Author: bugman
Date: Mon Apr 7 13:57:27 2008
New Revision: 5348
URL: http://svn.gna.org/viewcvs/relax?rev=5348&view=rev
Log:
Spun out the centre_of_mass() function to its own module.
This new module will contain all functions related to mass and inertia.
Added:
1.3/generic_fns/structure/mass.py
- copied, changed from r5339, 1.3/generic_fns/structure/structure.py
Modified:
1.3/generic_fns/structure/structure.py
Copied: 1.3/generic_fns/structure/mass.py (from r5339,
1.3/generic_fns/structure/structure.py)
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/mass.py?p2=1.3/generic_fns/structure/mass.py&p1=1.3/generic_fns/structure/structure.py&r1=5339&r2=5348&rev=5348&view=diff
==============================================================================
--- 1.3/generic_fns/structure/structure.py (original)
+++ 1.3/generic_fns/structure/mass.py Mon Apr 7 13:57:27 2008
@@ -22,17 +22,11 @@
# Python module imports.
from numpy import float64, zeros
-from os import F_OK, access
-from warnings import warn
# relax module imports.
from data import Data as relax_data_store
-from generic_fns import molmol
-from generic_fns.sequence import load_PDB_sequence
-from generic_fns.selection import exists_mol_res_spin_data, return_molecule,
return_residue, return_spin, spin_loop
-from relax_errors import RelaxError, RelaxFileError, RelaxNoPdbError,
RelaxNoPipeError, RelaxNoSequenceError, RelaxPdbError
-from relax_io import get_file_path
-from relax_warnings import RelaxNoPDBFileWarning
+from generic_fns.selection import return_molecule, return_residue,
return_spin
+from relax_errors import RelaxNoPdbError
@@ -128,134 +122,3 @@
return R,M
else:
return R
-
-
-def read_pdb(run=None, file=None, dir=None, model=None, load_seq=1, fail=1,
verbosity=1):
- """The pdb loading function."""
-
- # Tests.
- ########
-
- # Test if the current data pipe exists.
- if not relax_data_store.current_pipe:
- raise RelaxNoPipeError
-
- # Alias the current data pipe.
- cdp = relax_data_store[relax_data_store.current_pipe]
-
- # Test if PDB data corresponding to the run already exists.
- if hasattr(cdp, 'struct'):
- raise RelaxPdbError
-
- # Test if sequence data is loaded.
- if not load_seq and not exists_mol_res_spin_data():
- raise RelaxNoSequenceError
-
- # The file path.
- file_path = get_file_path(file, dir)
-
- # Test if the file exists.
- if not access(file_path, F_OK):
- if fail:
- raise RelaxFileError, ('PDB', file_path)
- else:
- warn(RelaxNoPDBFileWarning(file_path))
- return
-
-
- # Data creation.
- ################
-
- # File name.
- cdp.structure.file_name = file_path
-
- # Model.
- cdp.structure.model = model
-
-
- # Load the structures.
- ######################
-
- load_structures(file_path, model, verbosity)
-
-
- # Finish.
- #########
-
- # Sequence loading.
- if load_seq and not exists_mol_res_spin_data():
- load_PDB_sequence()
-
- # Load into Molmol (if running).
- molmol.open_pdb()
-
-
-def set_vector(spin=None, xh_vect=None):
- """Place the XH unit vector into the spin container object.
-
- @keyword spin: The spin container object.
- @type spin: SpinContainer instance
- @keyword xh_vect: The unit vector parallel to the XH bond.
- @type xh_vect: array of len 3
- """
-
- # Place the XH unit vector into the container.
- spin.xh_vect = xh_vect
-
-
-def vectors(heteronuc=None, proton=None, spin_id=None, verbosity=1):
- """Function for calculating/extracting the XH unit vector from the
loaded structure.
-
- @param heteronuc: The name of the heteronucleus.
- @type heteronuc: str
- @param proton: The name of the proton.
- @type proton: str
- @param spin_id: The molecule, residue, and spin identifier string.
- @type spin_id: str
- @param verbosity: The higher the value, the more information is
printed to screen.
- @type verbosity: int
- """
-
- # Alias the current data pipe.
- cdp = relax_data_store[relax_data_store.current_pipe]
-
- # Test if the PDB file has been loaded.
- if not hasattr(cdp, 'structure'):
- raise RelaxPdbError
-
- # Test if sequence data is loaded.
