Author: bugman
Date: Sun Nov 4 20:48:09 2007
New Revision: 3454
URL: http://svn.gna.org/viewcvs/relax?rev=3454&view=rev
Log:
Removed the out of date spin system module.
Removed:
1.3/generic_fns/spin.py
Removed: 1.3/generic_fns/spin.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/spin.py?rev=3453&view=auto
==============================================================================
--- 1.3/generic_fns/spin.py (original)
+++ 1.3/generic_fns/spin.py (removed)
@@ -1,312 +1,0 @@
-###############################################################################
-#
#
-# Copyright (C) 2003-2004, 2007 Edward d'Auvergne
#
-#
#
-# This file is part of the program relax.
#
-#
#
-# relax is free software; you can redistribute it and/or modify
#
-# it under the terms of the GNU General Public License as published by
#
-# the Free Software Foundation; either version 2 of the License, or
#
-# (at your option) any later version.
#
-#
#
-# relax is distributed in the hope that it will be useful,
#
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
-# GNU General Public License for more details.
#
-#
#
-# You should have received a copy of the GNU General Public License
#
-# along with relax; if not, write to the Free Software
#
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
-#
#
-###############################################################################
-
-# relax module imports.
-from data import Data as relax_data_store
-from relax_errors import RelaxError, RelaxFileEmptyError,
RelaxNoPdbChainError, RelaxNoPipeError, RelaxNoSequenceError,
RelaxSequenceError
-
-
-# The relax data storage object.
-
-
-def copy(res_num_from=None, res_name_from=None, res_num_to=None,
res_name_to=None):
- """Copy the contents of the residue structure from one residue to a new
residue.
-
- For copying to be successful, the res_num_from and res_name_from must
match an existant residue.
- The res_name_from and res_name_to arguments need not be supplied. The
new residue number must
- be unique.
-
- @param res_num_from: The residue number identifying the structure to
copy the data from.
- This argument must be supplied.
- @type res_num_from: int
- @param res_name_from: The residue name identifying the structure to
copy the data from. This
- argument is optional.
- @type res_name_from: str
- @param res_num_to: The residue number identifying the structure to
copy the data to. This
- argument must be supplied.
- @type res_num_to: int
- @param res_name_to: The residue name identifying the structure to
copy the data to. This
- argument is optional but if supplied will rename the copied residue.
- @type res_name_to: str
- """
-
- # Alias the current data pipe.
- cdp = relax_data_store[relax_data_store.current_pipe]
-
- # Test if the residue number already exists.
- for i in xrange(len(cdp.mol[0].res)):
- if cdp.mol[0].res[i].num == res_num_to:
- raise RelaxError, "The residue number '" + `res_num_to` + "'
already exists in the sequence."
-
- # Find the index corresponding to the residue number and name.
- index = None
- for i in xrange(len(cdp.mol[0].res)):
- # Residue number match.
- if cdp.mol[0].res[i].num == res_num_from:
- # Residue name match (if required).
- if res_name_from:
- if cdp.mol[0].res[i].name == res_name_from:
- index = i
- else:
- index = i
-
- # No residue to copy data from.
- if index == None:
- if res_name_from:
- raise RelaxError, "The residue '" + `res_num_from` + " " +
res_name_from + "' does not exist."
- else:
- raise RelaxError, "The residue number '" + `res_num_from` + "'
does not exist."
-
- # Copy the data.
- cdp.mol[0].res.append(cdp.mol[0].res[index].__clone__())
-
- # Change the new residue number.
- cdp.mol[0].res[-1].num = res_num_to
-
- # Change the new residue name.
- if res_name_to:
- cdp.mol[0].res[-1].name = res_name_to
-
-
-def create(res_num=None, res_name=None):
- """Function for adding a residue into the relax data store."""
-
- # 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 the residue number already exists.
- for i in xrange(len(cdp.mol[0].res)):
- if cdp.mol[0].res[i].num == res_num:
- raise RelaxError, "The residue number '" + `res_num` + "'
already exists in the sequence."
-
- # If no residue data exists, replace the empty first residue with this
residue.
- if cdp.mol[0].res[0].num == None and cdp.mol[0].res[0].name == None and
len(cdp.mol[0].res) == 1:
- cdp.mol[0].res[0].num = res_num
- cdp.mol[0].res[0].name = res_name
-
- # Append the residue.
- else:
- cdp.mol[0].res.add_item(res_num=res_num, res_name=res_name)
-
-
-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 delete(self, run=None):
- """Function for deleting the sequence."""
-
- # 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
-
- # Delete the data.
- del(relax_data_store.res[run])
-
- # Clean up the runs.
- self.relax.generic.runs.eliminate_unused_runs()
-
-
- def display(self, run=None):
- """Function for displaying the sequence."""
-
- # 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
-
- # Print a header.
- print "%-8s%-8s%-10s" % ("Number", "Name", "Selected")
-
- # Print the sequence.
- for i in xrange(len(relax_data_store.res[run])):
- print "%-8i%-8s%-10i" % (relax_data_store.res[run][i].num,
relax_data_store.res[run][i].name, relax_data_store.res[run][i].select)
-
-
- 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()
r3454 - /1.3/generic_fns/spin.py