Author: bugman
Date: Sun May 4 15:59:34 2008
New Revision: 6102
URL: http://svn.gna.org/viewcvs/relax?rev=6102&view=rev
Log:
Merged revisions 6013,6015-6068,6070-6101 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/mol_res_spin_module_rename
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r6013 | bugman | 2008-04-28 13:55:21 +0200 (Mon, 28 Apr 2008) | 3 lines
Created a temporary branch for some heavy duty module rearrangements.
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r6056 | bugman | 2008-05-02 19:16:06 +0200 (Fri, 02 May 2008) | 8 lines
Split up of the generic_fns.selection module.
All of the methods relating to the molecules, residues, and spins
(including the spin selection
string and associated functions and the spin selection object) have been
shifted into the
generic_fns.mol_res_spin module. The functions remaining in
generic_fns.selection are related to
purely the selection and deselection of spins.
........
r6057 | bugman | 2008-05-04 11:34:42 +0200 (Sun, 04 May 2008) | 3 lines
Wrote a module docstring.
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r6058 | bugman | 2008-05-04 11:37:06 +0200 (Sun, 04 May 2008) | 5 lines
Renamed all the functions of the residue, molecule, and spin modules.
This is in preparation for merging into the generic_fns.mol_res_spin module.
........
r6059 | bugman | 2008-05-04 11:39:01 +0200 (Sun, 04 May 2008) | 3 lines
Shifted all the copy functions into generic_fns.mol_res_spin.
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r6060 | bugman | 2008-05-04 11:40:38 +0200 (Sun, 04 May 2008) | 3 lines
Shifted all the create functions into generic_fns.mol_res_spin.
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r6061 | bugman | 2008-05-04 11:41:39 +0200 (Sun, 04 May 2008) | 3 lines
Shifted all the delete functions into generic_fns.mol_res_spin.
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r6062 | bugman | 2008-05-04 11:43:00 +0200 (Sun, 04 May 2008) | 4 lines
Shifted all the display functions into generic_fns.mol_res_spin.
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r6063 | bugman | 2008-05-04 11:44:58 +0200 (Sun, 04 May 2008) | 3 lines
Renamed all the 'rename' and 'renumber' fns to 'name' and 'number'.
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r6064 | bugman | 2008-05-04 11:46:52 +0200 (Sun, 04 May 2008) | 3 lines
Shifted all the naming functions into generic_fns.mol_res_spin.
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r6065 | bugman | 2008-05-04 11:48:17 +0200 (Sun, 04 May 2008) | 3 lines
Shifted all the numbering functions into generic_fns.mol_res_spin.
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r6066 | bugman | 2008-05-04 11:54:18 +0200 (Sun, 04 May 2008) | 3 lines
Big simplifications to the molecule and residue naming functions.
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r6067 | bugman | 2008-05-04 11:56:33 +0200 (Sun, 04 May 2008) | 3 lines
Converted the number_residue() fn to the form of the number_spin() fn.
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r6068 | bugman | 2008-05-04 11:57:17 +0200 (Sun, 04 May 2008) | 3 lines
Removed the empty molecule, residue, and spin modules.
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r6070 | bugman | 2008-05-04 12:16:26 +0200 (Sun, 04 May 2008) | 3 lines
Fixed all the broken imports.
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r6071 | bugman | 2008-05-04 12:26:45 +0200 (Sun, 04 May 2008) | 3 lines
Shifted all the unit tests of test_selection to test_mol_spin_res, and
fixed the import and calls.
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r6072 | bugman | 2008-05-04 13:27:54 +0200 (Sun, 04 May 2008) | 3 lines
Updated the molecule, residue, and spin unit test base classes.
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r6073 | bugman | 2008-05-04 13:31:07 +0200 (Sun, 04 May 2008) | 3 lines
Shifted all the molecule, residue, and spin unit tests into
test_mol_spin_res.
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r6074 | bugman | 2008-05-04 13:32:11 +0200 (Sun, 04 May 2008) | 3 lines
Import fix.
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r6075 | bugman | 2008-05-04 13:34:23 +0200 (Sun, 04 May 2008) | 3 lines
Made the names of the molecule unit tests unique.
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r6076 | bugman | 2008-05-04 13:36:11 +0200 (Sun, 04 May 2008) | 3 lines
Made the names of the residue unit tests unique.
