Author: bugman
Date: Tue Nov 7 06:44:04 2006
New Revision: 2760
URL: http://svn.gna.org/viewcvs/relax?rev=2760&view=rev
Log:
Monte Carlo simulations are now included in the diffusion tensor PDB
representation.
If Monte Carlo simulations exist and the diffusion tensor parameters were
allowed to vary then the
PDB file of the diffusion tensor representation will contain multiple 'SIM'
residues, one for each
simulation. The atoms of these residues represent the axes of the simulated
tensors and they will
appear as a distribution.
The code for generating the 'AXS' residues has been shifted from
'self.create_tensor_pdb()' into the
functions 'self.generate_spheroid_axes()' and
'self.generate_ellipsoid_axes()'. The code has been
modified to create the 'SIM' residues as well.
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=2760&r1=2759&r2=2760&view=diff
==============================================================================
--- branches/tensor_pdb/generic_fns/pdb.py (original)
+++ branches/tensor_pdb/generic_fns/pdb.py Tue Nov 7 06:44:04 2006
@@ -350,87 +350,182 @@
if self.relax.data.diff[self.run].type == 'spheroid':
# Print out.
print "\nGenerating the unique axis of the diffusion tensor."
-
- # The Dpar vector.
- Dpar_vect = self.relax.data.diff[self.run].Dpar_unit *
self.relax.data.diff[self.run].Dpar * scale
-
- # The negative Dpar vector.
- Dpar_vect_neg = -Dpar_vect
-
- # Position of both vectors relative to the centre of mass.
- Dpar_vect = R + Dpar_vect
- Dpar_vect_neg = R + Dpar_vect_neg
-
- # Create the 'AXS' residue.
- self.atom_add(atom_id='R_axes', atom_name='R', res_name='AXS',
chain_id=chain_id, res_num=res_num, pos=R, element='C')
- self.atom_add(atom_id='Dpar', atom_name='Dpar', res_name='AXS',
chain_id=chain_id, res_num=res_num, pos=Dpar_vect, element='C')
- self.atom_add(atom_id='Dpar_neg', atom_name='Dpar',
res_name='AXS', chain_id=chain_id, res_num=res_num, pos=Dpar_vect_neg,
element='C')
- self.atom_connect(atom_id='Dpar', bonded_id='R_axes')
- self.atom_connect(atom_id='Dpar_neg', bonded_id='R_axes')
-
- # Print out.
print " Scaling factor: " + `scale`
- print " Dpar vector (scaled + shifted to R): " + `Dpar_vect`
+
+ # Create the axis.
+ self.generate_spheroid_axes(scale=scale, chain_id=chain_id,
res_num=res_num, R=R)
+
+ # Simulations.
+ if hasattr(self.relax.data.diff[self.run], 'tm_sim'):
+ # Print out.
+ print " Creating the MC simulation axes."
+
+ # 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)
+
# 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."
-
- # The Dx, Dy, and Dz vectors.
- Dx_vect = self.relax.data.diff[self.run].Dx_unit *
self.relax.data.diff[self.run].Dx * scale
- 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 centre 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
-
- # Create the 'AXS' residue.
- self.atom_add(atom_id='R_axes', atom_name='R', res_name='AXS',
chain_id=chain_id, res_num=res_num, pos=R, element='C')
- self.atom_add(atom_id='Dx', atom_name='Dx', res_name='AXS',
chain_id=chain_id, res_num=res_num, pos=Dx_vect, element='C')
- self.atom_add(atom_id='Dy', atom_name='Dy', res_name='AXS',
chain_id=chain_id, res_num=res_num, pos=Dy_vect, element='C')
- self.atom_add(atom_id='Dz', atom_name='Dz', res_name='AXS',
chain_id=chain_id, res_num=res_num, pos=Dz_vect, element='C')
- self.atom_add(atom_id='Dx_neg', atom_name='Dx', res_name='AXS',
chain_id=chain_id, res_num=res_num, pos=Dx_vect_neg, element='C')
- self.atom_add(atom_id='Dy_neg', atom_name='Dy', res_name='AXS',
chain_id=chain_id, res_num=res_num, pos=Dy_vect_neg, element='C')
- self.atom_add(atom_id='Dz_neg', atom_name='Dz', res_name='AXS',
chain_id=chain_id, res_num=res_num, pos=Dz_vect_neg, element='C')
- self.atom_connect(atom_id='Dx', bonded_id='R_axes')
- self.atom_connect(atom_id='Dy', bonded_id='R_axes')
- self.atom_connect(atom_id='Dz', bonded_id='R_axes')
- self.atom_connect(atom_id='Dx_neg', bonded_id='R_axes')
- self.atom_connect(atom_id='Dy_neg', bonded_id='R_axes')
- self.atom_connect(atom_id='Dz_neg', bonded_id='R_axes')
-
- # Print out.
