BioSimSpace.IO.saveMolecules¶
-
BioSimSpace.IO.
saveMolecules
(filebase, system, fileformat, property_map={})¶ Save a molecular system to file.
- Parameters
filebase (str) – The base name of the output files.
system (
System
,Molecule
Molecule
) – The molecular system.fileformat (str, [str]) – The file format (or formats) to save to.
property_map (dict) – A dictionary that maps system “properties” to their user defined values. This allows the user to refer to properties with their own naming scheme, e.g. { “charge” : “my-charge” }
- Returns
files – The list of files that were generated.
- Return type
[str]
Examples
Load a molecular system from AMBER coordinate and topology files then try to save it to all supported file formats.
>>> import BioSimSpace as BSS >>> system = BSS.IO.readMolecules(["ala.rst7", "ala.prm7"]) >>> for format in BSS.IO.fileFormats(): ... try: ... BSS.IO.saveMolecules("test", system, format) ... except: ... print("Could not convert to format: '%s'" % format)
Load a molecular system from AMBER coordinate and topology files then try to save it to GROMACS format, mapping and un-mapping the charge property along the way.
>>> import BioSimSpace as BSS >>> system = BSS.IO.readMolecules(["ala.rst7", "ala.prm7"], property_map={"charge" : "my-charge"}) >>> BSS.IO.saveMolecules("test", system, ["gro87", "grotop"], property_map={"charge" : "my-charge"})