Author: bugman
Date: Mon Jan 12 14:21:18 2009
New Revision: 8411
URL: http://svn.gna.org/viewcvs/relax?rev=8411&view=rev
Log:
Shifted __atom_index() from the Internal class to the MolContainer.
Modified:
branches/multi_structure/generic_fns/structure/internal.py
Modified: branches/multi_structure/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_structure/generic_fns/structure/internal.py?rev=8411&r1=8410&r2=8411&view=diff
==============================================================================
--- branches/multi_structure/generic_fns/structure/internal.py (original)
+++ branches/multi_structure/generic_fns/structure/internal.py Mon Jan 12
14:21:18 2009
@@ -109,34 +109,6 @@
self.structural_data[struct_index] = str
else:
self.structural_data.append(str)
-
-
- def __atom_index(self, atom_num, struct_index):
- """Find the atom index corresponding to the given atom number.
-
- @param atom_num: The atom number to find the index of.
- @type atom_num: int
- @param struct_index: The index of the structural container to
extract the atom index
- from.
- @type struct_index: int
- @return: The atom index corresponding to the atom.
- @rtype: int
- """
-
- # Loop over the structures.
- for i in xrange(self.num):
- # Skip non-matching structures.
- if struct_index != None and struct_index != i:
- continue
-
- # Loop over the atoms.
- for j in xrange(len(self.structural_data[i].atom_num)):
- # Return the index.
- if self.structural_data[i].atom_num[j] == atom_num:
- return j
-
- # Should not be here, the PDB connect records are incorrect.
- warn(RelaxWarning("The atom number " + `atom_num` + " from the CONECT
record cannot be found within the ATOM and HETATM records."))
def __bonded_atom(self, attached_atom, index, struct_index):
@@ -1181,6 +1153,34 @@
self.z = []
+ def __atom_index(self, atom_num, struct_index):
+ """Find the atom index corresponding to the given atom number.
+
+ @param atom_num: The atom number to find the index of.
+ @type atom_num: int
+ @param struct_index: The index of the structural container to
extract the atom index
+ from.
+ @type struct_index: int
+ @return: The atom index corresponding to the atom.
+ @rtype: int
+ """
+
+ # Loop over the structures.
+ for i in xrange(self.num):
+ # Skip non-matching structures.
+ if struct_index != None and struct_index != i:
+ continue
+
+ # Loop over the atoms.
+ for j in xrange(len(self.structural_data[i].atom_num)):
+ # Return the index.
+ if self.structural_data[i].atom_num[j] == atom_num:
+ return j
+
+ # Should not be here, the PDB connect records are incorrect.
+ warn(RelaxWarning("The atom number " + `atom_num` + " from the CONECT
record cannot be found within the ATOM and HETATM records."))
+
+
def __parse_pdb_record(self, record):
"""Parse the PDB record string and return an array of the
corresponding atomic information.
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