Author: han87
Date: Mon Jun 27 18:55:51 2011
New Revision: 13246
URL: http://svn.gna.org/viewcvs/relax?rev=13246&view=rev
Log:
A new function vector_xyz() was generated.
A new function vector_xyz() was generated in '/prompt/structure.py' for
extracting a vector of two given atoms in a xyz file.
Modified:
branches/xyz/prompt/structure.py
Modified: branches/xyz/prompt/structure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/xyz/prompt/structure.py?rev=13246&r1=13245&r2=13246&view=diff
==============================================================================
--- branches/xyz/prompt/structure.py (original)
+++ branches/xyz/prompt/structure.py Mon Jun 27 18:55:51 2011
@@ -686,6 +686,76 @@
generic_fns.structure.main.vectors(attached=attached,
spin_id=spin_id, model=model, verbosity=verbosity, ave=ave, unit=unit)
+ def vectors_xyz(self, spin_id1=None, spin_id2=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
+ ~~~~~~~~~~~~~~~~~
+
+ spin_id1: The spin identification string of the spin 1.
+
+ spin_id2: The spin identification string of the spin 2.
+
+ 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 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.
+
+
+ Description
+ ~~~~~~~~~~~
+
+ 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 the loaded
+ structures. The bond vector will be that from the two atoms of a xyz
file loaded in relax.
+
+ 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 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
+ ~~~~~~~
+
+ To extract a vector of two atoms from xyz file, type:
+
+ relax> structure.vectors(spin_id1='#SSS-cluster4-new-test_mol1@2',
spin_id1='#SSS-cluster4-new-test_mol1@1')
+ """
+
+ # Function intro text.
+ if self._exec_info.intro:
+ text = self._exec_info.ps3 + "structure.vectors("
+ text = text + "spin_id1=" + repr(spin_id1)
+ text = text + ", spin_id2=" + repr(spin_id2)
+ text = text + ", model=" + repr(model)
+ text = text + ", verbosity=" + repr(verbosity)
+ text = text + ", ave=" + repr(ave)
+ text = text + ", unit=" + repr(unit) + ")"
+ print(text)
+
+ # The argument checks.
+ arg_check.is_str(spin_id1, 'spin_identification_string',
can_be_none=True)
+ arg_check.is_str(spin_id2, 'spin identification string',
can_be_none=True)
+ arg_check.is_int(model, 'model', can_be_none=True)
+ arg_check.is_int(verbosity, 'verbosity level')
+ arg_check.is_bool(ave, 'average vector flag')
+ arg_check.is_bool(unit, 'unit vector flag')
+
+ # Execute the functional code.
+ generic_fns.structure.main.vectors_xyz(spin_id1=spin_id1,
spin_id2=spin_id2, model=model, verbosity=verbosity, ave=ave, unit=unit)
+
+
def write_pdb(self, file=None, dir=None, model_num=None, force=False):
"""The PDB writing function.
r13246 - /branches/xyz/prompt/structure.py