Loading from multiple files

It is often the case that molecular information needs to be read from multiple files, e.g. a separate topology and coordinate file.

You load from multiple files simply by passing multiple filenames and/or URLs to sire.load().

>>> mols = sr.load("https://sire.openbiosim.org/m/ala.top",
...                "https://sire.openbiosim.org/m/ala.crd")
Downloading from 'https://sire.openbiosim.org/m/ala.top'...
Unzipping './ala.top.bz2'...
Downloading from 'https://sire.openbiosim.org/m/ala.crd'...
Unzipping './ala.crd.bz2'...

>>> print(mols)
System( name=ACE num_molecules=631 num_residues=633 num_atoms=1912 )

You can pass in the filenames as multiple arguments or as a list, whichever you find easiest.

>>> mols = sr.load(["https://sire.openbiosim.org/m/ala.top",
...                 "https://sire.openbiosim.org/m/ala.crd"])

If the files or URLs have a common base, then you can save some typing by using sire.expand(), e.g.

>>> mols = sr.load(sr.expand("https://sire.openbiosim.org/m",
...                          "ala.top", "ala.crd"))

or

>>> mols = sr.load(sr.expand(sr.tutorial_url,
...                          ["ala.top", "ala.crd"]))

Note

sr.tutorial_url expands to the base URL for tutorial files (https://sire.openbiosim.org/m). It is worth using this variable for the tutorial as it auto-completes and will reduce errors.

If you are loading files, you can also make use of glob expressions (wildcard expansions), e.g.

>>> mols = sr.load("ala.???")

Note

This line loads the ala.top and ala.crd files that were downloaded by the above lines. This is because Sire downloads files at URLs to the current directory. You can tell it to use a different directory by passing that in via the directory argument, e.g. sr.load(sr.expand(sr.tutorial_url,"cholesterol.sdf"), directory="tmp"). The directory will be created automatically if it doesn’t exist.

Note

We couldn’t use ala.* because the directory contains the compressed input files, ala.crd.bz2 and ala.top.bz2, which were downloaded by sr.load. If you remove both these files, then you could use sr.load("ala.*").