the data pipes."""
# Heading.
- print(("%-20s%-20s" % ("Data pipe name", "Data pipe type")))
+ print(("%-20s%-20s%-20s" % ("Data pipe name", "Data pipe type",
"Current")))
# Loop over the data pipes.
for pipe_name in ds:
- print(("%-20s%-20s" % (pipe_name, get_type(pipe_name))))
+ # The current data pipe.
+ current = ''
+ if pipe_name == cdp_name():
+ current = '*'
+
+ # Print out.
+ print("%-20s%-20s%-20s" % ("'"+pipe_name+"'", get_type(pipe_name),
current))
def get_pipe(name=None):
Modified: branches/bieri_gui/sample_scripts/full_analysis.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/sample_scripts/full_analysis.py?rev=11387&r1=11386&r2=11387&view=diff
==============================================================================
--- branches/bieri_gui/sample_scripts/full_analysis.py (original)
+++ branches/bieri_gui/sample_scripts/full_analysis.py Tue Aug 3 09:00:27
2010
@@ -156,8 +156,9 @@
# The sequence data (file name, dir, mol_name_col, res_num_col,
res_name_col, spin_num_col, spin_name_col, sep). These are the arguments to
the sequence.read() user function, for more information please see the
documentation for that function.
SEQ_ARGS = ['noe.600.out', None, None, 1, 2, None, None, None]
-# The heteronucleus atom name corresponding to that of the PDB file (used if
the spin name is not in the sequence data).
+# The heteronucleus and attached proton names corresponding to those in the
PDB file (used if the spin name is not in the sequence data).
HET_NAME = 'N'
+ATTACHED_NAME = 'H'
# The relaxation data (data type, frequency label, frequency, file name,
dir, mol_name_col, res_num_col, res_name_col, spin_num_col, spin_name_col,
data_col, error_col, sep). These are the arguments to the relax_data.read()
user function, please see the documentation for that function for more
information.
RELAX_DATA = [['R1', '600', 599.719 * 1e6, 'r1.600.out', None, None, 1, 2,
None, None, 3, 4, None],
@@ -194,4 +195,4 @@
# Execution (do not change!).
-dAuvergne_protocol(diff_model=DIFF_MODEL, mf_models=MF_MODELS,
local_tm_models=LOCAL_TM_MODELS, pdb_file=PDB_FILE, seq_args=SEQ_ARGS,
het_name=HET_NAME, relax_data=RELAX_DATA, unres=UNRES, exclude=EXCLUDE,
bond_length=BOND_LENGTH, csa=CSA, hetnuc=HETNUC, proton=PROTON,
grid_inc=GRID_INC, min_algor=MIN_ALGOR, mc_num=MC_NUM, conv_loop=CONV_LOOP)
+dAuvergne_protocol(diff_model=DIFF_MODEL, mf_models=MF_MODELS,
local_tm_models=LOCAL_TM_MODELS, pdb_file=PDB_FILE, seq_args=SEQ_ARGS,
het_name=HET_NAME,attached_name=ATTACHED_NAME, relax_data=RELAX_DATA,
unres=UNRES, exclude=EXCLUDE, bond_length=BOND_LENGTH, csa=CSA,
hetnuc=HETNUC, proton=PROTON, grid_inc=GRID_INC, min_algor=MIN_ALGOR,
mc_num=MC_NUM, conv_loop=CONV_LOOP)
Modified: branches/bieri_gui/scripts/code_validator
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/scripts/code_validator?rev=11387&r1=11386&r2=11387&view=diff
==============================================================================
--- branches/bieri_gui/scripts/code_validator (original)
+++ branches/bieri_gui/scripts/code_validator Tue Aug 3 09:00:27 2010
@@ -58,9 +58,6 @@
# Empty line after docstring.
self.docstring_clearance()
- # Docstring length.
- self.docstring_length()
-
# Variable, function, and class names.
######################################
@@ -173,7 +170,7 @@
"""Test for proper class naming."""
# Heading.
- sys.stdout.write(self.indent + "Class naming (must start with a
capital).\n")
+ sys.stdout.write(self.indent + "Class naming (should start with a
capital).\n")
# Flags.
ok = 1
@@ -461,72 +458,6 @@
self.terminate(ok)
- def docstring_length(self):
- """Test that the docstring is less than 100 char long."""
