Author: bugman
Date: Mon Jan 19 11:24:12 2009
New Revision: 8510
URL: http://svn.gna.org/viewcvs/relax?rev=8510&view=rev
Log:
Modified __bonded_atom() and __find_bonded_atoms() for the new structural
object design.
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=8510&r1=8509&r2=8510&view=diff
==============================================================================
--- branches/multi_structure/generic_fns/structure/internal.py (original)
+++ branches/multi_structure/generic_fns/structure/internal.py Mon Jan 19
11:24:12 2009
@@ -66,15 +66,15 @@
self.pack_structs([[MolContainer()]], orig_model_num=[model],
set_mol_name=[name])
- def __bonded_atom(self, attached_atom, index, struct_index):
+ 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.
@type attached_atom: str
@param index: The index of the atom which the attached atom
is attached to.
@type index: int
- @param struct_index: The index of the structure.
- @type struct_index: int
+ @param mol: The molecule container.
+ @type mol: MolContainer instance
@return: A tuple of information about the bonded atom.
@rtype: tuple consisting of the atom number (int),
atom name (str), element
name (str), and atomic position (Numeric array
of len 3)
@@ -82,16 +82,15 @@
# Init.
bonded_found = False
- struct = self.structural_data[struct_index]
# No bonded atoms, so go find everything within 1.2 Angstroms and say
they are bonded.
- if not struct.bonded[index]:
- self.__find_bonded_atoms(index, struct_index)
+ if not mol.bonded[index]:
+ self.__find_bonded_atoms(index, mol)
# Loop over the bonded atoms.
matching_list = []
- for bonded_index in struct.bonded[index]:
- if relax_re.search(struct.atom_name[bonded_index], attached_atom):
+ for bonded_index in mol.bonded[index]:
+ if relax_re.search(mol.atom_name[bonded_index], attached_atom):
matching_list.append(bonded_index)
num_attached = len(matching_list)
@@ -100,7 +99,7 @@
# Get the atom names.
matching_names = []
for i in matching_list:
- matching_names.append(struct.atom_name[i])
+ matching_names.append(mol.atom_name[i])
# Return nothing but a warning.
return None, None, None, None, None, 'More than one attached atom
found: ' + `matching_names`
@@ -111,17 +110,17 @@
# The bonded atom info.
index = matching_list[0]
- bonded_num = struct.atom_num[index]
- bonded_name = struct.atom_name[index]
- element = struct.element[index]
- pos = [struct.x[index], struct.y[index], struct.z[index]]
- attached_name = struct.atom_name[index]
+ bonded_num = mol.atom_num[index]
+ bonded_name = mol.atom_name[index]
+ element = mol.element[index]
+ pos = [mol.x[index], mol.y[index], mol.z[index]]
+ attached_name = mol.atom_name[index]
# Return the information.
return bonded_num, bonded_name, element, pos, attached_name, None
- def __find_bonded_atoms(self, index, struct_index, 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.
@@ -129,20 +128,17 @@
@param index: The index of the central atom.
@type index: int
- @param struct_index: The index of the structure.
- @type struct_index: int
- """
-
- # Init.
- struct = self.structural_data[struct_index]
+ @param mol: The molecule container.
+ @type mol: MolContainer instance
+ """
# Central atom info.
- centre = array([struct.x[index], struct.y[index], struct.z[index]],
float64)
+ centre = array([mol.x[index], mol.y[index], mol.z[index]], float64)
# Atom loop.
- for i in xrange(len(struct.atom_num)):
+ for i in xrange(len(mol.atom_num)):
# The atom's position.
- pos = array([struct.x[i], struct.y[i], struct.z[i]], float64)
+ pos = array([mol.x[i], mol.y[i], mol.z[i]], float64)
# The distance from the centre.
dist = linalg.norm(centre-pos)
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