Author: bugman
Date: Thu Jan 22 15:48:45 2009
New Revision: 8594
URL: http://svn.gna.org/viewcvs/relax?rev=8594&view=rev
Log:
Modified create_diff_tensor_pdb() for the new structural data design.
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=8594&r1=8593&r2=8594&view=diff
==============================================================================
--- branches/multi_structure/generic_fns/structure/geometric.py (original)
+++ branches/multi_structure/generic_fns/structure/geometric.py Thu Jan 22
15:48:45 2009
@@ -183,6 +183,9 @@
# Add a structure.
structure.add_molecule(name='diff_tensor')
+ # Alias the single molecule from the single model.
+ mol = structure.structural_data[0].mol[0]
+
# Loop over the pipes.
for pipe_index in xrange(len(pipe_list)):
# Get the pipe container.
@@ -228,7 +231,7 @@
CoM = centre_of_mass()
# Add the central atom.
- structure.atom_add(pdb_record='HETATM', atom_num=1,
atom_name='R'+atom_id_ext, res_name='COM', chain_id=chain_id, res_num=res_num,
pos=CoM, segment_id=None, element='C', struct_index=None)
+ mol.atom_add(pdb_record='HETATM', atom_num=1,
atom_name='R'+atom_id_ext, res_name='COM', chain_id=chain_id, res_num=res_num,
pos=CoM, segment_id=None, element='C', struct_index=None)
# Increment the residue number.
res_num = res_num + 1
@@ -241,7 +244,7 @@
print "\nGenerating the geometric object."
# The distribution.
- generate_vector_dist(structure=structure, res_name='TNS',
res_num=res_num, chain_id=chain_id, centre=CoM, R=pipe.diff_tensor.rotation,
warp=pipe.diff_tensor.tensor, scale=scale, inc=20)
+ generate_vector_dist(molecule=mol, res_name='TNS', res_num=res_num,
chain_id=chain_id, centre=CoM, R=pipe.diff_tensor.rotation,
warp=pipe.diff_tensor.tensor, scale=scale, inc=20)
# Increment the residue number.
res_num = res_num + 1
@@ -263,7 +266,7 @@
sim_vectors = None
# Generate the axes representation.
- res_num = generate_vector_residues(structure=structure,
vector=pipe.diff_tensor.Dpar*pipe.diff_tensor.Dpar_unit, atom_name='Dpar',
res_name_vect='AXS', sim_vectors=sim_vectors, chain_id=chain_id,
res_num=res_num, origin=CoM, scale=scale, neg=True)
+ res_num = generate_vector_residues(molecule=mol,
vector=pipe.diff_tensor.Dpar*pipe.diff_tensor.Dpar_unit, atom_name='Dpar',
res_name_vect='AXS', sim_vectors=sim_vectors, chain_id=chain_id,
res_num=res_num, origin=CoM, scale=scale, neg=True)
# Create the three axes of the ellipsoid.
@@ -283,9 +286,9 @@
sim_Dz_vectors = None
# Generate the axes representation.
- res_num = generate_vector_residues(structure=structure,
vector=pipe.diff_tensor.Dx*pipe.diff_tensor.Dx_unit, atom_name='Dpar',
res_name_vect='AXS', sim_vectors=sim_Dx_vectors, chain_id=chain_id,
res_num=res_num, origin=CoM, scale=scale, neg=True)
- res_num = generate_vector_residues(structure=structure,
vector=pipe.diff_tensor.Dy*pipe.diff_tensor.Dy_unit, atom_name='Dpar',
res_name_vect='AXS', sim_vectors=sim_Dy_vectors, chain_id=chain_id,
res_num=res_num, origin=CoM, scale=scale, neg=True)
- res_num = generate_vector_residues(structure=structure,
vector=pipe.diff_tensor.Dz*pipe.diff_tensor.Dz_unit, atom_name='Dpar',
res_name_vect='AXS', sim_vectors=sim_Dz_vectors, chain_id=chain_id,
res_num=res_num, origin=CoM, scale=scale, neg=True)
+ res_num = generate_vector_residues(molecule=mol,
vector=pipe.diff_tensor.Dx*pipe.diff_tensor.Dx_unit, atom_name='Dpar',
res_name_vect='AXS', sim_vectors=sim_Dx_vectors, chain_id=chain_id,
res_num=res_num, origin=CoM, scale=scale, neg=True)
+ res_num = generate_vector_residues(molecule=mol,
vector=pipe.diff_tensor.Dy*pipe.diff_tensor.Dy_unit, atom_name='Dpar',
res_name_vect='AXS', sim_vectors=sim_Dy_vectors, chain_id=chain_id,
res_num=res_num, origin=CoM, scale=scale, neg=True)
+ res_num = generate_vector_residues(molecule=mol,
vector=pipe.diff_tensor.Dz*pipe.diff_tensor.Dz_unit, atom_name='Dpar',
res_name_vect='AXS', sim_vectors=sim_Dz_vectors, chain_id=chain_id,
res_num=res_num, origin=CoM, scale=scale, neg=True)
# Create the PDB file.
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