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r6077 | bugman | 2008-05-04 13:37:10 +0200 (Sun, 04 May 2008) | 3 lines
Made the names of the spin unit tests unique.
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r6078 | bugman | 2008-05-04 13:43:37 +0200 (Sun, 04 May 2008) | 3 lines
Set up some objects containing the molecule, residue, and spin fns of
generic_fns.mol_res_spin.
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r6079 | bugman | 2008-05-04 13:44:21 +0200 (Sun, 04 May 2008) | 3 lines
Fixed the naming of the test_mol_spin_res.py file.
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r6080 | bugman | 2008-05-04 13:51:18 +0200 (Sun, 04 May 2008) | 3 lines
Lots of unit test fixes.
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r6081 | bugman | 2008-05-04 14:07:18 +0200 (Sun, 04 May 2008) | 3 lines
A bit of code rearrangement as a test.
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r6082 | bugman | 2008-05-04 14:11:40 +0200 (Sun, 04 May 2008) | 3 lines
Renamed all the function calls.
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r6083 | bugman | 2008-05-04 14:13:00 +0200 (Sun, 04 May 2008) | 3 lines
Added a dummy molecule module for the unit tests.
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r6084 | bugman | 2008-05-04 14:18:57 +0200 (Sun, 04 May 2008) | 3 lines
Created more dummy modules.
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r6085 | bugman | 2008-05-04 14:24:44 +0200 (Sun, 04 May 2008) | 3 lines
Manually reverted r6073.
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r6086 | bugman | 2008-05-04 14:25:40 +0200 (Sun, 04 May 2008) | 3 lines
Removed the dummy modules.
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r6087 | bugman | 2008-05-04 14:27:31 +0200 (Sun, 04 May 2008) | 3 lines
Import of the dummy modules into the correct location.
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r6088 | bugman | 2008-05-04 14:29:27 +0200 (Sun, 04 May 2008) | 3 lines
Shifted the test_reverse unit test back into test_selection.py.
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r6089 | bugman | 2008-05-04 14:30:58 +0200 (Sun, 04 May 2008) | 3 lines
Added a missing import.
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r6090 | bugman | 2008-05-04 14:32:46 +0200 (Sun, 04 May 2008) | 3 lines
Removed a broken import.
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r6091 | bugman | 2008-05-04 14:54:44 +0200 (Sun, 04 May 2008) | 3 lines
Fixed all the residue_name and residue_number unit tests.
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r6092 | bugman | 2008-05-04 14:56:47 +0200 (Sun, 04 May 2008) | 3 lines
Fixed all the molecule_name unit tests.
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r6093 | bugman | 2008-05-04 15:04:35 +0200 (Sun, 04 May 2008) | 3 lines
Renamed 'rename' and 'renumber' to 'name' and 'number' in the residue user
function class.
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r6094 | bugman | 2008-05-04 15:07:58 +0200 (Sun, 04 May 2008) | 3 lines
Renamed 'rename' to 'name' in the molecule user function class.
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r6095 | bugman | 2008-05-04 15:09:18 +0200 (Sun, 04 May 2008) | 3 lines
Fixes for the molecule.name() user function unit tests.
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r6096 | bugman | 2008-05-04 15:10:48 +0200 (Sun, 04 May 2008) | 3 lines
Fixes for the residue.name() and residue.number() user function unit tests.
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r6097 | bugman | 2008-05-04 15:13:10 +0200 (Sun, 04 May 2008) | 3 lines
Added the missing numbering functions.
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r6098 | bugman | 2008-05-04 15:14:35 +0200 (Sun, 04 May 2008) | 3 lines
Docstring fix.
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r6099 | bugman | 2008-05-04 15:49:31 +0200 (Sun, 04 May 2008) | 3 lines
Re-added tests for disallowed residue and spin selections.
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r6100 | bugman | 2008-05-04 15:53:46 +0200 (Sun, 04 May 2008) | 3 lines
Added the has_molecules(), has_residues(), and has_spins() methods to the
Selection object.
