Author: bugman
Date: Thu Nov 3 10:28:09 2011
New Revision: 14962
URL: http://svn.gna.org/viewcvs/relax?rev=14962&view=rev
Log:
All private methods have been renamed by replacing '__*()' with '_*()'.
Modified:
1.3/generic_fns/structure/internal.py
Modified: 1.3/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/internal.py?rev=14962&r1=14961&r2=14962&view=diff
==============================================================================
--- 1.3/generic_fns/structure/internal.py (original)
+++ 1.3/generic_fns/structure/internal.py Thu Nov 3 10:28:09 2011
@@ -68,7 +68,7 @@
self.pack_structs([[MolContainer()]], orig_model_num=[model],
orig_mol_num=[None], set_mol_name=[name])
- def __bonded_atom(self, attached_atom, index, mol):
+ def _bonded_atom(self, attached_atom, index, mol):
"""Find the atom named attached_atom directly bonded to the atom
located at the index.
@param attached_atom: The name of the attached atom to return.
@@ -152,7 +152,7 @@
return bonded_num, bonded_name, element, pos, attached_name, None
- def __find_bonded_atoms(self, index, mol, radius=1.2):
+ def _find_bonded_atoms(self, index, mol, radius=1.2):
"""Find all atoms within a sphere and say that they are attached to
the central atom.
The found atoms will be added to the 'bonded' data structure.
@@ -212,7 +212,7 @@
mol.atom_connect(index, connect_list[dist_list[i]])
- def __get_chemical_name(self, hetID):
+ def _get_chemical_name(self, hetID):
"""Return the chemical name corresponding to the given residue ID.
The following names are currently returned::
@@ -267,7 +267,7 @@
return 'Average vector'
- def __parse_models_pdb(self, file_path):
+ def _parse_models_pdb(self, file_path):
"""Generator function for looping over the models in the PDB file.
@param file_path: The full path of the PDB file.
@@ -321,7 +321,7 @@
yield model, records
- def __parse_models_xyz(self, file_path):
+ def _parse_models_xyz(self, file_path):
"""Generator function for looping over the models in the XYZ file.
@param file_path: The full path of the XYZ file.
@@ -376,7 +376,7 @@
yield records
- def __parse_mols(self, records):
+ def _parse_mols(self, records):
"""Generator function for looping over the molecules in the PDB
records of a model.
@param records: The list of PDB records for the model, or if no
models exist the entire
@@ -438,7 +438,7 @@
yield mol_num, mol_records
- def __validate_data_arrays(self, struct):
+ def _validate_data_arrays(self, struct):
"""Check the validity of the data arrays in the given structure
object.
@param struct: The structural object.
@@ -1568,7 +1568,7 @@
self.z = []
- def __atom_index(self, atom_num):
+ def _atom_index(self, atom_num):
"""Find the atom index corresponding to the given atom number.
@param atom_num: The atom number to find the index of.
@@ -1587,7 +1587,7 @@
warn(RelaxWarning("The atom number " + repr(atom_num) + " from the
CONECT record cannot be found within the ATOM and HETATM records."))
- def __det_pdb_element(self, atom_name):
+ def _det_pdb_element(self, atom_name):
"""Try to determine the element from the PDB atom name.
@param atom_name: The PDB atom name.
@@ -1627,7 +1627,7 @@
warn(RelaxWarning("Cannot determine the element associated with atom
'%s'." % atom_name))
- def __parse_pdb_record(self, record):
+ def _parse_pdb_record(self, record):
"""Parse the PDB record string and return an array of the
corresponding atomic information.
The format of the ATOM and HETATM records is::
@@ -1782,7 +1782,7 @@
return fields
- def __parse_xyz_record(self, record):
+ def _parse_xyz_record(self, record):
"""Parse the XYZ record string and return an array of the
corresponding atomic information.
The format of the XYZ records is::
r14962 - /1.3/generic_fns/structure/internal.py