Author: bugman
Date: Wed Oct 26 16:54:59 2011
New Revision: 14935
URL: http://svn.gna.org/viewcvs/relax?rev=14935&view=rev
Log:
Synchronised the atom_loop() method args in the structural API.
Modified:
1.3/generic_fns/structure/api_base.py
1.3/generic_fns/structure/scientific.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=14935&r1=14934&r2=14935&view=diff
==============================================================================
--- 1.3/generic_fns/structure/api_base.py (original)
+++ 1.3/generic_fns/structure/api_base.py Wed Oct 26 16:54:59 2011
@@ -74,7 +74,7 @@
raise RelaxImplementError
- def atom_loop(self, atom_id=None, str_id=None, model_num_flag=False,
mol_name_flag=False, res_num_flag=False, res_name_flag=False,
atom_num_flag=False, atom_name_flag=False, element_flag=False,
pos_flag=False, ave=False):
+ def atom_loop(self, atom_id=None, str_id=None, model_num=None,
model_num_flag=False, mol_name_flag=False, res_num_flag=False,
res_name_flag=False, atom_num_flag=False, atom_name_flag=False,
element_flag=False, pos_flag=False, ave=False):
"""Prototype generator method stub for looping over all atoms in the
structural data object.
This method should be designed as a generator
(http://www.python.org/dev/peps/pep-0255/).
@@ -92,19 +92,17 @@
8. The position of the atom in Euclidean space.
- @keyword atom_id: The molecule, residue, and atom
identifier string. Only atoms
- matching this selection will be yielded.
+ @keyword atom_id: The molecule, residue, and atom
identifier string. Only atoms matching this selection will be yielded.
@type atom_id: str
- @keyword str_id: The structure identifier. This can be
the file name, model
- number, or structure number. If None,
then all structures will
- be looped over.
+ @keyword str_id: The structure identifier. This can be
the file name, model number, or structure number. If None, then all
structures will be looped over.
@type str_id: str, int, or None
+ @keyword model_num: Only loop over a specific model.
+ @type model_num: int or None
@keyword model_num_flag: A flag which if True will cause the
model number to be yielded.
@type model_num_flag: bool
@keyword mol_name_flag: A flag which if True will cause the
molecule name to be yielded.
@type mol_name_flag: bool
- @keyword res_num_flag: A flag which if True will cause the
residue number to be
- yielded.
+ @keyword res_num_flag: A flag which if True will cause the
residue number to be yielded.
@type res_num_flag: bool
@keyword res_name_flag: A flag which if True will cause the
residue name to be yielded.
@type res_name_flag: bool
@@ -114,16 +112,12 @@
@type atom_name_flag: bool
@keyword element_flag: A flag which if True will cause the
element name to be yielded.
@type element_flag: bool
- @keyword pos_flag: A flag which if True will cause the
atomic position to be
- yielded.
+ @keyword pos_flag: A flag which if True will cause the
atomic position to be yielded.
@type pos_flag: bool
- @keyword ave: A flag which if True will result in this
method returning the
- average atom properties across all
loaded structures.
+ @keyword ave: A flag which if True will result in this
method returning the average atom properties across all loaded structures.
@type ave: bool
@return: A tuple of atomic information, as
described in the docstring.
- @rtype: tuple consisting of optional molecule
name (str), residue number
- (int), residue name (str), atom number
(int), atom name(str),
- element name (str), and atomic position
(array of len 3).
+ @rtype: tuple consisting of optional molecule
name (str), residue number (int), residue name (str), atom number (int), atom
name(str), element name (str), and atomic position (array of len 3).
"""
# Raise the error.
Modified: 1.3/generic_fns/structure/scientific.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/scientific.py?rev=14935&r1=14934&r2=14935&view=diff
==============================================================================
--- 1.3/generic_fns/structure/scientific.py (original)
+++ 1.3/generic_fns/structure/scientific.py Wed Oct 26 16:54:59 2011
@@ -154,7 +154,7 @@
yield res, res.number, res.name, res_index
- def atom_loop(self, atom_id=None, str_id=None, model_num_flag=False,
mol_name_flag=False, res_num_flag=False, res_name_flag=False,
atom_num_flag=False, atom_name_flag=False, element_flag=False,
pos_flag=False, ave=False):
+ def atom_loop(self, atom_id=None, str_id=None, model_num=None,
model_num_flag=False, mol_name_flag=False, res_num_flag=False,
res_name_flag=False, atom_num_flag=False, atom_name_flag=False,
element_flag=False, pos_flag=False, ave=False):
"""Generator function for looping over all atoms in the Scientific
Python data objects.
@keyword atom_id: The molecule, residue, and atom
identifier string. Only atoms
@@ -164,6 +164,8 @@
number, or structure number. If None,
then all structures will
be looped over.
@type str_id: str, int, or None
+ @keyword model_num: Only loop over a specific model.
+ @type model_num: int or None
@keyword model_num_flag: A flag which if True will cause the
model number to be yielded.
@type model_num_flag: bool
@keyword mol_name_flag: A flag which if True will cause the
molecule name to be yielded.
r14935 - in /1.3/generic_fns/structure: api_base.py scientific.py