Author: bugman
Date: Mon Jan 19 11:36:33 2009
New Revision: 8512
URL: http://svn.gna.org/viewcvs/relax?rev=8512&view=rev
Log:
Removed all dependence on the deleted __molecule_loop() method.
Modified:
branches/multi_structure/generic_fns/structure/internal.py
branches/multi_structure/generic_fns/structure/scientific.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=8512&r1=8511&r2=8512&view=diff
==============================================================================
--- branches/multi_structure/generic_fns/structure/internal.py (original)
+++ branches/multi_structure/generic_fns/structure/internal.py Mon Jan 19
11:36:33 2009
@@ -145,7 +145,7 @@
# Connect the atoms if within the radius value.
if dist < radius:
- self.atom_connect(index, i)
+ mol.atom_connect(index, i)
def __get_chemical_name(self, hetID):
Modified: branches/multi_structure/generic_fns/structure/scientific.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_structure/generic_fns/structure/scientific.py?rev=8512&r1=8511&r2=8512&view=diff
==============================================================================
--- branches/multi_structure/generic_fns/structure/scientific.py (original)
+++ branches/multi_structure/generic_fns/structure/scientific.py Mon Jan 19
11:36:33 2009
@@ -304,18 +304,18 @@
pos_array = []
# Loop over the models.
- for struct in self.structural_data:
+ for model in self.structural_data:
# Init.
atom_found = False
# Skip non-matching models.
- if model != None and model != struct.model:
+ if model != None and model != model.num:
continue
# Loop over each individual molecule.
- for mol, mol_name, mol_type in self.__molecule_loop(struct,
sel_obj):
+ for mol in model.mol:
# Loop over the residues of the protein in the PDB file.
- for res, res_num, res_name in self.__residue_loop(mol,
mol_type, sel_obj):
+ for res, res_num, res_name in self.__residue_loop(mol,
mol.mol_type, sel_obj):
# Loop over the atoms of the residue.
for atom in res:
# Atom number, name, and position.
@@ -323,7 +323,7 @@
atom_name = atom.name
# Skip non-matching atoms.
- if sel_obj and not sel_obj.contains_spin(atom_num,
atom_name, res_num, res_name, mol_name):
+ if sel_obj and not sel_obj.contains_spin(atom_num,
atom_name, res_num, res_name, mol.mol_name):
continue
# More than one matching atom!
@@ -334,7 +334,7 @@
atom_found = True
atom_num_match = atom_num
atom_name_match = atom_name
- mol_type_match = mol_type
+ mol_type_match = mol.mol_type
res_match = res
# Found the atom.
@@ -426,9 +426,9 @@
atom_found = False
# Loop over each individual molecule.
- for mol, mol_name, mol_type in self.__molecule_loop(model,
sel_obj):
+ for mol in model.mol:
# Loop over the residues of the protein in the PDB file.
- for res, res_num, res_name in self.__residue_loop(mol,
mol_name, mol_type, sel_obj):
+ for res, res_num, res_name in self.__residue_loop(mol,
mol.mol_name, mol.mol_type, sel_obj):
# Loop over the atoms of the residue.
for atom in res:
# Atom number, name, and position.
@@ -436,7 +436,7 @@
atom_name = atom.name
# Skip non-matching atoms.
- if sel_obj and not sel_obj.contains_spin(atom_num,
atom_name, res_num, res_name, mol_name):
+ if sel_obj and not sel_obj.contains_spin(atom_num,
atom_name, res_num, res_name, mol.mol_name):
continue
# More than one matching atom!
@@ -446,7 +446,7 @@
# The atom has been found, so store some info.
atom_found = True
pos_match = atom.position.array
- mol_type_match = mol_type
+ mol_type_match = mol.mol_type
res_match = res
# Found the atom.
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