Author: bugman
Date: Sat Mar 23 18:27:27 2013
New Revision: 19073
URL: http://svn.gna.org/viewcvs/relax?rev=19073&view=rev
Log:
Renamed the generic_fns.relax_re module to lib.regex.
Added:
trunk/lib/regex.py
- copied unchanged from r19067, trunk/generic_fns/relax_re.py
trunk/test_suite/unit_tests/_lib/test_regex.py
- copied, changed from r19067,
trunk/test_suite/unit_tests/_generic_fns/test_relax_re.py
Removed:
trunk/generic_fns/relax_re.py
trunk/test_suite/unit_tests/_generic_fns/test_relax_re.py
Modified:
trunk/generic_fns/__init__.py
trunk/generic_fns/mol_res_spin.py
trunk/generic_fns/structure/internal.py
trunk/generic_fns/structure/main.py
trunk/generic_fns/structure/scientific.py
trunk/lib/__init__.py
Modified: trunk/generic_fns/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/__init__.py?rev=19073&r1=19072&r2=19073&view=diff
==============================================================================
--- trunk/generic_fns/__init__.py (original)
+++ trunk/generic_fns/__init__.py Sat Mar 23 18:27:27 2013
@@ -51,7 +51,6 @@
'pymol_control',
'rdc',
'relax_data',
- 'relax_re',
'reset',
'result_files',
'results',
Modified: trunk/generic_fns/mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/mol_res_spin.py?rev=19073&r1=19072&r2=19073&view=diff
==============================================================================
--- trunk/generic_fns/mol_res_spin.py (original)
+++ trunk/generic_fns/mol_res_spin.py Sat Mar 23 18:27:27 2013
@@ -41,7 +41,8 @@
# relax module imports.
from data_store.mol_res_spin import MoleculeContainer, ResidueContainer,
SpinContainer
-from generic_fns import exp_info, pipes, relax_re
+from generic_fns import exp_info, pipes
+from lib import regex
from lib.check_types import is_unicode
from lib.errors import RelaxError, RelaxNoSpinError, RelaxMultiMolIDError,
RelaxMultiResIDError, RelaxMultiSpinIDError, RelaxResSelectDisallowError,
RelaxSpinSelectDisallowError
from lib.warnings import RelaxWarning
@@ -206,7 +207,7 @@
select_mol = True
# A true match.
- elif relax_re.search(self.molecules, mol.name):
+ elif regex.search(self.molecules, mol.name):
select_mol = True
else:
# No molecule container sent in, therefore the molecule is
assumed to match.
@@ -223,7 +224,7 @@
select_res = True
# A true match.
- elif res.num in self.residues or relax_re.search(self.residues,
res.name):
+ elif res.num in self.residues or regex.search(self.residues,
res.name):
select_res = True
else:
# No residue container sent in, therefore the residue is assumed
to match.
@@ -240,7 +241,7 @@
select_spin = True
# A true match.
- elif spin.num in self.spins or relax_re.search(self.spins,
spin.name):
+ elif spin.num in self.spins or regex.search(self.spins,
spin.name):
select_spin = True
else:
# No spin container sent in, therefore the spin is assumed to
match.
@@ -292,7 +293,7 @@
return self._intersect[0].contains_mol(mol) and
self._intersect[1].contains_mol(mol)
# The check.
- if relax_re.search(self.molecules, mol):
+ if regex.search(self.molecules, mol):
return True
# Nothingness.
@@ -331,7 +332,7 @@
select_res = False
# The residue checks.
- if res_num in self.residues or relax_re.search(self.residues,
res_name):
+ if res_num in self.residues or regex.search(self.residues, res_name):
select_res = True
# Nothingness.
@@ -377,7 +378,7 @@
select_spin = False
# The spin checks.
- if spin_num in self.spins or relax_re.search(self.spins, spin_name):
+ if spin_num in self.spins or regex.search(self.spins, spin_name):
select_spin = True
# Nothingness.
Removed: trunk/generic_fns/relax_re.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/relax_re.py?rev=19072&view=auto
==============================================================================
--- trunk/generic_fns/relax_re.py (original)
+++ trunk/generic_fns/relax_re.py (removed)
@@ -1,87 +1,0 @@
-###############################################################################
-#
#
-# Copyright (C) 2003-2012 Edward d'Auvergne
#
-#
#
-# This file is part of the program relax (http://www.nmr-relax.com).
