Author: bugman
Date: Fri Jul 4 10:34:56 2014
New Revision: 24449
URL: http://svn.gna.org/viewcvs/relax?rev=24449&view=rev
Log:
Added titles to the frame order geometric representation PDB files from
frame_order.pdb_model.
These are in the form of special Ti atoms placed 40 Angstrom away from the
pivot along the z-axis of
the system, or shifted 3 more Angstrom for the Monte Carlo simulations.
These are used to label the
alternative representations or the Monte Carlo simulation representations.
The residue type is set
to TLE and this has been registered in the internal structural object.
The pymol.frame_order user function now calls the represent_titles() function
to select these atoms,
hide them, and then add a long descriptive title. The atom name is used to
distinguish between
different titles.
Modified:
branches/frame_order_cleanup/lib/structure/internal/object.py
branches/frame_order_cleanup/pipe_control/pymol_control.py
branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py
Modified: branches/frame_order_cleanup/lib/structure/internal/object.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/structure/internal/object.py?rev=24449&r1=24448&r2=24449&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/structure/internal/object.py
(original)
+++ branches/frame_order_cleanup/lib/structure/internal/object.py Fri
Jul 4 10:34:56 2014
@@ -210,6 +210,7 @@
| CNX | Axis of the cone geometric object |
| CNE | Edge of the cone geometric object |
| AXE | The axis geometric object |
+ | TLE | The title for the object |
|________|________________________________________________|
For any other residues, no description is returned.
@@ -236,6 +237,7 @@
"CNX": "Axis of the cone geometric object",
"CNE": "Edge of the cone geometric object",
"AXE": "The axis geometric object",
+ "TLE": "The title for the object",
}
# Return the description, if one exists.
Modified: branches/frame_order_cleanup/pipe_control/pymol_control.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/pymol_control.py?rev=24449&r1=24448&r2=24449&view=diff
==============================================================================
--- branches/frame_order_cleanup/pipe_control/pymol_control.py (original)
+++ branches/frame_order_cleanup/pipe_control/pymol_control.py Fri Jul 4
10:34:56 2014
@@ -416,6 +416,9 @@
pymol_obj.exec_cmd("hide ('sele')")
pymol_obj.exec_cmd("cmd.delete('sele')")
+ # Set up the titles.
+ represent_titles(id=id)
+
# Set up the pivot points.
represent_pivots(id=id)
@@ -685,6 +688,48 @@
pymol_obj.exec_cmd("cmd.delete('sele')")
+def represent_titles(id=None):
+ """Set up the PyMOL title object representation.
+
+ @keyword id: The PyMOL object ID.
+ @type id: str
+ """
+
+ # Sanity check.
+ if id == None:
+ raise RelaxError("The PyMOL object ID must be supplied.")
+
+ # Frame order positive representation.
+ pymol_obj.exec_cmd("select (%s & resn TLE & name p)" % id)
+ pymol_obj.exec_cmd("hide ('sele')")
+ pymol_obj.exec_cmd("label 'sele', 'Positive representation'")
+ pymol_obj.exec_cmd("cmd.delete('sele')")
+
+ # Frame order negative representation.
+ pymol_obj.exec_cmd("select (%s & resn TLE & name n)" % id)
+ pymol_obj.exec_cmd("hide ('sele')")
+ pymol_obj.exec_cmd("label 'sele', 'Negative representation'")
+ pymol_obj.exec_cmd("cmd.delete('sele')")
+
+ # Frame order MC sim representation.
+ pymol_obj.exec_cmd("select (%s & resn TLE & name mc)" % id)
+ pymol_obj.exec_cmd("hide ('sele')")
+ pymol_obj.exec_cmd("label 'sele', 'MC sim representation'")
+ pymol_obj.exec_cmd("cmd.delete('sele')")
+
+ # Frame order MC sim positive representation.
+ pymol_obj.exec_cmd("select (%s & resn TLE & name p-mc)" % id)
+ pymol_obj.exec_cmd("hide ('sele')")
+ pymol_obj.exec_cmd("label 'sele', 'Positive MC sim representation'")
+ pymol_obj.exec_cmd("cmd.delete('sele')")
+
+ # Frame order MC sim negative representation.
+ pymol_obj.exec_cmd("select (%s & resn TLE & name n-mc)" % id)
+ pymol_obj.exec_cmd("hide ('sele')")
+ pymol_obj.exec_cmd("label 'sele', 'Negative MC sim representation'")
+ pymol_obj.exec_cmd("cmd.delete('sele')")
+
+
def represent_rotor_object(id=None):
"""Set up the PyMOL rotor object representation.
