Author: bugman
Date: Thu Jan 22 14:59:41 2009
New Revision: 8589
URL: http://svn.gna.org/viewcvs/relax?rev=8589&view=rev
Log:
Fixes for create_vector_dist() for the new structural data design.
The atoms are added to the single molecule, and the struct_index has been
eliminated.
Modified:
branches/multi_structure/generic_fns/structure/geometric.py
Modified: branches/multi_structure/generic_fns/structure/geometric.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_structure/generic_fns/structure/geometric.py?rev=8589&r1=8588&r2=8589&view=diff
==============================================================================
--- branches/multi_structure/generic_fns/structure/geometric.py (original)
+++ branches/multi_structure/generic_fns/structure/geometric.py Thu Jan 22
14:59:41 2009
@@ -353,6 +353,9 @@
# Add a structure.
structure.add_molecule(name='vector_dist')
+ # Alias the single molecule from the single model.
+ mol = structure.structural_data[0].mol[0]
+
# Initialise the residue and atom numbers.
res_num = 1
atom_num = 1
@@ -385,13 +388,13 @@
vector = spin.xh_vect * length * 1e10
# Add the central X atom.
- structure.atom_add(pdb_record='ATOM', atom_num=atom_num,
atom_name=spin.name, res_name=res_name, chain_id='A', res_num=res_num, pos=R,
segment_id=None, element=spin.element, struct_index=None)
+ mol.atom_add(pdb_record='ATOM', atom_num=atom_num,
atom_name=spin.name, res_name=res_name, chain_id='A', res_num=res_num, pos=R,
segment_id=None, element=spin.element)
# Add the H atom.
- structure.atom_add(pdb_record='ATOM', atom_num=atom_num+1,
atom_name='H', res_name=res_name, chain_id='A', res_num=res_num, pos=R+vector,
segment_id=None, element='H', struct_index=None)
+ mol.atom_add(pdb_record='ATOM', atom_num=atom_num+1, atom_name='H',
res_name=res_name, chain_id='A', res_num=res_num, pos=R+vector,
segment_id=None, element='H')
# Connect the two atoms.
- structure.atom_connect(index1=atom_num-1, index2=atom_num)
+ mol.atom_connect(index1=atom_num-1, index2=atom_num)
# Increment the atom number.
atom_num = atom_num + 2
@@ -412,13 +415,13 @@
vector = spin.xh_vect * length * 1e10
# Add the central X atom.
- structure.atom_add(pdb_record='ATOM', atom_num=atom_num,
atom_name=spin.name, res_name=res_name, chain_id='B', res_num=res_num, pos=R,
segment_id=None, element=spin.element, struct_index=None)
+ mol.atom_add(pdb_record='ATOM', atom_num=atom_num,
atom_name=spin.name, res_name=res_name, chain_id='B', res_num=res_num, pos=R,
segment_id=None, element=spin.element)
# Add the H atom.
- structure.atom_add(pdb_record='ATOM', atom_num=atom_num+1,
atom_name='H', res_name=res_name, chain_id='B', res_num=res_num, pos=R-vector,
segment_id=None, element='H', struct_index=None)
+ mol.atom_add(pdb_record='ATOM', atom_num=atom_num+1,
atom_name='H', res_name=res_name, chain_id='B', res_num=res_num, pos=R-vector,
segment_id=None, element='H')
# Connect the two atoms.
- structure.atom_connect(index1=atom_num-1, index2=atom_num)
+ mol.atom_connect(index1=atom_num-1, index2=atom_num)
# Increment the atom number.
atom_num = atom_num + 2
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