Python keys Exemples

Exemple #1

Fichier : simlist.py Projet : jeiros/htmd

def _autoDetectTopology(folder):
    from htmd.molecule.readers import _TOPOLOGY_READERS
    topotypes = ['pdb', 'prmtop', 'psf'] + list(_TOPOLOGY_READERS.keys())  # Prepending PDB, PSF, PRMTOP so that they are the default
    topo = None
    for tt in topotypes:
        files = glob(path.join(folder, '*.{}'.format(tt)))
        if len(files) > 0:
            if len(files) > 1:
                logger.warning('Multiple "{}" files were found in folder {}. '
                               'Picking {} as the topology'.format(tt, folder, files[0]))
            topo = files[0]
            break
    if topo is None:
        raise RuntimeError('No topology file found in folder {}. '
                           'Supported extensions are {}'.format(folder, list(_TOPOLOGY_READERS.keys())))
    return topo

Exemple #2

def _autoDetectTopology(folder):
    from htmd.molecule.readers import _TOPOLOGY_READERS
    topotypes = ['pdb', 'prmtop', 'psf'] + list(_TOPOLOGY_READERS.keys(
    ))  # Prepending PDB, PSF, PRMTOP so that they are the default
    topo = None
    for tt in topotypes:
        files = glob(path.join(folder, '*.{}'.format(tt)))
        if len(files) > 0:
            if len(files) > 1:
                logger.warning('Multiple "{}" files were found in folder {}. '
                               'Picking {} as the topology'.format(
                                   tt, folder, files[0]))
            topo = files[0]
            break
    if topo is None:
        raise RuntimeError('No topology file found in folder {}. '
                           'Supported extensions are {}'.format(
                               folder, list(_TOPOLOGY_READERS.keys())))
    return topo

Exemple #3

def _autoDetectTopology(folder):
    topo = {}
    for tt in __topotypes:
        files = glob(path.join(folder, '*.{}'.format(tt)))
        if len(files) > 0:
            if len(files) > 1:
                logger.warning('Multiple "{}" files were found in folder {}. '
                               'Picking {} as the topology'.format(tt, folder, files[0]))
            topo[tt] = files[0]
    if len(topo) == 0:
        raise RuntimeError('No topology file found in folder {}. '
                           'Supported extensions are {}'.format(folder, list(_TOPOLOGY_READERS.keys())))
    return list(topo.values())

Exemple #4

Fichier : simlist.py Projet : alejandrovr/htmd

def _autoDetectTopology(folder):
    topo = {}
    for tt in __topotypes:
        files = glob(path.join(folder, '*.{}'.format(tt)))
        if len(files) > 0:
            if len(files) > 1:
                logger.warning('Multiple "{}" files were found in folder {}. '
                               'Picking {} as the topology'.format(tt, folder, files[0]))
            topo[tt] = files[0]
    if len(topo) == 0:
        raise RuntimeError('No topology file found in folder {}. '
                           'Supported extensions are {}'.format(folder, list(_TOPOLOGY_READERS.keys())))
    return list(topo.values())

Exemple #5

                logger.warning(
                    'Filtering was not able to write {} due to error: {}'.
                    format(filttopo, e))


def _autoDetectTrajectories(folder):
    from htmd.molecule.readers import _TRAJECTORY_READERS
    import natsort
    for tt in _TRAJECTORY_READERS:
        trajectories = glob(path.join(folder, '*.{}'.format(tt)))
        if len(trajectories) > 0:
            return natsort.natsorted(trajectories)


from htmd.molecule.readers import _TOPOLOGY_READERS
__readers = list(_TOPOLOGY_READERS.keys())
__defaultReaders = ['pdb', 'prmtop', 'psf']
__otherReaders = list(np.setdiff1d(__readers, __defaultReaders))
__topotypes = __defaultReaders + __otherReaders  # Prepending PDB, PSF, PRMTOP so that they are the default


def _autoDetectTopology(folder):
    topo = {}
    for tt in __topotypes:
        files = glob(path.join(folder, '*.{}'.format(tt)))
        if len(files) > 0:
            if len(files) > 1:
                logger.warning('Multiple "{}" files were found in folder {}. '
                               'Picking {} as the topology'.format(
                                   tt, folder, files[0]))
            topo[tt] = files[0]

Exemple #6

Fichier : simlist.py Projet : alejandrovr/htmd

                mol.write(filttopo, filtsel)
            except Exception as e:
                logger.warning('Filtering was not able to write {} due to error: {}'.format(filttopo, e))


def _autoDetectTrajectories(folder):
    from htmd.molecule.readers import _TRAJECTORY_READERS
    import natsort
    for tt in _TRAJECTORY_READERS:
        trajectories = glob(path.join(folder, '*.{}'.format(tt)))
        if len(trajectories) > 0:
            return natsort.natsorted(trajectories)


from htmd.molecule.readers import _TOPOLOGY_READERS
__readers = list(_TOPOLOGY_READERS.keys())
__defaultReaders = ['pdb', 'prmtop', 'psf']
__otherReaders = list(np.setdiff1d(__readers, __defaultReaders))
__topotypes =  __defaultReaders + __otherReaders  # Prepending PDB, PSF, PRMTOP so that they are the default

def _autoDetectTopology(folder):
    topo = {}
    for tt in __topotypes:
        files = glob(path.join(folder, '*.{}'.format(tt)))
        if len(files) > 0:
            if len(files) > 1:
                logger.warning('Multiple "{}" files were found in folder {}. '
                               'Picking {} as the topology'.format(tt, folder, files[0]))
            topo[tt] = files[0]
    if len(topo) == 0:
        raise RuntimeError('No topology file found in folder {}. '