Modified:
branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py?rev=24449&r1=24448&r2=24449&view=diff
==============================================================================
--- branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py
(original)
+++ branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py
Fri Jul 4 10:34:56 2014
@@ -296,6 +296,97 @@
mols[i].atom_add(atom_num=atom_nums[i], atom_name=atom_names[i],
res_name='PIV', res_num=1, pos=pivots[i], element='C', pdb_record='HETATM')
+def add_titles(structure=None, representation=None, displacement=40.0,
sims=False):
+ """Add atoms to be used for the titles for the frame order geometric
objects.
+
+ @keyword structure: The internal structural object to add the
rotor objects to.
+ @type structure: lib.structure.internal.object.Internal
instance
+ @keyword representation: The representation to create. If this is
set to None or 'pos', the standard representation will be created. If set to
'neg', the axis system will be inverted.
+ @type representation: None or str
+ @keyword displacement: The distance away from the pivot point, in
Angstrom, to place the title. The simulation title will be shifted by a few
extra Angstrom to avoid clashes.
+ @type displacement: float
+ @keyword sims: A flag which if True will add the Monte
Carlo simulation pivots to the structural object. There must be one model
for each Monte Carlo simulation already present in the structural object.
+ @type sims: bool
+ """
+
+ # The title atom names.
+ atom_name = None
+ if representation == None and sims:
+ atom_name = 'mc'
+ elif representation == 'pos':
+ if sims:
+ atom_name = 'p-mc'
+ else:
+ atom_name = 'p'
+ elif representation == 'neg':
+ if sims:
+ atom_name = 'n-mc'
+ else:
+ atom_name = 'n'
+
+ # Nothing to do.
+ if atom_name == None:
+ return
+
+ # Avoid name overlaps.
+ if sims:
+ displacement += 3
+
+ # Create the molecule.
+ mol_name = 'titles'
+ structure.add_molecule(name=mol_name)
+
+ # The transformation matrix (identity matrix or inversion matrix).
+ if representation == 'neg':
+ T = -eye(3)
+ else:
+ T = eye(3)
+
+ # The pivot points.
+ pivot1 = generate_pivot(order=1)
+ pivot2 = generate_pivot(order=2)
+
+ # The models to loop over.
+ model_nums = [None]
+ sim_indices = [None]
+ if sims:
+ model_nums = [i+1 for i in range(cdp.sim_number)]
+ sim_indices = list(range(cdp.sim_number))
+
+ # Loop over the models.
+ for i in range(len(model_nums)):
+ # Alias the molecule.
+ mol = structure.get_molecule(mol_name, model=model_nums[i])
+
+ # The single rotor models.
+ if cdp.model not in ['double rotor']:
+ # Generate the rotor axis.
+ if cdp.model in ['rotor', 'free rotor']:
+ axis = create_rotor_axis_alpha(alpha=cdp.axis_alpha,
pivot=pivot1, point=com[i])
+ elif cdp.model in ['iso cone', 'iso cone, free rotor']:
+ axis = create_rotor_axis_spherical(theta=cdp.axis_theta,
phi=cdp.axis_phi)
+ else:
+ axis = create_rotor_axis_euler(alpha=cdp.eigen_alpha,
beta=cdp.eigen_beta, gamma=cdp.eigen_gamma)
+
+ # The double rotor models.
+ else:
+ # Generate the eigenframe of the motion.
+ frame = zeros((3, 3), float64)
+ euler_to_R_zyz(cdp.eigen_alpha, cdp.eigen_beta, cdp.eigen_gamma,
frame)
+
+ # Add the z axis.
+ axis = frame[:, 2]
+
+ # Transform the central axis.
+ axis = dot(T, axis)
+
+ # The label position.
+ pos = pivot1 + displacement*axis
+
+ # Add the atom.
+ mol.atom_add(atom_name=atom_name, res_name='TLE', res_num=1,
pos=pos, element='Ti', pdb_record='HETATM')
+
+
def add_rotors(structure=None, sims=False):
"""Add all rotor objects for the current frame order model to the
structural object.
@@ -627,6 +718,9 @@
if cdp.model not in ['rotor', 'free rotor', 'double rotor']:
add_cones(structure=structures[i],
representation=representation[i], size=size, inc=inc, sims=sims[i])
+ # Add atoms for creating titles.
+ add_titles(structure=structures[i],
representation=representation[i], sims=sims[i])
+
# Create the PDB file.
if format == 'PDB':
pdb_file = open_write_file(file_root[i]+'.pdb', dir,
compress_type=compress_type, force=force)
r24449 - in /branches/frame_order_cleanup: lib/structure/internal/ pipe_control/ specific_analyses/frame_order/