#
-#
#
-# This program is free software: you can redistribute it and/or modify
#
-# it under the terms of the GNU General Public License as published by
#
-# the Free Software Foundation, either version 3 of the License, or
#
-# (at your option) any later version.
#
-#
#
-# This program is distributed in the hope that it will be useful,
#
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
-# GNU General Public License for more details.
#
-#
#
-# You should have received a copy of the GNU General Public License
#
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
-#
#
-###############################################################################
-
-# Module docstring.
-"""Module implementing relax regular expression."""
-
-# Python module imports.
-import re
-
-
-def search(pattern, id):
- """Determine if id matches the pattern, or vice versa, allowing for
regular expressions.
-
- This method converts from relax's RE syntax to that of the re python
module.
-
- The changes include:
-
- 1. All '*' to '.*'.
- 2. The identifier is bracketed, '^' is added to the start and '$'
to the end.
-
- After conversion of both the string and patterns, the comparison is then
performed both ways from the converted string matching the original string
(using re.search()).
-
-
- @param pattern: The pattern to match the string to. This can be a
list of patterns. All elements will be converted to strings, so the pattern
or list can consist of anything.
- @type pattern: anything
- @param id: The identification object.
- @type id: None, str, or number
- @return: True if there is a match, False otherwise.
- @rtype: bool
- """
-
- # Catch None.
- if id == None:
- return False
-
- # Convert to a string.
- id = str(id)
-
- # If pattern is not a list, convert it to one.
- if not isinstance(pattern, list):
- patterns = [pattern]
- else:
- patterns = pattern
-
- # Loop over the patterns.
- for pattern in patterns:
- # Force a conversion to str.
- pattern = str(pattern)
-
- # Quick string check.
- if id == pattern:
- return True
-
- # First replace any '*' with '.*' (relax to re conversion).
- pattern_re = pattern.replace('*', '.*')
- id_re = id.replace('*', '.*')
-
- # Bracket the pattern.
- pattern_re = '^%s$' % pattern_re
- id_re = '^%s$' % id_re
-
- # String matches (both ways).
- if re.search(pattern_re, id):
- return True
- if re.search(id_re, pattern):
- return True
-
- # No matches.
- return False
Modified: trunk/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/structure/internal.py?rev=19073&r1=19072&r2=19073&view=diff
==============================================================================
--- trunk/generic_fns/structure/internal.py (original)
+++ trunk/generic_fns/structure/internal.py Sat Mar 23 18:27:27 2013
@@ -33,11 +33,12 @@
# relax module imports.
from data_store.relax_xml import fill_object_contents, xml_to_object
-from generic_fns import pipes, relax_re
+from generic_fns import pipes
from generic_fns.mol_res_spin import spin_loop
from generic_fns.mol_res_spin import Selection
from generic_fns.structure import pdb_read, pdb_write
from generic_fns.structure.api_base import Base_struct_API, ModelList,
Displacements
+from lib import regex
from lib.check_types import is_float
from lib.errors import RelaxError, RelaxNoneIntError, RelaxNoPdbError
from lib.io import file_root, open_read_file
@@ -91,7 +92,7 @@
# Loop over the bonded atoms.
matching_list = []
for bonded_index in mol.bonded[index]:
- if relax_re.search(mol.atom_name[bonded_index], attached_atom):
+ if regex.search(mol.atom_name[bonded_index], attached_atom):
matching_list.append(bonded_index)
num_attached = len(matching_list)
@@ -107,7 +108,7 @@
# No attached atoms.
if num_attached == 0:
- if relax_re.search('@*', attached_atom):
+ if regex.search('@*', attached_atom):
matching_list = []
bonded_num=[]
bonded_name=[]
Modified: trunk/generic_fns/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/structure/main.py?rev=19073&r1=19072&r2=19073&view=diff
==============================================================================
--- trunk/generic_fns/structure/main.py (original)
