Author: bugman
Date: Wed Nov 13 18:46:51 2013
New Revision: 21435
URL: http://svn.gna.org/viewcvs/relax?rev=21435&view=rev
Log:
Merged revisions 21391,21407-21434 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r21391 | bugman | 2013-11-06 10:21:38 +0100 (Wed, 06 Nov 2013) | 7 lines
Improvements to the pymol.view and molmol.view user functions for finding
the PDB files.
Now the possibility that this is being run from a results subdirectory is
taken into consideration.
If the file cannot be found, the os.pardir parent directory is added to the
start of the relative
path and the file checked for.
........
r21407 | bugman | 2013-11-12 16:47:16 +0100 (Tue, 12 Nov 2013) | 5 lines
The rdc.read user function will now skip all lines of the RDC file starting
with '#'.
To include molecule identifiers at the start of the line will now require
quotation marks.
........
r21408 | bugman | 2013-11-12 19:35:23 +0100 (Tue, 12 Nov 2013) | 3 lines
Shifted the RDC and PCS assembly methods from the main class to the data
module for the N-state analysis.
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r21409 | bugman | 2013-11-12 19:45:04 +0100 (Tue, 12 Nov 2013) | 3 lines
Created the pipe_control.mol_res_spin.is_pseudoatom() function to simplify
pseudo-atom handling.
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r21410 | bugman | 2013-11-12 19:54:20 +0100 (Tue, 12 Nov 2013) | 5 lines
Created the pipe_control.mol_res_spin.pseudoatom_loop() function.
This is used to loop over the spin containers corresponding to a given
pseudo-atom.
........
r21411 | bugman | 2013-11-13 09:57:41 +0100 (Wed, 13 Nov 2013) | 5 lines
Added a PDB file and RDC values (and absolute J+D and J) for propylene
carbonate.
This will be used for testing of pseudo-atoms in the N-state model analysis.
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r21412 | bugman | 2013-11-13 10:04:28 +0100 (Wed, 13 Nov 2013) | 3 lines
Renamed the propylene carbonate files to the correct name of pyrotartaric
anhydride.
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r21413 | bugman | 2013-11-13 10:47:37 +0100 (Wed, 13 Nov 2013) | 8 lines
Created two new system tests based on the new pyrotarctic anhydride long
range (1J, 2J & 3J) RDC data.
The first (N_state_model.test_pyrotartaric_anhydride_rdcs) optimises an
alignment tensor using long
range signed RDC data. The second
(N_state_model.test_pyrotartaric_anhydride_absT) optimises an
alignment tensor using long range absolute T (J+D) data. Both test long
range data together with
methyl group pseudo-atom data.
........
r21414 | bugman | 2013-11-13 11:06:59 +0100 (Wed, 13 Nov 2013) | 5 lines
Added all of the pyrotartaric anhydride RDC generation scripts and files.
This is simply for reference and reproducibility.
........
r21415 | bugman | 2013-11-13 11:09:09 +0100 (Wed, 13 Nov 2013) | 5 lines
Modifications for the pyrotartaric anhydride system test script.
The grid search now is much quicker, and the RDC correlation plots are now
sent to DEVNULL.
........
r21416 | bugman | 2013-11-13 11:12:12 +0100 (Wed, 13 Nov 2013) | 6 lines
Added the return_id argument to the
pipe_control.mol_res_spin.pseudoatom_loop() function.
This will then yield both the spin container and spin ID string. This
mimics the spin_loop()
function.
........
r21417 | bugman | 2013-11-13 14:05:03 +0100 (Wed, 13 Nov 2013) | 12 lines
Added proper pseudo-atom support for the RDCs in the N-state model analysis.
This involves a number of changes. The pseudo-atom specific functions
ave_rdc_tensor_pseudoatom()
and ave_rdc_tensor_pseudoatom_dDij_dAmn() have been added to the
lib.alignment.rdc module. These
simply average the values from the equivalent non-pseudo-atom functions.
The return_rdc_data()
function in the specific_analyses.n_state_model.data module has been
modified to assemble the RDC
constants and unit vectors for all members of the pseudo-atom and add these
to the returned
structures, as well as a new list of flags specifying if the interatom pair
contains pseudo-atoms.
The N-state model target function and gradient have been updated to send
the pseudo-atom data to the
new lib.alignment.rdc module functions.
........
r21418 | bugman | 2013-11-13 14:18:01 +0100 (Wed, 13 Nov 2013) | 6 lines
J couplings for the N-state analysis are now properly handled for
pseudo-atoms.
