Author: bugman
Date: Thu Oct 26 07:50:36 2006
New Revision: 2666
URL: http://svn.gna.org/viewcvs/relax?rev=2666&view=rev
Log:
Created functions for calculating the center of mass of the selected residues.
The function 'self.center_of_mass()' in the file 'generic_fns/pdb.py' has
been created to calculate
the center of mass. All unselected residues are skipped to allow hybrid
models, two fused runs of
non-overlapping residues, to be handled. Hence the center of mass will be
biased!
The function 'self.atomic_mass()' has also been added to the file. This
function returns the atomic
mass corresponding to the supplied element string.
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=2666&r1=2665&r2=2666&view=diff
==============================================================================
--- branches/tensor_pdb/generic_fns/pdb.py (original)
+++ branches/tensor_pdb/generic_fns/pdb.py Thu Oct 26 07:50:36 2006
@@ -37,6 +37,95 @@
self.print_flag = 1
+ def atomic_mass(self, element=None):
+ """Return the atomic mass of the given element."""
+
+ # Proton.
+ if element == 'H' or element == 'Q':
+ return 1.00794
+
+ # Carbon.
+ elif element == 'C':
+ return 12.0107
+
+ # Nitrogen.
+ elif element == 'N':
+ return 14.0067
+
+ # Oxygen.
+ elif element == 'O':
+ return 15.9994
+
+ # Sulphur.
+ elif element == 'S':
+ return 32.065
+
+ # Unknown.
+ else:
+ raise RelaxError, "The mass of the element " + `element` + " has
not yet been programmed into relax."
+
+
+ def center_of_mass(self):
+ """Calculate and return the center of mass of the structure."""
+
+ # Print out.
+ print "Calculating the center of mass."
+
+ # Initialise the center of mass.
+ R = zeros(3, Float64)
+
+ # Initialise the total mass.
+ M = 0.0
+
+ # Loop over the structures.
+ for struct in self.relax.data.pdb[self.run].structures:
+ # Protein.
+ if struct.peptide_chains:
+ chains = struct.peptide_chains
+
+ # RNA/DNA.
+ elif struct.nucleotide_chains:
+ chains = struct.nucleotide_chains
+
+ # Loop over the residues of the protein in the PDB file.
+ for res in chains[0].residues:
+ # Find the corresponding residue in 'self.relax.data'.
+ found = 0
+ for res_data in self.relax.data.res[self.run]:
+ if res.number == res_data.num:
+ found = 1
+ break
+
+ # Doesn't exist.
+ if not found:
+ continue
+
+ # Skip unselected residues.
+ if not res_data.select:
+ continue
+
+ # Loop over the atoms of the residue.
+ for atom in res:
+ # Atomic mass.
+ mass = self.atomic_mass(atom.properties['element'])
+
+ # Total mass.
+ M = M + mass
+
+ # Sum of mass * position.
+ R = R + mass * atom.position.array
+
+ # Normalise.
+ R = R / M
+
+ # Final print out.
+ print " Total mass: M = " + `M`
+ print " Center of mass: R = " + `R`
+
+ # Return the center of mass.
+ return R
+
+
def create_tensor_pdb(self, run=None, file=None, dir=None, force=0):
"""The pdb loading function."""
@@ -60,6 +149,9 @@
# Open the PDB file for writing.
tensor_pdb_file = self.relax.IO.open_write_file(self.file, self.dir,
self.force)
+
+ # Calculate the center of mass.
+ R = self.center_of_mass()
# Close the PDB file.
tensor_pdb_file.close()
r2666 - /branches/tensor_pdb/generic_fns/pdb.py