print " Scaling factor: " + `scale`
+
+ # Create the axes.
+ self.generate_ellipsoid_axes(scale=scale, chain_id=chain_id,
res_num=res_num, R=R)
+
+ # Simulations.
+ if hasattr(self.relax.data.diff[self.run], 'tm_sim'):
+ # Print out.
+ print " Creating the MC simulation axes."
+
+ # 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)
+
+
+ # Create the PDB file.
+ ######################
+
+ # Print out.
+ print "\nGenerating the PDB file."
+
+ # Open the PDB file for writing.
+ tensor_pdb_file = self.relax.IO.open_write_file(self.file, self.dir,
force=self.force)
+
+ # Write the data.
+ self.write_pdb_file(tensor_pdb_file, chain_id, res_num, res_name,
chemical_name, occupancy)
+
+ # Close the file.
+ tensor_pdb_file.close()
+
+
+ def generate_ellipsoid_axes(self, scale=None, 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.
+ @type res_num: int
+ @param R: The center of mass.
+ @type R: Numeric array (Float64)
+ @param i: The Monte Carlo simulation index.
+ @type i: int
+ @return: None
+ """
+
+ # Alias the relevant data.
+ if i == None:
+ Dx = self.relax.data.diff[self.run].Dx
+ Dy = self.relax.data.diff[self.run].Dy
+ Dz = self.relax.data.diff[self.run].Dz
+ Dx_unit = self.relax.data.diff[self.run].Dx_unit
+ Dy_unit = self.relax.data.diff[self.run].Dy_unit
+ Dz_unit = self.relax.data.diff[self.run].Dz_unit
+ res_name = 'AXS'
+ atom_id_ext = ''
+ else:
+ Dx = self.relax.data.diff[self.run].Dx_sim[i]
+ Dy = self.relax.data.diff[self.run].Dy_sim[i]
+ Dz = self.relax.data.diff[self.run].Dz_sim[i]
+ Dx_unit = self.relax.data.diff[self.run].Dx_unit_sim[i]
+ Dy_unit = self.relax.data.diff[self.run].Dy_unit_sim[i]
+ Dz_unit = self.relax.data.diff[self.run].Dz_unit_sim[i]
+ res_name = 'SIM'
+ atom_id_ext = '_sim' + `i`
+
+ # The Dx, Dy, and Dz vectors.
+ Dx_vect = Dx_unit * Dx * scale
+ Dy_vect = Dy_unit * Dy * scale
+ Dz_vect = Dz_unit * 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 centre 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
+
+ # Create the 'AXS' residue.
+ self.atom_add(atom_id='R_axes'+atom_id_ext, atom_name='R',
res_name=res_name, chain_id=chain_id, res_num=res_num, pos=R, element='C')
+ self.atom_add(atom_id='Dx'+atom_id_ext, atom_name='Dx',
res_name=res_name, chain_id=chain_id, res_num=res_num, pos=Dx_vect,
element='C')
+ self.atom_add(atom_id='Dy'+atom_id_ext, atom_name='Dy',
res_name=res_name, chain_id=chain_id, res_num=res_num, pos=Dy_vect,
element='C')
+ self.atom_add(atom_id='Dz'+atom_id_ext, atom_name='Dz',
res_name=res_name, chain_id=chain_id, res_num=res_num, pos=Dz_vect,
element='C')
+ self.atom_add(atom_id='Dx_neg'+atom_id_ext, atom_name='Dx',
res_name=res_name, chain_id=chain_id, res_num=res_num, pos=Dx_vect_neg,
element='C')
+ self.atom_add(atom_id='Dy_neg'+atom_id_ext, atom_name='Dy',
res_name=res_name, chain_id=chain_id, res_num=res_num, pos=Dy_vect_neg,
element='C')
+ self.atom_add(atom_id='Dz_neg'+atom_id_ext, atom_name='Dz',
res_name=res_name, chain_id=chain_id, res_num=res_num, pos=Dz_vect_neg,
element='C')
+ self.atom_connect(atom_id='Dx'+atom_id_ext,
bonded_id='R_axes'+atom_id_ext)
+ self.atom_connect(atom_id='Dy'+atom_id_ext,
bonded_id='R_axes'+atom_id_ext)
+ self.atom_connect(atom_id='Dz'+atom_id_ext,
bonded_id='R_axes'+atom_id_ext)
+ self.atom_connect(atom_id='Dx_neg'+atom_id_ext,
bonded_id='R_axes'+atom_id_ext)
+ self.atom_connect(atom_id='Dy_neg'+atom_id_ext,
bonded_id='R_axes'+atom_id_ext)
+ self.atom_connect(atom_id='Dz_neg'+atom_id_ext,
bonded_id='R_axes'+atom_id_ext)
+
+ # Print out.
