Author: bugman
Date: Wed Aug 20 21:10:20 2008
New Revision: 7215
URL: http://svn.gna.org/viewcvs/relax?rev=7215&view=rev
Log:
Fixed the creation of the PIV and AVE residues for the cone models.
Modified:
1.3/generic_fns/structure/geometric.py
1.3/specific_fns/n_state_model.py
Modified: 1.3/generic_fns/structure/geometric.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/geometric.py?rev=7215&r1=7214&r2=7215&view=diff
==============================================================================
--- 1.3/generic_fns/structure/geometric.py (original)
+++ 1.3/generic_fns/structure/geometric.py Wed Aug 20 21:10:20 2008
@@ -133,15 +133,15 @@
# Connect across the radial array (to generate the circular cone
edge).
if i != 0:
neighbour_id = 'T' + `i-1`
- structure.atom_connect(index1=atom_id, index2=neighbour_id)
+ #structure.atom_connect(index1=atom_id, index2=neighbour_id)
# Connect the last radial array to the first (to zip up the circle).
if i == inc-1:
neighbour_id = 'T' + `0`
- structure.atom_connect(index1=atom_id, index2=neighbour_id)
+ #structure.atom_connect(index1=atom_id, index2=neighbour_id)
# Join the atom to the cone apex.
- structure.atom_connect(index1=atom_id, index2='Apex')
+ #structure.atom_connect(index1=atom_id, index2='Apex')
# Increment the atom number.
atom_num = atom_num + 1
@@ -610,20 +610,25 @@
else:
atom_id_ext = ''
+ # The atom numbers (and indices).
+ origin_num = structure.structural_data[0].atom_num[-1]+1
+ atom_num = structure.structural_data[0].atom_num[-1]+2
+ atom_neg_num = structure.structural_data[0].atom_num[-1]+3
+
# The origin atom.
- structure.atom_add(pdb_record='HETATM', atom_num='R_vect'+atom_id_ext,
atom_name='R', res_name=res_name_vect, chain_id=chain_id, res_num=res_num,
pos=origin, segment_id=None, element='C', struct_index=None)
+ structure.atom_add(pdb_record='HETATM', atom_num=origin_num,
atom_name='R', res_name=res_name_vect, chain_id=chain_id, res_num=res_num,
pos=origin, segment_id=None, element='C', struct_index=None)
# Create the PDB residue representing the vector.
- structure.atom_add(pdb_record='HETATM', atom_num=atom_name+atom_id_ext,
atom_name=atom_name, res_name=res_name_vect, chain_id=chain_id,
res_num=res_num, pos=origin+vector*scale, segment_id=None, element='C',
struct_index=None)
- structure.atom_connect(index1=atom_name+atom_id_ext,
index2='R_vect'+atom_id_ext)
+ structure.atom_add(pdb_record='HETATM', atom_num=atom_num,
atom_name=atom_name, res_name=res_name_vect, chain_id=chain_id,
res_num=res_num, pos=origin+vector*scale, segment_id=None, element='C',
struct_index=None)
+ structure.atom_connect(index1=atom_num-1, index2=origin_num-1)
if neg:
- structure.atom_add(pdb_record='HETATM',
atom_num=atom_name+'_neg'+atom_id_ext, atom_name=atom_name,
res_name=res_name_vect, chain_id=chain_id, res_num=res_num,
pos=origin+vector*scale, segment_id=None, element='C', struct_index=None)
- structure.atom_connect(index1=atom_name+'_neg'+atom_id_ext,
index2='R_vect'+atom_id_ext)
+ structure.atom_add(pdb_record='HETATM', atom_num=atom_neg_num,
atom_name=atom_name, res_name=res_name_vect, chain_id=chain_id,
res_num=res_num, pos=origin+vector*scale, segment_id=None, element='C',
struct_index=None)
+ structure.atom_connect(index1=atom_neg_num-1, index2=origin_num-1)
# Add another atom to allow the axis labels to be shifted just outside
of the vector itself.
