Hi Edward,
in the function __bonded_atom() I found following code:
# Problem.
if num_attached > 1:
# Get the atom names.
matching_names = []
for i in matching_list:
matching_names.append(mol.atom_name[i])
# Return nothing but a warning.
return None, None, None, None, None, 'More than one
attached atom found: ' + repr(matching_names)
This means that it can only load one atom. But this is often not the
case for small molecule. For example if I have a CH3 group and I
asked it to load protons, all three protons should be loaded.
Best,
Han
On Jun 27, 2011, at 7:26 PM, Edward d'Auvergne wrote:
Hi Han,
This is another case were the current code can be used, and if it
doesn't work then it should be fixed rather than a new function added.
The structure.vectors() method is independent of the format of the
structural file. Normally when I use it, the PDB file has been read
in and is in the internal structure format. After reading the XYZ
file, it should also be in the internal format. So the
structure.vectors() user function should work on both. So if you load
all the carbons as spins from the organic molecule, the CH vectors
should be extractable with:
relax> structure.vectors(attached='H', spin_id='@C')
The 'H' needs no '*' characters as all protons in the XYZ file are
called 'H'. The internal structural object will then determine which
'H' atoms are attached to the C atoms. This is either taken from the
structural file, or it uses a very basic distance based algorithm in
__bonded_atom() and __find_bonded_atoms(). I have a feeling that this
will work automatically.
Regards,
Edward
On 27 June 2011 18:55, <[email protected]> wrote:
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.
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