<commit_before>"""
This file contains the base classes for topology proposals
"""

import simtk.openmm.app as app
from collections import namedtuple
TopologyProposal = namedtuple('Proposal',['old_topology','new_topology','ln_selection', 'new_to_old_atom_map'])

class Transformation(object):
    """
    This defines a type which, given the requisite metadata, can produce Proposals (namedtuple)
    of new topologies.
    
    Arguments
    --------
    current_topology : simtk.openmm.app.Topology object
        The topology which currently defines the system
    current_system : simtk.openmm.System object
        The system object with all relevant parameters
    metadata : object
        Data necessary for the generation of proposals<commit_msg>changed name of proposal probability ratio<commit_after>"""
This file contains the base classes for topology proposals
"""

import simtk.openmm.app as app
from collections import namedtuple
TopologyProposal = namedtuple('Proposal',['old_topology','new_topology','logp', 'new_to_old_atom_map'])

class Transformation(object):
    """
    This defines a type which, given the requisite metadata, can produce Proposals (namedtuple)
    of new topologies.
    
    Arguments
    --------
    current_topology : simtk.openmm.app.Topology object
        The topology which currently defines the system
    current_system : simtk.openmm.System object
        The system object with all relevant parameters
    metadata : object
        Data necessary for the generation of proposals
{'fraction_non_alphanumeric': 0.07455853499018966, 'fraction_numerical': 0.0, 'mean_word_length': 3.872611464968153, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '5791514', 'n_tokens_mistral': 393, 'n_tokens_neox': 382, 'n_words': 142}