Author: bugman
Date: Fri Jan 9 10:23:51 2009
New Revision: 8348
URL: http://svn.gna.org/viewcvs/relax?rev=8348&view=rev
Log:
Started to redesign the internal structural object load_pdb() method.
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=8348&r1=8347&r2=8348&view=diff
==============================================================================
--- branches/multi_structure/generic_fns/structure/internal.py (original)
+++ branches/multi_structure/generic_fns/structure/internal.py Fri Jan 9
10:23:51 2009
@@ -841,7 +841,7 @@
return data
- def load_pdb(self, file_path, read_mol=None, set_mol_name=None,
read_model=None, set_model_num=None, struct_index=None, verbosity=False):
+ def load_pdb(self, file_path, read_mol=None, set_mol_name=None,
read_model=None, set_model_num=None, verbosity=False):
"""Method for loading structures from a PDB file.
@param file_path: The full path of the PDB file.
@@ -861,9 +861,6 @@
@keyword set_model_num: Set the model number of the loaded molecule.
If set to None, then
the PDB model numbers will be preserved, if
they exist.
@type set_model_num: None, int, or list of int
- @param struct_index: The index of the structure. This optional
argument can be useful
- for reloading a structure.
- @type struct_index: int
@keyword verbosity: A flag which if True will cause messages to
be printed.
@type verbosity: bool
@return: The status of the loading of the PDB file.
@@ -882,59 +879,67 @@
# Separate the file name and path.
path, file = os.path.split(file_path)
+ # Convert the structure reading args into lists.
+ if read_mol and type(read_mol) != list:
+ read_mol = [read_mol]
+ if set_mol_name and type(set_mol_name) != list:
+ set_mol_name = [set_mol_name]
+ if read_model and type(read_model) != list:
+ read_model = [read_model]
+ if set_model_num and type(set_model_num) != list:
+ set_model_num = [set_model_num]
+
# The ID name.
- name = file
- if model != None:
- name = name + "_" + `model`
+ #name = file
+ #if model != None:
+ # name = name + "_" + `model`
# Use pointers (references) if the PDB data exists in another pipe.
- for data_pipe, pipe_name in pipes.pipe_loop(name=True):
- # Skip the current pipe.
- if pipe_name == pipes.cdp_name():
- continue
-
- # Structure exists.
- if hasattr(data_pipe, 'structure'):
- # Loop over the structures.
- for i in xrange(data_pipe.structure.num):
- if data_pipe.structure.name[i] == name and
data_pipe.structure.id == 'internal':
- # Add the structure.
- self.add_struct(name=name, model=model, file=file,
path=path, str=data_pipe.structure.structural_data[i],
struct_index=struct_index)
-
- # Print out.
- if verbosity:
- print "Using the structures from the data pipe "
+ `pipe_name` + "."
- print self.structural_data[i]
-
- # Exit this function.
- return True
+ #for data_pipe, pipe_name in pipes.pipe_loop(name=True):
+ # # Skip the current pipe.
+ # if pipe_name == pipes.cdp_name():
+ # continue
+
+ # # Structure exists.
+ # if hasattr(data_pipe, 'structure'):
+ # # Loop over the structures.
+ # for i in xrange(data_pipe.structure.num):
+ # if data_pipe.structure.name[i] == name and
data_pipe.structure.id == 'internal':
+ # # Add the structure.
+ # self.add_struct(name=name, model=model, file=file,
path=path, str=data_pipe.structure.structural_data[i],
struct_index=struct_index)
+
+ # # Print out.
+ # if verbosity:
+ # print "Using the structures from the data pipe
" + `pipe_name` + "."
+ # print self.structural_data[i]
+
+ # # Exit this function.
+ # return True
# Print out.
- if verbosity:
- if type(model) == int:
- print "Loading structure " + `model` + " from the PDB file."
- else:
- print "Loading all structures from the PDB file."
+ #if verbosity:
+ # if type(model) == int:
+ # print "Loading structure " + `model` + " from the PDB file."
+ # else:
+ # print "Loading all structures from the PDB file."
# Loop over all models in the PDB file.
- i = 0
- for model_num, records in self.__parse_models(file_path):
+ for model_num, model_records in self.__parse_models(file_path):
# Only load the desired model.
- if model != None and model != model_num:
+ if read_model and model_num not in read_model:
continue
# Print out.
if model_num != None:
print "Loading model: " + `model_num`
- # 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(records,
struct_index=len(self.structural_data)-1)
-
- # Increment the structure index.
- i = i + 1
+ # 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)
# Loading worked.
return True
r8348 - /branches/multi_structure/generic_fns/structure/internal.py