Author: bugman
Date: Fri Mar 22 17:14:20 2013
New Revision: 18993
URL: http://svn.gna.org/viewcvs/relax?rev=18993&view=rev
Log:
Next block of the manual merger of the frame_order_testing branch.
The commands used were:
svn merge -r18460:18461
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18466:18467
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18467:18468
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18468:18469
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18469:18470
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18472:18473
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18546:18547
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18547:18548
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
The console messages were:
[edau@localhost relax-trunk]$ svn merge -r18460:18461
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18461 into '.':
U specific_fns/frame_order.py
[edau@localhost relax-trunk]$ svn merge -r18466:18467
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
Conflict discovered in 'generic_fns/structure/main.py'.
Select: (p) postpone, (df) diff-full, (e) edit,
(mc) mine-conflict, (tc) theirs-conflict,
(s) show all options: p
--- Merging r18467 into '.':
C generic_fns/structure/main.py
Summary of conflicts:
Text conflicts: 1
[edau@localhost relax-trunk]$ svn merge -r18467:18468
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18468 into '.':
G specific_fns/frame_order.py
[edau@localhost relax-trunk]$ svn merge -r18468:18469
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18469 into '.':
G specific_fns/frame_order.py
[edau@localhost relax-trunk]$ svn merge -r18469:18470
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18470 into '.':
U test_suite/shared_data/frame_order/cam/full_analysis.py
[edau@localhost relax-trunk]$ svn merge -r18472:18473
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18473 into '.':
U auto_analyses/frame_order.py
[edau@localhost relax-trunk]$ svn merge -r18546:18547
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
Conflict discovered in 'generic_fns/structure/main.py'.
Select: (p) postpone, (df) diff-full, (e) edit,
(mc) mine-conflict, (tc) theirs-conflict,
(s) show all options: p
--- Merging r18547 into '.':
C generic_fns/structure/main.py
Summary of conflicts:
Text conflicts: 1
[edau@localhost relax-trunk]$ svn merge -r18547:18548
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18548 into '.':
G specific_fns/frame_order.py
[edau@localhost relax-trunk]$
Modified:
trunk/auto_analyses/frame_order.py
trunk/generic_fns/structure/main.py
trunk/specific_fns/frame_order.py
trunk/test_suite/shared_data/frame_order/cam/full_analysis.py
Modified: trunk/auto_analyses/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/auto_analyses/frame_order.py?rev=18993&r1=18992&r2=18993&view=diff
==============================================================================
--- trunk/auto_analyses/frame_order.py (original)
+++ trunk/auto_analyses/frame_order.py Fri Mar 22 17:14:20 2013
@@ -45,7 +45,7 @@
class Frame_order_analysis:
"""The frame order auto-analysis protocol."""
- def __init__(self, data_pipe_full=None, data_pipe_subset=None,
pipe_bundle=None, results_dir=None, grid_inc=11, grid_inc_rigid=21,
min_algor='simplex', num_int_pts_grid=50, num_int_pts_subset=[20, 100],
func_tol_subset=[1e-2, 1e-2], num_int_pts_full=[100, 1000, 200000],
func_tol_full=[1e-2, 1e-3, 1e-4], mc_sim_num=500, mc_int_pts=1000,
mc_func_tol=1e-3, models=['rigid', 'free rotor', 'rotor', 'iso cone,
torsionless', 'iso cone, free rotor', 'iso cone', 'pseudo-ellipse,
torsionless', 'pseudo-ellipse']):
+ def __init__(self, data_pipe_full=None, data_pipe_subset=None,
pipe_bundle=None, results_dir=None, grid_inc=11, grid_inc_rigid=21,
min_algor='simplex', num_int_pts_grid=50, num_int_pts_subset=[20, 100],
func_tol_subset=[1e-2, 1e-2], num_int_pts_full=[100, 1000, 200000],
func_tol_full=[1e-2, 1e-3, 1e-4], mc_sim_num=500, mc_int_pts=1000,
mc_func_tol=1e-3, models=['rigid', 'free rotor', 'rotor', 'iso cone, free
rotor', 'iso cone, torsionless', 'iso cone', 'pseudo-ellipse, torsionless',
'pseudo-ellipse']):
"""Perform the full frame order analysis.
