Author: bugman
Date: Thu Jan 22 16:01:16 2009
New Revision: 8596
URL: http://svn.gna.org/viewcvs/relax?rev=8596&view=rev
Log:
Fixes for the cone_pdb() method for the new structural data design.
Modified:
branches/multi_structure/specific_fns/n_state_model.py
Modified: branches/multi_structure/specific_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_structure/specific_fns/n_state_model.py?rev=8596&r1=8595&r2=8596&view=diff
==============================================================================
--- branches/multi_structure/specific_fns/n_state_model.py (original)
+++ branches/multi_structure/specific_fns/n_state_model.py Thu Jan 22 16:01:16
2009
@@ -1007,15 +1007,18 @@
# Add a structure.
structure.add_struct(name='cone')
+ # Alias the single molecule from the single model.
+ mol = structure.structural_data[0].mol[0]
+
# Add the pivot point.
- structure.atom_add(pdb_record='HETATM', atom_num=1, atom_name='R',
res_name='PIV', res_num=1, pos=cdp.pivot_point, element='C')
+ mol.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."
sim_vectors = None
if hasattr(cdp, 'ave_pivot_CoM_sim'):
sim_vectors = cdp.ave_pivot_CoM_sim
- res_num =
generic_fns.structure.geometric.generate_vector_residues(structure=structure,
vector=cdp.ave_pivot_CoM, atom_name='Ave', res_name_vect='AVE',
sim_vectors=sim_vectors, res_num=2, origin=cdp.pivot_point, scale=scale)
+ res_num =
generic_fns.structure.geometric.generate_vector_residues(mol=mol,
vector=cdp.ave_pivot_CoM, atom_name='Ave', res_name_vect='AVE',
sim_vectors=sim_vectors, res_num=2, origin=cdp.pivot_point, scale=scale)
# Generate the cone outer edge.
print "\nGenerating the cone outer edge."
@@ -1023,15 +1026,15 @@
angle = cdp.theta_diff_in_cone
elif cone_type == 'diff on cone':
angle = cdp.theta_diff_on_cone
- cap_start_atom = structure.structural_data[0].atom_num[-1]+1
- generic_fns.structure.geometric.cone_edge(structure=structure,
res_name='CON', res_num=3, apex=cdp.pivot_point, R=R, angle=angle,
length=norm(cdp.pivot_CoM), inc=inc)
+ cap_start_atom = mol.atom_num[-1]+1
+ generic_fns.structure.geometric.cone_edge(mol=mol, res_name='CON',
res_num=3, apex=cdp.pivot_point, R=R, angle=angle, length=norm(cdp.pivot_CoM),
inc=inc)
# Generate the cone cap, and stitch it to the cone edge.
if cone_type == 'diff in cone':
print "\nGenerating the cone cap."
- cone_start_atom = structure.structural_data[0].atom_num[-1]+1
-
generic_fns.structure.geometric.generate_vector_dist(structure=structure,
res_name='CON', res_num=3, centre=cdp.pivot_point, R=R, max_angle=angle,
scale=norm(cdp.pivot_CoM), inc=inc)
-
generic_fns.structure.geometric.stitch_cap_to_cone(structure=structure,
cone_start=cone_start_atom, cap_start=cap_start_atom+1, max_angle=angle,
inc=inc)
+ cone_start_atom = mol.atom_num[-1]+1
+ generic_fns.structure.geometric.generate_vector_dist(mol=mol,
res_name='CON', res_num=3, centre=cdp.pivot_point, R=R, max_angle=angle,
scale=norm(cdp.pivot_CoM), inc=inc)
+ generic_fns.structure.geometric.stitch_cap_to_cone(mol=mol,
cone_start=cone_start_atom, cap_start=cap_start_atom+1, max_angle=angle,
inc=inc)
# Create the PDB file.
print "\nGenerating the PDB file."
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