Author: bugman
Date: Sun May 4 11:37:06 2008
New Revision: 6058
URL: http://svn.gna.org/viewcvs/relax?rev=6058&view=rev
Log:
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.
Modified:
branches/mol_res_spin_module_rename/generic_fns/molecule.py
branches/mol_res_spin_module_rename/generic_fns/residue.py
branches/mol_res_spin_module_rename/generic_fns/spin.py
Modified: branches/mol_res_spin_module_rename/generic_fns/molecule.py
URL:
http://svn.gna.org/viewcvs/relax/branches/mol_res_spin_module_rename/generic_fns/molecule.py?rev=6058&r1=6057&r2=6058&view=diff
==============================================================================
--- branches/mol_res_spin_module_rename/generic_fns/molecule.py (original)
+++ branches/mol_res_spin_module_rename/generic_fns/molecule.py Sun May 4
11:37:06 2008
@@ -33,7 +33,7 @@
"""
-def copy(pipe_from=None, mol_from=None, pipe_to=None, mol_to=None):
+def copy_molecule(pipe_from=None, mol_from=None, pipe_to=None, mol_to=None):
"""Copy the contents of a molecule container to a new molecule.
For copying to be successful, the mol_from identification string must
match an existent molecule.
@@ -98,7 +98,7 @@
relax_data_store[pipe_to].mol[-1].name = mol_name_to
-def create(mol_name=None):
+def create_molecule(mol_name=None):
"""Function for adding a molecule into the relax data store."""
# Test if the current data pipe exists.
@@ -118,7 +118,7 @@
cdp.mol.add_item(mol_name=mol_name)
-def delete(mol_id=None):
+def delete_molecule(mol_id=None):
"""Function for deleting molecules from the current data pipe.
@param mol_id: The molecule identifier string.
@@ -163,7 +163,7 @@
cdp.mol.add_item()
-def display(mol_id=None):
+def display_molecule(mol_id=None):
"""Function for displaying the information associated with the molecule.
@param mol_id: The molecule identifier string.
@@ -194,7 +194,7 @@
print "%-15s %-15s" % (mol.name, `len(mol.res)`)
-def rename(mol_id, new_name=None):
+def rename_molecule(mol_id, new_name=None):
"""Function for renaming molecules.
@param mol_id: The identifier string for the molecule to rename.
Modified: branches/mol_res_spin_module_rename/generic_fns/residue.py
URL:
http://svn.gna.org/viewcvs/relax/branches/mol_res_spin_module_rename/generic_fns/residue.py?rev=6058&r1=6057&r2=6058&view=diff
==============================================================================
--- branches/mol_res_spin_module_rename/generic_fns/residue.py (original)
+++ branches/mol_res_spin_module_rename/generic_fns/residue.py Sun May 4
11:37:06 2008
@@ -33,7 +33,7 @@
"""
-def copy(pipe_from=None, res_from=None, pipe_to=None, res_to=None):
+def copy_residue(pipe_from=None, res_from=None, pipe_to=None, res_to=None):
"""Copy the contents of the residue structure from one residue to a new
residue.
For copying to be successful, the res_from identification string must
match an existent residue.
@@ -102,7 +102,7 @@
mol_to_container.res[-1].name = res_name_to
-def create(res_num=None, res_name=None, mol_id=None):
+def create_residue(res_num=None, res_name=None, mol_id=None):
"""Function for adding a residue into the relax data store.
@param res_num: The identification number of the new residue.
@@ -138,7 +138,7 @@
mol_to_cont.res.add_item(res_num=res_num, res_name=res_name)
-def delete(res_id=None):
+def delete_residue(res_id=None):
"""Function for deleting residues from the current data pipe.
@param res_id: The molecule and residue identifier string.
@@ -178,7 +178,7 @@
mol.res.add_item()
-def display(res_id=None):
+def display_residue(res_id=None):
"""Function for displaying the information associated with the residue.
@param res_id: The molecule and residue identifier string.
@@ -200,7 +200,7 @@
print "%-15s %-15s %-15s %-15s" % (mol_name, `res.num`, res.name,
`len(res.spin)`)
-def rename(res_id, new_name=None):
+def rename_residue(res_id, new_name=None):
"""Function for renaming residues.
@param res_id: The identifier string for the residue(s) to rename.
@@ -226,7 +226,7 @@
res.name = new_name
-def renumber(res_id, new_number=None):
+def renumber_residue(res_id, new_number=None):
"""Function for renumbering residues.
@param res_id: The identifier string for the residue to renumber.
Modified: branches/mol_res_spin_module_rename/generic_fns/spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/mol_res_spin_module_rename/generic_fns/spin.py?rev=6058&r1=6057&r2=6058&view=diff
==============================================================================
--- branches/mol_res_spin_module_rename/generic_fns/spin.py (original)
+++ branches/mol_res_spin_module_rename/generic_fns/spin.py Sun May 4
11:37:06 2008
@@ -33,7 +33,7 @@
"""
-def copy(pipe_from=None, spin_from=None, pipe_to=None, spin_to=None):
+def copy_spin(pipe_from=None, spin_from=None, pipe_to=None, spin_to=None):
"""Copy the contents of the spin structure from one spin to a new spin.
For copying to be successful, the spin_from identification string must
match an existent spin.
@@ -103,7 +103,7 @@
res_to_cont.spin[-1].name = spin_name_to
-def create(spin_num=None, spin_name=None, res_id=None):
+def create_spin(spin_num=None, spin_name=None, res_id=None):
"""Function for adding a spin into the relax data store.
@param spin_num: The identification number of the new spin.
@@ -137,7 +137,7 @@
res_to_cont.spin.add_item(spin_num=spin_num, spin_name=spin_name)
-def delete(spin_id=None):
+def delete_spin(spin_id=None):
"""Function for deleting spins from the current data pipe.
@param spin_id: The molecule, residue, and spin identifier string.
@@ -173,7 +173,7 @@
res.spin.add_item()
-def display(spin_id=None):
+def display_spin(spin_id=None):
"""Function for displaying the information associated with the spin.
@param spin_id: The molecule and residue identifier string.
@@ -189,7 +189,7 @@
print "%-15s %-15s %-15s %-15s %-15s" % (mol_name, `res_num`,
res_name, `spin.num`, spin.name)
-def name(spin_id=None, name=None):
+def name_spin(spin_id=None, name=None):
"""Name the spins.
@param spin_id: The spin identification string.
@@ -203,7 +203,7 @@
spin.name = name
-def number(spin_id=None, number=None):
+def number_spin(spin_id=None, number=None):
"""Number the spins.
@param spin_id: The spin identification string.
r6058 - in /branches/mol_res_spin_module_rename/generic_fns: molecule.py residue.py spin.py