Author: bugman
Date: Mon Jan 23 13:04:15 2012
New Revision: 15218
URL: http://svn.gna.org/viewcvs/relax?rev=15218&view=rev
Log:
Shifted the last of the CaM frame order test data into its subdirectory.
Added:
branches/frame_order_testing/test_suite/shared_data/frame_order/cam/README
- copied unchanged from r15215,
branches/frame_order_testing/test_suite/shared_data/frame_order/README
branches/frame_order_testing/test_suite/shared_data/frame_order/cam/rotate.log
- copied unchanged from r15215,
branches/frame_order_testing/test_suite/shared_data/frame_order/rotate.log
branches/frame_order_testing/test_suite/shared_data/frame_order/cam/rotate.py
- copied unchanged from r15215,
branches/frame_order_testing/test_suite/shared_data/frame_order/rotate.py
branches/frame_order_testing/test_suite/shared_data/frame_order/cam/rotor2/
- copied from r15215,
branches/frame_order_testing/test_suite/shared_data/frame_order/rotor2/
branches/frame_order_testing/test_suite/shared_data/frame_order/cam/tensors.py
- copied unchanged from r15215,
branches/frame_order_testing/test_suite/shared_data/frame_order/tensors.py
Removed:
branches/frame_order_testing/test_suite/shared_data/frame_order/README
branches/frame_order_testing/test_suite/shared_data/frame_order/rotate.log
branches/frame_order_testing/test_suite/shared_data/frame_order/rotate.py
branches/frame_order_testing/test_suite/shared_data/frame_order/rotor2/
branches/frame_order_testing/test_suite/shared_data/frame_order/tensors.py
Removed:
branches/frame_order_testing/test_suite/shared_data/frame_order/README
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/shared_data/frame_order/README?rev=15217&view=auto
==============================================================================
--- branches/frame_order_testing/test_suite/shared_data/frame_order/README
(original)
+++ branches/frame_order_testing/test_suite/shared_data/frame_order/README
(removed)
@@ -1,73 +1,0 @@
-Frame order test models
-=======================
-
-
-The PDB files
--------------
-
-The frame order test models herein are constructed from the original
reference structures:
-
- N-domain: 1J7O_1st_NH.pdb
- C-domain: 1J7P_1st_NH.pdb
-
-The C-domain structure is used to create distributions of structures
matching the various frame order models. These, together with a set of
alignment tensors, are used to create lists of RDCs and PCSs representing the
various motional models. Then reduced tensors are calculated for the
out-of-frame rotated C-domain structure:
-
- C-domain rotated: 1J7P_1st_NH_rot.pdb
-
-This rotation is to simulate the experimental experience whereby the
starting structures are not located at the rigid body average position (which
in this case is the original C-domain position).
-
-
-The numbers
------------
-
-The pivot point is defined as being between C_alpha of residue Met 76 of
model 1 of 1J7O:
- pos1 = array([40.325, 1.549, 13.359])
-and the backbone N of residue Glu 82 of model 1 of 1J7P:
- pos2 = array([34.183, -0.549, 20.134]).