+ if i == None:
print " Dx vector (scaled + shifted to R): " + `Dx_vect`
print " Dy vector (scaled + shifted to R): " + `Dy_vect`
print " Dz vector (scaled + shifted to R): " + `Dz_vect`
- # Create the PDB file.
- ######################
+ def generate_spheroid_axes(self, scale=None, 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.
+ @type res_num: int
+ @param R: The center of mass.
+ @type R: Numeric array (Float64)
+ @param i: The Monte Carlo simulation index.
+ @type i: int
+ @return: None
+ """
+
+ # Alias the relevant data.
+ if i == None:
+ Dpar = self.relax.data.diff[self.run].Dpar
+ Dpar_unit = self.relax.data.diff[self.run].Dpar_unit
+ res_name = 'AXS'
+ atom_id_ext = ''
+ else:
+ Dpar = self.relax.data.diff[self.run].Dpar_sim[i]
+ Dpar_unit = self.relax.data.diff[self.run].Dpar_unit_sim[i]
+ res_name = 'SIM'
+ atom_id_ext = '_sim' + `i`
+
+ # The Dpar vector.
+ Dpar_vect = Dpar_unit * Dpar * scale
+
+ # The negative Dpar vector.
+ Dpar_vect_neg = -Dpar_vect
+
+ # Position of both vectors relative to the centre of mass.
+ Dpar_vect = R + Dpar_vect
+ Dpar_vect_neg = R + Dpar_vect_neg
+
+ # Create the 'AXS' residue.
+ self.atom_add(atom_id='R_axes'+atom_id_ext, atom_name='R',
res_name=res_name, chain_id=chain_id, res_num=res_num, pos=R, element='C')
+ self.atom_add(atom_id='Dpar'+atom_id_ext, atom_name='Dpar',
res_name=res_name, chain_id=chain_id, res_num=res_num, pos=Dpar_vect,
element='C')
+ self.atom_add(atom_id='Dpar_neg'+atom_id_ext, atom_name='Dpar',
res_name=res_name, chain_id=chain_id, res_num=res_num, pos=Dpar_vect_neg,
element='C')
+ self.atom_connect(atom_id='Dpar'+atom_id_ext,
bonded_id='R_axes'+atom_id_ext)
+ self.atom_connect(atom_id='Dpar_neg'+atom_id_ext,
bonded_id='R_axes'+atom_id_ext)
# Print out.
- print "\nGenerating the PDB file."
-
- # Open the PDB file for writing.
- tensor_pdb_file = self.relax.IO.open_write_file(self.file, self.dir,
force=self.force)
-
- # Write the data.
- self.write_pdb_file(tensor_pdb_file, chain_id, res_num, res_name,
chemical_name, occupancy)
-
- # Close the file.
- tensor_pdb_file.close()
+ if i == None:
+ print " Dpar vector (scaled + shifted to R): " + `Dpar_vect`
def get_chemical_name(self, hetID):
@@ -1080,8 +1175,8 @@
- @type file: str
- @param file: The PDB file name.
+ @param file: The PDB file object. This object must be writable.
+ @type file: file object
@return: None
"""
r2760 - /branches/tensor_pdb/generic_fns/pdb.py