def CoM(pivot_point=None, centre=None):
"""Centre of mass analysis.
This function does an analysis of the centre of mass (CoM) of the N states. This includes
calculating the order parameter associated with the pivot-CoM vector, and the associated
cone of motions. The pivot_point argument must be supplied. If centre is None, then the
CoM will be calculated from the selected parts of the loaded structure. Otherwise it will
be set to the centre arg.
@param pivot_point: The pivot point in the structural file(s).
@type pivot_point: list of float of length 3
@param centre: The optional centre of mass vector.
@type centre: list of float of length 3
"""
# Test if the current data pipe exists.
check_pipe()
# Set the pivot point.
cdp.pivot_point = pivot_point
# The centre has been supplied.
if centre:
cdp.CoM = centre
# Calculate from the structure file.
else:
cdp.CoM = centre_of_mass()
# Calculate the vector between the pivot and CoM points.
cdp.pivot_CoM = array(cdp.CoM, float64) - array(cdp.pivot_point, float64)
# Calculate the unit vector between the pivot and CoM points.
unit_vect = cdp.pivot_CoM / norm(cdp.pivot_CoM)
# Initilise some data structures.
R = zeros((3, 3), float64)
vectors = zeros((cdp.N, 3), float64)
# Loop over the N states.
for c in range(cdp.N):
# Generate the rotation matrix.
euler_to_R_zyz(cdp.alpha[c], cdp.beta[c], cdp.gamma[c], R)
# Rotate the unit vector.
vectors[c] = dot(R, unit_vect)
# Multiply by the probability.
vectors[c] = vectors[c] * cdp.probs[c]
# Average of the unit vectors.
cdp.ave_unit_pivot_CoM = sum(vectors)
# The length reduction.
cdp.ave_pivot_CoM_red = norm(cdp.ave_unit_pivot_CoM)
# The aveage pivot-CoM vector.
cdp.ave_pivot_CoM = norm(cdp.pivot_CoM) * cdp.ave_unit_pivot_CoM
# The full length rotated pivot-CoM vector.
cdp.full_ave_pivot_CoM = cdp.ave_pivot_CoM / cdp.ave_pivot_CoM_red
# The cone angle for diffusion on an axially symmetric cone.
cdp.theta_diff_on_cone = acos(cdp.ave_pivot_CoM_red)
cdp.S_diff_on_cone = (3.0 * cos(cdp.theta_diff_on_cone)**2 - 1.0) / 2.0
# The cone angle and order parameter for diffusion in an axially symmetric cone.
cdp.theta_diff_in_cone = acos(2. * cdp.ave_pivot_CoM_red - 1.)
cdp.S_diff_in_cone = cos(
cdp.theta_diff_in_cone) * (1 + cos(cdp.theta_diff_in_cone)) / 2.0
# Print out.
print("\n%-40s %-20s" % ("Pivot point:", repr(cdp.pivot_point)))
print("%-40s %-20s" %
("Moving domain CoM (prior to rotation):", repr(cdp.CoM)))
print("%-40s %-20s" % ("Pivot-CoM vector", repr(cdp.pivot_CoM)))
print("%-40s %-20s" % ("Pivot-CoM unit vector:", repr(unit_vect)))
print("%-40s %-20s" % ("Average of the unit pivot-CoM vectors:",
repr(cdp.ave_unit_pivot_CoM)))
print("%-40s %-20s" %
("Average of the pivot-CoM vector:", repr(cdp.ave_pivot_CoM)))
print("%-40s %-20s" % ("Full length rotated pivot-CoM vector:",
repr(cdp.full_ave_pivot_CoM)))
print("%-40s %-20s" %
("Length reduction from unity:", repr(cdp.ave_pivot_CoM_red)))
print("%-40s %.5f rad (%.5f deg)" %
("Cone angle (diffusion on a cone)", cdp.theta_diff_on_cone,
cdp.theta_diff_on_cone / (2 * pi) * 360.))
print("%-40s S_cone = %.5f (S^2 = %.5f)" %
("S_cone (diffusion on a cone)", cdp.S_diff_on_cone,
cdp.S_diff_on_cone**2))
print("%-40s %.5f rad (%.5f deg)" %
("Cone angle (diffusion in a cone)", cdp.theta_diff_in_cone,
cdp.theta_diff_in_cone / (2 * pi) * 360.))
print("%-40s S_cone = %.5f (S^2 = %.5f)" %
("S_cone (diffusion in a cone)", cdp.S_diff_in_cone,
cdp.S_diff_in_cone**2))
print("\n\n")
# Script for determining the centre of mass of the reference structures.
# The CoM is not the real one as only the N, H, and Ca2+ atoms are used.
# relax module imports.
from pipe_control.structure.mass import centre_of_mass
# The PDB files.
files = [
'1J7O_1st_NH.pdb',
'1J7P_1st_NH.pdb',
'1J7P_1st_NH_rot.pdb'
]
# Loop over each PDB file.
for name in files:
# Create a separate data pipe for each.
pipe.create(name, 'N-state')
# Load the file.
structure.read_pdb(name)
# Calculate the CoM.
centre_of_mass()
def CoM(pivot_point=None, centre=None):
"""Centre of mass analysis.
