Author: bugman
Date: Fri Apr 4 16:56:01 2008
New Revision: 5312
URL: http://svn.gna.org/viewcvs/relax?rev=5312&view=rev
Log:
Updated the methods of the Scientific Python PDB specific structural object
class.
These now use the structure of the new 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=5312&r1=5311&r2=5312&view=diff
==============================================================================
--- 1.3/generic_fns/structure/scientific.py (original)
+++ 1.3/generic_fns/structure/scientific.py Fri Apr 4 16:56:01 2008
@@ -53,30 +53,24 @@
@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.
+ @keyword 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:
+ if hasattr(data_pipe, 'structure') 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
+ self.structural_data = data_pipe.structure.structural_data
# 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]
+ for i in xrange(len(self.structural_data)):
+ print self.structural_data[i]
# Exit this function.
return
-
- # Initialisation.
- cdp.structure.structures = []
# Load the structure i from the PDB file.
if type(model) == int:
@@ -95,8 +89,8 @@
if verbosity:
print str
- # Place the structure in 'cdp.structure'.
- cdp.structure.structures.append(str)
+ # Place the structure in 'self.structural_data'.
+ self.structural_data.append(str)
# Load all structures.
@@ -128,24 +122,25 @@
if verbosity:
print str
- # Place the structure in 'cdp.structure'.
- cdp.structure.structures.append(str)
+ # Place the structure in 'self.structural_data'.
+ self.structural_data.append(str)
# Increment i.
i = i + 1
- def xh_vector(self, data, structure=None, unit=1):
+ def xh_vector(self, spin, structure=None, unit=True):
"""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.
+ @param spin: The spin system data container.
+ @type spin: SpinContainer instance
+ @keyword 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
+ @keyword unit: A flag which if set will cause the function to
return the unit XH vector
+ rather than the full vector.
+ @type unit: bool
@return: The XH vector (or unit vector if the unit flag
is set).
@rtype: list or None
"""
@@ -154,11 +149,8 @@
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)
+ num_str = len(self.structural_data)
# Loop over the structures.
for i in xrange(num_str):
@@ -167,37 +159,37 @@
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
+ if self.structural_data[i].peptide_chains:
+ pdb_residues =
self.structural_data[i].peptide_chains[0].residues
+ elif self.structural_data[i].nucleotide_chains:
+ pdb_residues =
self.structural_data[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:
+ if spin.num == pdb_residues[k].number:
pdb_res = pdb_residues[k]
break
if pdb_res == None:
- raise RelaxNoResError, data.num
+ raise RelaxNoResError, spin.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))
+ if not pdb_res.atoms.has_key(spin.proton):
+ warn(RelaxNoAtomWarning(spin.proton, spin.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))
+ elif not pdb_res.atoms.has_key(spin.heteronuc):
+ warn(RelaxNoAtomWarning(spin.heteronuc, spin.num))
# Calculate the vector.
else:
# Get the proton position.
- posH = pdb_res.atoms[data.proton].position.array
+ posH = pdb_res.atoms[spin.proton].position.array
# Get the heteronucleus position.
- posX = pdb_res.atoms[data.heteronuc].position.array
+ posX = pdb_res.atoms[spin.heteronuc].position.array
# Calculate the XH bond vector.
vector = posH - posX
@@ -209,7 +201,7 @@
# Test for zero length.
if norm_factor == 0.0:
- warn(RelaxZeroVectorWarning(data.num))
+ warn(RelaxZeroVectorWarning(spin.num))
# Calculate the normalised vector.
else:
r5312 - /1.3/generic_fns/structure/scientific.py