[MDAKit/ Hackathon] Pocket Volume calculation

[H-EKE]

Hi,

We are trying to implement Fpocket (https://github.com/Discngine/fpocket) into MDAnalysis

[H-EKE]

###DRAFT

We are starting by adapting the same procedure as with HOLE for Fpocket :)

def run_fpocket(outfile, infile_text, executable):
    """Run the HOLE program.

    Parameters
    ----------
    outfile: str
        Output file name
    infile_text: str
        HOLE input text
        (typically generated by :func:`set_up_hole_input`)
    executable: str
        HOLE executable

    Returns
    -------
    str
        Output file name
    """
    with open(outfile, 'w') as output:
        proc = subprocess.Popen(executable, stdin=subprocess.PIPE,
                                stdout=output)
        stdout, stderr = proc.communicate(infile_text.encode('utf-8'))

    # check output in case of errors
    with open(outfile, 'r') as output:
        for line in output:
            if line.strip().startswith(('*** ERROR ***', 'ERROR')):
                proc.returncode = 255
                break

    # die in case of error
    if proc.returncode != 0:
        msg = 'HOLE failure ({}). Check output {}'
        logger.fatal(msg.format(proc.returncode, outfile))
        if stderr is not None:
            logger.fatal(stderr)
        raise ApplicationError(proc.returncode,
                               msg.format(executable, outfile))

    logger.info('HOLE finished. Output: {}'.format(outfile))
    return outfile

    def fpocket(pdbfile,
         outfile='hole.out',
         executable='hole',
         tmpdir=os.path.curdir,
         sample=0.2,
         end_radius=22.0,
         cpoint=None,
         cvect=None,
         random_seed=None,
         ignore_residues=IGNORE_RESIDUES,
         output_level=0,
         dcd=None,
         dcd_iniskip=0,
         dcd_step=1,
         keep_files=True):
         

def collect_fpocket(outfile='hole.out'):
    """Collect data from HOLE output.

    Parameters
    ----------
    outfile: str, optional
        HOLE output file to read. Default: 'hole.out'


    Returns
    -------
    dict
        Dictionary of HOLE profiles as record arrays
    """
    fmt = util.FORTRANReader('3F12')
    recarrays = {}

    with open(outfile, 'r') as output:
        toggle_read = False
        profile = 0
        records = []
        for line in output:
            line = line.rstrip()  # preserve columns in FORTRAN output
            # multiple frames from dcd in?
            if line.startswith(" Starting calculation for position number"):
                fields = line.split()
                profile = int(fields[5])
                records = []
                logger.debug('Started reading profile {}'.format(profile))
                continue

            # found data
            if line.startswith(' cenxyz.cvec'):
                toggle_read = True
                logger.debug('Started reading data')
                continue

            if toggle_read:
                if len(line.strip()) != 0:
                    try:
                        rxncoord, radius, cenlineD = fmt.read(line)
                    except:
                        msg = 'Problem parsing line: {}. Check output file {}'
                        logger.exception(msg.format(line, outfile))
                        raise
                    records.append((rxncoord, radius, cenlineD))
                    continue
                # end of data
                else:
                    toggle_read = False
                    names = ['rxn_coord', 'radius', 'cen_line_D']
                    recarr = np.rec.fromrecords(records,
                                                formats='f8, f8, f8',
                                                names=names)
                    recarrays[profile] = recarr

        return recarrays

profiles = hole2.hole(PDB_HOLE, executable='~/hole2/exe/hole')