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List: relax-commits
Subject: r2693 - /branches/tensor_pdb/generic_fns/pdb.py
From: edward.dauvergne () domain ! hid
Date: 2006-10-29 5:10:10
Message-ID: E1Ge2w0-0007ux-1v () domain ! hid
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Author: bugman
Date: Sun Oct 29 06:10:07 2006
New Revision: 2693
URL: http://svn.gna.org/viewcvs/relax?rev=2693&view=rev
Log:
Because of the diffusion tensor symmetry, the axes where extended in both the pos and \
neg directions.
Modified:
branches/tensor_pdb/generic_fns/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=2693&r1=2692&r2=2693&view=diff
==============================================================================
--- branches/tensor_pdb/generic_fns/pdb.py (original)
+++ branches/tensor_pdb/generic_fns/pdb.py Sun Oct 29 06:10:07 2006
@@ -262,12 +262,18 @@
# The Dpar vector.
Dpar_vect = self.relax.data.diff[self.run].Dpar_unit * \
self.relax.data.diff[self.run].Dpar * scale
- # Position relative to the center of mass.
+ # The negative Dpar vector.
+ Dpar_vect_neg = -Dpar_vect
+
+ # Position of both vectors relative to the center of mass.
Dpar_vect = R + Dpar_vect
+ Dpar_vect_neg = R + Dpar_vect_neg
# Add the atom and connect it to the center of mass.
self.atom_add(atom_id='Dpar', element='C', pos=Dpar_vect)
+ self.atom_add(atom_id='Dpar_neg', element='C', pos=Dpar_vect_neg)
self.atom_connect(atom_id='Dpar', bonded_id='R')
+ self.atom_connect(atom_id='Dpar_neg', bonded_id='R')
# Print out.
print " Scaling factor: " + `scale`
@@ -284,18 +290,32 @@
Dy_vect = self.relax.data.diff[self.run].Dy_unit * \
self.relax.data.diff[self.run].Dy * scale
Dz_vect = self.relax.data.diff[self.run].Dz_unit * \
self.relax.data.diff[self.run].Dz * scale
+ # The negative Dx, Dy, and Dz vectors.
+ Dx_vect_neg = -Dx_vect
+ Dy_vect_neg = -Dy_vect
+ Dz_vect_neg = -Dz_vect
+
# Positions relative to the center of mass.
Dx_vect = R + Dx_vect
Dy_vect = R + Dy_vect
Dz_vect = R + Dz_vect
+ Dx_vect_neg = R + Dx_vect_neg
+ Dy_vect_neg = R + Dy_vect_neg
+ Dz_vect_neg = R + Dz_vect_neg
# Add the atoms and connect them to the center of mass.
self.atom_add(atom_id='Dx', element='C', pos=Dx_vect)
self.atom_add(atom_id='Dy', element='C', pos=Dy_vect)
self.atom_add(atom_id='Dz', element='C', pos=Dz_vect)
+ self.atom_add(atom_id='Dx_neg', element='C', pos=Dx_vect_neg)
+ self.atom_add(atom_id='Dy_neg', element='C', pos=Dy_vect_neg)
+ self.atom_add(atom_id='Dz_neg', element='C', pos=Dz_vect_neg)
self.atom_connect(atom_id='Dx', bonded_id='R')
self.atom_connect(atom_id='Dy', bonded_id='R')
self.atom_connect(atom_id='Dz', bonded_id='R')
+ self.atom_connect(atom_id='Dx_neg', bonded_id='R')
+ self.atom_connect(atom_id='Dy_neg', bonded_id='R')
+ self.atom_connect(atom_id='Dz_neg', bonded_id='R')
# Print out.
print " Scaling factor: " + `scale`
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