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licence clean-up: all LGPL v3
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- Andre Caldas commented on the fact that the licence was not
  named correctly in AUTHORS
- all files are now properly distributed under LGPLv3 (updated
  all comment headers and AUTHORS and setup.py):
  The next release on PyPi should properly display LPGL
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@orbeckst
orbeckst committed Apr 28, 2014
1 parent 27f66f7 commit 940ea7b
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Showing 6 changed files with 99 additions and 113 deletions.
15 changes: 12 additions & 3 deletions AUTHORS
View file
@@ -1,3 +1,12 @@
gridDataFormats
Copyright (c) 2007-2010 Oliver Beckstein <orbeckst@gmail.com>
Published under the GNU Public Licence, version 3
=================
gridDataFormats
=================

Copyright (c) 2007-2014 Oliver Beckstein <orbeckst@gmail.com>

Published under the GNU Lesser General Public Licence, version 3


* releases: https://pypi.python.org/pypi/GridDataFormats

* source code repository: https://github.com/orbeckst/GridDataFormats
72 changes: 36 additions & 36 deletions gridData/OpenDX.py
View file
@@ -1,6 +1,6 @@
# gridData --- python modules to read and write gridded data
# Copyright (c) 2009-2010 Oliver Beckstein <orbeckst@gmail.com>
# Released under the GNU Lesser Public License, version 3 or later.
# Copyright (c) 2009-2014 Oliver Beckstein <orbeckst@gmail.com>
# Released under the GNU Lesser General Public License, version 3 or later.

"""
:mod:`OpenDX` --- routines to read and write simple OpenDX files
Expand Down Expand Up @@ -31,11 +31,11 @@
grid numpy nD array (typically a nD histogram)
grid.shape the shape of the array
origin the cartesian coordinates of the center of the
origin the cartesian coordinates of the center of the
(0,0,..,0) grid cell
delta n x n array with the length of a grid cell along
each axis; for regular rectangular grids the off-diagonal
elements are 0 and the diagonal ones correspond to the
delta n x n array with the length of a grid cell along
each axis; for regular rectangular grids the off-diagonal
elements are 0 and the diagonal ones correspond to the
'bin width' of the histogram, eg delta[0,0] = 1.0 (Angstrom)
>>> dx = OpenDX.field('density')
Expand All @@ -46,8 +46,8 @@
or
>>> dx = OpenDX.field('density',components=dict(
positions=OpenDX.gridpositions(1,grid.shape,d.origin,d.delta),
connections=OpenDX.gridconnections(2,grid.shape),
positions=OpenDX.gridpositions(1,grid.shape,d.origin,d.delta),
connections=OpenDX.gridconnections(2,grid.shape),
data=OpenDX.array(3,grid)) )
Expand Down Expand Up @@ -79,7 +79,7 @@ def sorted(iterable, cmp=None, key=None, reverse=False):
Naive pre python 2.4 compatibility fudge.
With key, cmp must make use of triplets (key,int,value).
It's a fudge after all.
It's a fudge after all.
"""
L = list(iterable)
args = ()
Expand All @@ -91,11 +91,11 @@ def sorted(iterable, cmp=None, key=None, reverse=False):
# decorate-sort-undecorate
deco = [(key(x),i,x) for i,x in enumerate(L)]
deco.sort(*args)
L[:] = [y[2] for y in deco]
L[:] = [y[2] for y in deco]
if reverse:
L.reverse()
return L

class DXclass(object):
"""'class' object as defined by OpenDX"""
def __init__(self,classid):
Expand All @@ -113,7 +113,7 @@ def write(self,file,optstring="",quote=False):
# spaces. (Chimera 1.4.1, PyMOL 1.3)
file.write('object '+classid+' class '+str(self.name)+' '+\
optstring+'\n')

def read(self,file):
raise NotImplementedError('Reading is currently not supported.')

Expand All @@ -124,7 +124,7 @@ def ndformat(self,s):

def __repr__(self):
return '<OpenDX.'+str(self.name)+' object, id='+str(self.id)+'>'


class gridpositions(DXclass):
"""OpenDX gridpositions class.
Expand Down Expand Up @@ -189,7 +189,7 @@ def write(self,file):
self.array.size)
# grid data, serialized as a C array (z fastest varying)
# (flat iterator is equivalent to: for x: for y: for z: grid[x,y,z])
# VMD's DX reader requires exactly 3 values per line
# VMD's DX reader requires exactly 3 values per line
values_per_line = 3
anext = self.array.flat.next
while 1:
Expand Down Expand Up @@ -228,7 +228,7 @@ def __init__(self,classid='0',components=None,comments=None):
individual ids!) which correspond to
positions
connections
data
data
comments list of strings; each string becomes a comment line
prefixed with '#'. Avoid newlines.
Expand All @@ -237,7 +237,7 @@ def __init__(self,classid='0',components=None,comments=None):
write() write a dx file
add() add a component to the field
add_comments() add comments
A field must have at least the components 'positions',
'connections', and 'data'. Those components are associated
with objects belonging to the field. When writing a dx file
Expand Down Expand Up @@ -405,7 +405,7 @@ class DXParser(object):
"""Brain-dead baroque implementation to read a simple (VMD) dx file.
Requires a OpenDX.field instance.
1) scan for 'object' lines:
'object' id 'class' class [data]
[data ...]
Expand Down Expand Up @@ -452,12 +452,12 @@ def __init__(self,filename):
'array':self.__array, 'field':self.__field,
}