-The pivot is therefore located at:
- pivot = array([ 37.254, 0.5, 16.7465])
-
-The mass and CoM positions for the 3 structures are:
-
-1J7O_1st_NH.pdb:
- Total mass: M = 1219.2527599999992
- Centre of mass: R = array([ 41.73908729, 6.02977539, -0.76356475])
-
-1J7P_1st_NH.pdb:
- Total mass: M = 1085.12894
- Centre of mass: R = array([ 26.83678091, -12.37906417, 28.34154128])
-
-1J7P_1st_NH_rot.pdb:
- Total mass: M = 1085.12894
- Centre of mass: R = array([ 48.10599831, -9.25645351, 30.74219371])
-
-The rotations used were:
- The pivot rotation matrix is:
- [[ 0.94362558 -0.32261441 -0.07409926]
- [ 0.07417985 0.42425993 -0.90249701]
- [ 0.32259589 0.8461226 0.42427402]]
- Or:
- [[50, 144, 193, 70, 46, 50, 238, 63], [20, 226, 242, 237, 182, 165, 212,
191], [186, 246, 92, 83, 43, 248, 178, 191]]
- [[58, 194, 151, 108, 115, 253, 178, 63], [172, 96, 219, 34, 19, 39, 219,
63], [196, 113, 90, 106, 65, 225, 236, 191]]
- [[242, 101, 13, 63, 105, 165, 212, 63], [50, 198, 13, 178, 111, 19, 235,
63], [205, 235, 128, 52, 78, 39, 219, 63]]
-
- The torsion rotation matrix is:
- [[ 0.01589352 -0.09970727 -0.99488987]
- [ 0.9789945 0.20383041 -0.00478817]
- [ 0.20326622 -0.97391562 0.10085245]]
- Or:
- [[128, 201, 194, 7, 100, 70, 144, 63], [160, 250, 209, 98, 106, 134,
185, 191], [24, 152, 178, 72, 35, 214, 239, 191]]
- [[220, 59, 87, 72, 236, 83, 239, 63], [140, 208, 234, 93, 29, 23, 202,
63], [192, 18, 211, 106, 195, 156, 115, 191]]
- [[26, 230, 62, 166, 160, 4, 202, 63], [96, 107, 207, 20, 81, 42, 239,
191], [168, 128, 140, 89, 119, 209, 185, 63]]
-
- The full rotation matrix is:
- [[-0.31334613 -0.88922808 -0.33329811]
- [ 0.93737972 -0.23341205 -0.2585306 ]
- [ 0.15209688 -0.39343645 0.90668313]]
- Or:
- [[141, 60, 4, 233, 220, 13, 212, 191], [103, 126, 203, 113, 142, 116,
236, 191], [62, 176, 27, 150, 193, 84, 213, 191]]
- [[1, 19, 253, 194, 3, 255, 237, 63], [170, 54, 95, 40, 114, 224, 205,
191], [15, 10, 120, 237, 195, 139, 208, 191]]
- [[3, 166, 36, 16, 233, 119, 195, 63], [89, 32, 75, 19, 16, 46, 217,
191], [21, 155, 147, 87, 140, 3, 237, 63]]
-
-The paramagnetic centre will be assumed to be the second calcium in the
1J7O_1st_NH PDB file (A1001). This position is:
- centre = array([35.934, 12.194, -4.206])
Removed:
branches/frame_order_testing/test_suite/shared_data/frame_order/rotate.log
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/shared_data/frame_order/rotate.log?rev=15217&view=auto
==============================================================================
---
branches/frame_order_testing/test_suite/shared_data/frame_order/rotate.log
(original)
+++
branches/frame_order_testing/test_suite/shared_data/frame_order/rotate.log
(removed)
@@ -1,161 +1,0 @@
-
-
-
- relax repository checkout
-
- Molecular dynamics by NMR data analysis
-
- Copyright (C) 2001-2006 Edward d'Auvergne
- Copyright (C) 2006-2011 the relax development team
-
-This is free software which you are welcome to modify and redistribute under
the conditions of the
-GNU General Public License (GPL). This program, including all modules, is
licensed under the GPL
-and comes with absolutely no warranty. For details type 'GPL' within the
relax prompt.
-
-Assistance in using the relax prompt and scripting interface can be accessed
by typing 'help' within
-the prompt.
-
-Processor fabric: Uni-processor.
-
-script = 'rotate.py'
-----------------------------------------------------------------------------------------------------
-# Script for shifting the C-domain to be out of the average rigid body
position.
-
-# Python module imports.
-from numpy import array, dot, float64, zeros
-from numpy.linalg import norm
-from sys import stdout
-
-# relax module imports.
-from float import floatAsByteArray
-from maths_fns.rotation_matrix import axis_angle_to_R, R_random_axis
-
-
-def to_ieee_754(R):
- """Convert and return the rotation matrix as the full precision IEEE 754
byte array."""
