Author: bugman
Date: Fri Apr 4 16:03:20 2008
New Revision: 5305
URL: http://svn.gna.org/viewcvs/relax?rev=5305&view=rev
Log:
Created the Scientific Python specific data object.
The functions specific to Scientific Python have been converted into methods
of the object. The new
object inherits from api_base.Str_object.
Modified:
1.3/generic_fns/structure/scientific.py
Modified: 1.3/generic_fns/structure/scientific.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/scientific.py?rev=5305&r1=5304&r2=5305&view=diff
==============================================================================
--- 1.3/generic_fns/structure/scientific.py (original)
+++ 1.3/generic_fns/structure/scientific.py Fri Apr 4 16:03:20 2008
@@ -33,89 +33,59 @@
module_avail = False
# relax module imports.
+from api_base import Str_object
from data import Data as relax_data_store
from relax_errors import RelaxNoPdbChainError, RelaxNoResError,
RelaxPdbLoadError
from relax_warnings import RelaxNoAtomWarning, RelaxZeroVectorWarning
-
-def load_structures(file_path, model, verbosity=False):
- """Function for loading the structures from the PDB file.
-
- @param file_path: The full path of the file.
- @type file_path: str
- @param model: The PDB model to use.
- @type model: int
- @param verbosity: A flag which if True will cause messages to be
printed.
- @type verbosity: bool
- """
-
- # Alias the current data pipe.
- cdp = relax_data_store[relax_data_store.current_pipe]
-
- # Use pointers (references) if the PDB data exists in another run.
- for data_pipe in relax_data_store:
- if hasattr(data_pipe, 'structure') and hasattr(cdp.structure,
'structures') and data_pipe.structure.file_name == file_path and
data_pipe.structure.model == model:
- # Make a pointer to the data.
- cdp.structure.structures = data_pipe.structure.structures
-
+class Scientific_data(Str_object):
+ """The Scientific Python specific data object."""
+
+ def load_structures(self, file_path, model, verbosity=False):
+ """Function for loading the structures from the PDB file.
+
+ @param file_path: The full path of the file.
+ @type file_path: str
+ @param model: The PDB model to use.
+ @type model: int
+ @param verbosity: A flag which if True will cause messages to be
printed.
+ @type verbosity: bool
+ """
+
+ # Alias the current data pipe.
+ cdp = relax_data_store[relax_data_store.current_pipe]
+
+ # Use pointers (references) if the PDB data exists in another run.
+ for data_pipe in relax_data_store:
+ if hasattr(data_pipe, 'structure') and hasattr(cdp.structure,
'structures') and data_pipe.structure.file_name == file_path and
data_pipe.structure.model == model:
+ # Make a pointer to the data.
+ cdp.structure.structures = data_pipe.structure.structures
+
+ # Print out.
+ if verbosity:
+ print "Using the structures from the data pipe " +
`data_pipe.pipe_name` + "."
+ for i in xrange(len(cdp.structure.structures)):
+ print cdp.structure.structures[i]
+
+ # Exit this function.
+ return
+
+ # Initialisation.
+ cdp.structure.structures = []
+
+ # Load the structure i from the PDB file.
+ if type(model) == int:
# Print out.
if verbosity:
- print "Using the structures from the data pipe " +
`data_pipe.pipe_name` + "."
- for i in xrange(len(cdp.structure.structures)):
- print cdp.structure.structures[i]
-
- # Exit this function.
- return
-
- # Initialisation.
- cdp.structure.structures = []
-
- # Load the structure i from the PDB file.
- if type(model) == int:
- # Print out.
- if verbosity:
- print "Loading structure " + `model` + " from the PDB file."
-
- # Load the structure into 'str'.
- str = Scientific.IO.PDB.Structure(file_path, model)
-
- # Test the structure.
- if len(str) == 0:
- raise RelaxPdbLoadError, file_path
-
- # Print the PDB info.
- if verbosity:
- print str
-
- # Place the structure in 'cdp.structure'.
- cdp.structure.structures.append(str)
-
-
- # Load all structures.
- else:
- # Print out.
- if verbosity:
- print "Loading all structures from the PDB file."
-
- # First model.
- i = 1
-
- # Loop over all the other structures.
