[ENH]: Adding option to export/return PDB as a raw string

[hedderi4]

Problem

It would be very useful to be able to return the cavities as a string in PDB format instead of immediately writing it to a file.
Thanks a lot!

Proposed solution

This should be done by editing the _export function, since the PDB string is anyways generated, right? Or are there any other possibilities that I am missing?

[jvsguerra]

Hi @jbHedderich,

Thank you for your suggestion.

Are you interested in obtaining the coordinates of the cavity points from the string? If so, we shared a function (grid2coords) to export coordinates in a numpy.ndarray in this #110 (comment).

Please let us know if this meets your needs.

[jvsguerra]

I have implemented an option to export PDB as a raw string in pyKVFinder v0.6.14.

To use this feature, you can follow the examples below.

Example 1: Using full workflow (pyKVFinder.run_workflow) to detect cavities and export the cavity PDB-formatted file as a string. The pyKVFindeResults.export method now accepts None as an input for the output filename (output), returning the PDB-formatted data as a raw string instead of writing it to a file.

>>> import pyKVFinder
>>> pdb = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.pdb')
>>> results = pyKVFinder.run_workflow(pdb)
>>> string = results.export(output=None)
>>> print(string)
ATOM     1  H   KAA     0       0.000   0.000   0.000  1.00  0.00
...
ATOM  1000  H   KAA     0       0.000   0.000   0.000  1.00  0.00
>>> string = results.export_all(output=None)
>>> print(string)
ATOM     1  H   KAA     0       0.000   0.000   0.000  1.00  0.00
...
ATOM  1000  H   KAA     0       0.000   0.000   0.000  1.00  0.00

Example 2: Using the stepwise workflow (pyKVFinder.read_pdb, pyKVFinder.get_vertices, pyKVFinder.detect) to detect cavities and export the cavity PDB-formatted file as a string. The pyKVFinder.export function now accepts None as an input for the output filename (fn), returning the PDB-formatted data as a raw string instead of writing it to a file.

>>> import pyKVFinder
>>> pdb = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.pdb')
>>> atomic = pyKVFinder.read_pdb(pdb)
>>> vertices = pyKVFinder.get_vertices(atomic)
>>> ncav, cavities = pyKVFinder.detect(atomic, vertices)
>>> string = pyKVFinder.export(None, cavities, None, vertices)
>>> print(string)
ATOM     1  H   KAA     0       0.000   0.000   0.000  1.00  0.00
...
ATOM  1000  H   KAA     0       0.000   0.000   0.000  1.00  0.00

Please let me know if this meets your needs. If you encounter any further issues or have additional questions, feel free to ask for assistance.

[hedderi4]

Thanks, that helped a lot :)!