Author: bugman
Date: Sun Nov 25 20:28:23 2007
New Revision: 3957
URL: http://svn.gna.org/viewcvs/relax?rev=3957&view=rev
Log:
Converted all the methods of the Angles class into module functions.
Modified:
1.3/generic_fns/angles.py
Modified: 1.3/generic_fns/angles.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/angles.py?rev=3957&r1=3956&r2=3957&view=diff
==============================================================================
--- 1.3/generic_fns/angles.py (original)
+++ 1.3/generic_fns/angles.py Sun Nov 25 20:28:23 2007
@@ -30,99 +30,91 @@
+def angles(self, run):
+ """Function for calculating the angle defining the XH vector in the
diffusion frame."""
-class Angles:
- def __init__(self, relax):
- """Class containing the functions relating to angles."""
+ # Test if the run exists.
+ if not run in relax_data_store.run_names:
+ raise RelaxNoPipeError, run
- self.relax = relax
+ # Test if the PDB file has been loaded.
+ if not relax_data_store.pdb.has_key(run):
+ raise RelaxNoPdbError, run
+
+ # Test if sequence data is loaded.
+ if not relax_data_store.res.has_key(run):
+ raise RelaxNoSequenceError, run
+
+ # Test if the diffusion tensor data is loaded.
+ if not relax_data_store.diff.has_key(run):
+ raise RelaxNoTensorError, run
+
+ # Arguments.
+ self.run = run
+
+ # Sphere.
+ if relax_data_store.diff[self.run].type == 'sphere':
+ return
+
+ # Spheroid.
+ elif relax_data_store.diff[self.run].type == 'spheroid':
+ self.spheroid_frame()
+
+ # Ellipsoid.
+ elif relax_data_store.diff[self.run].type == 'ellipsoid':
+ raise RelaxError, "No coded yet."
- def angles(self, run):
- """Function for calculating the angle defining the XH vector in the
diffusion frame."""
+def ellipsoid_frame(self):
+ """Function for calculating the spherical angles of the XH vector in the
ellipsoid frame."""
- # Test if the run exists.
- if not run in relax_data_store.run_names:
- raise RelaxNoPipeError, run
+ # Get the unit vectors Dx, Dy, and Dz of the diffusion tensor axes.
+ Dx, Dy, Dz = self.relax.generic.diffusion_tensor.unit_axes()
- # Test if the PDB file has been loaded.
- if not relax_data_store.pdb.has_key(run):
- raise RelaxNoPdbError, run
+ # Loop over the sequence.
+ for i in xrange(len(relax_data_store.res[self.run])):
+ # Test if the vector exists.
+ if not hasattr(relax_data_store.res[self.run][i], 'xh_vect'):
+ print "No angles could be calculated for residue '" +
`relax_data_store.res[self.run][i].num` + " " +
relax_data_store.res[self.run][i].name + "'."
+ continue
- # Test if sequence data is loaded.
- if not relax_data_store.res.has_key(run):
- raise RelaxNoSequenceError, run
+ # dz and dx direction cosines.
+ dz = dot(Dz, relax_data_store.res[self.run][i].xh_vect)
+ dx = dot(Dx, relax_data_store.res[self.run][i].xh_vect)
- # Test if the diffusion tensor data is loaded.
- if not relax_data_store.diff.has_key(run):
- raise RelaxNoTensorError, run
+ # Calculate the polar angle theta.
+ relax_data_store.res[self.run][i].theta = acos(dz)
- # Arguments.
- self.run = run
-
- # Sphere.
- if relax_data_store.diff[self.run].type == 'sphere':
- return
-
- # Spheroid.
- elif relax_data_store.diff[self.run].type == 'spheroid':
- self.spheroid_frame()
-
- # Ellipsoid.
- elif relax_data_store.diff[self.run].type == 'ellipsoid':
- raise RelaxError, "No coded yet."
+ # Calculate the azimuthal angle phi.
+ relax_data_store.res[self.run][i].phi = acos(dx /
sin(relax_data_store.res[self.run][i].theta))
- def ellipsoid_frame(self):
- """Function for calculating the spherical angles of the XH vector in
the ellipsoid frame."""
+def spheroid_frame(self):
+ """Function for calculating the angle alpha of the XH vector within the
spheroid frame."""
- # Get the unit vectors Dx, Dy, and Dz of the diffusion tensor axes.
- Dx, Dy, Dz = self.relax.generic.diffusion_tensor.unit_axes()
+ # Get the unit vector Dpar of the diffusion tensor axis.
+ Dpar = self.relax.generic.diffusion_tensor.unit_axes()
- # Loop over the sequence.
- for i in xrange(len(relax_data_store.res[self.run])):
- # Test if the vector exists.
- if not hasattr(relax_data_store.res[self.run][i], 'xh_vect'):
- print "No angles could be calculated for residue '" +
`relax_data_store.res[self.run][i].num` + " " +
relax_data_store.res[self.run][i].name + "'."
- continue
+ # Loop over the sequence.
+ for i in xrange(len(relax_data_store.res[self.run])):
+ # Test if the vector exists.
+ if not hasattr(relax_data_store.res[self.run][i], 'xh_vect'):
+ print "No angles could be calculated for residue '" +
`relax_data_store.res[self.run][i].num` + " " +
relax_data_store.res[self.run][i].name + "'."
+ continue
- # dz and dx direction cosines.
- dz = dot(Dz, relax_data_store.res[self.run][i].xh_vect)
- dx = dot(Dx, relax_data_store.res[self.run][i].xh_vect)
-
- # Calculate the polar angle theta.
- relax_data_store.res[self.run][i].theta = acos(dz)
-
- # Calculate the azimuthal angle phi.
- relax_data_store.res[self.run][i].phi = acos(dx /
sin(relax_data_store.res[self.run][i].theta))
+ # Calculate alpha.
+ relax_data_store.res[self.run][i].alpha = acos(dot(Dpar,
relax_data_store.res[self.run][i].xh_vect))
- def spheroid_frame(self):
- """Function for calculating the angle alpha of the XH vector within
the spheroid frame."""
+def wrap_angles(self, angle, lower, upper):
+ """Convert the given angle to be between the lower and upper values."""
- # Get the unit vector Dpar of the diffusion tensor axis.
- Dpar = self.relax.generic.diffusion_tensor.unit_axes()
+ while 1:
+ if angle > upper:
+ angle = angle - upper
+ elif angle < lower:
+ angle = angle + upper
+ else:
+ break
- # Loop over the sequence.
- for i in xrange(len(relax_data_store.res[self.run])):
- # Test if the vector exists.
- if not hasattr(relax_data_store.res[self.run][i], 'xh_vect'):
- print "No angles could be calculated for residue '" +
`relax_data_store.res[self.run][i].num` + " " +
relax_data_store.res[self.run][i].name + "'."
- continue
-
- # Calculate alpha.
- relax_data_store.res[self.run][i].alpha = acos(dot(Dpar,
relax_data_store.res[self.run][i].xh_vect))
-
-
- def wrap_angles(self, angle, lower, upper):
- """Convert the given angle to be between the lower and upper values."""
-
- while 1:
- if angle > upper:
- angle = angle - upper
- elif angle < lower:
- angle = angle + upper
- else:
- break
-
- return angle
+ return angle
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