- if not exists_mol_res_spin_data():
- raise RelaxNoSequenceError
-
- # Test that the nuclei have been correctly set.
- if heteronuc == proton:
- raise RelaxError, "The proton and heteronucleus are set to the same
atom."
-
- # Number of structures.
- num_str = len(cdp.structure.structures)
-
- # Print out.
- if verbosity:
- if num_str > 1:
- print "\nCalculating and averaging the unit XH vectors from all
structures."
- else:
- print "\nCalculating the unit XH vectors from the structure."
-
- # Loop over the sequence.
- for spin in spin_loop(spin_id):
- # Skip unselected residues.
- if not spin.select:
- continue
-
- # Set the proton and heteronucleus names.
- spin.proton = proton
- spin.heteronuc = heteronuc
-
- # Calculate the vector.
- vector = xh_vector(spin)
-
- # Set the vector and deselect the spin if the vector doesn't exist.
- if vector != None:
- spin.xh_vect = vector
- else:
- spin.select = False
Modified: 1.3/generic_fns/structure/structure.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/structure.py?rev=5348&r1=5347&r2=5348&view=diff
==============================================================================
--- 1.3/generic_fns/structure/structure.py (original)
+++ 1.3/generic_fns/structure/structure.py Mon Apr 7 13:57:27 2008
@@ -21,7 +21,6 @@
###############################################################################
# Python module imports.
-from numpy import float64, zeros
from os import F_OK, access
from warnings import warn
@@ -29,105 +28,11 @@
from data import Data as relax_data_store
from generic_fns import molmol
from generic_fns.sequence import load_PDB_sequence
-from generic_fns.selection import exists_mol_res_spin_data, return_molecule,
return_residue, return_spin, spin_loop
-from relax_errors import RelaxError, RelaxFileError, RelaxNoPdbError,
RelaxNoPipeError, RelaxNoSequenceError, RelaxPdbError
+from generic_fns.selection import exists_mol_res_spin_data, spin_loop
+from relax_errors import RelaxError, RelaxFileError, RelaxNoPipeError,
RelaxNoSequenceError, RelaxPdbError
from relax_io import get_file_path
from relax_warnings import RelaxNoPDBFileWarning
-
-
-def centre_of_mass(return_mass=False):
- """Calculate and return the centre of mass of the structure.
-
- @param return_mass: A flag which if False will cause only the centre of
mass to be returned, but
- if True will cause the centre of mass and the mass
itself to be returned as
- a tuple.
- @type return_mass: bool
- @return: The centre of mass vector, and additionally the mass.
- @rtype: list of 3 floats (or tuple of a list of 3 floats and
one float)
- """
-
- # Alias the current data pipe.
- cdp = relax_data_store[relax_data_store.current_pipe]
-
- # Test if a structure has been loaded.
- if not hasattr(cdp.structure, 'structures'):
- raise RelaxNoPdbError
-
- # Print out.
- print "Calculating the centre of mass."
-
- # Initialise the centre of mass.
- R = zeros(3, float64)
-
- # Initialise the total mass.
- M = 0.0
-
- # Loop over the structures.
- for struct in cdp.structure.structures:
- # Get the corresponding molecule container.
- if cdp.mol[0].name == None:
- mol_cont = cdp.mol[0]
- else:
- mol_cont = return_molecule('#' + struct.name)
-
- # Deselected molecule.
- if not mol_cont.select:
- continue
-
- # 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:
- # Get the corresponding residue container.
- if mol_cont.res[0].name == None and mol_cont.res[0].num == None:
- res_cont = mol_cont.res[0]
- else:
- res_cont = return_residue(':' + `res.number`)
-
- # Deselected residue.
- if not res_cont.select:
- continue
-
- # Loop over the atoms of the residue.
- for atom in res:
- # Get the corresponding spin container.
- if res_cont.spin[0].name == None and res_cont.spin[0].num ==
None:
- spin_cont = res_cont.spin[0]
- else:
- spin_cont = return_spin('@' +
`atom.properties['serial_number']`)
-
- # Deselected spin.
- if not spin_cont.select:
- continue
-
- # Atomic mass.
- mass = return_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 " Centre of mass: R = " + `R`
-
- # Return the centre of mass.
- if return_mass:
- return R,M
- else:
- return R
def read_pdb(run=None, file=None, dir=None, model=None, load_seq=1, fail=1,
verbosity=1):
r5348 - in /1.3/generic_fns/structure: mass.py structure.py