Reading and writing molecular systems

BioSimSpace has support for reading and writing a large number of common molecular file formats. Unlike many other molecular parsers, BioSimSpace does not attempt to infer the format from the file extension. Instead, it reads the files in parallel using its blazing fast suite of parsers in order to automatically determine the correct format.

To read a system from file:

import BioSimSpace as BSS

# Load a molecular system from a set of files.
system = BSS.IO.readMolecules(["ala.crd", ""])

It is possible to mix and match formats as long as the molecular information in the different files is consistent. BioSimSpace will report an error whenever it is unable to parse a particular file, or whenever it encounters conflicting information.

It is possible to query the system to see the file formats from which it was constructed:


(Note that the file formats need not match the extensions of the original files.)

BioSimSpace also makes it easy to write a molecular system:

# Save the system using the original file format, i.e. "filename.prm7" and "filename.rst7"
BSS.IO.saveMolecules("filename", system, system.fileFormat())

Where possible, BioSimSpace can also interconvert between formats. For example:

# Save the molecular system to a PDB file.
BSS.IO.saveMolecules("filename", system, "PDB")

# Save the molecular system to a selection of formats.
BSS.IO.saveMolecules("flename", system, ["PDB", "Mol2", "Gro87"])

To see what file formats are available within BioSimSpace:


To get a description of a given fileformat:

'Protein Data Bank (PDB) format files.'