-
- array = []
-
- for i in range(3):
- array.append([])
- for j in range(3):
- array[i].append(floatAsByteArray(R[i, j]))
-
- return array
-
-
-# Init.
-PIVOT_ANGLE = 200.0 / 3.0
-PIVOT_ANGLE = PIVOT_ANGLE * (2.0*pi) / 360
-PIVOT = array([ 37.254, 0.5, 16.7465])
-R_PIVOT = zeros((3, 3), float64)
-
-TORSION_ANGLE = 100 / 3.0
-COM_C = array([ 26.83678091, -12.37906417, 28.34154128])
-R_TORSION = zeros((3, 3), float64)
-VECT_TORSION = COM_C - PIVOT
-VECT_TORSION = VECT_TORSION / norm(VECT_TORSION)
-
-
-# Generate a random pivot rotation.
-R_random_axis(R_PIVOT, PIVOT_ANGLE)
-
-# Print out.
-print("\nThe pivot rotation angle is: %20.40f" % PIVOT_ANGLE)
-print("The pivot rotation angle is: %s" % floatAsByteArray(PIVOT_ANGLE))
-print("\nThe pivot rotation matrix is:\n%s" % R_PIVOT)
-print("Or:")
-float_array = to_ieee_754(R_PIVOT)
-for i in range(3):
- print(float_array[i])
-
-# Generate the torsion angle rotation.
-axis_angle_to_R(VECT_TORSION, TORSION_ANGLE, R_TORSION)
-
-# Print out.
-print("\nThe torsion rotation matrix is:\n%s" % R_TORSION)
-print("Or:")
-float_array = to_ieee_754(R_TORSION)
-for i in range(3):
- print(float_array[i])
-
-# Combine the rotations.
-R = dot(R_TORSION, R_PIVOT)
-
-# Print out.
-print("\nThe full rotation matrix is:\n%s" % R)
-print("Or:")
-float_array = to_ieee_754(R)
-for i in range(3):
- print(float_array[i])
-
-# Create a data pipe.
-pipe.create('rot', 'N-state')
-
-# Load the C-domain PDB file.
-structure.read_pdb('1J7P_1st_NH.pdb')
-
-# Rotate all atoms.
-structure.rotate(R=R, origin=[ 37.254, 0.5, 16.7465])
-
-# Save the rotated PDB file.
-structure.write_pdb('1J7P_1st_NH_rot_new.pdb', force=True)
-----------------------------------------------------------------------------------------------------
-
-The pivot rotation angle is: 1.1635528346628865037359901180025190114975
-The pivot rotation angle is: [28, 185, 192, 147, 233, 157, 242, 63]
-
-The pivot rotation matrix is:
-[[ 0.94362558 -0.32261441 -0.07409926]
- [ 0.07417985 0.42425993 -0.90249701]
- [ 0.32259589 0.8461226 0.42427402]]
-Or:
-[[50, 144, 193, 70, 46, 50, 238, 63], [20, 226, 242, 237, 182, 165, 212,
191], [186, 246, 92, 83, 43, 248, 178, 191]]
-[[58, 194, 151, 108, 115, 253, 178, 63], [172, 96, 219, 34, 19, 39, 219,
63], [196, 113, 90, 106, 65, 225, 236, 191]]
-[[242, 101, 13, 63, 105, 165, 212, 63], [50, 198, 13, 178, 111, 19, 235,
63], [205, 235, 128, 52, 78, 39, 219, 63]]
-
-The torsion rotation matrix is:
-[[ 0.01589352 -0.09970727 -0.99488987]
- [ 0.9789945 0.20383041 -0.00478817]
- [ 0.20326622 -0.97391562 0.10085245]]
-Or:
-[[128, 201, 194, 7, 100, 70, 144, 63], [160, 250, 209, 98, 106, 134, 185,
191], [24, 152, 178, 72, 35, 214, 239, 191]]
-[[220, 59, 87, 72, 236, 83, 239, 63], [140, 208, 234, 93, 29, 23, 202, 63],
[192, 18, 211, 106, 195, 156, 115, 191]]
-[[26, 230, 62, 166, 160, 4, 202, 63], [96, 107, 207, 20, 81, 42, 239, 191],
