Author: bugman
Date: Fri Apr 4 17:57:34 2014
New Revision: 22653
URL: http://svn.gna.org/viewcvs/relax?rev=22653&view=rev
Log:
Updated the ancient
test_suite/shared_data/frame_order/cam/rotor2/pcs_only/frame_order.py script.
This now matches the script of its parent directory.
Modified:
trunk/test_suite/shared_data/frame_order/cam/rotor2/pcs_only/frame_order.py
Modified:
trunk/test_suite/shared_data/frame_order/cam/rotor2/pcs_only/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/rotor2/pcs_only/frame_order.py?rev=22653&r1=22652&r2=22653&view=diff
==============================================================================
---
trunk/test_suite/shared_data/frame_order/cam/rotor2/pcs_only/frame_order.py
(original)
+++
trunk/test_suite/shared_data/frame_order/cam/rotor2/pcs_only/frame_order.py
Fri Apr 4 17:57:34 2014
@@ -1,34 +1,12 @@
# Script for optimising the free rotor frame order test model of CaM.
# Python module imports.
-from numpy import array, float64, transpose, zeros
-
-# relax module imports.
-from lib.geometry.rotations import euler_to_R_zyz
+from numpy import array
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', force=True)
-
-
- def optimisation(self):
- """Optimise the frame order model."""
# Create the data pipe.
pipe.create(pipe_name='frame order', pipe_type='frame order')
@@ -37,26 +15,25 @@
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')
+ # Set up the 15N and 1H spins.
+ structure.load_spins(spin_id='@N', ave_pos=False)
+ structure.load_spins(spin_id='@H', ave_pos=False)
+ spin.isotope(isotope='15N', spin_id='@N')
+ spin.isotope(isotope='1H', spin_id='@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")
+ # Define the magnetic dipole-dipole relaxation interaction.
+ interatom.define(spin_id1='@N', spin_id2='@H', direct_bond=True)
+ interatom.set_dist(spin_id1='@N', spin_id2='@H', ave_dist=1.041 *
1e-10)
+ interatom.unit_vectors()
# 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], dir='..',
res_num_col=2, spin_name_col=5, data_col=6, error_col=7)
+ # Load the RDCs.
+ #rdc.read(align_id=ln[i], file='rdc_%s.txt'%ln[i], dir='..',
spin_id1_col=1, spin_id2_col=2, data_col=3, error_col=4)
# The PCS.
- pcs.read(align_id=ln[i], file='pcs_%s.txt'%ln[i], dir='..',
res_num_col=2, spin_name_col=5, data_col=6, error_col=7)
+ pcs.read(align_id=ln[i], file='pcs_%s.txt'%ln[i], dir='..',
mol_name_col=1, res_num_col=2, spin_name_col=5, data_col=6, error_col=7)
# The temperature and field strength.
spectrometer.temperature(id=ln[i], temp=303)
@@ -67,14 +44,15 @@
# Define the domains.
domain(id='N', spin_id=":1-78")
- domain(id='C', spin_id=":80-144")
+ domain(id='C', spin_id=":80-148")
# 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']
+ ids = ['dy', 'tb', 'tm', 'er']
for i in range(len(full)):
# Initialise the reduced tensor.
- align_tensor.init(tensor=red[i], params=(0, 0, 0, 0, 0))
+ align_tensor.init(tensor=red[i], align_id=ids[i], params=(0, 0,
0, 0, 0))
# Set the domain info.
align_tensor.set_domain(tensor=full[i], domain='N')
@@ -86,15 +64,22 @@
# Select the model.
frame_order.select_model('rotor')
+ # Set up the mechanics of the displacement to the average domain
position.
+ frame_order.average_position(pivot='motional', translation=False)
+
# 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)
+ frame_order.pivot(pivot, fix=True)
# Set the paramagnetic centre.
paramag.centre(pos=[35.934, 12.194, -4.206])
+
+ # The optimisation settings.
+ frame_order.num_int_pts(num=50)
+ frame_order.quad_int(flag=False)
# Check the minimum.
cdp.ave_pos_alpha = 1.2017352840543052
@@ -104,7 +89,7 @@
cdp.axis_phi = 0.89069389677025046
cdp.cone_sigma_max = 0.52757207875029488
calc()
- print cdp.chi2
+ print("\nchi2: %s" % repr(cdp.chi2))
# Optimise.
#grid_search(inc=5)
@@ -119,64 +104,17 @@
#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.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')
+ # Create the PDB representation.
+ frame_order.pdb_model(force=True)
# PyMOL.
pymol.view()
pymol.command('show spheres')
- pymol.cone_pdb('cone.pdb')
+ pymol.cone_pdb('frame_order.pdb')
+ # Save the state.
+ state.save('frame_order', force=True)
- 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', force=True)
# Execute the analysis.
r22653 - /trunk/test_suite/shared_data/frame_order/cam/rotor2/pcs_only/frame_order.py