Author: bugman
Date: Sat Jul 5 11:54:54 2008
New Revision: 6731
URL: http://svn.gna.org/viewcvs/relax?rev=6731&view=rev
Log:
Deleted all the PDB terminate() function calls and methods.
These are not necessary as the TER record is now automatically generated.
Modified:
branches/rdc_analysis/generic_fns/structure/api_base.py
branches/rdc_analysis/generic_fns/structure/geometric.py
branches/rdc_analysis/generic_fns/structure/internal.py
branches/rdc_analysis/specific_fns/n_state_model.py
Modified: branches/rdc_analysis/generic_fns/structure/api_base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/rdc_analysis/generic_fns/structure/api_base.py?rev=6731&r1=6730&r2=6731&view=diff
==============================================================================
--- branches/rdc_analysis/generic_fns/structure/api_base.py (original)
+++ branches/rdc_analysis/generic_fns/structure/api_base.py Sat Jul 5
11:54:54 2008
@@ -231,18 +231,6 @@
return len(self.structural_data)
- def terminate(self, model=None):
- """Prototype method stub for terminating the structural chain.
-
- @keyword model: The model to add the atom to. If not supplied
and multiple models
- exist, then the atom will be added to all models.
- @type model: None or int
- """
-
- # Raise the error.
- raise RelaxImplementError
-
-
def write_pdb(self, file):
"""Prototype method stub for the creation of a PDB file from the
structural data.
Modified: branches/rdc_analysis/generic_fns/structure/geometric.py
URL:
http://svn.gna.org/viewcvs/relax/branches/rdc_analysis/generic_fns/structure/geometric.py?rev=6731&r1=6730&r2=6731&view=diff
==============================================================================
--- branches/rdc_analysis/generic_fns/structure/geometric.py (original)
+++ branches/rdc_analysis/generic_fns/structure/geometric.py Sat Jul 5
11:54:54 2008
@@ -283,12 +283,6 @@
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=R, 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=R, 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=R, scale=scale, neg=True)
-
-
- # Terminate the chain (the TER record).
- #######################################
-
- structure.terminate(atom_id_ext=atom_id_ext, res_num=res_num)
# Create the PDB file.
Modified: branches/rdc_analysis/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/branches/rdc_analysis/generic_fns/structure/internal.py?rev=6731&r1=6730&r2=6731&view=diff
==============================================================================
--- branches/rdc_analysis/generic_fns/structure/internal.py (original)
+++ branches/rdc_analysis/generic_fns/structure/internal.py Sat Jul 5
11:54:54 2008
@@ -640,34 +640,6 @@
self.__fill_object_from_pdb(records, len(self.structural_data)-1)
- def terminate(self, model=None):
- """Method for terminating the chain by adding a TER record to the
structural data object.
-
- The residue number and name are taken from the last atom in the
current structural object.
-
-
- @keyword model: The model to add the atom to. If not supplied
and multiple models
- exist, then the atom will be added to all models.
- @type model: None or int
- """
-
- # Loop over the models.
- for i in xrange(len(self.structural_data)):
- # Alias the structure.
- struct = self.structural_data[i]
-
- # Skip non-matching models.
- if model != None and model != struct.model:
- continue
-
- # The name and number of the last residue.
- res_name = struct.res_name[-1]
- res_num = struct.res_num[-1]
-
- # Add the TER 'atom'.
- self.atom_add(pdb_record='TER', res_name=res_name,
res_num=res_num, model=i)
-
-
def write_pdb(self, file, struct_index=None):
"""Method for the creation of a PDB file from the structural data.
Modified: branches/rdc_analysis/specific_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/rdc_analysis/specific_fns/n_state_model.py?rev=6731&r1=6730&r2=6731&view=diff
==============================================================================
--- branches/rdc_analysis/specific_fns/n_state_model.py (original)
+++ branches/rdc_analysis/specific_fns/n_state_model.py Sat Jul 5 11:54:54
2008
@@ -245,9 +245,6 @@
print "\nGenerating the cone cap."
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,
max_angle=angle, inc=inc)
-
- # Terminate the chain.
- structure.terminate(res_num=res_num)
# Create the PDB file.
print "\nGenerating the PDB file."
r6731 - in /branches/rdc_analysis: generic_fns/structure/ specific_fns/