Author: bugman
Date: Sat Sep 27 16:20:16 2008
New Revision: 7404
URL: http://svn.gna.org/viewcvs/relax?rev=7404&view=rev
Log:
Redesigned the internal and Scientific load_pdb() methods.
An auxiliary method __add_struct() was created for looking after the
structure additions.
Modified:
1.3/generic_fns/structure/internal.py
1.3/generic_fns/structure/scientific.py
Modified: 1.3/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/internal.py?rev=7404&r1=7403&r2=7404&view=diff
==============================================================================
--- 1.3/generic_fns/structure/internal.py (original)
+++ 1.3/generic_fns/structure/internal.py Sat Sep 27 16:20:16 2008
@@ -51,6 +51,56 @@
# Identification string.
id = 'internal'
+
+
+ def __add_struct(self, name=None, model=None, file=None, path=None,
str=None, struct_index=None):
+ """Add the given structure to the store.
+
+ @keyword name: The structural identifier.
+ @type name: str
+ @keyword model: The structural model.
+ @type model: int or None
+ @keyword file: The name of the file containing the
structure.
+ @type file: str
+ @keyword path: The optional path where the file is located.
+ @type path: str
+ @keyword str: The object containing the structural data.
+ @type str: Structure_container instance
+ @keyword struct_index: The index of the structural container, used
for replacing the
+ structure.
+ @type struct_index: int or None.
+ """
+
+ # Some checks.
+ if struct_index != None:
+ # Index check.
+ if struct_index >= self.num:
+ raise RelaxError, "The structure index of " + `struct_index`
+ " cannot be more than the total number of structures of " + `self.num` + "."
+
+ # ID check.
+ if name != self.name[struct_index]:
+ raise RelaxError, "The ID names " + `name` + " and " +
`self.name[struct_index]` + " do not match."
+
+ # Model.
+ if model != self.model[struct_index]:
+ raise RelaxError, "The models " + `model` + " and " +
`self.model[struct_index]` + " do not match."
+
+ # File name.
+ if file != self.file[struct_index]:
+ raise RelaxError, "The file names of " + `file` + " and " +
`self.file[struct_index]` + " do not match."
+
+ # Path.
+ if path != self.path[struct_index]:
+ raise RelaxError, "The paths of " + `path` + " and " +
`self.path[struct_index]` + " do not match."
+
+ # Initialise.
+ else:
+ self.num = self.num + 1
+ self.name.append(name)
+ self.model.append(model)
+ self.file.append(file)
+ self.path.append(path)
+ self.structural_data.append(str)
def __atom_index(self, atom_num, struct_index):
@@ -775,8 +825,8 @@
@param file_path: The full path of the PDB file.
@type file_path: str
- @param model: The structural model to use.
- @type model: int
+ @param model: The PDB model to use. If None, all models
will be loaded.
+ @type model: int or None
@param struct_index: The index of the structure. This optional
argument can be useful
for reloading a structure.
@type struct_index: int
@@ -788,37 +838,45 @@
# Initial print out.
if verbosity:
- print "Internal relax PDB parser.\n"
+ print "\nInternal relax PDB parser."
# Test if the file exists.
if not access(file_path, F_OK):
+ # Exit indicating failure.
return False
- # Set the file name and path.
- expanded = path.split(file_path)
- self.path.append(expanded[0])
- self.file.append(expanded[1])
-
- # Store the model number.
- self.model = model
+ # Separate the file name and path.
+ path, file = path.split(file_path)
+
+ # The ID name.
+ name = file
+ if model != None:
+ name = name + "_" + `model`
# Use pointers (references) if the PDB data exists in another pipe.
- for data_pipe in ds:
+ for key in ds:
+ # Skip the current pipe.
+ if key == ds.current_pipe:
+ continue
+
+ # Get the data pipe.
+ data_pipe = ds[key]
+
+ # Structure exists.
if hasattr(data_pipe, 'structure'):
# Loop over the structures.
- for i in xrange(len(data_pipe.structure)):
- if data_pipe.structure.file[i] == expanded[1] and
data_pipe.structure[i].model == model and data_pipe.structure.id ==
'internal':
- # Make a pointer to the data.
- self.structural_data =
data_pipe.structure.structural_data[i]
-
+ for i in xrange(data_pipe.structure.num):
+ if data_pipe.structure.name[i] == name and
data_pipe.structure.id == 'internal':
# Print out.
if verbosity:
- print "Using the structures from the data pipe "
+ `data_pipe.pipe_name` + "."
- for i in xrange(len(self.structural_data)):
- print self.structural_data[i]
+ print "Using the structures from the data pipe "
+ `key` + "."
+ print self.structural_data[i]
+
+ # 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)
# Exit this function.
- return
+ return True
# Print out.
if verbosity:
@@ -833,9 +891,10 @@
if model != None and model != model_num:
continue
- # Initialise and fill the structural data object.