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Added:
1.3/generic_fns/mol_res_spin.py
- copied, changed from r6068,
branches/mol_res_spin_module_rename/generic_fns/mol_res_spin.py
1.3/test_suite/unit_tests/_generic_fns/molecule.py
- copied unchanged from r6100,
branches/mol_res_spin_module_rename/test_suite/unit_tests/_generic_fns/molecule.py
1.3/test_suite/unit_tests/_generic_fns/residue.py
- copied unchanged from r6100,
branches/mol_res_spin_module_rename/test_suite/unit_tests/_generic_fns/residue.py
1.3/test_suite/unit_tests/_generic_fns/spin.py
- copied unchanged from r6100,
branches/mol_res_spin_module_rename/test_suite/unit_tests/_generic_fns/spin.py
1.3/test_suite/unit_tests/_generic_fns/test_mol_res_spin.py
- copied unchanged from r6100,
branches/mol_res_spin_module_rename/test_suite/unit_tests/_generic_fns/test_mol_res_spin.py
Removed:
1.3/generic_fns/molecule.py
1.3/generic_fns/residue.py
1.3/generic_fns/spin.py
Modified:
1.3/ (props changed)
1.3/generic_fns/angles.py
1.3/generic_fns/grace.py
1.3/generic_fns/intensity.py
1.3/generic_fns/minimise.py
1.3/generic_fns/model_selection.py
1.3/generic_fns/molmol.py
1.3/generic_fns/palmer.py
1.3/generic_fns/pymol.py
1.3/generic_fns/selection.py
1.3/generic_fns/sequence.py
1.3/generic_fns/structure/geometric.py
1.3/generic_fns/structure/main.py
1.3/generic_fns/structure/mass.py
1.3/generic_fns/structure/scientific.py
1.3/generic_fns/value.py
1.3/prompt/molecule.py
1.3/prompt/residue.py
1.3/prompt/spin.py
1.3/specific_fns/base_class.py
1.3/specific_fns/consistency_tests.py
1.3/specific_fns/jw_mapping.py
1.3/specific_fns/model_free/mf_minimise.py
1.3/specific_fns/model_free/model_free.py
1.3/specific_fns/relax_data.py
1.3/specific_fns/relax_fit.py
1.3/test_suite/system_tests/consistency_tests.py
1.3/test_suite/system_tests/jw_mapping.py
1.3/test_suite/unit_tests/_generic_fns/_structure/test_scientific.py
1.3/test_suite/unit_tests/_generic_fns/test_molecule.py
1.3/test_suite/unit_tests/_generic_fns/test_residue.py
1.3/test_suite/unit_tests/_generic_fns/test_selection.py
1.3/test_suite/unit_tests/_generic_fns/test_spin.py
1.3/test_suite/unit_tests/_prompt/test_molecule.py
1.3/test_suite/unit_tests/_prompt/test_residue.py
1.3/test_suite/unit_tests/molecule_testing_base.py
1.3/test_suite/unit_tests/residue_testing_base.py
1.3/test_suite/unit_tests/spin_testing_base.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: 1.3/generic_fns/angles.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/angles.py?rev=6102&r1=6101&r2=6102&view=diff
Modified: 1.3/generic_fns/grace.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/grace.py?rev=6102&r1=6101&r2=6102&view=diff
Modified: 1.3/generic_fns/intensity.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/intensity.py?rev=6102&r1=6101&r2=6102&view=diff
Modified: 1.3/generic_fns/minimise.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/minimise.py?rev=6102&r1=6101&r2=6102&view=diff
Modified: 1.3/generic_fns/model_selection.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/model_selection.py?rev=6102&r1=6101&r2=6102&view=diff
Copied: 1.3/generic_fns/mol_res_spin.py (from r6068,
branches/mol_res_spin_module_rename/generic_fns/mol_res_spin.py)
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/mol_res_spin.py?p2=1.3/generic_fns/mol_res_spin.py&p1=branches/mol_res_spin_module_rename/generic_fns/mol_res_spin.py&r1=6068&r2=6102&rev=6102&view=diff
Removed: 1.3/generic_fns/molecule.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/molecule.py?rev=6101&view=auto
Modified: 1.3/generic_fns/molmol.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/molmol.py?rev=6102&r1=6101&r2=6102&view=diff
Modified: 1.3/generic_fns/palmer.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/palmer.py?rev=6102&r1=6101&r2=6102&view=diff
Modified: 1.3/generic_fns/pymol.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/pymol.py?rev=6102&r1=6101&r2=6102&view=diff
Removed: 1.3/generic_fns/residue.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/residue.py?rev=6101&view=auto
Modified: 1.3/generic_fns/selection.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/selection.py?rev=6102&r1=6101&r2=6102&view=diff
Modified: 1.3/generic_fns/sequence.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/sequence.py?rev=6102&r1=6101&r2=6102&view=diff
Removed: 1.3/generic_fns/spin.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/spin.py?rev=6101&view=auto
