[Biopython-dev] report: what happens on 'from Bio import PDB'?

[Kristian Rother]

Hi,

I'm currently checking what my application is using its memory for
(because it uses way too much for non-Biopython related things). However,
as soon as the simple command

from Bio import PDB

is executed, these are the objects that Python has in memory after running
the gc:

1 <class 'codecs.CodecInfo'>
1 <class 'ctypes.PyDLL'>
1 <class 'ctypes._endian._swapped_meta'>
1 <class 'numpy.core.numeric._unspecified'>
1 <class 'numpy.lib._datasource._FileOpeners'>
1 <class 'numpy.lib.index_tricks.CClass'>
1 <class 'numpy.lib.index_tricks.RClass'>
1 <class 'numpy.ma.core.MaskedArray'>
1 <class 'numpy.ma.core._maximum_operation'>
1 <class 'numpy.ma.core._minimum_operation'>
1 <class 'numpy.ma.extras.mr_class'>
1 <class 'random.Random'>
1 <class 'site._Helper'>
1 <class 'string._TemplateMetaclass'>
1 <class 'unittest.TestLoader'>
1 <type 'NoneType'>
1 <type 'NotImplementedType'>
1 <type '_ctypes.ArrayType'>
1 <type '_ctypes.StructType'>
1 <type '_ctypes.UnionType'>
1 <type 'ellipsis'>
1 <type 'exceptions.MemoryError'>
1 <type 'exceptions.RuntimeError'>
1 <type 'mtrand.RandomState'>
1 <type 'numpy.ndarray'>
1 <type 'sys.flags'>
1 <type 'sys.floatinfo'>
1 <type 'thread.lock'>
1 <type 'unicode'>
1 from module:Bio.GenBank.utils
1 from module:Bio.PDB.PDBIO
1 from module:Bio.PropertyManager
1 from module:os
2 <class 'Bio.PropertyManager.CreateDict'>
2 <class 'ctypes.LibraryLoader'>
2 <class 'numpy.lib.index_tricks.IndexExpression'>
2 <class 'numpy.lib.index_tricks.nd_grid'>
2 <class 'site.Quitter'>
2 <type 'bool'>
2 <type 'numpy.bool_'>
2 <type 'numpy.float64'>
2 <type 'object'>
2 from module:Bio.GenBank.LocationParser
2 from module:xml.sax.handler
3 <class 'site._Printer'>
3 <type '_ctypes.PointerType'>
3 <type 'file'>
3 <type 'frame'>
4 <type 'PyCObject'>
5 <class 'ctypes.CFunctionType'>
6 <class 'numpy.core.numerictypes._typedict'>
6 <type 'complex'>
6 from module:numpy.ma.extras
7 <type 'imp.NullImporter'>
7 from module:Bio.Alphabet.IUPAC
7 from module:__future__
8 <type '_ctypes.CFuncPtrType'>
9 <class 'numpy.ma.core._arraymethod'>
10 <type 'classmethod_descriptor'>
13 <type 'Struct'>
14 <type 'frozenset'>
15 <class 'numpy.testing.nosetester.NoseTester'>
16 <class 'abc.ABCMeta'>
16 <type 'staticmethod'>
19 <type 'classmethod'>
27 <type '_ctypes.SimpleType'>
35 <type 'cell'>
35 <type 'operator.itemgetter'>
36 <type 'StgDict'>
38 <type '_sre.SRE_Pattern'>
49 <type 'set'>
56 <type 'long'>
56 from module:Bio.Alphabet
68 <type 'instancemethod'>
76 <type 'numpy.ufunc'>
91 <type 'property'>
95 from module:numpy.ma.core
201 <type 'member_descriptor'>
203 <type 'classobj'>
225 <type 'module'>
350 <type 'type'>
351 from module:Bio.Data.CodonTable
360 <type 'int'>
385 <type 'float'>
393 <type 'getset_descriptor'>
407 <type 'weakref'>
579 <type 'method_descriptor'>
837 <type 'builtin_function_or_method'>
1365 <type 'wrapper_descriptor'>
2073 <type 'dict'>
3191 <type 'function'>
3289 <type 'code'>
4099 <type 'list'>
11989 <type 'tuple'>
19718 <type 'str'>
total 50912

Hope this is useful ;-)

Best Regards,
   Kristian