Author: bugman
Date: Thu Jul 3 15:04:20 2014
New Revision: 24433
URL: http://svn.gna.org/viewcvs/relax?rev=24433&view=rev
Log:
Redesign of the average domain position part of the frame_order.pdb_model
user function.
The Monte Carlo simulations are now represented. If the file root is set to
the default of
'ave_pos', then these will be placed in the file 'ave_pos.pdb', or a
compressed version. Each
simulation is in a different model, matching the geometric representation
'*_sim.pdb' files. The
original structure is copied for each model, and then rotated to the MC
simulation average position.
Modified:
branches/frame_order_cleanup/pipe_control/pymol_control.py
branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py
branches/frame_order_cleanup/user_functions/pymol_control.py
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=24433&r1=24432&r2=24433&view=diff
==============================================================================
--- branches/frame_order_cleanup/pipe_control/pymol_control.py (original)
+++ branches/frame_order_cleanup/pipe_control/pymol_control.py Thu Jul 3
15:04:20 2014
@@ -353,6 +353,7 @@
# Find all PDB files.
pdb_files = find_pdb_files(path=path, file_root=root)
+ pdb_files += find_pdb_files(path=path, file_root=root+'_sim')
# Read in the PDB files.
print pdb_files
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=24433&r1=24432&r2=24433&view=diff
==============================================================================
--- branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py
(original)
+++ branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py
Thu Jul 3 15:04:20 2014
@@ -446,26 +446,70 @@
# Printout.
subsection(file=sys.stdout, text="Creating a PDB file with the moving
domains shifted to the average position.")
- # Make a copy of the structural object (so as to preserve the original
structure).
- structure = deepcopy(cdp.structure)
-
- # First rotate the moving domain to the average position.
- R = zeros((3, 3), float64)
- if hasattr(cdp, 'ave_pos_alpha'):
- euler_to_R_zyz(cdp.ave_pos_alpha, cdp.ave_pos_beta,
cdp.ave_pos_gamma, R)
- else:
- euler_to_R_zyz(0.0, cdp.ave_pos_beta, cdp.ave_pos_gamma, R)
- origin = pipe_centre_of_mass(atom_id=domain_moving(), verbosity=0)
- structure.rotate(R=R, origin=origin, atom_id=domain_moving())
-
- # Then translate the moving domain.
- structure.translate(T=[cdp.ave_pos_x, cdp.ave_pos_y, cdp.ave_pos_z],
atom_id=domain_moving())
-
- # Output to PDB format.
- if format == 'PDB':
- file = open_write_file(file_name=file+'.pdb', dir=dir,
compress_type=compress_type, force=force)
- structure.write_pdb(file=file)
- file.close()
+ # Initialise.
+ titles = []
+ sims = []
+ file_root = []
+ models = []
+
+ # The real average position.
+ titles.append("real average position")
+ sims.append(False)
+ file_root.append(file)
+ models.append([None])
+
+ # The positive MC simulation representation.
+ if hasattr(cdp, 'sim_number'):
+ titles.append("MC simulation representation")
+ sims.append(True)
+ file_root.append("%s_sim" % file)
+ models.append([i+1 for i in range(cdp.sim_number)])
+
+ # Loop over each representation and add the contents.
+ for i in range(len(titles)):
+ # Printout.
+ subsubsection(file=sys.stdout, text="Creating the %s." % titles[i])
+
+ # Make a copy of the structural object (so as to preserve the
original structure).
+ structure = deepcopy(cdp.structure)
+
+ # Loop over each model.
+ for j in range(len(models[i])):
+ # Create or set the models, if needed.
+ if models[i][j] == 1:
+ structure.set_model(model_new=1)
+ elif models[i][j] != None:
+ structure.add_model(model=models[i][j])
+
+ # Loop over each model.
+ for j in range(len(models[i])):
+ # First rotate the moving domain to the average position.