+++ trunk/generic_fns/structure/main.py Sat Mar 23 18:27:27 2013
@@ -30,7 +30,7 @@
from warnings import warn
# relax module imports.
-from generic_fns import molmol, relax_re
+from generic_fns import molmol
from generic_fns.interatomic import interatomic_loop
from generic_fns.mol_res_spin import create_spin, exists_mol_res_spin_data,
generate_spin_id_unique, linear_ave, return_molecule, return_residue,
return_spin, spin_loop
from generic_fns import pipes
Modified: trunk/generic_fns/structure/scientific.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/structure/scientific.py?rev=19073&r1=19072&r2=19073&view=diff
==============================================================================
--- trunk/generic_fns/structure/scientific.py (original)
+++ trunk/generic_fns/structure/scientific.py Sat Mar 23 18:27:27 2013
@@ -37,9 +37,10 @@
# relax module imports.
from data_store.relax_xml import fill_object_contents, xml_to_object
-from generic_fns import pipes, relax_re
+from generic_fns import pipes
from generic_fns.mol_res_spin import Selection, generate_spin_id,
parse_token, tokenise
from generic_fns.structure.api_base import Base_struct_API
+from lib import regex
from lib.errors import RelaxError, RelaxPdbLoadError
from lib.io import file_root
from lib.warnings import RelaxWarning, RelaxNoAtomWarning,
RelaxNoPDBFileWarning, RelaxZeroVectorWarning
@@ -79,7 +80,7 @@
# The find the attached atom in the residue (FIXME).
matching_list = []
for atom in list(res.atoms.keys()):
- if relax_re.search(atom, attached_atom):
+ if regex.search(atom, attached_atom):
matching_list.append(atom)
num_attached = len(matching_list)
Modified: trunk/lib/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/__init__.py?rev=19073&r1=19072&r2=19073&view=diff
==============================================================================
--- trunk/lib/__init__.py (original)
+++ trunk/lib/__init__.py Sat Mar 23 18:27:27 2013
@@ -40,6 +40,7 @@
'model_selection',
'order',
'physical_constants',
+ 'regex',
'spectral_densities',
'structure',
'text',
Removed: trunk/test_suite/unit_tests/_generic_fns/test_relax_re.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_generic_fns/test_relax_re.py?rev=19072&view=auto
==============================================================================
--- trunk/test_suite/unit_tests/_generic_fns/test_relax_re.py (original)
+++ trunk/test_suite/unit_tests/_generic_fns/test_relax_re.py (removed)
@@ -1,51 +1,0 @@
-###############################################################################
-#
#
-# Copyright (C) 2008 Edward d'Auvergne
#
-#
#
-# This file is part of the program relax (http://www.nmr-relax.com).
#
-#
#
-# This program is free software: you can redistribute it and/or modify
#
-# it under the terms of the GNU General Public License as published by
#
-# the Free Software Foundation, either version 3 of the License, or
#
-# (at your option) any later version.
#
-#
#
-# This program is distributed in the hope that it will be useful,
#
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
-# GNU General Public License for more details.
#
-#
#
-# You should have received a copy of the GNU General Public License
#
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
-#
#
-###############################################################################
-
-# Python module imports.
-from unittest import TestCase
-
-# relax module imports.
-from generic_fns import relax_re
-
-
-class Test_relax_re(TestCase):
- """Unit tests for the functions of the 'generic_fns.relax_re' module."""
-
- # Place the generic_fns.relax_re module into the class namespace.
- relax_re_fns = relax_re
-
-
- def test_search(self):
- """Test the proper behaviour of the generic_fns.relax_re.search()
function."""
-
- # Test a number of calls which should return True.
