Author: bugman
Date: Wed Nov 8 08:16:51 2006
New Revision: 2773
URL: http://svn.gna.org/viewcvs/relax?rev=2773&view=rev
Log:
Added hybrid run support for the 'pdb.create_tensor_pdb()' user function.
The function 'self.create_tensor_pdb()' in the file 'generic_fns/pdb.py' has
been modified to loop
over an array of runs. This array is normally the single standard run.
However when a hybrid run
is encountered, the runs of the hybrid are looped over.
The chain ID letter is now taken from the 'string.ascii_uppercase' string.
The letter is extracted
using the run index.
All atom IDs have had the chain ID appended to the end to make then unique
when multiple chains
exist.
The data structure 'self.atomic_data' of 'generic_fns/pdb.py' has been
modified to include the
record name (ATOM, HETATM, or TER) at position 1. Hence all other elements
have been shifted by
one. This is to allow multiple TER records one at the end of each chain,
each having their own atom
number.
The 'het_data' array in 'self.write_pdb_file()' is no longer sorted as it
already is sorted because
of the sorting of atomic data arrays. This allows the HET records to be
sorted first by chain ID
then by residue number.
The HETNAM and FORMUL records are now only created if the residue has not
been previously
encountered. This avoids duplicated records.
All the atomic coordinate records (ATOM, HETATM, or TER) are now created
sequentially by looping
over the atomic data sorted by atom number.
Modified:
branches/tensor_pdb/generic_fns/pdb.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/tensor_pdb/generic_fns/pdb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/tensor_pdb/generic_fns/pdb.py?rev=2773&r1=2772&r2=2773&view=diff
r2773 - /branches/tensor_pdb/generic_fns/pdb.py