recognising multiple molecules in pdb output from flare about biosimspace HOT 3 CLOSED

This is because the Flare file is not a properly formatted PDB file. We only break the contents into multiple molecules if the PDB contains multiple MODEL entries (with appropriate ENDMDL records) or if there are TER records between the molecules. The Flare file has neither, but just concatenates together a bunch of individual PDB files. (There should only be one MASTER and END per file.) We also can't use the CONECT records to break the system into molecules, since these are often incomplete or entirely missing.

I'd recommend writing to separate PDB files, then loading all of them at one go. You could also load them individually and add them to a system. Something like:

# Load molecules from a bunch of files into the same system.
system = BSS.IO.readMolecules(BSS.IO.glob("file_prefix_*.pdb"))

# Or...

# Load the files one-by-one and add the molecules to a system.
for idx, file in enumerate(pdb_files):
    # Create the initial system.
    if idx == 0:
        system = BSS.IO.readMolecules(file)
    # Add the molecule to the system.
    else:
        system += BSS.IO.readMolecules(file).getMolecules()

from biosimspace.

ok, I thought it was something like that. I'll find a way to write them out individually.

from biosimspace.

No problem. If we end up using these Flare files a lot then it would be easy for me to modify the PDB parser (since we know what the format is). In the short term, splitting to multiple files is probably the best option.

from biosimspace.