- self.assertEqual(True, self.relax_re_fns.search('H', 'H'))
- self.assertEqual(True, self.relax_re_fns.search('H*', 'H'))
- self.assertEqual(True, self.relax_re_fns.search('H*', 'H1'))
- self.assertEqual(True, self.relax_re_fns.search('H1', 'H1'))
- self.assertEqual(True, self.relax_re_fns.search('^H*', 'H'))
- self.assertEqual(True, self.relax_re_fns.search('^H*$', 'H'))
- self.assertEqual(True, self.relax_re_fns.search('^H*$', 'H'))
-
- # Test a number of calls which should return False.
- self.assertEqual(False, self.relax_re_fns.search('H*', 'NH'))
- self.assertEqual(False, self.relax_re_fns.search('H', 'HN'))
- self.assertEqual(False, self.relax_re_fns.search('H', 'H1'))
Copied: trunk/test_suite/unit_tests/_lib/test_regex.py (from r19067,
trunk/test_suite/unit_tests/_generic_fns/test_relax_re.py)
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_lib/test_regex.py?p2=trunk/test_suite/unit_tests/_lib/test_regex.py&p1=trunk/test_suite/unit_tests/_generic_fns/test_relax_re.py&r1=19067&r2=19073&rev=19073&view=diff
==============================================================================
--- trunk/test_suite/unit_tests/_generic_fns/test_relax_re.py (original)
+++ trunk/test_suite/unit_tests/_lib/test_regex.py Sat Mar 23 18:27:27 2013
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2008 Edward d'Auvergne
#
+# Copyright (C) 2008-2013 Edward d'Auvergne
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
@@ -23,29 +23,29 @@
from unittest import TestCase
# relax module imports.
-from generic_fns import relax_re
+from lib import regex
-class Test_relax_re(TestCase):
- """Unit tests for the functions of the 'generic_fns.relax_re' module."""
+class Test_regex(TestCase):
+ """Unit tests for the functions of the 'lib.regex' module."""
- # Place the generic_fns.relax_re module into the class namespace.
- relax_re_fns = relax_re
+ # Place the lib.regex module into the class namespace.
+ regex = regex
def test_search(self):
- """Test the proper behaviour of the generic_fns.relax_re.search()
function."""
+ """Test the proper behaviour of the lib.regex.search() function."""
# Test a number of calls which should return True.
- self.assertEqual(True, self.relax_re_fns.search('H', 'H'))
- self.assertEqual(True, self.relax_re_fns.search('H*', 'H'))
- self.assertEqual(True, self.relax_re_fns.search('H*', 'H1'))
- self.assertEqual(True, self.relax_re_fns.search('H1', 'H1'))
- self.assertEqual(True, self.relax_re_fns.search('^H*', 'H'))
- self.assertEqual(True, self.relax_re_fns.search('^H*$', 'H'))
- self.assertEqual(True, self.relax_re_fns.search('^H*$', 'H'))
+ self.assertEqual(True, self.regex.search('H', 'H'))
+ self.assertEqual(True, self.regex.search('H*', 'H'))
+ self.assertEqual(True, self.regex.search('H*', 'H1'))
+ self.assertEqual(True, self.regex.search('H1', 'H1'))
+ self.assertEqual(True, self.regex.search('^H*', 'H'))
+ self.assertEqual(True, self.regex.search('^H*$', 'H'))
+ self.assertEqual(True, self.regex.search('^H*$', 'H'))
# Test a number of calls which should return False.
- self.assertEqual(False, self.relax_re_fns.search('H*', 'NH'))
- self.assertEqual(False, self.relax_re_fns.search('H', 'HN'))
- self.assertEqual(False, self.relax_re_fns.search('H', 'H1'))
+ self.assertEqual(False, self.regex.search('H*', 'NH'))
+ self.assertEqual(False, self.regex.search('H', 'HN'))
+ self.assertEqual(False, self.regex.search('H', 'H1'))
r19073 - in /trunk: generic_fns/ generic_fns/structure/ lib/ test_suite/unit_tests/_generic_fns/ test_suite/unit_tests/_lib/