Author: bugman
Date: Mon Jul 7 11:54:03 2008
New Revision: 6786
URL: http://svn.gna.org/viewcvs/relax?rev=6786&view=rev
Log:
Redesign of the structure.vectors() user function to allow more flexibility
with multiple structures.
Modified:
1.3/prompt/structure.py
Modified: 1.3/prompt/structure.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/structure.py?rev=6786&r1=6785&r2=6786&view=diff
==============================================================================
--- 1.3/prompt/structure.py (original)
+++ 1.3/prompt/structure.py Mon Jul 7 11:54:03 2008
@@ -362,37 +362,56 @@
generic_fns.structure.main.read_pdb(file=file, dir=dir, model=model,
parser=parser)
- def vectors(self, proton='H', spin_id=None, verbosity=1):
- """Function for calculating/extracting XH vectors from the structure.
+ def vectors(self, attached='H', spin_id=None, struct_index=None,
verbosity=1, ave=True, unit=True):
+ """Extract unit bond vectors from the structure.
Keyword arguments
~~~~~~~~~~~~~~~~~
- proton: The name of the proton attached to the spin, as specified
in the structural file.
+ attached: The type of atom attached to the spin. Regular
expression is allowed, for
+ example 'H*'.
spin_id: The spin identification string.
+
+ struct_index: The index of the structure to extract bond vectors
from (which if set to None
+ will cause all vectors to be extracted).
verbosity: The amount of information to print to screen. Zero
corresponds to minimal
output while higher values increase the amount of output. The
default value is 1.
+ ave: A flag which if True will cause all extracted bond vectors to
be averaged. If only
+ one vector is extracted, this argument will have no effect.
+
+ unit: A flag which if True will cause the unit vector to calculated
rather than the full
+ length bond vector.
+
Description
~~~~~~~~~~~
- Once the structures have been loaded, the unit XH bond vectors must
be extracted for the
- non-spherical diffusion models. The vectors are calculated using
the atomic coordinates
- of the atoms specified by spin itself and its singly attached proton.
-
- If more than one model structure is loaded, the unit XH vectors for
each model will be
- calculated and the final unit XH vector will be taken as the average.
+ For a number of types of analysis, bond vectors or unit bond vectors
are required for the
+ calculations. This user function allows these vectors to be
extracted from a loaded
+ structure. The bond vector will be that from the spin system loaded
in relax to the bonded
+ atom specified by the 'attached' argument. For example if
'attached' is set to 'H', all
+ attached protons will be searched for. If set to 'CA', all atoms
named 'CA' in the
+ structure will be searched for.
+
+ The extraction of vectors can occur in a number of ways. For
example if an NMR structure
+ with N models is loaded (or if multiple structures from any source
of the same compound are
+ loaded), there are three options for extracting the bond vector.
Firstly the bond vector of
+ a single model or structure can be extracted by specifying the
structural index
+ 'struct_index', where 0 corresponds to the first structure/model.
Secondly the bond vectors
+ from all structures/models can be extracted if 'struct_index' is
None and 'ave' is set to
+ False. Thirdly, if 'struct_index' is None and 'ave' is set to True,
then a single vector
+ which is the average of all structures/models will be calculated.
Example
~~~~~~~
- To calculate the XH vectors of the backbone amide nitrogens where in
the PDB file the
- backbone nitrogen is called 'N' and the attached proton is called
'H', assuming multiple
- types of spin have already been loaded, type one of:
+ To extract the XH vectors of the backbone amide nitrogens where in
the PDB file the backbone
+ nitrogen is called 'N' and the attached proton is called 'H',
assuming multiple types of
+ spin have already been loaded, type one of:
relax> structure.vectors(spin_id='@N')
relax> structure.vectors('H', spin_id='@N')
@@ -402,7 +421,7 @@
relax> structure.vectors(proton='HN', spin_id='@N')
- For the Ca, type:
+ For the 'CA' spin bonded to the 'HA' proton, type:
relax> structure.vectors(proton='HA', spin_id='@CA')
@@ -429,25 +448,40 @@
# Function intro text.
if self.__relax__.interpreter.intro:
text = sys.ps3 + "structure.vectors("
- text = text + "proton=" + `proton`
+ text = text + "attached=" + `attached`
text = text + ", spin_id=" + `spin_id`
- text = text + ", verbosity=" + `verbosity` + ")"
+ text = text + ", struct_index=" + `struct_index`
+ text = text + ", verbosity=" + `verbosity`
+ text = text + ", ave=" + `ave`
+ text = text + ", unit=" + `unit` + ")"
print text
- # The attached proton argument.
- if type(proton) != str:
- raise RelaxStrError, ('the attached proton', proton)
+ # The attached atom argument.
+ if type(attached) != str:
+ raise RelaxStrError, ('the attached atom', attached)
# Spin identification string.
if spin_id != None and type(spin_id) != str:
raise RelaxNoneStrError, ('Spin identification string', spin_id)
+ # The struct_index argument.
+ if struct_index != None and type(struct_index) != int:
+ raise RelaxNoneIntError, ('structure index', struct_index)
+
# The verbosity level.
if type(verbosity) != int:
raise RelaxIntError, ('verbosity level', verbosity)
+ # The average vector flag.
+ if type(ave) != bool:
+ raise RelaxBoolError, ('average vector flag', ave)
+
+ # The unit vector flag.
+ if type(unit) != bool:
+ raise RelaxBoolError, ('unit vector flag', unit)
+
# Execute the functional code.
- generic_fns.structure.main.vectors(proton=proton, spin_id=spin_id,
verbosity=verbosity)
+ generic_fns.structure.main.vectors(attached=attached,
spin_id=spin_id, struct_index=struct_index, verbosity=verbosity, ave=ave,
unit=unit)
def write_pdb(self, file=None, dir=None, struct_index=None, force=False):
r6786 - /1.3/prompt/structure.py