@param data_pipe_full: The name of the data pipe containing
all of the RDC and PCS data.
Modified: trunk/generic_fns/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/structure/main.py?rev=18993&r1=18992&r2=18993&view=diff
==============================================================================
--- trunk/generic_fns/structure/main.py (original)
+++ trunk/generic_fns/structure/main.py Fri Mar 22 17:14:20 2013
@@ -427,7 +427,6 @@
mol_names.append(mol_name_target)
else:
mol_names.append(mol_name)
- mol_names.append(mol_name)
res_nums.append(res_num)
res_names.append(res_name)
spin_nums.append(atom_num)
@@ -612,7 +611,7 @@
for model in models:
coord.append([])
for pos in cdp.structure.atom_loop(atom_id=atom_id, model_num=model,
pos_flag=True):
- coord[-1].append(pos)
+ coord[-1].append(pos[0])
coord[-1] = array(coord[-1])
# Calculate the RMSD.
Modified: trunk/specific_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_fns/frame_order.py?rev=18993&r1=18992&r2=18993&view=diff
==============================================================================
--- trunk/specific_fns/frame_order.py (original)
+++ trunk/specific_fns/frame_order.py Fri Mar 22 17:14:20 2013
@@ -28,7 +28,7 @@
from minfx.generic import generic_minimise
from minfx.grid import grid_point_array
from numpy import arccos, array, dot, eye, float64, identity, ones,
transpose, zeros
-from numpy.linalg import inv
+from numpy.linalg import inv, norm
from re import search
import sys
from warnings import warn
@@ -639,7 +639,7 @@
continue
# A single atomic position.
- if len(spin.pos) == 1:
+ if spin.pos.shape == (3,):
atomic_pos.append(spin.pos[0])
# Average multiple atomic positions.
@@ -810,12 +810,8 @@
continue
# A single unit vector.
- if arg_check.is_float(interatom.vector[0], raise_error=False):
+ if interatom.vector.shape == (3,):
unit_vect.append(interatom.vector)
-
- # A single unit vector.
- elif len(interatom.vector) == 1:
- unit_vect.append(interatom.vector[0])
# Average multiple unit vectors.
else:
@@ -829,6 +825,9 @@
# Store.
unit_vect.append(ave_vector)
+
+ # Normalise (to be sure).
+ unit_vect[-1] = unit_vect[-1] / norm(unit_vect[-1])
# Gyromagnetic ratios.
g1 = return_gyromagnetic_ratio(spin1.isotope)
@@ -1354,9 +1353,9 @@
rdcs, rdc_err, rdc_weight, rdc_vect, rdc_const, absolute_rdc =
self._minimise_setup_rdcs(sim_index=sim_index)
# Data checks.
- if not len(pcs):
+ if pcs != None and not len(pcs):
raise RelaxNoPCSError
- if not len(rdcs):
+ if rdcs != None and not len(rdcs):
raise RelaxNoRDCError
# Get the atomic_positions.
Modified: trunk/test_suite/shared_data/frame_order/cam/full_analysis.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/full_analysis.py?rev=18993&r1=18992&r2=18993&view=diff
==============================================================================
--- trunk/test_suite/shared_data/frame_order/cam/full_analysis.py (original)
+++ trunk/test_suite/shared_data/frame_order/cam/full_analysis.py Fri Mar 22
17:14:20 2013
@@ -164,6 +164,7 @@
# Duplicate the PCS data subset data pipe to create a data pipe containing
all the PCS data.
DATA = "Data - " + PIPE_BUNDLE
pipe.copy(pipe_from=SUBSET, pipe_to=DATA, bundle_to=PIPE_BUNDLE)
+pipe.switch(DATA)
# Load the complete PCS data into the already filled data pipe.
for i in range(len(ln)):
r18993 - in /trunk: auto_analyses/ generic_fns/structure/ specific_fns/ test_suite/shared_data/frame_order/cam/