Author: bugman
Date: Tue Jul 8 01:15:32 2008
New Revision: 6818
URL: http://svn.gna.org/viewcvs/relax?rev=6818&view=rev
Log:
Added 2 new methods to the internal relax structural object.
These are __find_bonded_atom() and bond_vectors().
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=6818&r1=6817&r2=6818&view=diff
==============================================================================
--- 1.3/generic_fns/structure/internal.py (original)
+++ 1.3/generic_fns/structure/internal.py Tue Jul 8 01:15:32 2008
@@ -32,6 +32,7 @@
# relax module imports.
from api_base import Base_struct_API
from data import Relax_data_store; ds = Relax_data_store()
+from generic_fns import relax_re
from generic_fns.mol_res_spin import Selection
from relax_errors import RelaxError
from relax_io import open_read_file
@@ -105,6 +106,55 @@
# Make the connection.
self.atom_connect(index1=self.__atom_index(record[1],
struct_index), index2=self.__atom_index(record[i+2], struct_index),
struct_index=struct_index)
+
+
+ def __find_bonded_atom(self, attached_atom, index, struct_index):
+ """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
+ @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)
+ """
+
+ # Init.
+ bonded_found = False
+ struct = self.structural_data[struct_index]
+
+ # 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):
+ matching_list.append(bonded_index)
+ num_attached = len(matching_list)
+
+ # Problem.
+ if num_attached > 1:
+ # Get the atom names.
+ matching_names = []
+ for i in matching_list:
+ matching_names.append(struct.atom_name[i])
+
+ # Return nothing.
+ return None, None, None, None
+
+ # No attached atoms.
+ if num_attached == 0:
+ return None, None, None, None
+
+ # The bonded atom info.
+ bonded_num = struct.atom_num[bonded_index]
+ bonded_name = struct.atom_name[bonded_index]
+ element = struct.element[bonded_index]
+ pos = [struct.x[bonded_index], struct.y[bonded_index],
struct.z[bonded_index]]
+
+ # Return the information.
+ return bonded_num, bonded_name, element, pos
def __get_chemical_name(self, hetID):
@@ -585,6 +635,74 @@
yield atomic_tuple
+ def bond_vectors(self, atom_id=None, attached_atom=None,
struct_index=None):
+ """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
+ """
+
+ # Generate the selection object.
+ sel_obj = Selection(atom_id)
+
+ # Initialise some objects.
+ vectors = []
+
+ # Loop over the structures.
+ for i in xrange(len(self.structural_data)):
+ # Single structure.
+ if struct_index and struct_index != i:
+ continue
+
+ # Alias.
+ struct = self.structural_data[i]
+
+ # Init.
+ atom_found = False
+
+ # Loop over all atoms.
+ for j in xrange(len(struct.atom_name)):
+ # Skip non-matching atoms.
+ if sel_obj and not sel_obj.contains_spin(struct.atom_num[j],
struct.atom_name[j], struct.res_num[j], struct.res_name[j]):
+ continue
+
+ # More than one matching atom!
+ if atom_found:
+ raise RelaxError, "The atom_id argument " + `atom_id` +
" must correspond to a single atom."
+
+ # The atom has been found, so store some info.
+ atom_found = True
+ index = j
+
+ # 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)
+
+ # No bonded atom.
+ if (bonded_num, bonded_name, element) == (None, None, None):
+ continue
+
+ # The bond vector.
+ vector = array(pos, float64) - array([struct.x[index],
struct.y[index], struct.z[index]], float64)
+
+ # Append the vector to the vectors array.
+ vectors.append(vector)
+
+ # Return the bond vectors.
+ return vectors
+
+
def load_pdb(self, file_path, model=None, verbosity=False):
"""Method for loading structures from a PDB file.
r6818 - /1.3/generic_fns/structure/internal.py