def add_trajectory(self, name, overwrite=False, shape=(0,), title='',
                       chunksize=2**19, comp_filter=default_compression,
                       atom=tables.Float64Atom(), params=dict(),
                       chunkslice='bytes'):
        """Add an trajectory array in '/trajectories'.
        """
        group = self.h5file.root.trajectories
        if name in group:
            print("%s already exists ..." % name, end='')
            if overwrite:
                self.h5file.remove_node(group, name)
                print(" deleted.")
            else:
                print(" old returned.")
                return group.get_node(name)

        nparams = self.numeric_params
        num_t_steps = nparams['t_max'] / nparams['t_step']

        chunkshape = self.calc_chunkshape(chunksize, shape, kind=chunkslice)
        store_array = self.h5file.create_earray(
            group, name, atom=atom,
            shape = shape,
            chunkshape = chunkshape,
            expectedrows = num_t_steps,
            filters = comp_filter,
            title = title)

        # Set the array parameters/attributes
        for key, value in params.items():
            store_array.set_attr(key, value)
        store_array.set_attr('PyBroMo', __version__)
        store_array.set_attr('creation_time', current_time())
        return store_array
def add_trajectory(self, name, overwrite=False, shape=(0,), title='',
                       chunksize=2**19, comp_filter=default_compression,
                       atom=tables.Float64Atom(), params=dict(),
                       chunkslice='bytes'):
        """Add an trajectory array in '/trajectories'.
        """
        group = self.h5file.root.trajectories
        if name in group:
            print("%s already exists ..." % name, end='')
            if overwrite:
                self.h5file.remove_node(group, name)
                print(" deleted.")
            else:
                print(" old returned.")
                return group.get_node(name)

        nparams = self.numeric_params
        num_t_steps = nparams['t_max'] / nparams['t_step']

        chunkshape = self.calc_chunkshape(chunksize, shape, kind=chunkslice)
        store_array = self.h5file.create_earray(
            group, name, atom=atom,
            shape = shape,
            chunkshape = chunkshape,
            expectedrows = num_t_steps,
            filters = comp_filter,
            title = title)

        # Set the array parameters/attributes
        for key, value in params.items():
            store_array.set_attr(key, value)
        store_array.set_attr('PyBroMo', __version__)
        store_array.set_attr('creation_time', current_time())
        return store_array
def add_trajectory ( self , name , overwrite = False , shape = ( 0 , ) , title = '' , chunksize = 2 ** 19 , comp_filter = default_compression , atom = tables . Float64Atom ( ) , params = dict ( ) , chunkslice = 'bytes' ) : group = self . h5file . root . trajectories if name in group : print ( "%s already exists ..." % name , end = '' ) if overwrite : self . h5file . remove_node ( group , name ) print ( " deleted." ) else : print ( " old returned." ) return group . get_node ( name ) nparams = self . numeric_params num_t_steps = nparams [ 't_max' ] / nparams [ 't_step' ] chunkshape = self . calc_chunkshape ( chunksize , shape , kind = chunkslice ) store_array = self . h5file . create_earray ( group , name , atom = atom , shape = shape , chunkshape = chunkshape , expectedrows = num_t_steps , filters = comp_filter , title = title ) # Set the array parameters/attributes for key , value in params . items ( ) : store_array . set_attr ( key , value ) store_array . set_attr ( 'PyBroMo' , __version__ ) store_array . set_attr ( 'creation_time' , current_time ( ) ) return store_array
Add an trajectory array in '/trajectories'.
Add an trajectory array in / trajectories .