Author: bugman
Date: Thu Jan 15 13:42:44 2009
New Revision: 8468
URL: http://svn.gna.org/viewcvs/relax?rev=8468&view=rev
Log:
Redesign of the set up of the molecule container data structures.
The file info is now set by the pack_structs() base API method rather than
the MolContainer internal
object or the ScientificPython code.
Modified:
branches/multi_structure/generic_fns/structure/api_base.py
branches/multi_structure/generic_fns/structure/internal.py
branches/multi_structure/generic_fns/structure/scientific.py
Modified: branches/multi_structure/generic_fns/structure/api_base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_structure/generic_fns/structure/api_base.py?rev=8468&r1=8467&r2=8468&view=diff
==============================================================================
--- branches/multi_structure/generic_fns/structure/api_base.py (original)
+++ branches/multi_structure/generic_fns/structure/api_base.py Thu Jan 15
13:42:44 2009
@@ -276,7 +276,7 @@
return len(self.structural_data)
- def pack_structs(self, data_matrix, orig_model_num=None,
set_model_num=None, orig_mol_num=None, set_mol_name=None):
+ def pack_structs(self, data_matrix, orig_model_num=None,
set_model_num=None, orig_mol_num=None, set_mol_name=None, file_name=None,
file_path=None):
"""From the given structural data, expand the structural data data
structure.
@param data_matrix: A matrix of structural objects.
@@ -287,8 +287,13 @@
@type set_model_num: list of int
@keyword orig_mol_num: The original molecule numbers (for
storage).
@type orig_mol_num: list of int
- @keyword set_mol_name: The molecule names (for naming the
molecules).
- @type set_mol_name: list of str
+ @keyword mol_name: The molecule ID string.
+ @type mol_name: str
+ @keyword file_name: The name of the file from which the
molecular data has been
+ extracted.
+ @type file_name: None or str
+ @keyword file_path: The full path to the file specified by
'file_name'.
+ @type file_path: None or str
"""
# Test the number of models.
@@ -346,6 +351,14 @@
# Pack the structures.
model.mol.add_item(mol_name=set_mol_name[j],
mol_cont=data_matrix[i][j])
+
+ # Set the molecule name and store the structure file info.
+ model.mol[-1].mol_name = set_mol_name[j]
+ model.mol[-1].file_name = file_name
+ model.mol[-1].file_path = file_path
+ model.mol[-1].file_mol_num = orig_mol_num[j]
+ model.mol[-1].file_model = orig_model_num[j]
+
def target_mol_name(self, set=None, target=None, index=None,
mol_num=None, file=None):
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=8468&r1=8467&r2=8468&view=diff
==============================================================================
--- branches/multi_structure/generic_fns/structure/internal.py (original)
+++ branches/multi_structure/generic_fns/structure/internal.py Thu Jan 15
13:42:44 2009
@@ -416,7 +416,7 @@
mol = model.mol[mol_index]
# Skip non-matching molecules.
- if sel_obj and not sel_obj.contains_mol(mol.name):
+ if sel_obj and not sel_obj.contains_mol(mol.mol_name):
continue
# Loop over all atoms.
@@ -453,7 +453,7 @@
pos = array([mol.x[i], mol.y[i], mol.z[i]], float64)
# The molecule name.
- mol_name = mol.name
+ mol_name = mol.mol_name
# Build the tuple to be yielded.
atomic_tuple = ()
@@ -652,7 +652,7 @@
orig_mol_num.append(mol_num)
# Generate the molecule container.
- mol = MolContainer(mol_name=new_mol_name[-1],
file_name=file, file_path=path, file_model=model_num, file_mol_num=mol_num)
+ mol = MolContainer()
# Fill the molecular data object.
mol.fill_object_from_pdb(mol_records)
@@ -667,7 +667,7 @@
model_index = model_index + 1
# Create the structural data data structures.
- self.pack_structs(mol_conts, orig_model_num=orig_model_num,
set_model_num=set_model_num, orig_mol_num=orig_mol_num,
set_mol_name=new_mol_name)
+ self.pack_structs(mol_conts, orig_model_num=orig_model_num,
set_model_num=set_model_num, orig_mol_num=orig_mol_num,
set_mol_name=new_mol_name, file_name=file, file_path=path)
# Loading worked.
return True
@@ -1044,28 +1044,8 @@
"""
- def __init__(self, mol_name=None, file_name=None, file_path=None,
file_model=None, file_mol_num=None):
- """Initialise the molecular container.
-
- @keyword mol_name: The molecule ID string.
- @type mol_name: str
- @keyword file_name: The name of the file from which the
molecular data has been
- extracted.
- @type file_name: None or str
- @keyword file_path: The full path to the file specified by
'file_name'.
- @type file_path: None or str
- @keyword file_model: The model in the file from which this
data has been extracted.
- @type file_model: None or str
- @keyword file_mol_num: The molecule in the file from which this
data has been extracted.
- @type file_mol_num: None or str
- """
-
- # Set the molecule info.
- self.mol_name = mol_name
- self.file_name = file_name
- self.file_path = file_path
- self.file_model = file_model
- self.file_mol_num = file_mol_num
+ def __init__(self):
+ """Initialise the molecular container."""
# The atom num (array of int).
self.atom_num = []
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=8468&r1=8467&r2=8468&view=diff
==============================================================================
--- branches/multi_structure/generic_fns/structure/scientific.py (original)
+++ branches/multi_structure/generic_fns/structure/scientific.py Thu Jan 15
13:42:44 2009
@@ -193,7 +193,7 @@
res_index = res_index + 1
# Skip non-matching residues.
- if sel_obj and not sel_obj.contains_res(res_num, res_name,
mol.name):
+ if sel_obj and not sel_obj.contains_res(res_num, res_name,
mol.mol_name):
continue
# Yield the residue info.
@@ -207,7 +207,7 @@
res_index = res_index + 1
# Skip non-matching residues.
- if sel_obj and not sel_obj.contains_res(res.number,
res.name, mol.name):
+ if sel_obj and not sel_obj.contains_res(res.number,
res.name, mol.mol_name):
continue
# Yield the residue info.
@@ -262,7 +262,7 @@
mol = model.mol[mol_index]
# Skip non-matching molecules.
- if sel_obj and not sel_obj.contains_mol(mol.name):
+ if sel_obj and not sel_obj.contains_mol(mol.mol_name):
continue
# Loop over the residues.
@@ -277,7 +277,7 @@
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.name):
+ if sel_obj and not sel_obj.contains_spin(atom_num,
atom_name, res_num, res_name, mol.mol_name):
continue
# The atom position.
@@ -287,10 +287,10 @@
pos = atom.position.array
# The molecule name.
- mol_name = mol.name
+ mol_name = mol.mol_name
# Replace empty variables with None.
- if not mol.name:
+ if not mol.mol_name:
mol_name = None
if not res_num:
res_num = None
@@ -646,7 +646,7 @@
model_num = model_num + 1
# Create the structural data data structures.
- self.pack_structs(mol_conts, orig_model_num=orig_model_num,
set_model_num=set_model_num, orig_mol_num=range(1, len(mol_conts[0])+1),
set_mol_name=new_mol_name)
+ self.pack_structs(mol_conts, orig_model_num=orig_model_num,
set_model_num=set_model_num, orig_mol_num=range(1, len(mol_conts[0])+1),
set_mol_name=new_mol_name, file_name=file, file_path=path)
# Loading worked.
return True
r8468 - in /branches/multi_structure/generic_fns/structure: api_base.py internal.py scientific.py