/usr/lib/python2.7/dist-packages/chempy/mmtf/io.py is in pymol 1.8.4.0+dfsg-1build1.
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Experimental MMTF (Macromolecular Transmission Format) I/O library
'''
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import os
import sys
import itertools
import numpy
import struct
import msgpack
if sys.version_info[0] < 3:
from urllib import urlopen
izip = itertools.izip
izip_longest = itertools.izip_longest
as_msgpack_key = lambda k: k
else:
# python3
from urllib.request import urlopen
izip = zip
izip_longest = itertools.zip_longest
as_msgpack_key = lambda k: k if isinstance(k, bytes) else k.encode()
buffer = lambda s, i=0: memoryview(s)[i:]
# should be replaced with a more efficient numpy-array aware iterator
def simpleiter(iterable):
if isinstance(iterable, numpy.ndarray):
# Iterating over a numpy array is unreasonably slow. Iterating
# over it's list copy is much faster!
return iter(iterable.tolist())
return iter(iterable)
def asarray(arr, dtype='i'):
if hasattr(arr, '__len__'):
return numpy.asarray(arr, dtype)
return numpy.fromiter(arr, dtype)
MMTF_ENDIAN = '>' # big-endian
########### ENCODINGS ################
class RunLength:
@staticmethod
def encode(iterable):
in_iter = simpleiter(iterable)
curr = next(in_iter)
counter = 1
for item in in_iter:
if item == curr:
counter += 1
else:
yield curr
yield counter
curr = item
counter = 1
yield curr
yield counter
@staticmethod
def decode(iterable):
in_iter = simpleiter(iterable)
out = []
extend = out.extend
for item in in_iter:
extend([item] * next(in_iter))
return out
class Delta:
@staticmethod
def encode(iterable):
return numpy.diff(asarray(iterable, 'i4'))
@staticmethod
def decode(iterable):
return asarray(iterable).cumsum(dtype='i4')
class RecursiveIndex:
def __init__(self, min, max):
self.limits = (min, max)
def encode(self, iterable):
min, max = self.limits
for curr in simpleiter(iterable):
while curr >= max:
yield max
curr -= max
while curr <= min:
yield min
curr -= min
yield curr
def decode(self, iterable):
min, max = self.limits
decoded_val = 0
for item in simpleiter(iterable):
decoded_val += item
if item != max and item != min:
yield decoded_val
decoded_val = 0
class IntegerFloats:
def __init__(self, factor):
self.factor = factor
def encode(self, in_floats):
return (asarray(in_floats, 'f4') * self.factor).astype('i4')
def decode(self, in_ints):
return asarray(in_ints, 'f4') / self.factor
class IntegerChars:
@staticmethod
def encode(in_chars):
return [ord(x) for x in in_chars]
@staticmethod
def decode(in_ints):
return [(chr(x) if x else '') for x in simpleiter(in_ints)]
######## BUFFERS ###########
class NumbersBuffer:
def __init__(self, basetype='i', dectype=''):
self.enctype = numpy.dtype(MMTF_ENDIAN + basetype)
self.dectype = numpy.dtype(dectype or basetype)
def decode(self, in_bytes):
return numpy.frombuffer(in_bytes, self.enctype).astype(self.dectype)
def encode(self, in_ints):
return asarray(in_ints, self.enctype).tostring()
class StringsBuffer:
def __init__(self, nbytes, encoding='ascii'):
self.enctype = numpy.dtype('S' + str(nbytes))
self.encoding = encoding
def decode(self, in_bytes):
bstrings = numpy.frombuffer(in_bytes, self.enctype)
return [b.decode(self.encoding) for b in bstrings]
def encode(self, strings):
bstrings = numpy.fromiter((s.encode(self.encoding) for s in strings),
self.enctype, len(strings))
return bstrings.tostring()
########## STRATEGIES #############
def _PackedIntBufStrategy(nbytes=1, dectype='i4'):
m = 1 << (nbytes * 8 - 1)
return [
NumbersBuffer('i' + str(nbytes), dectype),
RecursiveIndex(-m, m - 1),
]
strategies = {
1: [NumbersBuffer('f4')],
2: [NumbersBuffer('i1')],
3: [NumbersBuffer('i2')],
4: [NumbersBuffer('i4')],
5: lambda length: [StringsBuffer(length)],
6: [NumbersBuffer('i4'), RunLength, IntegerChars],
7: [NumbersBuffer('i4'), RunLength],
8: [NumbersBuffer('i4'), RunLength, Delta],
9: lambda factor: [NumbersBuffer('i4'), RunLength, IntegerFloats(factor)],
10: lambda factor: _PackedIntBufStrategy(2) + [Delta, IntegerFloats(factor)],
11: lambda factor: [NumbersBuffer('i2'), IntegerFloats(factor)],
12: lambda factor: _PackedIntBufStrategy(2) + [IntegerFloats(factor)],
13: lambda factor: _PackedIntBufStrategy(1) + [IntegerFloats(factor)],
14: _PackedIntBufStrategy(2),
15: _PackedIntBufStrategy(1),
}
# optional parameters format (defaults to 'i' -> one int32 argument)
strategyparamsfmt = {
}
########## MEDIUM LEVEL ARRAY ENCODE/DECODE API ##############
def encode(arr, codec, param=0):
strategy = strategies[codec]
if not isinstance(strategy, list):
strategy = strategy(param)
buf = struct.pack(MMTF_ENDIAN + 'iii', codec, len(arr), param)
for handler in reversed(strategy):
arr = handler.encode(arr)
buf += arr
return buf
def encode_int(arr):
'''Find the best compression for a 32bit int array'''
return min((encode(arr, codec) for codec in (4, 7, 8)), key=len)
def decode(value):
codec, length = struct.unpack(MMTF_ENDIAN + 'ii', value[:8])
strategy = strategies[codec]
if not isinstance(strategy, list):
fmt = strategyparamsfmt.get(codec, 'i')
params = struct.unpack(MMTF_ENDIAN + fmt, value[8:12])
strategy = strategy(*params)
value = buffer(value, 12)
for handler in strategy:
value = handler.decode(value)
return value
############### HIGH LEVEL READER API ################
class MmtfReader:
def __init__(self, data):
if isinstance(data, bytes):
if data[:2] != b'\x1f\x8b': # gzip magic number
self._data = msgpack.unpackb(data)
return
import io, gzip
data = gzip.GzipFile(fileobj=io.BytesIO(data))
self._data = msgpack.unpack(data)
@classmethod
def from_url(cls, url):
handle = open(url, 'rb') if os.path.isfile(url) else urlopen(url)
return cls(handle.read())
def get(self, key, default=None):
key = as_msgpack_key(key)
try:
value = self._data[key]
except KeyError:
return default
if not (key.endswith(b'List') and isinstance(value, bytes)):
return value
return decode(value)
def get_iter(self, key, default=()):
return simpleiter(self.get(key, default))
def get_table_iter(self, keys, defaults=None):
if defaults is None:
return izip_longest(*[self.get_iter(k) for k in keys])
return izip(*[self.get_iter(k, itertools.repeat(d))
for (k, d) in zip(keys, defaults)])
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