Author: bugman
Date: Sun Nov 4 14:56:03 2007
New Revision: 3408
URL: http://svn.gna.org/viewcvs/relax?rev=3408&view=rev
Log:
Removed junk code, left over from the copy from 'generic_fns/sequence.py'.
Modified:
1.3/generic_fns/residue.py
Modified: 1.3/generic_fns/residue.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/residue.py?rev=3408&r1=3407&r2=3408&view=diff
==============================================================================
--- 1.3/generic_fns/residue.py (original)
+++ 1.3/generic_fns/residue.py Sun Nov 4 14:56:03 2007
@@ -262,167 +262,3 @@
# Rename the residue is there is a match.
if mol.res[i].num in residues or mol.res[i].name in residues:
mol.res[i].num = new_number
-
-
-class Residue:
- def __init__(self, relax):
- """Class containing functions specific to amino-acid sequence."""
-
- self.relax = relax
-
-
- def data_names(self):
- """Function for returning a list of names of data structures
associated with the sequence."""
-
- return [ 'res' ]
-
-
-
- def load_PDB_sequence(self, run=None):
- """Function for loading the sequence out of a PDB file.
-
- This needs to be modified to handle multiple peptide chains.
- """
-
- # Print out.
- print "\nLoading the sequence from the PDB file.\n"
-
- # Reassign the sequence of the first structure.
- if relax_data_store.pdb[run].structures[0].peptide_chains:
- res =
relax_data_store.pdb[run].structures[0].peptide_chains[0].residues
- molecule = 'protein'
- elif relax_data_store.pdb[run].structures[0].nucleotide_chains:
- res =
relax_data_store.pdb[run].structures[0].nucleotide_chains[0].residues
- molecule = 'nucleic acid'
- else:
- raise RelaxNoPdbChainError
-
- # Add the run to 'relax_data_store.res'.
- relax_data_store.res.add_list(run)
-
- # Loop over the sequence.
- for i in xrange(len(res)):
- # Append a data container.
- relax_data_store.res[run].add_item()
-
- # Residue number.
- relax_data_store.res[run][i].num = res[i].number
-
- # Residue name.
- if molecule == 'nucleic acid':
- relax_data_store.res[run][i].name = res[i].name[-1]
- else:
- relax_data_store.res[run][i].name = res[i].name
-
- # Select the residue.
- relax_data_store.res[run][i].select = 1
-
-
- def read(self, run=None, file=None, dir=None, num_col=0, name_col=1,
sep=None):
- """Function for reading sequence data."""
-
- # Test if the run exists.
- if not run in relax_data_store.run_names:
- raise RelaxNoPipeError, run
-
- # Test if the sequence data has already been read.
- if relax_data_store.res.has_key(run):
- raise RelaxSequenceError, run
-
- # Extract the data from the file.
- file_data = self.relax.IO.extract_data(file, dir)
-
- # Count the number of header lines.
- header_lines = 0
- for i in xrange(len(file_data)):
- try:
- int(file_data[i][num_col])
- except:
- header_lines = header_lines + 1
- else:
- break
-
- # Remove the header.
- file_data = file_data[header_lines:]
-
- # Strip data.
- file_data = self.relax.IO.strip(file_data)
-
- # Do nothing if the file does not exist.
- if not file_data:
- raise RelaxFileEmptyError
-
- # Test if the sequence data is valid.
- for i in xrange(len(file_data)):
- try:
- int(file_data[i][num_col])
- except ValueError:
- raise RelaxError, "Sequence data is invalid."
-
- # Add the run to 'relax_data_store.res'.
- relax_data_store.res.add_list(run)
-
- # Fill the array 'relax_data_store.res[run]' with data containers
and place sequence data into the array.
- for i in xrange(len(file_data)):
- # Append a data container.
- relax_data_store.res[run].add_item()
-
- # Insert the data.
- relax_data_store.res[run][i].num = int(file_data[i][num_col])
- relax_data_store.res[run][i].name = file_data[i][name_col]
- relax_data_store.res[run][i].select = 1
-
-
- def sort(self, run=None):
- """Function for sorting the sequence by residue number."""
-
- # Test if the run exists.
- if not run in relax_data_store.run_names:
- raise RelaxNoPipeError, run
-
- # Test if the sequence data is loaded.
- if not relax_data_store.res.has_key(run):
- raise RelaxNoSequenceError, run
-
- # Sort the sequence.
- relax_data_store.res[run].sort(self.sort_cmpfunc)
-
-
- def sort_cmpfunc(self, x, y):
- """Sequence comparison function given to the ListType function
'sort'."""
-
- if x.num > y.num:
- return 1
- elif x.num < y.num:
- return -1
- elif x.num == y.num:
- return 0
-
-
- def write(self, run=None, file=None, dir=None, force=0):
- """Function for writing sequence data."""
-
- # Test if the run exists.
- if not run in relax_data_store.run_names:
- raise RelaxNoPipeError, run
-
- # Test if the sequence data is loaded.
- if not relax_data_store.res.has_key(run):
- raise RelaxNoSequenceError, run
-
- # Open the file for writing.
- seq_file = self.relax.IO.open_write_file(file, dir, force)
-
- # Loop over the sequence.
- for i in xrange(len(relax_data_store.res[run])):
- # Residue number.
- seq_file.write("%-5i" % relax_data_store.res[run][i].num)
-
- # Residue name.
- seq_file.write("%-6s" % relax_data_store.res[run][i].name)
-
- # New line.
- seq_file.write("\n")
-
- # Close the results file.
- seq_file.close()
r3408 - /1.3/generic_fns/residue.py