The measured J couplings for the members of the pseudo-atom should not be
used, but rather that of
the pseudo-atom spin itself (as the former does not exist).
........
r21419 | bugman | 2013-11-13 14:26:23 +0100 (Wed, 13 Nov 2013) | 6 lines
Fix for the pyrotartaric_anhydride.py N-state model system test script.
This is used in two system tests. The user function call for reading the
inter-spin distances was
instead reading the J couplings as the distance.
........
r21420 | bugman | 2013-11-13 14:58:54 +0100 (Wed, 13 Nov 2013) | 3 lines
The interatomic loop now skips the element if either of the spin systems
are deselected.
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r21421 | bugman | 2013-11-13 15:02:27 +0100 (Wed, 13 Nov 2013) | 6 lines
Eliminated the old pseudo-atom handling in the N-state model specific
return_rdc_data() function.
This was multiplying the RDCs by -3 to handle the tetrahedral geometry of
the 1J methyl RDCs.
However this approach is not valid for non-methyl pseudo-atoms or for 2J,
3J, etc. data.
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r21422 | bugman | 2013-11-13 15:06:50 +0100 (Wed, 13 Nov 2013) | 17 lines
Reverted r21420 as the spin containers and interatomic data containers
should be handled separately.
The command used was:
svn merge -r21420:r21419 .
This is important to allow interatomic containers with good RDC data to be
selected while one of the
spin pairs deselected (for example if its PCS data is bad).
.....
r21420 | bugman | 2013-11-13 14:58:54 +0100 (Wed, 13 Nov 2013) | 3 lines
Changed paths:
M /trunk/pipe_control/interatomic.py
The interatomic loop now skips the element if either of the spin systems
are deselected.
.....
........
r21423 | bugman | 2013-11-13 15:33:18 +0100 (Wed, 13 Nov 2013) | 6 lines
A RelaxError is now raised for the N-state model optimisation with
gradients when T = J+D data is used.
The gradients for this data type are not implemented yet, so it is better
to prevent the user from
using this.
........
r21424 | bugman | 2013-11-13 15:34:40 +0100 (Wed, 13 Nov 2013) | 5 lines
The N_state_model.test_pyrotartaric_anhydride_absT system test now uses
simplex optimisation to pass.
The Newton algorithm cannot be used as the gradients for T = J+D type data
have not been implemented.
........
r21425 | bugman | 2013-11-13 16:51:00 +0100 (Wed, 13 Nov 2013) | 5 lines
An RDC error of 0.0 will now deselect the corresponding interatomic data
container.
This can be used for simpler pseudo-atom handling.
........
r21426 | bugman | 2013-11-13 16:51:59 +0100 (Wed, 13 Nov 2013) | 3 lines
Updated the menthol long range RDC data file to include pseudo-atom member
distances.
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r21427 | bugman | 2013-11-13 16:59:10 +0100 (Wed, 13 Nov 2013) | 5 lines
Renamed the interatomic_loop() function 'selected' argument to 'skip_desel'.
This is to match the spin_loop() function arguments.
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r21428 | bugman | 2013-11-13 17:02:06 +0100 (Wed, 13 Nov 2013) | 6 lines
The interatom.unit_vectors user function now calculates the unit vectors
for deselected containers.
This is useful for pseudo-atom handling where the interatomic containers to
the pseudo-atom members
have already been deselected.
........
r21429 | bugman | 2013-11-13 17:05:05 +0100 (Wed, 13 Nov 2013) | 5 lines
Updated the value checking for the N_state_model.test_absolute_rdc_menthol
system test.
The pseudo-atoms are now properly handled so the result is now much better.
........
r21430 | bugman | 2013-11-13 17:35:30 +0100 (Wed, 13 Nov 2013) | 5 lines
The stereochemistry auto-analysis can now accept a file of interatomic
distances.
This is for better pseudo-atom support.
........
r21431 | bugman | 2013-11-13 17:46:19 +0100 (Wed, 13 Nov 2013) | 3 lines
The N-state model specific check_rdcs() function now properly handles
pseudo-atoms.
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r21432 | bugman | 2013-11-13 17:52:22 +0100 (Wed, 13 Nov 2013) | 5 lines
The pipe_control.rdc.q_factors() function now properly handles pseudo-atoms.
If pseudo-atoms are present, then 2Da^2(4 + 3R)/5 normalised Q factor is
skipped.
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r21433 | bugman | 2013-11-13 18:12:05 +0100 (Wed, 13 Nov 2013) | 5 lines
Fix for the N_state_model.test_stereochem_analysis system test for the
pseudo-atom handling.