- structure.atom_add(pdb_record='HETATM', atom_num='vect
label'+atom_id_ext, atom_name=atom_name, res_name=res_name_vect,
chain_id=chain_id, res_num=res_num, pos=origin+label_placement*vector*scale,
segment_id=None, element='N', struct_index=None)
+ structure.atom_add(pdb_record='HETATM', atom_num=atom_neg_num,
atom_name=atom_name, res_name=res_name_vect, chain_id=chain_id,
res_num=res_num, pos=origin+label_placement*vector*scale, segment_id=None,
element='N', struct_index=None)
if neg:
- structure.atom_add(pdb_record='HETATM', atom_num='vect neg
label'+atom_id_ext, atom_name=atom_name, res_name=res_name_vect,
chain_id=chain_id, res_num=res_num, pos=origin-label_placement*vector*scale,
segment_id=None, element='N', struct_index=None)
+ structure.atom_add(pdb_record='HETATM', atom_num=atom_neg_num_ext,
atom_name=atom_name, res_name=res_name_vect, chain_id=chain_id,
res_num=res_num, pos=origin-label_placement*vector*scale, segment_id=None,
element='N', struct_index=None)
# Print out.
print " " + atom_name + " vector (scaled + shifted to origin): " +
`origin+vector*scale`
@@ -634,16 +639,17 @@
for i in xrange(sim_vectors):
# Increment the residue number, so each simulation is a new
residue.
res_num = res_num + 1
-
- # Modify the atom_id for each simulation.
- atom_id_ext_sim = atom_id_ext + '_sim' + `i`
+
+ # The atom numbers (and indices).
+ atom_num = structure.structural_data[0].atom_num[-1]+1
+ atom_neg_num = structure.structural_data[0].atom_num[-1]+2
# Create the PDB residue representing the vector.
- structure.atom_add(pdb_record='HETATM',
atom_num=atom_name+atom_id_ext_sim, atom_name=atom_name,
res_name=res_name_sim, chain_id=chain_id, res_num=res_num,
pos=origin+sim_vectors[i]*scale, segment_id=None, element='C',
struct_index=None)
- structure.atom_connect(index1=atom_name+atom_id_ext_sim,
index2='R_vect'+atom_id_ext_sim)
+ structure.atom_add(pdb_record='HETATM', atom_num=atom_num,
atom_name=atom_name, res_name=res_name_sim, chain_id=chain_id,
res_num=res_num, pos=origin+sim_vectors[i]*scale, segment_id=None,
element='C', struct_index=None)
+ structure.atom_connect(index1=atom_num-1, index2=origin_num-1)
if neg:
- structure.atom_add(pdb_record='HETATM',
atom_num=atom_name+'_neg'+atom_id_ext_sim, atom_name=atom_name,
res_name=res_name_sim, chain_id=chain_id, res_num=res_num,
pos=origin-sim_vectors[i]*scale, segment_id=None, element='C',
struct_index=None)
-
structure.atom_connect(index1=atom_name+'_neg'+atom_id_ext_sim,
index2='R_vect'+atom_id_ext_sim)
+ structure.atom_add(pdb_record='HETATM', atom_num=atom_num+1,
atom_name=atom_name, res_name=res_name_sim, chain_id=chain_id,
res_num=res_num, pos=origin-sim_vectors[i]*scale, segment_id=None,
element='C', struct_index=None)
+ structure.atom_connect(index1=atom_neg_num-1,
index2=origin_num-1)
# Return the new residue number.
return res_num
Modified: 1.3/specific_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/n_state_model.py?rev=7215&r1=7214&r2=7215&view=diff
==============================================================================
--- 1.3/specific_fns/n_state_model.py (original)
+++ 1.3/specific_fns/n_state_model.py Wed Aug 20 21:10:20 2008
@@ -226,7 +226,7 @@
structure.structural_data.append(Structure_container())
# Add the pivot point.
- structure.atom_add(pdb_record='HETATM', atom_name='R',
res_name='PIV', res_num=1, pos=cdp.pivot_point, element='C')
+ structure.atom_add(pdb_record='HETATM', atom_num=1, atom_name='R',
res_name='PIV', res_num=1, pos=cdp.pivot_point, element='C')
# Generate the average pivot-CoM vectors.
print "\nGenerating the average pivot-CoM vectors."
r7215 - in /1.3: generic_fns/structure/geometric.py specific_fns/n_state_model.py