+ R = zeros((3, 3), float64)
+ if hasattr(cdp, 'ave_pos_alpha'):
+ if sims[i]:
+ euler_to_R_zyz(cdp.ave_pos_alpha_sim[j],
cdp.ave_pos_beta_sim[j], cdp.ave_pos_gamma_sim[j], R)
+ else:
+ euler_to_R_zyz(cdp.ave_pos_alpha, cdp.ave_pos_beta,
cdp.ave_pos_gamma, R)
+ else:
+ if sims[i]:
+ euler_to_R_zyz(0.0, cdp.ave_pos_beta_sim[j],
cdp.ave_pos_gamma_sim[j], R)
+ else:
+ euler_to_R_zyz(0.0, cdp.ave_pos_beta, cdp.ave_pos_gamma,
R)
+ origin = pipe_centre_of_mass(atom_id=domain_moving(),
verbosity=0)
+ structure.rotate(R=R, origin=origin, model=models[i][j],
atom_id=domain_moving())
+
+ # Then translate the moving domain.
+ if sims[i]:
+ T = [cdp.ave_pos_x_sim[j], cdp.ave_pos_y_sim[j],
cdp.ave_pos_z_sim[j]]
+ else:
+ T = [cdp.ave_pos_x, cdp.ave_pos_y, cdp.ave_pos_z]
+ structure.translate(T=T, model=models[i][j],
atom_id=domain_moving())
+
+ # Output to PDB format.
+ if format == 'PDB':
+ pdb_file = open_write_file(file_name=file_root[i]+'.pdb',
dir=dir, compress_type=compress_type, force=force)
+ structure.write_pdb(file=pdb_file)
+ pdb_file.close()
def create_distribution(format='PDB', file=None, dir=None, compress_type=0,
force=False):
Modified: branches/frame_order_cleanup/user_functions/pymol_control.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/user_functions/pymol_control.py?rev=24433&r1=24432&r2=24433&view=diff
==============================================================================
--- branches/frame_order_cleanup/user_functions/pymol_control.py
(original)
+++ branches/frame_order_cleanup/user_functions/pymol_control.py Thu
Jul 3 15:04:20 2014
@@ -189,7 +189,11 @@
# Description.
uf.desc.append(Desc_container())
uf.desc[-1].add_paragraph("This user function is designed to be combined
with the frame_order.pdb_model user function. It will take the three PDB
representations created by frame_order.pdb_model - the molecular structure
with the averaged domain positions, the frame order dynamics representation
files, and the moving domain distribution file - and display them in PyMOL.
Rather than loading the three representations into PyMOL manually, this user
function will change the representation to significantly improve the
visualisation.")
-uf.desc[-1].add_paragraph("For the frame order representation files,if the
file root is left to the default of 'frame_order' then all of the following
files will be loaded: 'frame_order.pdb', 'frame_order_pos.pdb',
'frame_order_neg.pdb', 'frame_order_sim.pdb', 'frame_order_sim_pos.pdb',
'frame_order_sim_neg.pdb'. The user function will not only search for these
files, but also all *.gz and *.bz2 versions of these files. This is to
support all output files from the frame_order.pdb_model user function.")
+uf.desc[-1].add_paragraph("For the frame order position files, if the file
roots are left to the defaults then the following files will be loaded:")
+uf.desc[-1].add_list_element("The file root 'ave_pos' will load the
'ave_pos.pdb' and 'ave_pos_sim.pdb' files.")
+uf.desc[-1].add_list_element("The file root 'frame_order' will load the
'frame_order.pdb', 'frame_order_pos.pdb', 'frame_order_neg.pdb',
'frame_order_sim.pdb', 'frame_order_sim_pos.pdb' and
'frame_order_sim_neg.pdb' files.")
+uf.desc[-1].add_list_element("The file root 'dist' will load the 'dist.pdb'
file.")
+uf.desc[-1].add_paragraph("The user function will not only search for these
files, but also all *.gz and *.bz2 versions of these files. This is to
support all output files from the frame_order.pdb_model user function.")
uf.backend = pymol_control.frame_order
uf.menu_text = "&frame_order"
uf.gui_icon = "relax.frame_order"
r24433 - in /branches/frame_order_cleanup: pipe_control/ specific_analyses/frame_order/ user_functions/