Author: bugman
Date: Tue Nov 7 06:51:20 2006
New Revision: 2764
URL: http://svn.gna.org/viewcvs/relax?rev=2764&view=rev
Log:
Added extra atoms to the 'AXS' residue of the tensor PDB representation for
labelling.
Two or six extra atoms are added for the spheroid and ellipsoid axes
respectively. These are set to
be nitrogen atoms to allow easy selection of just those atoms. They are also
placed 3 Angstrom
outside of the geometric object so that the labels do not clash with the
latitudinal and
longitudinal lines as well as the Monte Carlo simulation axes.
The code for generating the PDB chemical formula in 'self.write_pdb_file()'
was modified to handle
nitrogen atoms.
The PyMOL user function 'pymol.tensor_pdb()' has been modified to use the new
representation. The
final selection is also deleted at the end of the user function.
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=2764&r1=2763&r2=2764&view=diff
==============================================================================
--- branches/tensor_pdb/generic_fns/pdb.py (original)
+++ branches/tensor_pdb/generic_fns/pdb.py Tue Nov 7 06:51:20 2006
@@ -468,6 +468,21 @@
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)
+ # Add six more atoms to allow the axis labels to be shifted just
outside of the geometric object.
+ if i == None:
+ # A slightly longer vector (by 3 Angstrom).
+ Dx_vect = Dx_unit * (Dx * scale + 3.0)
+ Dy_vect = Dy_unit * (Dy * scale + 3.0)
+ Dz_vect = Dz_unit * (Dz * scale + 3.0)
+
+ # Add the atoms.
+ self.atom_add(atom_id='Dx label', atom_name='Dx',
res_name=res_name, chain_id=chain_id, res_num=res_num, pos=R+Dx_vect,
element='N')
+ self.atom_add(atom_id='Dx neg label', atom_name='Dx',
res_name=res_name, chain_id=chain_id, res_num=res_num, pos=R-Dx_vect,
element='N')
+ self.atom_add(atom_id='Dy label', atom_name='Dy',
res_name=res_name, chain_id=chain_id, res_num=res_num, pos=R+Dy_vect,
element='N')
+ self.atom_add(atom_id='Dy neg label', atom_name='Dy',
res_name=res_name, chain_id=chain_id, res_num=res_num, pos=R-Dy_vect,
element='N')
+ self.atom_add(atom_id='Dz label', atom_name='Dz',
res_name=res_name, chain_id=chain_id, res_num=res_num, pos=R+Dz_vect,
element='N')
+ self.atom_add(atom_id='Dz neg label', atom_name='Dz',
res_name=res_name, chain_id=chain_id, res_num=res_num, pos=R-Dz_vect,
element='N')
+
# Print out.
if i == None:
print " Dx vector (scaled + shifted to R): " + `Dx_vect`
@@ -519,6 +534,15 @@
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)
+
+ # Add two more atoms to allow the axis labels to be shifted just
outside of the geometric object.
+ if i == None:
+ # A slightly longer vector (by 3 Angstrom).
+ vect = Dpar_unit * (Dpar * scale + 3.0)
+
+ # Add the atoms.
+ self.atom_add(atom_id='Dpar label', atom_name='Dpar',
res_name=res_name, chain_id=chain_id, res_num=res_num, pos=R+vect,
element='N')
+ self.atom_add(atom_id='Dpar neg label', atom_name='Dpar',
res_name=res_name, chain_id=chain_id, res_num=res_num, pos=R-vect,
element='N')
# Print out.
if i == None:
@@ -1200,9 +1224,9 @@
element = array[9]
# If the residue is not already stored initialise a new het_data
element.
- # (residue number, residue name, chain ID, number of atoms,
number of H, number of C).
+ # (residue number, residue name, chain ID, number of atoms,
number of H, number of C, number of N).
if not het_data or not res_num == het_data[-1][0]:
- het_data.append([array[4], array[2], array[3], 0, 0, 0])
+ het_data.append([array[4], array[2], array[3], 0, 0, 0, 0])
# Total atom count.
het_data[-1][3] = het_data[-1][3] + 1
@@ -1215,9 +1239,13 @@
elif element == 'C':
het_data[-1][5] = het_data[-1][5] + 1
+ # Nitrogen count.
+ elif element == 'N':
+ het_data[-1][6] = het_data[-1][6] + 1
+
# Unsupported element type.
else:
- raise RelaxError, "The element " + `element` + " was
expected to be one of ['H', 'C']."
+ raise RelaxError, "The element " + `element` + " was
expected to be one of ['H', 'C', 'N']."
# Sort by residue number.
het_data.sort()
@@ -1255,18 +1283,28 @@
# Print out.
print "Creating the FORMUL records."
- # Loop over the non-standard residues.
+ # Loop over the non-standard residues and generate and write the
chemical formula.
for het in het_data:
- # Chemical formula.
+ # Initialise the chemical formula.
formula = ''
+
+ # Protons.
if het[4]:
if formula:
formula = formula + ' '
formula = formula + 'H' + `het[4]`
+
+ # Carbon.
if het[5]:
if formula:
formula = formula + ' '
formula = formula + 'C' + `het[5]`
+
+ # Nitrogen
+ if het[6]:
+ if formula:
+ formula = formula + ' '
+ formula = formula + 'N' + `het[6]`
# The FORMUL record (chemical formula).
file.write("%-6s %2s %3s %2s%1s%-51s\n" % ('FORMUL', het[0],
het[1], '', '', formula))
r2764 - /branches/tensor_pdb/generic_fns/pdb.py