Author: bugman
Date: Mon Jan 26 15:01:10 2009
New Revision: 8646
URL: http://svn.gna.org/viewcvs/relax?rev=8646&view=rev
Log:
Created the Xplor module for handling Xplor formatted files.
The function parse_noe_restraints() has been added to parse the NOE
restraints. The function
strip_comments() has been written to remove Xplor comments from the input
data.
Added:
branches/ave_noe/generic_fns/xplor.py
Added: branches/ave_noe/generic_fns/xplor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/generic_fns/xplor.py?rev=8646&view=auto
==============================================================================
--- branches/ave_noe/generic_fns/xplor.py (added)
+++ branches/ave_noe/generic_fns/xplor.py Mon Jan 26 15:01:10 2009
@@ -1,0 +1,161 @@
+###############################################################################
+#
#
+# Copyright (C) 2009 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
#
+#
#
+###############################################################################
+
+# Module docstring.
+"""Module containing functions for the parsing and creation of Xplor
formatted files."""
+
+# Python module imports.
+from re import search
+from string import split
+
+
+def parse_noe_restraints(lines):
+ """Parse and return the NOE restraints from the Xplor lines.
+
+ @param lines: The Xplor formatted file, or file fragment, split into
lines.
+ @type lines: list of str
+ @return: The NOE restraint list in the format of two atom
identification strings and the
+ lower and upper restraints.
+ @rtype: list of lists of [str, str, float, float]
+ """
+
+ # Strip all comments from the data.
+ lines = strip_comments(lines)
+
+ # Extract the data.
+ data = []
+ line_index = 0
+ while 1:
+ # Break out!
+ if line_index >= len(lines):
+ break
+
+ # Find the starting assign.
+ if search('^assign', lines[line_index]):
+ # Add a new data line.
+ data.append([None, None, None, None])
+
+ # Init.
+ char_index = -1
+
+ # Extract the first atom string.
+ atom = ''
+ inside = False
+ while 1:
+ # Inc the character index.
+ char_index = char_index + 1
+
+ # Start.
+ if not inside:
+ if lines[line_index][char_index] == '(':
+ inside = True
+ continue
+
+ # End.
+ if inside and lines[line_index][char_index] == ')':
+ break
+
+ # Append the character.
+ atom = atom + lines[line_index][char_index]
+
+ # Convert the atom data to a relax atom id.
+ data[-1][0] = atom
+
+ # Extract the second atom string.
+ atom = ''
+ inside = False
+ while 1:
+ # Inc the character index.
+ char_index = char_index + 1
+
+ # Check if we need to go to the next line.
+ if char_index > len(lines[line_index]):
+ line_index = line_index + 1
+ char_index = -1
+ continue
+
+ # Start.
+ if not inside:
+ if lines[line_index][char_index] == '(':
+ inside = True
+ continue
+
+ # End.
+ if inside and lines[line_index][char_index] == ')':
+ break
+
+ # Append the character.
+ atom = atom + lines[line_index][char_index]
+
+ # Convert the atom data to a relax atom id.
+ data[-1][1] = atom
+
+ # The rest of the data (NOE restraint info).
+ info = split(lines[line_index][char_index+1:])
+
+ # NOE dist, lower, upper.
+ noe = float(info[0])
+ lower = float(info[1])
+ upper = float(info[2])
+
+ # Convert to upper and lower bounds.
+ data[-1][2] = noe - lower
+ data[-1][3] = noe + upper
+
+ # Line index.
+ line_index = line_index + 1
+
+ # Return the data.
+ return data
+
+
+def strip_comments(lines):
+ """Remove all Xplor comments from the data.
+
+ @param lines: The Xplor formatted file, or file fragment, split into
lines.
+ @type lines: list of str
+ @return: The file data with all comments removed.
+ @rtype: list of str
+ """
+
+ # Loop over the lines.
+ new_lines = []
+ for line in lines:
+ # Comment lines.
+ if search('^!', line):
+ continue
+
+ # Partial comment lines.
+ new_line = ''
+ for char in line:
+ # Comment - so skip the rest of the line.
+ if char == '!':
+ continue
+
+ # Build the new line.
+ new_line = new_line + char
+
+ # Add the new line.
+ new_lines.append(new_line)
+
+ # Return the stripped data.
+ return new_lines
r8646 - /branches/ave_noe/generic_fns/xplor.py