Allow PDBIO to write to an open IO object without closing it

[jgreener64]

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Recent changes to PDBIO in be77131 switched to using a with fhandle block for the open file handle. This is fine in the case of the file being opened by PDBIO, but another useful situation is having an open file handle or string object that you can read from or write to again.

This PR only closes the file handle if PDBIO opened it, allowing for example:

from Bio.PDB import *
from io import StringIO

parser = PDBParser()
structure = parser.get_structure("6YYT", "6YYT.pdb")
res = structure[0]["A"][31]

io_pdb = PDBIO()
io_pdb.set_structure(res)
io_str = StringIO()
io_pdb.save(io_str)
print(io_str.getvalue())

ATOM      1  N   VAL A  31     125.110  92.109  68.636  1.00 52.46           N  
ATOM      2  CA  VAL A  31     124.229  91.412  69.563  1.00 52.46           C  
ATOM      3  C   VAL A  31     122.990  92.264  69.821  1.00 52.46           C  
ATOM      4  O   VAL A  31     122.766  93.266  69.142  1.00 52.46           O  
ATOM      5  CB  VAL A  31     124.958  91.076  70.879  1.00 52.46           C  
ATOM      6  CG1 VAL A  31     126.011  90.005  70.641  1.00 52.46           C  
ATOM      7  CG2 VAL A  31     125.585  92.327  71.479  1.00 52.46           C  
TER       8      VAL A  31                                                       
END   

whereas on Biopython 1.79 the last line errors as io_str has been closed by save:

ValueError: I/O operation on closed file

Most of the code change is white space, it just adds a flag that closes the handle depending on whether open was called.

This initially came to my attention due to a downstream error in NGLView (https://bioinformatics.stackexchange.com/questions/20151/file-i-o-error-using-nglview-show-biopythonstructure) which uses this behaviour to access the string of a written PDB file without writing a file (https://github.com/nglviewer/nglview/blob/master/nglview/adaptor.py#L193-L200).

[peterjc]

Might be able to use isinstance(file, str) here instead of a flag variable?

[jgreener64]

Sure, done.

[peterjc]

Looks good to me.

Tip: append ?w=1 on the diff view in GitHub to hide the indentation change which makes this look more dramatic than it really is.

[JoaoRodrigues]

Looks good to me as well. I'll merge it. Thanks Joe!

@peterjc Nice trick with the ?w=1 to hide indentation, it took me a while to figure out what exactly had changed!

[peterjc]

To help remember this, it's a w for whitespace, just like the diff -w ... command line option.

[jgreener64]

There is also a checkbox to hide white space under the settings dropdown in the diff viewer.

[peterjc]

I see, via the cog icon - I wonder how long that's been there? Thanks!

[pippo1990]

Could you check if solution could be like PDBParser [PDBParser.py] handles it:

from Bio.File import as_handle ##github.com/biopython/biopython/blob/…

and in PDBIO.py save method #[https://github.com/biopython/biopython/blob/7ef56557bdca66eabd62334e61c4dc3153c997ff/Bio/PDB/PDBIO.py#L299]

change with fhandle to with as_handle(fhandle) , was referring to old PDBIO 1.80 that was using with fhandle

or betterr remove "if isinstance else ..." and change "with fhandle:" to "with as_handle(file, mode = 'w') as fhandle:"