Author: bugman
Date: Fri Jan 9 17:55:39 2009
New Revision: 8350
URL: http://svn.gna.org/viewcvs/relax?rev=8350&view=rev
Log:
Many fixes and much new code for the new structural container design.
Modified:
branches/multi_structure/generic_fns/structure/internal.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=8350&r1=8349&r2=8350&view=diff
==============================================================================
--- branches/multi_structure/generic_fns/structure/internal.py (original)
+++ branches/multi_structure/generic_fns/structure/internal.py Fri Jan 9
17:55:39 2009
@@ -194,13 +194,13 @@
return bonded_num, bonded_name, element, pos, attached_name, None
- def __fill_object_from_pdb(self, records, struct_index):
+ def __fill_object_from_pdb(self, records, struct_cont):
"""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
+ @param struct_cont: The structural data container.
+ @type struct_cont: StructContainer instance
"""
# Loop over the records.
@@ -366,6 +366,48 @@
# If records is not empty then there are no models, so yield the lot.
if len(records):
yield model, records
+
+
+ def __parse_mols(self, records):
+ """Generator function for looping over the molecules in the PDB
records of a model.
+
+ @param records: The list of PDB records for the model, or if no
models exist the entire
+ PDB file.
+ @type records: list of str
+ @return: The molecule number and all the records for that
molecule.
+ @rtype: tuple of int and list of str
+ """
+
+ # Check for empty records.
+ if records == []:
+ raise RelaxError, "There are no PDB records for this model."
+
+ # Init.
+ mol_num = 1
+ mol_records = []
+
+ # Loop over the data.
+ for record in records:
+ # A molecule termination record.
+ if search('^TER', record):
+ # Yield the info.
+ yield mol_num, mol_records
+
+ # Reset the records.
+ mol_records = []
+
+ # Increment the molecule number.
+ mol_num = mol_num + 1
+
+ # Skip the rest of this loop.
+ continue
+
+ # Append the line as a record of the molecule.
+ mol_records.append(record)
+
+ # If records is not empty then there is only a single molecule, so
yield the lot.
+ if len(mol_records):
+ yield mol_num, mol_records
def __parse_pdb_record(self, record):
@@ -521,50 +563,6 @@
# Return the atomic info.
return fields
-
-
- def __parse_structs(self, records):
- """Generator function for looping over the structures in the PDB
records of a model.
-
- @param records: The list of PDB records for the model, or if no
models exist the entire
- PDB file.
- @type records: list of str
- @return: The structure number and all the records for
that structure.
- @rtype: tuple of int and list of str
- """
-
- # Check for empty records.
- if records == []:
- raise RelaxError, "There are no PDB records for this model."
-
- print records
-
- # Init.
- struct_num = 1
- struct_records = []
-
- # Loop over the data.
- for record in records:
- # A structure termination record.
- if search('^TER', record):
- # Yield the info.
- yield struct_num, struct_records
-
- # Reset the records.
- struct_records = []
-
- # Increment the structure number.
- struct_num = struct_num + 1
-
- # Skip the rest of this loop.
- continue
-
- # Append the line as a record of the structure.
- struct_records.append(record)
-
- # If records is not empty then there is only a single structure, so
yield the lot.
- if len(struct_records):
- yield struct_num, struct_records
def __validate_data_arrays(self, struct):
@@ -968,6 +966,7 @@
# print "Loading all structures from the PDB file."
# Loop over all models in the PDB file.
+ model_index = 0
for model_num, model_records in self.__parse_models(file_path):
# Only load the desired model.
if read_model and model_num not in read_model:
@@ -975,15 +974,46 @@
# Print out.
if model_num != None:
- print "Loading model: " + `model_num`
-
- # Loop over the structures of the model.
- for struct_num, struct_records in
self.__parse_structs(model_records):
- # Add an empty structure.
- self.add_struct(name=name, model=model_num, file=file,
path=path, str=Structure_container(), struct_index=struct_index)
-
- # Fill the structural data object.
- self.__fill_object_from_pdb(struct_records,
struct_index=len(self.structural_data)-1)
+ print "%-25s %-10s" % ("Loading from model: ", `model_num`)
+
+ # Set the target model number.
+ if set_model_num:
+ new_model_num = set_model_num[model_index]
+ else:
+ new_model_num = model_num
+ print "%-25s %-10s\n" % ("Loading to model: ", `new_model_num`)
+
+ # Add a new model.
+ self.structural_data.add_item(new_model_num)
+
+ # Loop over the molecules of the model.
+ mol_index = 0
+ for mol_num, mol_records in self.__parse_mols(model_records):
+ # Set the target molecule name.
+ if set_mol_name:
+ new_mol_name = set_mol_name[mol_index]
+ else:
+ # Set the name to the file name plus the structure
number.
+ new_mol_name = file + '_mol' + `mol_num`
+
+ # Print out.
+ print "%-25s %-10s" % ("Loading from molecule: ", `mol_num`)
+ print "%-25s %-10s" % ("Structure ID string: ",
`new_mol_name`)
+
+ # Generate the molecule container.
+ mol = Molecule_container(mol_name=new_mol_name,
file_name=file, file_path=path, file_model=model_num, file_mol_num=mol_num)
+
+ # Add the molecule to the last model.
+ self.structural_data[-1].mol.add_item(mol_name=mol_name,
mol_cont=mol)
+
+ # Fill the molecular data object.
+ self.__fill_object_from_pdb(mol_records,
model_index=len(self.structural_data),
mol_index=len(self.structural_data[-1].mol))
+
+ # Increment the molecule index.
+ mol_index = mol_index + 1
+
+ # Increment the model index.
+ model_index = model_index + 1
# Loading worked.
return True
@@ -1336,8 +1366,8 @@
file.write("END\n")
-class Structure_container:
- """The container for the structural information.
+class Molecule_container:
+ """The container for the molecular information.
The structural data object for this class is a container possessing a
number of different arrays
corresponding to different structural information. These objects
include:
@@ -1360,11 +1390,28 @@
"""
- def __init__(self):
- """Initialise all the arrays."""
-
- # The model.
- self.model = None
+ 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
# The atom num (array of int).
self.atom_num = []
r8350 - /branches/multi_structure/generic_fns/structure/internal.py