BioSimSpace.Stream

The Stream package contains tools for streaming wrapped Sire objects, i.e. objects from BioSimSpace._SireWrappers.

Functions

save(sire_object, filebase)	Stream a wrapped Sire object to file.
load(file)	Stream a wrapped Sire object from file.

Examples

Stream a System object to and from file.

 import BioSimSpace as BSS

 files = BSS.IO.expand(BSS.tutorialUrl(), ["ala.top", "ala.crd"], ".bz2")

 # Load a molecular system.
 system0 = BSS.IO.readMolecules(files)

 # Stream to file.
 BSS.Stream.save(system0, "system")

 # Alternatively, stream the system object directly.
 system0.save("system")

 # Stream from file.
 system1 = BSS.Stream.load("system.s3")

 # Check the metadata associated with an existing stream. Streaming is
 # generally backwards compatible, but it can be useful to know check
 # the data if issues occur, or when you require an object from a specific
 # sandpit.
 BSS.Stream.getMetadata("system.bss")
 {'bss_object': 'BioSimSpace._SireWrappers._system.System',
 'bss_version': '2023.2.2',
 'bss_revisionid': '9d46295',
 'sire_version': '2023.3.0.dev',
 'sire_revisionid': '90eef20',
 'sandpit': 'None'}

 # You can also get more extensive metadata regarding the underlying Sire
 # object.
 BSS.Stream.getSireMetadata("system.bss")
{'Object type(s)': 'SireSystem::System',
 'Created by': 'lester',
 'Creation date': 'Thu Jun 29 09:38:21 2023',
 'Created on': 'porridge',
 'System': {'UNIX system': 'Linux',
  'UNIX release': '6.3.9-arch1-1',
  'UNIX version': '#1 SMP PREEMPT_DYNAMIC Wed, 21 Jun 2023 20:46:20 +0000',
  'UNIX machine': 'x86_64',
  'Compiler': 'GNU C++ (13.1.0)',
  'Wordsize': '64 bit',
  'ByteOrder': 'Little endian',
  'Qt runtime version': '5.15.8',
  'Qt compile version': '5.15.8',
  'Sire compile version': '2023.3.0',
  'Compile flags': '-std=c++17 -DSIRE_HAS_CPP_17 -DSIRE_HAS_CPP_14 -DSIRE_HAS_CPP_1Y -DSIRE_HAS_CPP_11 -Wall -Wno-attributes -pipe -DSIRE_ALWAYS_INLINE=inline -Wno-strict-aliasing -DSIRE_VISIBILITY_AVAILABLE -fvisibility=hidden -fvisibility-inlines-hidden -fopenmp-simd -mavx -DSIRE_USE_AVX  -std=c++17 -DSIRE_HAS_CPP_17 -DSIRE_HAS_CPP_14 -DSIRE_HAS_CPP_1Y -DSIRE_HAS_CPP_11 -O3 -ffast-math -fomit-frame-pointer',
  'Link flags': '-rdynamic -Wl,--no-undefined -lpthread'},
 'Repository': 'git@github.com:OpenBioSim/sire.git | devel',
 'Packed size': '317.173 kB',
 'Unpacked size': '3872.57 kB',
 'Country': 'United Kingdom',
 'Language': 'English'}