Author: bugman
Date: Sat Mar 23 18:08:56 2013
New Revision: 19069
URL: http://svn.gna.org/viewcvs/relax?rev=19069&view=rev
Log:
Shifted the generic_fns.xplor module to lib.xplor.
Added:
trunk/lib/xplor.py
- copied unchanged from r19067, trunk/generic_fns/xplor.py
Removed:
trunk/generic_fns/xplor.py
Modified:
trunk/generic_fns/__init__.py
trunk/generic_fns/noesy.py
trunk/lib/__init__.py
Modified: trunk/generic_fns/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/__init__.py?rev=19069&r1=19068&r2=19069&view=diff
==============================================================================
--- trunk/generic_fns/__init__.py (original)
+++ trunk/generic_fns/__init__.py Sat Mar 23 18:08:56 2013
@@ -64,6 +64,5 @@
'sys_info',
'temperature',
'value',
- 'vmd',
- 'xplor'
+ 'vmd'
]
Modified: trunk/generic_fns/noesy.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/noesy.py?rev=19069&r1=19068&r2=19069&view=diff
==============================================================================
--- trunk/generic_fns/noesy.py (original)
+++ trunk/generic_fns/noesy.py Sat Mar 23 18:08:56 2013
@@ -29,7 +29,7 @@
# relax module imports.
from generic_fns import pipes
from generic_fns.mol_res_spin import exists_mol_res_spin_data, return_spin,
tokenise
-from generic_fns import xplor
+from lib import xplor
from lib.errors import RelaxError, RelaxNoSequenceError
from lib.io import open_read_file
from lib.warnings import RelaxWarning
Removed: trunk/generic_fns/xplor.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/xplor.py?rev=19068&view=auto
==============================================================================
--- trunk/generic_fns/xplor.py (original)
+++ trunk/generic_fns/xplor.py (removed)
@@ -1,306 +1,0 @@
-###############################################################################
-#
#
-# Copyright (C) 2009-2013 Edward d'Auvergne
#
-#
#
-# This file is part of the program relax (http://www.nmr-relax.com).
#
-#
#
-# This program 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 3 of the License, or
#
-# (at your option) any later version.
#
-#
#
-# This program 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 this program. If not, see <http://www.gnu.org/licenses/>.
#
-#
#
-###############################################################################
-
-# Module docstring.
-"""Module containing functions for the parsing and creation of Xplor
formatted files."""
-
-# Python module imports.
-from re import search
-
-# relax module imports.
-from lib.errors import RelaxError
-
-
-def __convert_to_id(string):
- """Convert the string into a relax atom id representation.
-
- @param string: The Xplor atom string.
- @type string: str
- @return: The relax atom id.
- @rtype: str
- """
-
- # Split up the string by the 'and' statements.
- data = string.split('and')
-
- # Loop over the data.
- relax_id = ''
- for i in range(len(data)):
- # Split by whitespace.
- info = data[i].split()
-
- # Don't know what this is!
- if len(info) != 2:
- raise RelaxError("Cannot convert the Xplor atom string '%s' to
relax format." % string)
-
- # A molecule identifier.
- if info[0] == 'segid':
- relax_id = relax_id + '#' + info[1]
-
- # A residue identifier.
- elif info[0] == 'resid':
- relax_id = relax_id + ':' + info[1]
-
- # An atom identifier.
- elif info[0] == 'name':
- relax_id = relax_id + '@' + info[1]
-
- # Return the relax id.
- return relax_id
-
-
-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 (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 isinstance(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 isinstance(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.
- line_index = 0
- while True:
- # Break out!
- if line_index >= len(lines):
- break
-
- # Find the assign statements.
- if search('^assign', lines[line_index]):
- # Init.
- char_index = -1
-
- # Extract the atom ID strings.
- id = ['', '']
- id_index = 0
- inside = 0
- while True:
- # Inc the character index.
- char_index = char_index + 1
-
- # Break out!
- if line_index >= len(lines):
- break
-
- # 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
-
- # 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:
- continue
-
- # 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.
- 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 = lines[line_index][char_index+1:].split()
-
- # NOE dist, lower, upper.
- noe = float(info[0])
- lower = float(info[1])
- upper = float(info[2])
-
- # Non-data line.
- else:
- # Line index.
- line_index = line_index + 1
-
- # Skip to the next line without yielding.
- continue
-
- # 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 True:
- # 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.
- if not atoms[0]:
- return id
- else:
- return atoms
-
-
-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
Modified: trunk/lib/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/__init__.py?rev=19069&r1=19068&r2=19069&view=diff
==============================================================================
--- trunk/lib/__init__.py (original)
+++ trunk/lib/__init__.py Sat Mar 23 18:08:56 2013
@@ -39,5 +39,6 @@
'spectral_densities',
'structure',
'text',
- 'warnings'
+ 'warnings',
+ 'xplor'
]
r19069 - in /trunk: generic_fns/__init__.py generic_fns/noesy.py generic_fns/xplor.py lib/__init__.py lib/xplor.py