Author: macraild
Date: Wed Nov 8 19:20:15 2006
New Revision: 2776
URL: http://svn.gna.org/viewcvs/relax?rev=2776&view=rev
Log:
Preliminary implimentation of auto-scaling for viewing tensors.
As discussed at:
https://mail.gna.org/public/relax-devel/2006-10/msg00204.html
This revision provides a simple scaling based on molecular mass.
This option is selected with the scale='mass' option to the
pdb.create_tensor_pdb() command
Modified:
branches/tensor_pdb/generic_fns/pdb.py
branches/tensor_pdb/prompt/pdb.py
Modified: branches/tensor_pdb/generic_fns/pdb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/tensor_pdb/generic_fns/pdb.py?rev=2776&r1=2775&r2=2776&view=diff
==============================================================================
--- branches/tensor_pdb/generic_fns/pdb.py (original)
+++ branches/tensor_pdb/generic_fns/pdb.py Wed Nov 8 19:20:15 2006
@@ -169,8 +169,21 @@
else:
raise RelaxError, "The mass of the element " + `element` + " has
not yet been programmed into relax."
-
- def centre_of_mass(self):
+
+ def autoscale_tensor(self,method=None):
+ """Automatically determine an appropriate scaling factor for display
+ of the diffusion tensor"""
+
+ if method == 'mass':
+ com, mass = self.centre_of_mass(return_mass=True)
+ scale = mass * 6.8e-11
+ return scale
+
+ warn(RelaxWarning("Autoscale method %s not implimented. Reverting to
scale=1.8e-6 A.s" % method))
+ return 1.8e-6
+
+
+ def centre_of_mass(self, return_mass=False):
"""Calculate and return the centre of mass of the structure."""
# Print out.
@@ -228,7 +241,10 @@
print " Centre of mass: R = " + `R`
# Return the centre of mass.
- return R
+ if return_mass:
+ return R,M
+ else:
+ return R
def create_tensor_pdb(self, run=None, scale=1.8e-6, file=None, dir=None,
force=0):
@@ -239,6 +255,10 @@
self.file = file
self.dir = dir
self.force = force
+ if scale == 'mass':
+ self.scale = self.autoscale_tensor(scale)
+ else:
+ self.scale = scale
# Test if the run exists.
if not run in self.relax.data.run_names:
@@ -335,7 +355,7 @@
vector = dot(self.relax.data.diff[self.run].tensor,
vector)
# Scale the vector.
- vector = vector * scale
+ vector = vector * self.scale
# Position relative to the centre of mass.
pos = R + vector
@@ -372,10 +392,10 @@
if self.relax.data.diff[self.run].type == 'spheroid':
# Print out.
print "\nGenerating the unique axis of the diffusion tensor."
- print " Scaling factor: " + `scale`
+ print " Scaling factor: " +
`self.scale`
# Create the axis.
- self.generate_spheroid_axes(scale=scale, chain_id=chain_id,
res_num=res_num, R=R)
+ self.generate_spheroid_axes(chain_id=chain_id,
res_num=res_num, R=R)
# Simulations.
if hasattr(self.relax.data.diff[self.run], 'tm_sim'):
@@ -385,17 +405,17 @@
# Create each MC simulation axis as a new residue.
for i in
xrange(len(self.relax.data.diff[self.run].tm_sim)):
res_num = res_num + 1
- self.generate_spheroid_axes(scale=scale,
chain_id=chain_id, res_num=res_num, R=R, i=i)
+ self.generate_spheroid_axes(chain_id=chain_id,
res_num=res_num, R=R, i=i)
# Create the three axes of the ellipsoid.
if self.relax.data.diff[self.run].type == 'ellipsoid':
# Print out.
print "Generating the three axes of the ellipsoid."
- print " Scaling factor: " + `scale`
+ print " Scaling factor: " +
`self.scale`
# Create the axes.
- self.generate_ellipsoid_axes(scale=scale, chain_id=chain_id,
res_num=res_num, R=R)
+ self.generate_ellipsoid_axes(chain_id=chain_id,
res_num=res_num, R=R)
# Simulations.
if hasattr(self.relax.data.diff[self.run], 'tm_sim'):
@@ -405,7 +425,7 @@
# Create each MC simulation axis as a new residue.
for i in
xrange(len(self.relax.data.diff[self.run].tm_sim)):
res_num = res_num + 1
- self.generate_ellipsoid_axes(scale=scale,
chain_id=chain_id, res_num=res_num, R=R, i=i)
+ self.generate_ellipsoid_axes(chain_id=chain_id,
res_num=res_num, R=R, i=i)
# Terminate the chain (the TER record).
@@ -436,11 +456,9 @@
tensor_pdb_file.close()
- def generate_ellipsoid_axes(self, scale=None, chain_id=None,
res_num=None, R=None, i=None):
+ def generate_ellipsoid_axes(self, chain_id=None, res_num=None, R=None,
i=None):
"""Generate the AXS and SIM residues of the ellipsoidal PDB tensor
representation.
- @param scale: The scaling factor (with the units of second
Angstroms).
- @type scale: float
@param chain_id: The chain identification code.
@type chain_id: str
@param res_num: The residue number.
@@ -451,8 +469,10 @@
@type i: int
@return: None
"""
-
+
+
# Alias the relevant data.
+ scale = self.scale
if i == None:
Dx = self.relax.data.diff[self.run].Dx
Dy = self.relax.data.diff[self.run].Dy
@@ -527,11 +547,9 @@
print " Dz vector (scaled + shifted to R): " + `Dz_vect`
- def generate_spheroid_axes(self, scale=None, chain_id=None,
res_num=None, R=None, i=None):
+ def generate_spheroid_axes(self, chain_id=None, res_num=None, R=None,
i=None):
"""Generate the AXS and SIM residues of the spheroid PDB tensor
representation.
- @param scale: The scaling factor (with the units of second
Angstroms).
- @type scale: float
@param chain_id: The chain identification code.
@type chain_id: str
@param res_num: The residue number.
@@ -544,6 +562,7 @@
"""
# Alias the relevant data.
+ scale = self.scale
if i == None:
Dpar = self.relax.data.diff[self.run].Dpar
Dpar_unit = self.relax.data.diff[self.run].Dpar_unit
Modified: branches/tensor_pdb/prompt/pdb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/tensor_pdb/prompt/pdb.py?rev=2776&r1=2775&r2=2776&view=diff
==============================================================================
--- branches/tensor_pdb/prompt/pdb.py (original)
+++ branches/tensor_pdb/prompt/pdb.py Wed Nov 8 19:20:15 2006
@@ -150,8 +150,8 @@
raise RelaxStrError, ('run', run)
# Scaling.
- if type(scale) != float and type(scale) != int:
- raise RelaxNumError, ('scaling factor', scale)
+ #if type(scale) != float and type(scale) != int:
+ # raise RelaxNumError, ('scaling factor', scale)
# File name.
if type(file) != str:
r2776 - in /branches/tensor_pdb: generic_fns/pdb.py prompt/pdb.py