- self.structural_data.append(Structure_container())
- self.structural_data[-1].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, len(self.structural_data)-1)
# Loading worked.
Modified: 1.3/generic_fns/structure/scientific.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/scientific.py?rev=7404&r1=7403&r2=7404&view=diff
==============================================================================
--- 1.3/generic_fns/structure/scientific.py (original)
+++ 1.3/generic_fns/structure/scientific.py Sat Sep 27 16:20:16 2008
@@ -58,6 +58,56 @@
# Execute the base class __init__() method.
Base_struct_API.__init__(self)
+
+
+ def __add_struct(self, name=None, model=None, file=None, path=None,
str=None, struct_index=None):
+ """Add the given structure to the store.
+
+ @keyword name: The structural identifier.
+ @type name: str
+ @keyword model: The structural model.
+ @type model: int or None
+ @keyword file: The name of the file containing the
structure.
+ @type file: str
+ @keyword path: The optional path where the file is located.
+ @type path: str
+ @keyword str: The object containing the structural data.
+ @type str: Structure_container instance
+ @keyword struct_index: The index of the structural container, used
for replacing the
+ structure.
+ @type struct_index: int or None.
+ """
+
+ # Some checks.
+ if struct_index != None:
+ # Index check.
+ if struct_index >= self.num:
+ raise RelaxError, "The structure index of " + `struct_index`
+ " cannot be more than the total number of structures of " + `self.num` + "."
+
+ # ID check.
+ if name != self.name[struct_index]:
+ raise RelaxError, "The ID names " + `name` + " and " +
`self.name[struct_index]` + " do not match."
+
+ # Model.
+ if model != self.model[struct_index]:
+ raise RelaxError, "The models " + `model` + " and " +
`self.model[struct_index]` + " do not match."
+
+ # File name.
+ if file != self.file[struct_index]:
+ raise RelaxError, "The file names of " + `file` + " and " +
`self.file[struct_index]` + " do not match."
+
+ # Path.
+ if path != self.path[struct_index]:
+ raise RelaxError, "The paths of " + `path` + " and " +
`self.path[struct_index]` + " do not match."
+
+ # Initialise.
+ else:
+ self.num = self.num + 1
+ self.name.append(name)
+ self.model.append(model)
+ self.file.append(file)
+ self.path.append(path)
+ self.structural_data.append(str)
def __find_bonded_atom(self, attached_atom, mol_type, res):
@@ -466,12 +516,17 @@
def load_pdb(self, file_path, model=None, verbosity=False):
"""Function for loading the structures from the PDB file.
- @param file_path: The full path of the file.
- @type file_path: str
- @param model: The PDB model to use.
- @type model: None or int
- @keyword verbosity: A flag which if True will cause messages to be
printed.
- @type verbosity: bool
+ @param file_path: The full path of the file.
+ @type file_path: str
+ @param model: The PDB model to use. If None, all models
will be loaded.
+ @type model: int or None
+ @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.
+ @rtype: bool
"""
# Initial print out.
@@ -480,15 +535,16 @@
# Test if the file exists.
if not access(file_path, F_OK):
- return
-
- # Set the file name and path.
- expanded = path.split(file_path)
- self.path.append(expanded[0])
- self.file.append(expanded[1])
-
- # Store the model number.
- self.model = model
+ # Exit indicating failure.
+ return False
+
+ # Separate the file name and path.
+ path, file = path.split(file_path)
+
+ # The ID name.
+ name = file
+ if model != None:
+ name = name + "_" + `model`
# Use pointers (references) if the PDB data exists in another data
pipe.
for key in ds:
@@ -499,19 +555,18 @@
# Get the data pipe.
data_pipe = ds[key]
- # Structure already exists.
- if hasattr(data_pipe, 'structure') and
data_pipe.structure.file[0] == expanded[1] and data_pipe.structure.model ==
model:
- # Make a pointer to the data.
- self.structural_data = data_pipe.structure.structural_data
-
- # Print out.
- if verbosity:
- print "Using the structures from the data pipe " + `key`
+ "."
- for i in xrange(len(self.structural_data)):
- print self.structural_data[i]
-
- # Exit this function.
- return
+ # 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':
+ # Print out.
+ if verbosity:
+ print "Using the structures from the data pipe "
+ `key` + "."
+ print self.structural_data[i]
+
+ # Exit this function.
+ return True
# Load the structure i from the PDB file.
if type(model) == int:
@@ -530,8 +585,8 @@
if verbosity:
print str
- # Place the structure in 'self.structural_data'.
- self.structural_data.append(str)
+ # Add the structure.
+ self.__add_struct(name=name, model=model, file=file, path=path,
str=str, struct_index=struct_index)
# Load all structures.
@@ -564,7 +619,10 @@
print str
# Place the structure in 'self.structural_data'.
- self.structural_data.append(str)
+ self.__add_struct(name=name, model=i, file=file, path=path,
str=str, struct_index=struct_index)
# Increment i.
i = i + 1
+
+ # Loading worked.
+ return True
r7404 - in /1.3/generic_fns/structure: internal.py scientific.py