- while 1:
- # Load the pdb files.
- str = Scientific.IO.PDB.Structure(file_path, i)
-
- # No model 1.
- if len(str) == 0 and i == 1:
- str = Scientific.IO.PDB.Structure(file_path)
- if len(str) == 0:
- raise RelaxPdbLoadError, file_path
-
- # Test if the last structure has been reached.
+ print "Loading structure " + `model` + " from the PDB file."
+
+ # Load the structure into 'str'.
+ str = Scientific.IO.PDB.Structure(file_path, model)
+
+ # Test the structure.
if len(str) == 0:
- del str
- break
+ raise RelaxPdbLoadError, file_path
# Print the PDB info.
if verbosity:
@@ -124,109 +94,142 @@
# Place the structure in 'cdp.structure'.
cdp.structure.structures.append(str)
- # Increment i.
- i = i + 1
-
-
-def xh_vector(data, structure=None, unit=1):
- """Function for calculating/extracting the XH vector from the loaded
structure.
-
- @param data: The spin system data container.
- @type data: Residue instance
- @param structure: The structure number to get the XH vector from. If
set to None and
- multiple structures exist, then the XH vector will be averaged
across all structures.
- @type structure: int
- @param unit: A flag which if set will cause the function to
return the unit XH vector
- rather than the full vector.
- @type unit: int
- @return: The XH vector (or unit vector if the unit flag is
set).
- @rtype: list or None
- """
-
- # Initialise.
- vector_array = []
- ave_vector = zeros(3, float64)
-
- # Alias the current data pipe.
- cdp = relax_data_store[relax_data_store.current_pipe]
-
- # Number of structures.
- num_str = len(cdp.structure.structures)
-
- # Loop over the structures.
- for i in xrange(num_str):
- # The vectors from a specific structure.
- if structure != None and structure != i:
- continue
-
- # Reassign the first peptide or nucleotide chain of the first
structure.
- if cdp.structure.structures[i].peptide_chains:
- pdb_residues =
cdp.structure.structures[i].peptide_chains[0].residues
- elif cdp.structure.structures[i].nucleotide_chains:
- pdb_residues =
cdp.structure.structures[i].nucleotide_chains[0].residues
+
+ # Load all structures.
else:
- raise RelaxNoPdbChainError
-
- # Find the corresponding residue in the PDB.
- pdb_res = None
- for k in xrange(len(pdb_residues)):
- if data.num == pdb_residues[k].number:
- pdb_res = pdb_residues[k]
- break
- if pdb_res == None:
- raise RelaxNoResError, data.num
-
- # Test if the proton atom exists for residue i.
- if not pdb_res.atoms.has_key(data.proton):
- warn(RelaxNoAtomWarning(data.proton, data.num))
-
- # Test if the heteronucleus atom exists for residue i.
- elif not pdb_res.atoms.has_key(data.heteronuc):
- warn(RelaxNoAtomWarning(data.heteronuc, data.num))
-
- # Calculate the vector.
- else:
- # Get the proton position.
- posH = pdb_res.atoms[data.proton].position.array
-
- # Get the heteronucleus position.
- posX = pdb_res.atoms[data.heteronuc].position.array
-
- # Calculate the XH bond vector.
- vector = posH - posX
-
- # Unit vector.
- if unit:
- # Normalisation factor.
- norm_factor = sqrt(dot(vector, vector))
-
- # Test for zero length.
- if norm_factor == 0.0:
- warn(RelaxZeroVectorWarning(data.num))
-
- # Calculate the normalised vector.
+ # Print out.
+ if verbosity:
+ print "Loading all structures from the PDB file."
+
+ # First model.
+ i = 1
+
+ # Loop over all the other structures.
+ while 1:
+ # Load the pdb files.
+ str = Scientific.IO.PDB.Structure(file_path, i)
+
+ # No model 1.
+ if len(str) == 0 and i == 1:
+ str = Scientific.IO.PDB.Structure(file_path)
+ if len(str) == 0:
+ raise RelaxPdbLoadError, file_path
+
+ # Test if the last structure has been reached.
+ if len(str) == 0:
+ del str
+ break
+
+ # Print the PDB info.
