gromacs/utilities.py
def number_pdbs(*args, **kwargs):
    """Rename pdbs x1.pdb ... x345.pdb --> x0001.pdb ... x0345.pdb

    :Arguments:
       - *args*: filenames or glob patterns (such as "pdb/md*.pdb")
       - *format*: format string including keyword *num* ["%(num)04d"]
    """

    format = kwargs.pop('format', "%(num)04d")
    name_format = "%(prefix)s" + format +".%(suffix)s"

    for f in itertools.chain.from_iterable(map(glob.glob, args)):
        m = NUMBERED_PDB.search(f)
        if m is None:
            continue
        num = int(m.group('NUMBER'))
        prefix = m.group('PREFIX')
        suffix = m.group('SUFFIX')
        newname = name_format % vars()
        logger.info("Renaming {f!r} --> {newname!r}".format(**vars()))
        try:
            os.rename(f, newname)
        except OSError:
            logger.exception("renaming failed")
def number_pdbs(*args, **kwargs):
    """Rename pdbs x1.pdb ... x345.pdb --> x0001.pdb ... x0345.pdb

    :Arguments:
       - *args*: filenames or glob patterns (such as "pdb/md*.pdb")
       - *format*: format string including keyword *num* ["%(num)04d"]
    """

    format = kwargs.pop('format', "%(num)04d")
    name_format = "%(prefix)s" + format +".%(suffix)s"

    for f in itertools.chain.from_iterable(map(glob.glob, args)):
        m = NUMBERED_PDB.search(f)
        if m is None:
            continue
        num = int(m.group('NUMBER'))
        prefix = m.group('PREFIX')
        suffix = m.group('SUFFIX')
        newname = name_format % vars()
        logger.info("Renaming {f!r} --> {newname!r}".format(**vars()))
        try:
            os.rename(f, newname)
        except OSError:
            logger.exception("renaming failed")
def number_pdbs ( * args , * * kwargs ) : format = kwargs . pop ( 'format' , "%(num)04d" ) name_format = "%(prefix)s" + format + ".%(suffix)s" for f in itertools . chain . from_iterable ( map ( glob . glob , args ) ) : m = NUMBERED_PDB . search ( f ) if m is None : continue num = int ( m . group ( 'NUMBER' ) ) prefix = m . group ( 'PREFIX' ) suffix = m . group ( 'SUFFIX' ) newname = name_format % vars ( ) logger . info ( "Renaming {f!r} --> {newname!r}" . format ( * * vars ( ) ) ) try : os . rename ( f , newname ) except OSError : logger . exception ( "renaming failed" )
Rename pdbs x1.pdb ... x345.pdb --> x0001.pdb ... x0345.pdb

    :Arguments:
       - *args*: filenames or glob patterns (such as "pdb/md*.pdb")
       - *format*: format string including keyword *num* ["%(num)04d"]
Rename pdbs x1 . pdb ... x345 . pdb -- > x0001 . pdb ... x0345 . pdb