Modified: 1.3/generic_fns/structure/geometric.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/geometric.py?rev=6102&r1=6101&r2=6102&view=diff
Modified: 1.3/generic_fns/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/main.py?rev=6102&r1=6101&r2=6102&view=diff
Modified: 1.3/generic_fns/structure/mass.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/mass.py?rev=6102&r1=6101&r2=6102&view=diff
Modified: 1.3/generic_fns/structure/scientific.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/scientific.py?rev=6102&r1=6101&r2=6102&view=diff
Modified: 1.3/generic_fns/value.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/value.py?rev=6102&r1=6101&r2=6102&view=diff
Modified: 1.3/prompt/molecule.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/molecule.py?rev=6102&r1=6101&r2=6102&view=diff
Modified: 1.3/prompt/residue.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/residue.py?rev=6102&r1=6101&r2=6102&view=diff
Modified: 1.3/prompt/spin.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/spin.py?rev=6102&r1=6101&r2=6102&view=diff
Modified: 1.3/specific_fns/base_class.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/base_class.py?rev=6102&r1=6101&r2=6102&view=diff
Modified: 1.3/specific_fns/consistency_tests.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/consistency_tests.py?rev=6102&r1=6101&r2=6102&view=diff
Modified: 1.3/specific_fns/jw_mapping.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/jw_mapping.py?rev=6102&r1=6101&r2=6102&view=diff
Modified: 1.3/specific_fns/model_free/mf_minimise.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/model_free/mf_minimise.py?rev=6102&r1=6101&r2=6102&view=diff
Modified: 1.3/specific_fns/model_free/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/model_free/model_free.py?rev=6102&r1=6101&r2=6102&view=diff
Modified: 1.3/specific_fns/relax_data.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/relax_data.py?rev=6102&r1=6101&r2=6102&view=diff
Modified: 1.3/specific_fns/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/relax_fit.py?rev=6102&r1=6101&r2=6102&view=diff
Modified: 1.3/test_suite/system_tests/consistency_tests.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/consistency_tests.py?rev=6102&r1=6101&r2=6102&view=diff
Modified: 1.3/test_suite/system_tests/jw_mapping.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/jw_mapping.py?rev=6102&r1=6101&r2=6102&view=diff
Modified: 1.3/test_suite/unit_tests/_generic_fns/_structure/test_scientific.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/unit_tests/_generic_fns/_structure/test_scientific.py?rev=6102&r1=6101&r2=6102&view=diff
Modified: 1.3/test_suite/unit_tests/_generic_fns/test_molecule.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/unit_tests/_generic_fns/test_molecule.py?rev=6102&r1=6101&r2=6102&view=diff
Modified: 1.3/test_suite/unit_tests/_generic_fns/test_residue.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/unit_tests/_generic_fns/test_residue.py?rev=6102&r1=6101&r2=6102&view=diff
Modified: 1.3/test_suite/unit_tests/_generic_fns/test_selection.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/unit_tests/_generic_fns/test_selection.py?rev=6102&r1=6101&r2=6102&view=diff
Modified: 1.3/test_suite/unit_tests/_generic_fns/test_spin.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/unit_tests/_generic_fns/test_spin.py?rev=6102&r1=6101&r2=6102&view=diff
Modified: 1.3/test_suite/unit_tests/_prompt/test_molecule.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/unit_tests/_prompt/test_molecule.py?rev=6102&r1=6101&r2=6102&view=diff
Modified: 1.3/test_suite/unit_tests/_prompt/test_residue.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/unit_tests/_prompt/test_residue.py?rev=6102&r1=6101&r2=6102&view=diff
Modified: 1.3/test_suite/unit_tests/molecule_testing_base.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/unit_tests/molecule_testing_base.py?rev=6102&r1=6101&r2=6102&view=diff
Modified: 1.3/test_suite/unit_tests/residue_testing_base.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/unit_tests/residue_testing_base.py?rev=6102&r1=6101&r2=6102&view=diff
Modified: 1.3/test_suite/unit_tests/spin_testing_base.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/unit_tests/spin_testing_base.py?rev=6102&r1=6101&r2=6102&view=diff
r6102 - in /1.3: ./ generic_fns/ generic_fns/structure/ prompt/ specific_fns/ specific_fns/model_free/ test_suite/system_tes...