SYMBOL INDEX (77 symbols across 8 files)

FILE: Vizard/main.py
  function downsample (line 46) | def downsample(data, max_len):
  function running_average (line 52) | def running_average(data, length):
  function create_bar_plot (line 61) | def create_bar_plot(init_data, title):
  function create_hist_plot (line 71) | def create_hist_plot(init_data, title):
  function update (line 95) | def update():

FILE: data_structs.py
  class Vocabulary (line 13) | class Vocabulary(object):
    method __init__ (line 15) | def __init__(self, init_from_file=None, max_length=140):
    method encode (line 25) | def encode(self, char_list):
    method decode (line 32) | def decode(self, matrix):
    method tokenize (line 42) | def tokenize(self, smiles):
    method add_characters (line 57) | def add_characters(self, chars):
    method init_from_file (line 68) | def init_from_file(self, file):
    method __len__ (line 74) | def __len__(self):
    method __str__ (line 77) | def __str__(self):
  class MolData (line 80) | class MolData(Dataset):
    method __init__ (line 90) | def __init__(self, fname, voc):
    method __getitem__ (line 97) | def __getitem__(self, i):
    method __len__ (line 103) | def __len__(self):
    method __str__ (line 106) | def __str__(self):
    method collate_fn (line 110) | def collate_fn(cls, arr):
  class Experience (line 118) | class Experience(object):
    method __init__ (line 121) | def __init__(self, voc, max_size=100):
    method add_experience (line 126) | def add_experience(self, experience):
    method sample (line 142) | def sample(self, n):
    method initiate_from_file (line 158) | def initiate_from_file(self, fname, scoring_function, Prior):
    method print_memory (line 178) | def print_memory(self, path):
    method __len__ (line 191) | def __len__(self):
  function replace_halogen (line 194) | def replace_halogen(string):
  function tokenize (line 203) | def tokenize(smiles):
  function canonicalize_smiles_from_file (line 220) | def canonicalize_smiles_from_file(fname):
  function filter_mol (line 234) | def filter_mol(mol, max_heavy_atoms=50, min_heavy_atoms=10, element_list...
  function write_smiles_to_file (line 244) | def write_smiles_to_file(smiles_list, fname):
  function filter_on_chars (line 250) | def filter_on_chars(smiles_list, chars):
  function filter_file_on_chars (line 261) | def filter_file_on_chars(smiles_fname, voc_fname):
  function combine_voc_from_files (line 280) | def combine_voc_from_files(fnames):
  function construct_vocabulary (line 291) | def construct_vocabulary(smiles_list):

FILE: model.py
  class MultiGRU (line 10) | class MultiGRU(nn.Module):
    method __init__ (line 13) | def __init__(self, voc_size):
    method forward (line 21) | def forward(self, x, h):
    method init_h (line 30) | def init_h(self, batch_size):
  class RNN (line 34) | class RNN():
    method __init__ (line 37) | def __init__(self, voc):
    method likelihood (line 43) | def likelihood(self, target):
    method sample (line 71) | def sample(self, batch_size, max_length=140):
  function NLLLoss (line 114) | def NLLLoss(inputs, targets):

FILE: scoring_functions.py
  class no_sulphur (line 31) | class no_sulphur():
    method __init__ (line 36) | def __init__(self):
    method __call__ (line 38) | def __call__(self, smile):
  class tanimoto (line 45) | class tanimoto():
    method __init__ (line 53) | def __init__(self):
    method __call__ (line 57) | def __call__(self, smile):
  class activity_model (line 66) | class activity_model():
    method __init__ (line 72) | def __init__(self):
    method __call__ (line 76) | def __call__(self, smile):
    method fingerprints_from_mol (line 85) | def fingerprints_from_mol(cls, mol):
  class Worker (line 94) | class Worker():
    method __init__ (line 98) | def __init__(self, scoring_function=None):
    method __call__ (line 108) | def __call__(self, smile, index, result_list):
    method is_alive (line 117) | def is_alive(self):
  class Multiprocessing (line 120) | class Multiprocessing():
    method __init__ (line 124) | def __init__(self, num_processes=None, scoring_function=None):
    method alive_workers (line 128) | def alive_workers(self):
    method __call__ (line 131) | def __call__(self, smiles):
  class Singleprocessing (line 167) | class Singleprocessing():
    method __init__ (line 170) | def __init__(self, scoring_function=None):
    method __call__ (line 172) | def __call__(self, smiles):
  function get_scoring_function (line 176) | def get_scoring_function(scoring_function, num_processes=None, **kwargs):

FILE: train_agent.py
  function train_agent (line 16) | def train_agent(restore_prior_from='data/Prior.ckpt',

FILE: train_prior.py
  function pretrain (line 15) | def pretrain(restore_from=None):

FILE: utils.py
  function Variable (line 5) | def Variable(tensor):
  function decrease_learning_rate (line 16) | def decrease_learning_rate(optimizer, decrease_by=0.01):
  function seq_to_smiles (line 21) | def seq_to_smiles(seqs, voc):
  function fraction_valid_smiles (line 29) | def fraction_valid_smiles(smiles):
  function unique (line 37) | def unique(arr):

FILE: vizard_logger.py
  class VizardLog (line 4) | class VizardLog():
    method __init__ (line 5) | def __init__(self, log_dir):
    method log (line 18) | def log(self, data, name, dtype="array", log_every=1, overwrite=False):