Author: bugman
Date: Thu Sep 25 17:52:15 2008
New Revision: 7302
URL: http://svn.gna.org/viewcvs/relax?rev=7302&view=rev
Log:
Added support to the internal PDB structural object for determining connected
atoms.
This is for when no CONECT records exist. The method __find_bonded_atom()
has been renamed to
__bonded_atom(), and the new method __find_bonded_atoms() has been written.
This new method
connects all atoms located a certain distance from each other.
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=7302&r1=7301&r2=7302&view=diff
==============================================================================
--- 1.3/generic_fns/structure/internal.py (original)
+++ 1.3/generic_fns/structure/internal.py Thu Sep 25 17:52:15 2008
@@ -24,7 +24,7 @@
"""Module containing the internal relax structural object."""
# Python module imports.
-from numpy import array, float64, zeros
+from numpy import array, float64, linalg, zeros
from re import search
from string import split, strip
from warnings import warn
@@ -74,41 +74,7 @@
warn(RelaxWarning("The atom number " + `atom_num` + " from the
CONECT record cannot be found within the ATOM and HETATM records."))
- def __fill_object_from_pdb(self, records, struct_index):
- """Method for generating a complete Structure_container object from
the given PDB records.
-
- @param records: A list of structural PDB records.
- @type records: list of str
- @param struct_index: The index of the structural container to add
the data to.
- @type struct_index: int
- """
-
- # Loop over the records.
- for record in records:
- # Parse the record.
- record = self.__parse_pdb_record(record)
-
- # Nothing to do.
- if not record:
- continue
-
- # Add the atom.
- if record[0] == 'ATOM' or record[0] == 'HETATM':
- self.atom_add(pdb_record=record[0], atom_num=record[1],
atom_name=record[2], res_name=record[4], chain_id=record[5],
res_num=record[6], pos=[record[8], record[9], record[10]],
segment_id=record[13], element=record[14], struct_index=struct_index)
-
- # Connect atoms.
- if record[0] == 'CONECT':
- # Loop over the atoms of the record.
- for i in xrange(len(record)-2):
- # Skip if there is no record.
- if record[i+2] == None:
- continue
-
- # 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):
+ def __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.
@@ -126,6 +92,10 @@
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)
+
# Loop over the bonded atoms.
matching_list = []
for bonded_index in struct.bonded[index]:
@@ -157,6 +127,71 @@
# Return the information.
return bonded_num, bonded_name, element, pos, attached_name, None
+
+
+ def __fill_object_from_pdb(self, records, struct_index):
+ """Method for generating a complete Structure_container object from
the given PDB records.
+
+ @param records: A list of structural PDB records.
+ @type records: list of str
+ @param struct_index: The index of the structural container to add
the data to.
+ @type struct_index: int
+ """
+
+ # Loop over the records.
+ for record in records:
+ # Parse the record.
+ record = self.__parse_pdb_record(record)
+
+ # Nothing to do.
+ if not record:
+ continue
+
+ # Add the atom.
+ if record[0] == 'ATOM' or record[0] == 'HETATM':
+ self.atom_add(pdb_record=record[0], atom_num=record[1],
atom_name=record[2], res_name=record[4], chain_id=record[5],
res_num=record[6], pos=[record[8], record[9], record[10]],
segment_id=record[13], element=record[14], struct_index=struct_index)
+
+ # Connect atoms.
+ if record[0] == 'CONECT':
+ # Loop over the atoms of the record.
+ for i in xrange(len(record)-2):
+ # Skip if there is no record.
+ if record[i+2] == None:
+ continue
+
+ # 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_atoms(self, index, struct_index, 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.
+
+
+ @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]
+
+ # Central atom info.
+ centre = array([struct.x[index], struct.y[index], struct.z[index]],
float64)
+
+ # Atom loop.
+ for i in xrange(len(struct.atom_num)):
+ # The atom's position.
+ pos = array([struct.x[i], struct.y[i], struct.z[i]], float64)
+
+ # The distance from the centre.
+ dist = linalg.norm(centre-pos)
+
+ # Connect the atoms if within the radius value.
+ if dist < radius:
+ self.atom_connect(index, i)
def __get_chemical_name(self, hetID):
@@ -698,8 +733,8 @@
# Found the atom.
if atom_found:
- # Find the atom bonded to this
structure/molecule/residue/atom.
- bonded_num, bonded_name, element, pos, attached_name,
warnings = self.__find_bonded_atom(attached_atom, index, i)
+ # Get the atom bonded to this
structure/molecule/residue/atom.
+ bonded_num, bonded_name, element, pos, attached_name,
warnings = self.__bonded_atom(attached_atom, index, i)
# No bonded atom.
if (bonded_num, bonded_name, element) == (None, None, None):
r7302 - /1.3/generic_fns/structure/internal.py