An interatomic distance file is now used to explicitly set up all distances.
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r21434 | bugman | 2013-11-13 18:30:44 +0100 (Wed, 13 Nov 2013) | 6 lines
Fixes for the N-state model target function gradient and Hessian for the
data structure changes.
The unit vector data structure is no longer a pure numpy array but a mixed
list and array structure
to handle pseudo-atoms.
........
Added:
branches/relax_disp/test_suite/shared_data/align_data/pyrotartaric_anhydride/
- copied from r21434,
trunk/test_suite/shared_data/align_data/pyrotartaric_anhydride/
branches/relax_disp/test_suite/shared_data/structures/phthalic_acid/snapshots/distances
- copied unchanged from r21434,
trunk/test_suite/shared_data/structures/phthalic_acid/snapshots/distances
branches/relax_disp/test_suite/shared_data/structures/pyrotartaric_anhydride.pdb
- copied unchanged from r21434,
trunk/test_suite/shared_data/structures/pyrotartaric_anhydride.pdb
branches/relax_disp/test_suite/system_tests/scripts/n_state_model/pyrotartaric_anhydride.py
- copied unchanged from r21434,
trunk/test_suite/system_tests/scripts/n_state_model/pyrotartaric_anhydride.py
Modified:
branches/relax_disp/ (props changed)
branches/relax_disp/auto_analyses/stereochem_analysis.py
branches/relax_disp/lib/alignment/rdc.py
branches/relax_disp/pipe_control/interatomic.py
branches/relax_disp/pipe_control/mol_res_spin.py
branches/relax_disp/pipe_control/molmol.py
branches/relax_disp/pipe_control/pymol_control.py
branches/relax_disp/pipe_control/rdc.py
branches/relax_disp/pipe_control/selection.py
branches/relax_disp/specific_analyses/n_state_model/__init__.py
branches/relax_disp/specific_analyses/n_state_model/data.py
branches/relax_disp/target_functions/n_state_model.py
branches/relax_disp/test_suite/shared_data/align_data/menthol/long_range_rdc
branches/relax_disp/test_suite/system_tests/n_state_model.py
branches/relax_disp/test_suite/system_tests/scripts/n_state_model/stereochem_analysis.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/relax_disp/auto_analyses/stereochem_analysis.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/auto_analyses/stereochem_analysis.py?rev=21435&r1=21434&r2=21435&view=diff
Modified: branches/relax_disp/lib/alignment/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/lib/alignment/rdc.py?rev=21435&r1=21434&r2=21435&view=diff
Modified: branches/relax_disp/pipe_control/interatomic.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/pipe_control/interatomic.py?rev=21435&r1=21434&r2=21435&view=diff
Modified: branches/relax_disp/pipe_control/mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/pipe_control/mol_res_spin.py?rev=21435&r1=21434&r2=21435&view=diff
Modified: branches/relax_disp/pipe_control/molmol.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/pipe_control/molmol.py?rev=21435&r1=21434&r2=21435&view=diff
Modified: branches/relax_disp/pipe_control/pymol_control.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/pipe_control/pymol_control.py?rev=21435&r1=21434&r2=21435&view=diff
Modified: branches/relax_disp/pipe_control/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/pipe_control/rdc.py?rev=21435&r1=21434&r2=21435&view=diff
Modified: branches/relax_disp/pipe_control/selection.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/pipe_control/selection.py?rev=21435&r1=21434&r2=21435&view=diff
Modified: branches/relax_disp/specific_analyses/n_state_model/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/n_state_model/__init__.py?rev=21435&r1=21434&r2=21435&view=diff
Modified: branches/relax_disp/specific_analyses/n_state_model/data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/n_state_model/data.py?rev=21435&r1=21434&r2=21435&view=diff
Modified: branches/relax_disp/target_functions/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/target_functions/n_state_model.py?rev=21435&r1=21434&r2=21435&view=diff
Modified:
branches/relax_disp/test_suite/shared_data/align_data/menthol/long_range_rdc
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/align_data/menthol/long_range_rdc?rev=21435&r1=21434&r2=21435&view=diff
Modified: branches/relax_disp/test_suite/system_tests/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/n_state_model.py?rev=21435&r1=21434&r2=21435&view=diff
Modified:
branches/relax_disp/test_suite/system_tests/scripts/n_state_model/stereochem_analysis.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/scripts/n_state_model/stereochem_analysis.py?rev=21435&r1=21434&r2=21435&view=diff
r21435 - in /branches/relax_disp: ./ auto_analyses/ lib/alignment/ pipe_control/ specific_analyses/n_state_model/ target_fun...