+ if verbosity:
+ print str
+
+ # Place the structure in 'cdp.structure'.
+ cdp.structure.structures.append(str)
+
+ # Increment i.
+ i = i + 1
+
+
+ def xh_vector(self, data, structure=None, unit=1):
+ """Function for calculating/extracting the XH vector from the loaded
structure.
+
+ @param data: The spin system data container.
+ @type data: Residue instance
+ @param structure: The structure number to get the XH vector from.
If set to None and
+ multiple structures exist, then the XH vector will be averaged
across all structures.
+ @type structure: int
+ @param unit: A flag which if set will cause the function to
return the unit XH vector
+ rather than the full vector.
+ @type unit: int
+ @return: The XH vector (or unit vector if the unit flag
is set).
+ @rtype: list or None
+ """
+
+ # Initialise.
+ vector_array = []
+ ave_vector = zeros(3, float64)
+
+ # Alias the current data pipe.
+ cdp = relax_data_store[relax_data_store.current_pipe]
+
+ # Number of structures.
+ num_str = len(cdp.structure.structures)
+
+ # Loop over the structures.
+ for i in xrange(num_str):
+ # The vectors from a specific structure.
+ if structure != None and structure != i:
+ continue
+
+ # Reassign the first peptide or nucleotide chain of the first
structure.
+ if cdp.structure.structures[i].peptide_chains:
+ pdb_residues =
cdp.structure.structures[i].peptide_chains[0].residues
+ elif cdp.structure.structures[i].nucleotide_chains:
+ pdb_residues =
cdp.structure.structures[i].nucleotide_chains[0].residues
+ else:
+ raise RelaxNoPdbChainError
+
+ # Find the corresponding residue in the PDB.
+ pdb_res = None
+ for k in xrange(len(pdb_residues)):
+ if data.num == pdb_residues[k].number:
+ pdb_res = pdb_residues[k]
+ break
+ if pdb_res == None:
+ raise RelaxNoResError, data.num
+
+ # Test if the proton atom exists for residue i.
+ if not pdb_res.atoms.has_key(data.proton):
+ warn(RelaxNoAtomWarning(data.proton, data.num))
+
+ # Test if the heteronucleus atom exists for residue i.
+ elif not pdb_res.atoms.has_key(data.heteronuc):
+ warn(RelaxNoAtomWarning(data.heteronuc, data.num))
+
+ # Calculate the vector.
+ else:
+ # Get the proton position.
+ posH = pdb_res.atoms[data.proton].position.array
+
+ # Get the heteronucleus position.
+ posX = pdb_res.atoms[data.heteronuc].position.array
+
+ # Calculate the XH bond vector.
+ vector = posH - posX
+
+ # Unit vector.
+ if unit:
+ # Normalisation factor.
+ norm_factor = sqrt(dot(vector, vector))
+
+ # Test for zero length.
+ if norm_factor == 0.0:
+ warn(RelaxZeroVectorWarning(data.num))
+
+ # Calculate the normalised vector.
+ else:
+ vector_array.append(vector / norm_factor)
+
+ # Normal XH vector.
else:
- vector_array.append(vector / norm_factor)
-
- # Normal XH vector.
- else:
- vector_array.append(vector)
-
- # Return None if there are no vectors.
- if not len(vector_array):
- return
-
- # Sum the vectors.
- for vector in vector_array:
- # Sum.
- ave_vector = ave_vector + vector
-
- # Average the vector.
- ave_vector = ave_vector / len(vector_array)
-
- # Unit vector.
- if unit:
- ave_vector = ave_vector / sqrt(dot(ave_vector, ave_vector))
-
- # Return the vector.
- return ave_vector
+ vector_array.append(vector)
+
+ # Return None if there are no vectors.
+ if not len(vector_array):
+ return
+
+ # Sum the vectors.
+ for vector in vector_array:
+ # Sum.
+ ave_vector = ave_vector + vector
+
+ # Average the vector.
+ ave_vector = ave_vector / len(vector_array)
+
+ # Unit vector.
+ if unit:
+ ave_vector = ave_vector / sqrt(dot(ave_vector, ave_vector))
+
+ # Return the vector.
+ return ave_vector
r5305 - /1.3/generic_fns/structure/scientific.py