Author: bugman
Date: Wed May 6 17:03:00 2009
New Revision: 9040
URL: http://svn.gna.org/viewcvs/relax?rev=9040&view=rev
Log:
Rewrote how the Xplor NOE restraints are read.
Two new functions, first_parse() and second_parse() have been written to
first extract all assign
statements and then handle pseudoatoms.
Modified:
1.3/generic_fns/xplor.py
Modified: 1.3/generic_fns/xplor.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/xplor.py?rev=9040&r1=9039&r2=9040&view=diff
==============================================================================
--- 1.3/generic_fns/xplor.py (original)
+++ 1.3/generic_fns/xplor.py Wed May 6 17:03:00 2009
@@ -74,59 +74,84 @@
@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]
+ @return: The NOE restraint list in the format of two atom
identification strings (or list
+ of str for pseudoatoms) 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)
+ # Init.
+ data = []
+
+ # First level pass (assign statements).
+ for id1, id2, noe, lower, upper in first_parse(lines):
+ # Second parse (pseudoatoms).
+ id1 = second_parse(id1)
+ id2 = second_parse(id2)
+
+ # Convert to relax spin IDs.
+ if type(id1) == list:
+ relax_id1 = []
+ for i in range(len(id1)):
+ relax_id1.append(__convert_to_id(id1[i]))
+ else:
+ relax_id1 = __convert_to_id(id1)
+
+ if type(id2) == list:
+ relax_id2 = []
+ for i in range(len(id2)):
+ relax_id2.append(__convert_to_id(id2[i]))
+ else:
+ relax_id2 = __convert_to_id(id2)
+
+ # Convert to upper and lower bounds.
+ lower_bound = noe - lower
+ upper_bound = noe + upper
+
+ # Add the data to the list.
+ data.append([relax_id1, relax_id2, lower_bound, upper_bound])
+
+ # Return the data.
+ return data
+
+
+def first_parse(lines):
+ """Generator function to parse and extract the 2 atom IDs and NOE info
from the lines.
+
+ The first parse loops over and returns the data from assign statements,
returning pseudo atoms
+ as single strings. The second parse splits the pseudoatoms.
+
+ @param lines: The Xplor formatted file, or file fragment, split into
lines.
+ @type lines: list of str
+ @return: The 2 atom IDs, and NOE info (NOE, upper, and lower
bounds).
+ @rtype: str, str, float, float, float
+ """
+
# Extract the data.
- data = []
line_index = 0
while 1:
# Break out!
if line_index >= len(lines):
break
- # Find the starting assign.
+ # Find the assign statements.
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
+ # Extract the atom ID strings.
+ id = ['', '']
+ id_index = 0
+ inside = 0
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 out!
+ if line_index >= len(lines):
break
-
- # Append the character.
- atom = atom + lines[line_index][char_index]
-
- # Convert the atom data to a relax atom id.
- data[-1][0] = __convert_to_id(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]):
@@ -134,21 +159,36 @@
char_index = -1
continue
- # Start.
+ # A starting bracket, so increment the inside counter.
+ if lines[line_index][char_index] == '(':
+ inside = inside + 1
+
+ # Don't include the first bracket in the ID string.
+ if inside == 1:
+ continue
+
+ # Not inside, so jump to the next character.
if not inside:
- if lines[line_index][char_index] == '(':
- inside = True
continue
- # End.
- if inside and lines[line_index][char_index] == ')':
- break
+ # An ending bracket.
+ elif lines[line_index][char_index] == ')':
+ inside = inside - 1
+
+ # A logical test (debugging).
+ if inside < 0:
+ raise RelaxError, "Improperly formatted Xplor file,
unmatched ')'."
# Append the character.
- atom = atom + lines[line_index][char_index]
-
- # Convert the atom data to a relax atom id.
- data[-1][1] = __convert_to_id(atom)
+ if inside:
+ id[id_index] = id[id_index] +
lines[line_index][char_index]
+
+ # Go to the second id_index, or break.
+ if inside == 0:
+ if id_index == 1:
+ break
+ else:
+ id_index = 1
# The rest of the data (NOE restraint info).
info = split(lines[line_index][char_index+1:])
@@ -158,15 +198,73 @@
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.
+ yield id[0], id[1], noe, lower, upper
+
+
+def second_parse(id):
+ """Split up pseudoatoms.
+
+ @param id: The Xplor atom id without outer brackets, i.e. a single atom
or a list of atoms in
+ the case of pseudoatoms.
+ @type id: str
+ @return: For normal atoms, the id string is returned unmodified. For
pseudoatoms, a list of
+ strings, with brackets removed, is returned.
+ @rtype: str or list of str
+ """
+
+ # Loop over the characters.
+ atoms = ['']
+ index = -1
+ inside = False
+ while 1:
+ # Inc the character index.
+ index = index + 1
+
+ # Break out.
+ if index >= len(id):
+ break
+
+ # A starting bracket, so flip the inside flag.
+ if id[index] == '(':
+ # 2 brackets?!?
+ if inside:
+ raise RelaxError, "The Xplor pseudoatom ID string '%s' is
invalid." % id
+
+ # The flag.
+ inside = True
+
+ # Don't include the first bracket in the ID string.
+ continue
+
+ # Not inside, so jump to the next character.
+ if not inside:
+ continue
+
+ # An ending bracket.
+ if id[index] == ')':
+ inside = False
+
+ # Append the character.
+ if inside:
+ atoms[-1] = atoms[-1] + id[index]
+
+ # Add another atom.
+ if not inside:
+ atoms.append('')
+
+ # Remove the last empty atom string.
+ if atoms[0] and atoms[-1] == '':
+ atoms = atoms[:-1]
+
# Return the data.
- return data
+ if not atoms[0]:
+ return id
+ else:
+ return atoms
def strip_comments(lines):
r9040 - /1.3/generic_fns/xplor.py