-
- # Heading.
- sys.stdout.write(self.indent + "Docstring length. Should be less
than 100 characters including all leading whitespace (equations can be
longer).\n")
-
- # Flags.
- ok = 1
-
- # Loop over the file.
- for i in xrange(len(self.lines)):
- # Flags.
- too_long = 0
-
- # Find the functions.
- if search("^ *def ", self.lines[i]):
- # Skip functions without docstrings!
- if not search("^ *\"\"\"", self.lines[i+1]) and not
search("^ *\'\'\'", self.lines[i+1]):
- continue
-
- # Split the docstring line.
- if search("^ *\"\"\"", self.lines[i+1]):
- row = split(self.lines[i+1], "\"\"\"")
- else:
- row = split(self.lines[i+1], "\'\'\'")
-
- # Loop over the docstring.
- j = 0
- while 1:
- # Single line docstring.
- if len(row) == 3:
- # Test the length of the line.
- if len(row[0]) + 3 + len(row[1]) > 101:
- too_long = 1
- break
-
- # Test the length of the line.
- if len(self.lines[i+1+j]) > 101:
- too_long = 1
- break
-
- # Increment the line counter.
- j = j + 1
-
- # End of the docstring.
- if search("\"\"\"", self.lines[i+1+j]) or
search("\'\'\'", self.lines[i+1+j]):
- break
-
- # Docstring is ok.
- if not too_long:
- continue
-
- # Initial print out.
- if ok:
- sys.stdout.write(self.indent + " Line num: ")
- sys.stdout.write(`i+1+j+2`)
- ok = 0
-
- # Print the line number.
- else:
- sys.stdout.write(", " + `i+1+j+2`)
-
- # Termination.
- self.terminate(ok)
-
-
def function_args(self):
"""Test for proper function argment spacing."""
Modified: branches/bieri_gui/specific_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/specific_fns/frame_order.py?rev=11387&r1=11386&r2=11387&view=diff
==============================================================================
--- branches/bieri_gui/specific_fns/frame_order.py (original)
+++ branches/bieri_gui/specific_fns/frame_order.py Tue Aug 3 09:00:27 2010
@@ -36,7 +36,7 @@
from api_base import API_base
from api_common import API_common
from float import isNaN, isInf
-from generic_fns import pipes
+from generic_fns import align_tensor, pipes
from generic_fns.angles import wrap_angles
from generic_fns.structure.cones import Iso_cone
from generic_fns.structure.geometric import cone_edge, generate_vector_dist,
generate_vector_residues, stitch_cone_to_edge
@@ -114,6 +114,9 @@
# Make a single function call. This will cause back calculation and
the data will be stored in the class instance.
target.func(param_vector)
+
+ # Store the back-calculated tensors.
+ self._store_bc_tensors(target)
# Return the reduced tensors.
return target.red_tensors_bc
@@ -416,6 +419,22 @@
# Update the model.
self._update_model()
+
+
+ def _store_bc_tensors(self, target_fn):
+ """Store the back-calculated reduced alignment tensors.
+
+ @param target_fn: The frame-order target function class.
+ @type target_fn: class instance
+ """
+
+ # Loop over the reduced tensors.
+ for i, tensor in self._tensor_loop(red=True):
+ # New name.
+ name = tensor.name + ' bc'
+
+ # Initialise the new tensor.
+ align_tensor.init(tensor=name,
params=(target_fn.red_tensors_bc[5*i + 0], target_fn.red_tensors_bc[5*i + 1],
target_fn.red_tensors_bc[5*i + 2], target_fn.red_tensors_bc[5*i + 3],
target_fn.red_tensors_bc[5*i + 4]), param_types=2)
def _tensor_loop(self, red=False):
@@ -673,6 +692,9 @@
# Set the chi2.
cdp.chi2 = chi2
+
+ # Store the back-calculated tensors.
+ self._store_bc_tensors(target)
def create_mc_data(self, spin_id=None):
@@ -1073,6 +1095,10 @@
# Unpack the results.
self._unpack_opt_results(results, sim_index)
+ # Store the back-calculated tensors.
+ self._store_bc_tensors(target)
+
+
def model_loop(self):
"""Dummy generator method.
r11387 - in /branches/bieri_gui: ./ auto_analyses/ generic_fns/ sample_scripts/ scripts/ specific_fns/