[168, 128, 140, 89, 119, 209, 185, 63]]
-
-The full rotation matrix is:
-[[-0.31334613 -0.88922808 -0.33329811]
- [ 0.93737972 -0.23341205 -0.2585306 ]
- [ 0.15209688 -0.39343645 0.90668313]]
-Or:
-[[141, 60, 4, 233, 220, 13, 212, 191], [103, 126, 203, 113, 142, 116, 236,
191], [62, 176, 27, 150, 193, 84, 213, 191]]
-[[1, 19, 253, 194, 3, 255, 237, 63], [170, 54, 95, 40, 114, 224, 205, 191],
[15, 10, 120, 237, 195, 139, 208, 191]]
-[[3, 166, 36, 16, 233, 119, 195, 63], [89, 32, 75, 19, 16, 46, 217, 191],
[21, 155, 147, 87, 140, 3, 237, 63]]
-
-relax> pipe.create(pipe_name='rot', pipe_type='N-state')
-
-relax> structure.read_pdb(file='1J7P_1st_NH.pdb', dir=None, read_mol=None,
set_mol_name=None, read_model=None, set_model_num=None, parser='internal')
-
-Internal relax PDB parser.
-Opening the file '1J7P_1st_NH.pdb' for reading.
-Adding molecule '1J7P_1st_NH_mol1' to model None (from the original molecule
number 1 of model None)
-
-relax> structure.rotate(R=array([[-0.31334613, -0.88922808, -0.33329811],
- [ 0.93737972, -0.23341205, -0.2585306 ],
- [ 0.15209688, -0.39343645, 0.90668313]]), origin=[37.254, 0.5,
16.7465])
-
-relax> structure.write_pdb(file='1J7P_1st_NH_rot_new.pdb', dir=None,
model_num=None, force=True)
-Opening the file '1J7P_1st_NH_rot_new.pdb' for writing.
-
-Creating the PDB records
-
-REMARK
-HET
-HETNAM
-FORMUL
-ATOM, HETATM, TER
-CONECT
-
-MASTER
-END
-
Removed:
branches/frame_order_testing/test_suite/shared_data/frame_order/rotate.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/shared_data/frame_order/rotate.py?rev=15217&view=auto
==============================================================================
--- branches/frame_order_testing/test_suite/shared_data/frame_order/rotate.py
(original)
+++ branches/frame_order_testing/test_suite/shared_data/frame_order/rotate.py
(removed)
@@ -1,81 +1,0 @@
-# Script for shifting the C-domain to be out of the average rigid body
position.
-
-# Python module imports.
-from numpy import array, dot, float64, zeros
-from numpy.linalg import norm
-from sys import stdout
-
-# relax module imports.
-from float import floatAsByteArray
-from maths_fns.rotation_matrix import axis_angle_to_R, R_random_axis
-
-
-def to_ieee_754(R):
- """Convert and return the rotation matrix as the full precision IEEE 754
byte array."""
-
- array = []
-
- for i in range(3):
- array.append([])
- for j in range(3):
- array[i].append(floatAsByteArray(R[i, j]))
-
- return array
-
-
-# Init.
-PIVOT_ANGLE = 200.0 / 3.0
-PIVOT_ANGLE = PIVOT_ANGLE * (2.0*pi) / 360
-PIVOT = array([ 37.254, 0.5, 16.7465])
-R_PIVOT = zeros((3, 3), float64)
-
-TORSION_ANGLE = 100 / 3.0
-COM_C = array([ 26.83678091, -12.37906417, 28.34154128])
-R_TORSION = zeros((3, 3), float64)
-VECT_TORSION = COM_C - PIVOT
-VECT_TORSION = VECT_TORSION / norm(VECT_TORSION)
-
-
-# Generate a random pivot rotation.
