Author: bugman
Date: Fri Jan 16 11:26:44 2009
New Revision: 8493
URL: http://svn.gna.org/viewcvs/relax?rev=8493&view=rev
Log:
Modified the prompt interface of the structure.vectors() user function.
The struct_index arg is dead! Long live the model arg!
Modified:
branches/multi_structure/prompt/structure.py
Modified: branches/multi_structure/prompt/structure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_structure/prompt/structure.py?rev=8493&r1=8492&r2=8493&view=diff
==============================================================================
--- branches/multi_structure/prompt/structure.py (original)
+++ branches/multi_structure/prompt/structure.py Fri Jan 16 11:26:44 2009
@@ -464,25 +464,25 @@
generic_fns.structure.main.read_pdb(file=file, dir=dir,
read_mol=read_mol, set_mol_name=set_mol_name, read_model=read_model,
set_model_num=set_model_num, parser=parser)
- def vectors(self, attached='H', spin_id=None, struct_index=None,
verbosity=1, ave=True, unit=True):
- """Extract unit bond vectors from the structure.
+ def vectors(self, attached='H', spin_id=None, model=None, verbosity=1,
ave=True, unit=True):
+ """Extract and store the bond vectors from the loaded structures in
the spin container.
Keyword arguments
~~~~~~~~~~~~~~~~~
- attached: The type of atom attached to the spin. Regular expression
is allowed, for
- example 'H*'.
+ attached: The name of the second atom which attached to the spin of
interest. 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).
+ model: The model to extract bond vectors from (which if set to None
will cause the vectors
+ of all models 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.
+ ave: A flag which if True will cause the bond vectors from all models
to be averaged. If
+ vectors from only one model 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.
@@ -492,20 +492,20 @@
~~~~~~~~~~~
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.
+ calculations. This user function allows these vectors to be extracted
from the loaded
+ structures. The bond vector will be that from the atom associated
with the spin system
+ loaded in relax to the bonded atom specified by the 'attached'
argument. For example if
+ 'attached' is set to 'H' and the protein backbone amide spins 'N' are
loaded, the all 'N-H'
+ vectors will be extracted. But if set to 'CA', all atoms named 'CA'
in the structures will
+ be searched for and all 'N-Ca' bond vectors will be extracted.
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.
+ with N models is loaded or if multiple molecules, from any source, of
the same compound are
+ loaded as different models, there are three options for extracting the
bond vector. Firstly
+ the bond vector of a single model can be extracted by setting the
'model' argument.
+ Secondly the bond vectors from all models can be extracted if 'model'
is None and 'ave' is
+ set to False. Thirdly, if 'model' is None and 'ave' is set to True,
then a single vector
+ which is the average for all models will be calculated.
Example
@@ -552,7 +552,7 @@
text = sys.ps3 + "structure.vectors("
text = text + "attached=" + `attached`
text = text + ", spin_id=" + `spin_id`
- text = text + ", struct_index=" + `struct_index`
+ text = text + ", model=" + `model`
text = text + ", verbosity=" + `verbosity`
text = text + ", ave=" + `ave`
text = text + ", unit=" + `unit` + ")"
@@ -564,11 +564,11 @@
# 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)
+ raise RelaxNoneStrError, ('spin identification string', spin_id)
+
+ # The model argument.
+ if model != None and type(model) != int:
+ raise RelaxNoneIntError, ('model', model)
# The verbosity level.
if type(verbosity) != int:
@@ -583,7 +583,7 @@
raise RelaxBoolError, ('unit vector flag', unit)
# Execute the functional code.
- generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
struct_index=struct_index, verbosity=verbosity, ave=ave, unit=unit)
+ generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
def write_pdb(self, file=None, dir=None, struct_index=None, force=False):
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