def parse(self,DXfield):
"""Parse the dx file and construct a DX field object with component classes.
DXfield_object = OpenDX.field(*args)
parse(DXfield_object)
parse(DXfield_object)
A tokenizer turns the dx file into a stream of tokens. A
hierarchy of parsers examines the stream. The level-0 parser
Expand All @@ -471,7 +471,7 @@ def parse(self,DXfield):
not implemented yet.
* Unknown tokens raise an exception.
"""

self.DXfield = DXfield # OpenDX.field (used by comment parser)
self.currentobject = None # containers for data
self.objects = [] # |
Expand All @@ -495,12 +495,12 @@ def parse(self,DXfield):

# free space
del self.currentobject, self.objects



def __general(self):
"""Level-0 parser and main loop.
Look for a token that matches a level-1 parser and hand over control."""
while 1: # main loop
try:
Expand All @@ -510,7 +510,7 @@ def __general(self):
# (kludge in here as the last level-2 parser usually does not return
# via the object parser)
if self.currentobject and self.currentobject not in self.objects:
self.objects.append(self.currentobject)
self.objects.append(self.currentobject)
return # stop parsing and finish
# decision branches for all level-1 parsers:
# (the only way to get out of the lower level parsers!)
Expand All @@ -525,7 +525,7 @@ def __general(self):
# later we never formally switch back to __general
# (would create inifinite loop)
raise DXParseError('Unknown level-1 construct at '+str(tok))

self.apply_parser() # hand over to new parser
# (possibly been set further down the hierarchy!)

Expand Down Expand Up @@ -559,7 +559,7 @@ def __object(self):
# setup new DXInitObject
classtype = self.__consume().text
self.currentobject = DXInitObject(classtype=classtype,classid=classid)

self.use_parser(classtype)

# Level-2 parser (object parsers)
Expand All @@ -572,12 +572,12 @@ def __gridpositions(self):
delta 1 0 0
delta 0 1 0
delta 0 0 1
"""
"""
try:
tok = self.__consume()
except DXParserNoTokens:
return

if tok.equals('counts'):
shape = []
try:
Expand All @@ -592,7 +592,7 @@ def __gridpositions(self):
elif tok.equals('origin'):
origin = []
try:
while (self.__peek().iscode('INTEGER') or
while (self.__peek().iscode('INTEGER') or
self.__peek().iscode('REAL')):
tok = self.__consume()
origin.append(tok.value())
Expand All @@ -606,7 +606,7 @@ def __gridpositions(self):
try:
while (self.__peek().iscode('INTEGER') or
self.__peek().iscode('REAL')):
tok = self.__consume()
tok = self.__consume()
d.append(tok.value())
except DXParserNoTokens:
pass
Expand All @@ -618,7 +618,7 @@ def __gridpositions(self):
self.currentobject['delta'] = [d]
else:
raise DXParseError('gridpositions: '+str(tok)+' not recognized.')


def __gridconnections(self):
"""Level-2 parser for gridconnections.
Expand All @@ -631,7 +631,7 @@ def __gridconnections(self):
tok = self.__consume()
except DXParserNoTokens:
return

if tok.equals('counts'):
shape = []
try:
Expand All @@ -647,7 +647,7 @@ def __gridconnections(self):
raise DXParseError('gridconnections: '+str(tok)+' not recognized.')


def __array(self):
def __array(self):
"""Level-2 parser for arrays.
pattern:
Expand All @@ -662,7 +662,7 @@ def __array(self):
tok = self.__consume()
except DXParserNoTokens:
return

if tok.equals('type'):
tok = self.__consume()
if not tok.iscode('STRING'):
Expand Down Expand Up @@ -706,7 +706,7 @@ def __field(self):
"""Level-2 parser for a DX field object.
pattern:
object "site map 1" class field
object "site map 1" class field
component "positions" value 1
component "connections" value 2
component "data" value 3
Expand Down Expand Up @@ -790,9 +790,9 @@ def __consume(self,):
pass
"""
self.__refill_tokenbuffer()
#print "DEBUG consume: "+str(self.__parser)+' '+str(self.__peek())
#print "DEBUG consume: "+str(self.__parser)+' '+str(self.__peek())
try:
return self.tokens.pop(0) # singlet
except IndexError:
raise DXParserNoTokens

5 changes: 2 additions & 3 deletions gridData/__init__.py
View file
@@ -1,7 +1,6 @@
# $Id$
# gridDataFormats --- python modules to read and write gridded data
# Copyright (c) 2009-2010 Oliver Beckstein <orbeckst@gmail.com>
# Released under the GNU Lesser Public License, version 3 or later.
# Copyright (c) 2009-2014 Oliver Beckstein <orbeckst@gmail.com>
# Released under the GNU Lesser General Public License, version 3 or later.
# See the files COPYING and COPYING.LESSER for details.

"""
Expand Down

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