-R_random_axis(R_PIVOT, PIVOT_ANGLE)
-
-# Print out.
-print("\nThe pivot rotation angle is: %20.40f" % PIVOT_ANGLE)
-print("The pivot rotation angle is: %s" % floatAsByteArray(PIVOT_ANGLE))
-print("\nThe pivot rotation matrix is:\n%s" % R_PIVOT)
-print("Or:")
-float_array = to_ieee_754(R_PIVOT)
-for i in range(3):
- print(float_array[i])
-
-# Generate the torsion angle rotation.
-axis_angle_to_R(VECT_TORSION, TORSION_ANGLE, R_TORSION)
-
-# Print out.
-print("\nThe torsion rotation matrix is:\n%s" % R_TORSION)
-print("Or:")
-float_array = to_ieee_754(R_TORSION)
-for i in range(3):
- print(float_array[i])
-
-# Combine the rotations.
-R = dot(R_TORSION, R_PIVOT)
-
-# Print out.
-print("\nThe full rotation matrix is:\n%s" % R)
-print("Or:")
-float_array = to_ieee_754(R)
-for i in range(3):
- print(float_array[i])
-
-# Create a data pipe.
-pipe.create('rot', 'N-state')
-
-# Load the C-domain PDB file.
-structure.read_pdb('1J7P_1st_NH.pdb')
-
-# Rotate all atoms.
-structure.rotate(R=R, origin=PIVOT)
-
-# Save the rotated PDB file.
-structure.write_pdb('1J7P_1st_NH_rot_new.pdb', force=True)
Removed:
branches/frame_order_testing/test_suite/shared_data/frame_order/tensors.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/shared_data/frame_order/tensors.py?rev=15217&view=auto
==============================================================================
---
branches/frame_order_testing/test_suite/shared_data/frame_order/tensors.py
(original)
+++
branches/frame_order_testing/test_suite/shared_data/frame_order/tensors.py
(removed)
@@ -1,12 +1,0 @@
-# The full alignment tensors (real RDC tensors from CaM-IQ).
-align_tensor.init(tensor='Dy N-dom', params=(0.000622191953772,
1.35210609663e-05, -0.000133742852942, 0.000756743581636, 0.000550729840729),
param_types=2, align_id='dy')
-align_tensor.init(tensor='Dy N-dom', params=(2.35766523882e-05,
2.51785772774e-05, 1.99369755031e-05, 1.86674275393e-05, 2.01343581166e-05),
param_types=2, errors=True, align_id='dy')
-
-align_tensor.init(tensor='Tb N-dom', params=(0.000617222650166,
-0.000438128542649, -0.000375477068228, 0.000760687126774, 0.00034129025543),
param_types=2, align_id='tb')
-align_tensor.init(tensor='Tb N-dom', params=(1.63152405109e-05,
1.86581336167e-05, 1.34361351013e-05, 1.46648001703e-05, 1.76633948194e-05),
param_types=2, errors=True, align_id='tb')
-
-align_tensor.init(tensor='Tm N-dom', params=(-0.000385660891266,
0.000325292994524, 0.000318318888621, -0.00044409190064, -0.000473507384479),
param_types=2, align_id='tm')
-align_tensor.init(tensor='Tm N-dom', params=(1.47916817671e-05,
1.81460089395e-05, 1.27148330285e-05, 1.54915569205e-05, 1.55953362766e-05),
param_types=2, errors=True, align_id='tm')
-
-align_tensor.init(tensor='Er N-dom', params=(-0.000187529356988,
0.000130813961653, 7.14700966617e-05, -0.000264275852243,
-0.000343164086618), param_types=2, align_id='er')
-align_tensor.init(tensor='Er N-dom', params=(1.88459382279e-05,
1.66197299895e-05, 1.69306486018e-05, 2.12500669486e-05, 1.96610327688e-05),
param_types=2, errors=True, align_id='er')
r15218 - in /branches/frame_order_testing/test_suite/shared_data/frame_order: ./ cam/ cam/rotor2/ rotor2/