This function does an analysis of the centre of mass (CoM) of the N states. This includes
calculating the order parameter associated with the pivot-CoM vector, and the associated
cone of motions. The pivot_point argument must be supplied. If centre is None, then the
CoM will be calculated from the selected parts of the loaded structure. Otherwise it will
be set to the centre arg.
@param pivot_point: The pivot point in the structural file(s).
@type pivot_point: list of float of length 3
@param centre: The optional centre of mass vector.
@type centre: list of float of length 3
"""
# Test if the current data pipe exists.
check_pipe()
# Set the pivot point.
cdp.pivot_point = pivot_point
# The centre has been supplied.
if centre:
cdp.CoM = centre
# Calculate from the structure file.
else:
cdp.CoM = centre_of_mass()
# Calculate the vector between the pivot and CoM points.
cdp.pivot_CoM = array(cdp.CoM, float64) - array(cdp.pivot_point, float64)
# Calculate the unit vector between the pivot and CoM points.
unit_vect = cdp.pivot_CoM / norm(cdp.pivot_CoM)
# Initilise some data structures.
R = zeros((3, 3), float64)
vectors = zeros((cdp.N, 3), float64)
# Loop over the N states.
for c in range(cdp.N):
# Generate the rotation matrix.
euler_to_R_zyz(cdp.alpha[c], cdp.beta[c], cdp.gamma[c], R)
# Rotate the unit vector.
vectors[c] = dot(R, unit_vect)
# Multiply by the probability.
vectors[c] = vectors[c] * cdp.probs[c]
# Average of the unit vectors.
cdp.ave_unit_pivot_CoM = sum(vectors)
# The length reduction.
cdp.ave_pivot_CoM_red = norm(cdp.ave_unit_pivot_CoM)
# The aveage pivot-CoM vector.
cdp.ave_pivot_CoM = norm(cdp.pivot_CoM) * cdp.ave_unit_pivot_CoM
# The full length rotated pivot-CoM vector.
cdp.full_ave_pivot_CoM = cdp.ave_pivot_CoM / cdp.ave_pivot_CoM_red
# The cone angle for diffusion on an axially symmetric cone.
cdp.theta_diff_on_cone = acos(cdp.ave_pivot_CoM_red)
cdp.S_diff_on_cone = (3.0*cos(cdp.theta_diff_on_cone)**2 - 1.0) / 2.0
# The cone angle and order parameter for diffusion in an axially symmetric cone.
cdp.theta_diff_in_cone = acos(2.*cdp.ave_pivot_CoM_red - 1.)
cdp.S_diff_in_cone = cos(cdp.theta_diff_in_cone) * (1 + cos(cdp.theta_diff_in_cone)) / 2.0
# Print out.
print("\n%-40s %-20s" % ("Pivot point:", repr(cdp.pivot_point)))
print("%-40s %-20s" % ("Moving domain CoM (prior to rotation):", repr(cdp.CoM)))
print("%-40s %-20s" % ("Pivot-CoM vector", repr(cdp.pivot_CoM)))
print("%-40s %-20s" % ("Pivot-CoM unit vector:", repr(unit_vect)))
print("%-40s %-20s" % ("Average of the unit pivot-CoM vectors:", repr(cdp.ave_unit_pivot_CoM)))
print("%-40s %-20s" % ("Average of the pivot-CoM vector:", repr(cdp.ave_pivot_CoM)))
print("%-40s %-20s" % ("Full length rotated pivot-CoM vector:", repr(cdp.full_ave_pivot_CoM)))
print("%-40s %-20s" % ("Length reduction from unity:", repr(cdp.ave_pivot_CoM_red)))
print("%-40s %.5f rad (%.5f deg)" % ("Cone angle (diffusion on a cone)", cdp.theta_diff_on_cone, cdp.theta_diff_on_cone / (2*pi) *360.))
print("%-40s S_cone = %.5f (S^2 = %.5f)" % ("S_cone (diffusion on a cone)", cdp.S_diff_on_cone, cdp.S_diff_on_cone**2))
print("%-40s %.5f rad (%.5f deg)" % ("Cone angle (diffusion in a cone)", cdp.theta_diff_in_cone, cdp.theta_diff_in_cone / (2*pi) *360.))
print("%-40s S_cone = %.5f (S^2 = %.5f)" % ("S_cone (diffusion in a cone)", cdp.S_diff_in_cone, cdp.S_diff_in_cone**2))
print("\n\n")
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License for more details. #
# #
# You should have received a copy of the GNU General Public License #
# along with this program. If not, see <http://www.gnu.org/licenses/>. #
# #
###############################################################################
# Module docstring.
"""Script for determining the centre of mass of the reference structures.
The CoM is not the real one as only the N, H, and Ca2+ atoms are used.
"""
# relax module imports.
from pipe_control.structure.mass import centre_of_mass
# The PDB files.
files = ['1J7O_1st_NH.pdb', '1J7P_1st_NH.pdb', '1J7P_1st_NH_rot.pdb']
# Loop over each PDB file.
for name in files:
# Create a separate data pipe for each.
pipe.create(name, 'N-state')
# Load the file.
structure.read_pdb(name)
# Calculate the CoM.
centre_of_mass()
