Author: bugman
Date: Tue Jan 3 16:16:56 2012
New Revision: 15129
URL: http://svn.gna.org/viewcvs/relax?rev=15129&view=rev
Log:
Updated the scientific PDB reader atom_loop() method to match the changes to
the API.
Modified:
branches/frame_order_testing/generic_fns/structure/scientific.py
Modified: branches/frame_order_testing/generic_fns/structure/scientific.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/structure/scientific.py?rev=15129&r1=15128&r2=15129&view=diff
==============================================================================
--- branches/frame_order_testing/generic_fns/structure/scientific.py
(original)
+++ branches/frame_order_testing/generic_fns/structure/scientific.py Tue Jan
3 16:16:56 2012
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2003-2010 Edward d'Auvergne
#
+# Copyright (C) 2003-2012 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -190,78 +190,110 @@
element name (str), and atomic position
(array of len 3).
"""
+ # Check that the structure is loaded.
+ if not len(self.structural_data):
+ raise RelaxNoPdbError
+
# Generate the selection object.
- sel_obj = Selection(atom_id)
-
- # Model loop.
- for model in self.model_loop():
- # Loop over the molecules.
- for mol_index in range(len(model.mol)):
- mol = model.mol[mol_index]
-
- # Skip non-matching molecules.
- if sel_obj and not sel_obj.contains_mol(mol.mol_name):
- continue
-
- # Loop over the residues.
- for res, res_num, res_name, res_index in
self.__residue_loop(mol, sel_obj):
- # Loop over the atoms of the residue.
- atom_index = -1
- for atom in res:
- # Atom number, name, index, and element type.
- atom_num = atom.properties['serial_number']
- atom_name = atom.name
- element = atom.properties['element']
- atom_index = atom_index + 1
-
- # Skip non-matching atoms.
- if sel_obj and not sel_obj.contains_spin(atom_num,
atom_name, res_num, res_name, mol.mol_name):
- continue
-
- # The atom position.
+ sel_obj = None
+ if atom_id:
+ sel_obj = Selection(atom_id)
+
+ # Obtain all data from the first model (except the position data).
+ model = self.structural_data[0]
+
+ # Loop over the molecules.
+ for mol_index in range(len(model.mol)):
+ mol = model.mol[mol_index]
+
+ # Skip non-matching molecules.
+ if sel_obj and not sel_obj.contains_mol(mol.mol_name):
+ continue
+
+ # Loop over the residues.
+ for res, res_num, res_name, res_index in
self.__residue_loop(mol, sel_obj):
+ # Loop over the atoms of the residue.
+ atom_index = -1
+ for atom in res:
+ # Atom number, name, index, and element type.
+ atom_num = atom.properties['serial_number']
+ atom_name = atom.name
+ element = atom.properties['element']
+ atom_index = atom_index + 1
+
+ # Skip non-matching atoms.
+ if sel_obj and not sel_obj.contains_spin(atom_num,
atom_name, res_num, res_name, mol.mol_name):
+ continue
+
+ # The atom position.
+ if pos_flag:
+ # Average the position.
if ave:
pos = self.__ave_atom_pos(mol_index, res_index,
atom_index)
+
+ # All positions.
else:
- pos = atom.position.array
-
- # The molecule name.
- mol_name = mol.mol_name
-
- # Replace empty variables with None.
- if not mol.mol_name:
- mol_name = None
- if not res_num:
- res_num = None
- if not res_name:
- res_name = None
- if not atom_num:
- atom_num = None
- if not atom_name:
- atom_name = None
-
- # Build the tuple to be yielded.
- atomic_tuple = ()
- if mol_name_flag:
- atomic_tuple = atomic_tuple + (mol_name,)
- if res_num_flag:
- atomic_tuple = atomic_tuple + (res_num,)
- if res_name_flag:
- atomic_tuple = atomic_tuple + (res_name,)
- if atom_num_flag:
- atomic_tuple = atomic_tuple + (atom_num,)
- if atom_name_flag:
- atomic_tuple = atomic_tuple + (atom_name,)
- if element_flag:
- atomic_tuple = atomic_tuple + (element,)
- if pos_flag:
- atomic_tuple = atomic_tuple + (pos,)
-
- # Yield the information.
- yield atomic_tuple
-
- # Break out of the loop if the ave flag is set, as data from
only one model is used.
- if ave:
- break
+ # Initialise.
+ pos = []
+
+ # Loop over the models.
+ for j in range(len(self.structural_data)):
+ # A single model.
+ if model_num != None and
self.structural_data[j].num != model_num:
+ continue
+
+ # Alias.
+ mol2 = self.structural_data[j].mol[mol_index]
+
+ # The residue.
+ if mol2.mol_type != 'other':
+ res = mol2.data.residues[res_index]
+ else:
+ res = mol2.data[res_index]
+
+ # The atom.
+ atom = res[atom_index]
+
+ # Append the position.
+ pos.append(atom.position.array)
+
+ # Convert.
+ pos = array(pos, float64)
+
+ # The molecule name.
+ mol_name = mol.mol_name
+
+ # Replace empty variables with None.
+ if not mol.mol_name:
+ mol_name = None
+ if not res_num:
+ res_num = None
+ if not res_name:
+ res_name = None
+ if not atom_num:
+ atom_num = None
+ if not atom_name:
+ atom_name = None
+
+ # Build the tuple to be yielded.
+ atomic_tuple = ()
+ if mol_name_flag:
+ atomic_tuple = atomic_tuple + (mol_name,)
+ if res_num_flag:
+ atomic_tuple = atomic_tuple + (res_num,)
+ if res_name_flag:
+ atomic_tuple = atomic_tuple + (res_name,)
+ if atom_num_flag:
+ atomic_tuple = atomic_tuple + (atom_num,)
+ if atom_name_flag:
+ atomic_tuple = atomic_tuple + (atom_name,)
+ if element_flag:
+ atomic_tuple = atomic_tuple + (element,)
+ if pos_flag:
+ atomic_tuple = atomic_tuple + (pos,)
+
+ # Yield the information.
+ yield atomic_tuple
def attached_atom(self, atom_id=None, attached_atom=None, model=None):
@@ -348,9 +380,9 @@
pos = zeros(3, float64)
# Loop over the models.
- for model in self.model_loop():
+ for j in range(len(self.structural_data)):
# The exact molecule.
- mol = model.mol[mol_index]
+ mol = self.structural_data[j].mol[mol_index]
# The residue.
if mol.mol_type != 'other':
r15129 - /branches/frame_order_testing/generic_fns/structure/scientific.py