Author: bugman
Date: Tue Jan 13 18:03:18 2009
New Revision: 8434
URL: http://svn.gna.org/viewcvs/relax?rev=8434&view=rev
Log:
Redesigned the Scientific python structural object load_pdb() method.
The structural data structure is not yet created.
Modified:
branches/multi_structure/generic_fns/structure/scientific.py
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=8434&r1=8433&r2=8434&view=diff
==============================================================================
--- branches/multi_structure/generic_fns/structure/scientific.py (original)
+++ branches/multi_structure/generic_fns/structure/scientific.py Tue Jan 13
18:03:18 2009
@@ -520,7 +520,7 @@
return data
- def load_pdb(self, file_path, read_mol=None, set_mol_name=None,
read_model=None, set_model_num=None, verbosity=False):
+ def load_pdb(self, file_path, read_mol=None, set_mol_name=None,
read_model=None, set_model_num=None, verbosity=True):
"""Function for loading the structures from the PDB file.
@param file_path: The full path of the file.
@@ -558,98 +558,99 @@
# Separate the file name and path.
path, file = os.path.split(file_path)
- # The ID name.
- name = file
- if model != None:
- name = name + "_" + `model`
+ # 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]
# Use pointers (references) if the PDB data exists in another data
pipe.
- for data_pipe, pipe_name in pipes.pipe_loop(name=True):
- # Skip the current pipe.
- if pipe_name == pipes.cdp_name():
+ #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 == 'scientific' and
len(data_pipe.structure.structural_data):
+ # # 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
+
+ # Load the structure i from the PDB file.
+ #if type(model) == int:
+ # # Print out.
+ # if verbosity:
+ # print "Loading structure " + `model` + " from the PDB file."
+
+ # # Load the structure into 'str'.
+ # str = Scientific.IO.PDB.Structure(file_path, model)
+
+ # # Test the structure.
+ # if len(str) == 0:
+ # raise RelaxPdbLoadError, file_path
+
+ # # Print the PDB info.
+ # if verbosity:
+ # print str
+#
+# # Add the structure.
+# self.add_struct(name=name, model=model, file=file, path=path,
str=str, struct_index=struct_index)
+
+
+ # Print out.
+ if verbosity:
+ print "Loading all structures from the PDB file."
+
+ # Load all models.
+ models = []
+ model_flag = True
+ model_num = 1
+ while 1:
+ # Only load the desired model.
+ if read_model and model_num not in read_model:
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 == 'scientific' and
len(data_pipe.structure.structural_data):
- # 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
-
- # Load the structure i from the PDB file.
- if type(model) == int:
- # Print out.
- if verbosity:
- print "Loading structure " + `model` + " from the PDB file."
-
- # Load the structure into 'str'.
- str = Scientific.IO.PDB.Structure(file_path, model)
-
- # Test the structure.
- if len(str) == 0:
- raise RelaxPdbLoadError, file_path
+ # Load the pdb files.
+ model = Scientific.IO.PDB.Structure(file_path, model_num)
+
+ # No model 1.
+ if not len(model) and not len(models):
+ # Load the PDB without a model number.
+ model = Scientific.IO.PDB.Structure(file_path)
+ model_flag = False
+
+ # Ok, nothing is loadable from this file.
+ if not len(model):
+ raise RelaxPdbLoadError, file_path
+
+ # Test if the last structure has been reached.
+ if not len(model):
+ del model
+ break
# Print the PDB info.
if verbosity:
- print str
-
- # Add the structure.
- self.add_struct(name=name, model=model, file=file, path=path,
str=str, struct_index=struct_index)
-
-
- # Load all structures.
- else:
- # Print out.
- if verbosity:
- print "Loading all structures from the PDB file."
-
- # First model.
- i = 1
-
- # Loop over all the other structures.
- while 1:
- # Load the pdb files.
- str = Scientific.IO.PDB.Structure(file_path, i)
-
- # No model 1.
- if len(str) == 0 and i == 1:
- # Load the PDB without a model number.
- str = Scientific.IO.PDB.Structure(file_path)
-
- # Ok, nothing is loadable from this file.
- if len(str) == 0:
- raise RelaxPdbLoadError, file_path
-
- # Set the model number.
- model = None
-
- # Set the model number.
- else:
- model = i
-
- # Test if the last structure has been reached.
- if len(str) == 0:
- del str
- break
-
- # Print the PDB info.
- if verbosity:
- print str
-
- # Place the structure in 'self.structural_data'.
- self.add_struct(name=name, model=model, file=file,
path=path, str=str, struct_index=struct_index)
-
- # Increment i.
- i = i + 1
+ print model
+
+ # Append the model to the list.
+ models.append(model)
+
+ # Increment the model counter.
+ model_num = model_num + 1
# Loading worked.
return True
r8434 - /branches/multi_structure/generic_fns/structure/scientific.py