Author: bugman
Date: Thu Dec 8 16:02:28 2011
New Revision: 15070
URL: http://svn.gna.org/viewcvs/relax?rev=15070&view=rev
Log:
Removal of the frame_order_pcs_only.py script which is now in the pcs_only
directory.
Removed:
branches/frame_order_testing/test_suite/shared_data/frame_order/rotor2/frame_order_pcs_only.py
Removed:
branches/frame_order_testing/test_suite/shared_data/frame_order/rotor2/frame_order_pcs_only.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/shared_data/frame_order/rotor2/frame_order_pcs_only.py?rev=15069&view=auto
==============================================================================
---
branches/frame_order_testing/test_suite/shared_data/frame_order/rotor2/frame_order_pcs_only.py
(original)
+++
branches/frame_order_testing/test_suite/shared_data/frame_order/rotor2/frame_order_pcs_only.py
(removed)
@@ -1,184 +1,0 @@
-# Script for optimising the free rotor frame order test model of CaM.
-
-# Python module imports.
-from numpy import array, float64, transpose, zeros
-from os import sep
-
-# relax module imports.
-from maths_fns.rotation_matrix import euler_to_R_zyz
-
-
-class Analysis:
- def __init__(self):
- """Execute the frame order analysis."""
-
- # Optimise.
- self.optimisation()
-
- # Load the original structure.
- self.original_structure()
-
- # Domain transformation.
- self.transform()
-
- # Display in pymol.
- self.pymol_display()
-
- # Save the state.
- state.save('frame_order_pcs_only', force=True)
-
-
- def optimisation(self):
- """Optimise the frame order model."""
-
- # Create the data pipe.
- pipe.create(pipe_name='frame order', pipe_type='frame order')
-
- # Read the structures.
- structure.read_pdb('1J7O_1st_NH.pdb', dir='..', set_mol_name='N-dom')
- structure.read_pdb('1J7P_1st_NH_rot.pdb', dir='..',
set_mol_name='C-dom')
-
- # Load the spins.
- structure.load_spins('@N')
- structure.load_spins('@H')
-
- # Load the NH vectors.
- structure.vectors(spin_id='@N', attached='H', ave=False)
-
- # Set the values needed to calculate the dipolar constant.
- value.set(1.041 * 1e-10, 'bond_length', spin_id="@N")
- value.set('15N', 'heteronucleus', spin_id="@N")
- value.set('1H', 'proton', spin_id="@N")
-
- # Loop over the alignments.
- ln = ['dy', 'tb', 'tm', 'er']
- for i in range(len(ln)):
- ## Load the RDCs.
- #rdc.read(align_id=ln[i], file='rdc_%s.txt'%ln[i],
res_num_col=2, spin_name_col=5, data_col=6, error_col=7)
-
- # The PCS.
- pcs.read(align_id=ln[i], file='pcs_%s.txt'%ln[i], res_num_col=2,
spin_name_col=5, data_col=6, error_col=7)
-
- # The temperature and field strength.
- temperature(id=ln[i], temp=303)
- frq.set(id=ln[i], frq=900e6)
-
- # Load the N-domain tensors (the full tensors).
- script('../tensors.py')
-
- # Define the domains.
- domain(id='N', spin_id=":1-78")
- domain(id='C', spin_id=":80-144")
-
- # The tensor domains and reductions.
- full = ['Dy N-dom', 'Tb N-dom', 'Tm N-dom', 'Er N-dom']
- red = ['Dy C-dom', 'Tb C-dom', 'Tm C-dom', 'Er C-dom']
- for i in range(len(full)):
- # Initalise the reduced tensor.
- align_tensor.init(tensor=red[i], params=(0,0,0,0,0))
-
- # Set the domain info.
- align_tensor.set_domain(tensor=full[i], domain='N')
- align_tensor.set_domain(tensor=red[i], domain='C')
-
- # Specify which tensor is reduced.
- align_tensor.reduction(full_tensor=full[i], red_tensor=red[i])
-
- # Select the model.
- frame_order.select_model('rotor')
-
- # Set the reference domain.
- frame_order.ref_domain('N')
-
- # Set the initial pivot point.
- pivot = array([ 37.254, 0.5, 16.7465])
- frame_order.pivot(pivot)
-
- # Set the paramagnetic centre.
- paramag.centre(pos=[35.934, 12.194, -4.206])
-
- # Check the minimum.
- cdp.ave_pos_alpha = 1.2017352840543052
- cdp.ave_pos_beta = 5.8477792871424867
- cdp.ave_pos_gamma = 0.65969938507054027
- cdp.axis_theta = 0.69832655838992175
- cdp.axis_phi = 0.89069389677025046
- cdp.cone_sigma_max = 0.52757207875029488
- calc()
- print cdp.chi2
-
- # Optimise.
- #grid_search(inc=5)
- minimise('simplex', constraints=False)
-
- ## Test Monte Carlo simulations.
- #monte_carlo.setup(number=500)
- #monte_carlo.create_data()
- #monte_carlo.initial_values()
- #minimise('simplex', constraints=False)
- #eliminate()
- #monte_carlo.error_analysis()
-
-
- def original_structure(self):
- """Load the original structure into a dedicated data pipe."""
-
- # Create a special data pipe for the original rigid body position.
- pipe.create(pipe_name='orig pos', pipe_type='frame order')
-
- # Load the structure.
- structure.read_pdb('1J7P_1st_NH.pdb', dir='..')
-
-
- def pymol_display(self):
- """Display the results in PyMOL."""
-
- # Switch back to the main data pipe.
- pipe.switch('frame order')
-
- # Load the PDBs of the 2 domains.
- structure.read_pdb('1J7O_1st_NH.pdb', dir='..')
- structure.read_pdb('1J7P_1st_NH_rot.pdb', dir='..')
-
- # Create the cone PDB file.
- frame_order.cone_pdb(file='cone_pcs_only.pdb', force=True)
-
- # Set the domains.
- frame_order.domain_to_pdb(domain='N', pdb='1J7O_1st_NH.pdb')
- frame_order.domain_to_pdb(domain='C', pdb='1J7P_1st_NH_rot.pdb')
-
- # PyMOL.
- pymol.view()
- pymol.command('show spheres')
- pymol.cone_pdb('cone_pcs_only.pdb')
-
-
- def transform(self):
- """Transform the domain to the average position."""
-
- # Switch back to the main data pipe.
- pipe.switch('frame order')
-
- # The rotation matrix.
- R = zeros((3, 3), float64)
- euler_to_R_zyz(cdp.ave_pos_alpha, cdp.ave_pos_beta,
cdp.ave_pos_gamma, R)
- print("Rotation matrix:\n%s\n" % R)
- R = transpose(R)
- print("Inverted rotation:\n%s\n" % R)
- pivot = cdp.pivot
-
- # Create a special data pipe for the average rigid body position.
- pipe.create(pipe_name='ave pos', pipe_type='frame order')
-
- # Load the structure.
- structure.read_pdb('1J7P_1st_NH_rot.pdb', dir='..')
-
- # Rotate all atoms.
- structure.rotate(R=R, origin=pivot)
-
- # Write out the new PDB.
- structure.write_pdb('ave_pos_pcs_only', force=True)
-
-
-# Execute the analysis.
-Analysis()
r15070 - /branches/frame_order_testing/test_suite/shared_data/frame_order/rotor2/frame_order_pcs_only.py