Author: bugman
Date: Sat Sep 27 15:04:05 2008
New Revision: 7402
URL: http://svn.gna.org/viewcvs/relax?rev=7402&view=rev
Log:
The load_pdb() structural method now accepts the struct_index arg.
This is passed in by from_xml() to place the structure in the correct
position.
Modified:
1.3/generic_fns/structure/api_base.py
1.3/generic_fns/structure/internal.py
Modified: 1.3/generic_fns/structure/api_base.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/api_base.py?rev=7402&r1=7401&r2=7402&view=diff
==============================================================================
--- 1.3/generic_fns/structure/api_base.py (original)
+++ 1.3/generic_fns/structure/api_base.py Sat Sep 27 15:04:05 2008
@@ -232,15 +232,15 @@
# Loop over the structures and load them.
for i in xrange(self.num):
# Now load the structure from file again.
- loaded = self.load_pdb(file_path=self.path[i] + sep +
self.file[i], model=None)
+ loaded = self.load_pdb(file_path=self.path[i] + sep +
self.file[i], model=None, struct_index=i)
# Try without the path to search for the file in the current
directory.
if not loaded:
- loaded = self.load_pdb(file_path=self.file[i], model=None)
+ loaded = self.load_pdb(file_path=self.file[i], model=None,
struct_index=i)
# Try in the path of the results file.
if not loaded:
- loaded = self.load_pdb(file_path=dir + sep + self.file[i],
model=None)
+ loaded = self.load_pdb(file_path=dir + sep + self.file[i],
model=None, struct_index=i)
# Can't load the file.
if not loaded:
@@ -250,19 +250,24 @@
warn(RelaxWarning("The structure file " + `self.file[i]`
+ " cannot be found in the current directory or the directory of the results
file."))
- def load_pdb(self, file_path, model=None, verbosity=False):
+ def load_pdb(self, file_path, model=None, struct_index=None,
verbosity=False):
"""Prototype method stub for loading structures from a PDB file.
This inherited prototype method is a stub which, if the
functionality is desired, should be
overwritten by the derived class.
- @param file_path: The full path of the PDB file.
- @type file_path: str
- @param model: The structural model to use.
- @type model: 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 PDB file.
+ @type file_path: str
+ @param model: The structural model to use.
+ @type model: 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.
+ @rtype: bool
"""
# Raise the error.
Modified: 1.3/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/internal.py?rev=7402&r1=7401&r2=7402&view=diff
==============================================================================
--- 1.3/generic_fns/structure/internal.py (original)
+++ 1.3/generic_fns/structure/internal.py Sat Sep 27 15:04:05 2008
@@ -770,17 +770,20 @@
return data
- def load_pdb(self, file_path, model=None, verbosity=False):
+ def load_pdb(self, file_path, model=None, struct_index=None,
verbosity=False):
"""Method for loading structures from a PDB file.
- @param file_path: The full path of the PDB file.
- @type file_path: str
- @param model: The structural model to use.
- @type model: 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
+ @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 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.
r7402 - in /1.3/generic_fns/structure: api_base.py internal.py