Author: bugman
Date: Tue Jul 8 01:41:48 2008
New Revision: 6819
URL: http://svn.gna.org/viewcvs/relax?rev=6819&view=rev
Log:
Modified the __find_bonded_atom() and bond_vectors() methods to return more
data.
This additional data is the name of the attached atom and any warnings when
trying to find the
attached atom.
Modified:
1.3/generic_fns/structure/internal.py
1.3/generic_fns/structure/main.py
Modified: 1.3/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/internal.py?rev=6819&r1=6818&r2=6819&view=diff
==============================================================================
--- 1.3/generic_fns/structure/internal.py (original)
+++ 1.3/generic_fns/structure/internal.py Tue Jul 8 01:41:48 2008
@@ -140,12 +140,12 @@
for i in matching_list:
matching_names.append(struct.atom_name[i])
- # Return nothing.
- return None, None, None, None
+ # Return nothing but a warning.
+ return None, None, None, None, 'More than one attached atom
found: ' + `matching_names`
# No attached atoms.
if num_attached == 0:
- return None, None, None, None
+ return None, None, None, None, "No attached atom could be found."
# The bonded atom info.
bonded_num = struct.atom_num[bonded_index]
@@ -154,7 +154,7 @@
pos = [struct.x[bonded_index], struct.y[bonded_index],
struct.z[bonded_index]]
# Return the information.
- return bonded_num, bonded_name, element, pos
+ return bonded_num, bonded_name, element, pos, None
def __get_chemical_name(self, hetID):
@@ -635,21 +635,26 @@
yield atomic_tuple
- def bond_vectors(self, atom_id=None, attached_atom=None,
struct_index=None):
+ def bond_vectors(self, atom_id=None, attached_atom=None,
struct_index=None, return_name=False, return_warnings=False):
"""Find the bond vector between the atoms of 'attached_atom' and
'atom_id'.
- @keyword atom_id: The molecule, residue, and atom identifier
string. This must
- correspond to a single atom in the system.
- @type atom_id: str
- @keyword attached_atom: The name of the bonded atom.
- @type attached_atom: str
- @keyword struct_index: The index of the structure to return the
vectors from. If not
- supplied and multiple structures/models
exist, then vectors from all
- structures will be returned.
- @type struct_index: None or int
- @type struct_index: None or int.
- @return: The list of bond vectors for each structure.
- @rtype: list of numpy arrays
+ @keyword atom_id: The molecule, residue, and atom
identifier string. This must
+ correspond to a single atom in the
system.
+ @type atom_id: str
+ @keyword attached_atom: The name of the bonded atom.
+ @type attached_atom: str
+ @keyword struct_index: The index of the structure to return the
vectors from. If not
+ supplied and multiple structures/models
exist, then vectors from
+ all structures will be returned.
+ @type struct_index: None or int
+ @keyword return_name: A flag which if True will cause the name
of the attached atom to
+ be returned together with the bond
vectors.
+ @type return_name: bool
+ @keyword return_warnings: A flag which if True will cause warning
messages to be returned.
+ @type return_warnings: bool
+ @return: The list of bond vectors for each
structure.
+ @rtype: list of numpy arrays (or a tuple if
return_name or
+ return_warnings are set)
"""
# Generate the selection object.
@@ -687,7 +692,7 @@
# Found the atom.
if atom_found:
# Find the atom bonded to this
structure/molecule/residue/atom.
- bonded_num, bonded_name, element, pos =
self.__find_bonded_atom(attached_atom, index, i)
+ bonded_num, bonded_name, element, pos, warnings =
self.__find_bonded_atom(attached_atom, index, i)
# No bonded atom.
if (bonded_num, bonded_name, element) == (None, None, None):
@@ -699,8 +704,15 @@
# Append the vector to the vectors array.
vectors.append(vector)
- # Return the bond vectors.
- return vectors
+ # Build the tuple to be yielded.
+ data = (vectors,)
+ if return_name:
+ data = data + (struct.atom_name[index],)
+ if return_warnings:
+ data = data + (warnings,)
+
+ # Return the data.
+ return data
def load_pdb(self, file_path, model=None, verbosity=False):
Modified: 1.3/generic_fns/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/main.py?rev=6819&r1=6818&r2=6819&view=diff
==============================================================================
--- 1.3/generic_fns/structure/main.py (original)
+++ 1.3/generic_fns/structure/main.py Tue Jul 8 01:41:48 2008
@@ -304,7 +304,7 @@
continue
# Get the bond info.
- bond_vectors = cdp.structure.bond_vectors(atom_id=id,
attached_atom=attached, struct_index=struct_index)
+ bond_vectors, attached_name, warnings =
cdp.structure.bond_vectors(atom_id=id, attached_atom=attached,
struct_index=struct_index, return_name=True, return_warnings=True)
# No attached atom.
if not bond_vectors:
r6819 - in /1.3/generic_fns/structure: internal.py main.py