SYMBOL INDEX (89 symbols across 13 files)

FILE: deepdock/DockingFunction.py
  function score_compound (line 15) | def score_compound(ligand, target, model, dist_threshold=3., seed=None, ...
  function dock_compound (line 56) | def dock_compound(mol, target_ply, model, dist_threshold=3., popsize=150...
  class optimze_conformation (line 119) | class optimze_conformation():
    method __init__ (line 120) | def __init__(self, mol, target_coords, n_particles, pi, mu, sigma, sav...
    method score_conformation (line 138) | def score_conformation(self, values):
  function SetDihedral (line 178) | def SetDihedral(conf, atom_idx, new_vale):
  function GetDihedral (line 181) | def GetDihedral(conf, atom_idx):
  function GetTransformationMatrix (line 184) | def GetTransformationMatrix(transformations):
  function compute_euclidean_distances_matrix (line 192) | def compute_euclidean_distances_matrix(X, Y):
  function calculate_probablity (line 200) | def calculate_probablity(pi, sigma, mu, y):
  function apply_changes (line 208) | def apply_changes(mol, values, rotable_bonds):
  function get_torsions (line 219) | def get_torsions(mol_list):
  function get_random_conformation (line 261) | def get_random_conformation(mol, rotable_bonds=None, seed=None):
  function atom_scores (line 280) | def atom_scores(ligand, target, probabilities, batch):
  function calculate_atom_contribution (line 289) | def calculate_atom_contribution(ligand, target, model, dist_threshold=3....

FILE: deepdock/models.py
  function compute_cluster_batch_index (line 13) | def compute_cluster_batch_index(cluster, batch):
  class NodeSampling (line 21) | class NodeSampling(nn.Module):
    method __init__ (line 22) | def __init__(self, nodes_per_graph):
    method forward (line 27) | def forward(self, x):
  class ResBlock (line 45) | class ResBlock(nn.Module):
    method __init__ (line 46) | def __init__(self, in_channels, dropout_rate=0.15):
    method forward (line 64) | def forward(self, data):
  class EdgeModel (line 80) | class EdgeModel(torch.nn.Module):
    method __init__ (line 81) | def __init__(self, in_channels):
    method forward (line 85) | def forward(self, src, dest, edge_attr, u, batch):
  class NodeModel (line 94) | class NodeModel(torch.nn.Module):
    method __init__ (line 95) | def __init__(self, in_channels):
    method forward (line 100) | def forward(self, x, edge_index, edge_attr, u, batch):
  class TargetNet (line 114) | class TargetNet(nn.Module):
    method __init__ (line 115) | def __init__(self, in_channels, edge_features=3, hidden_dim=128, resid...
    method forward (line 126) | def forward(self, data):
  class LigandNet (line 140) | class LigandNet(nn.Module):
    method __init__ (line 141) | def __init__(self, in_channels, edge_features=6, hidden_dim=128, resid...
    method forward (line 152) | def forward(self, data):
  class DeepDock (line 163) | class DeepDock(nn.Module):
    method __init__ (line 164) | def __init__(self, ligand_model, target_model, hidden_dim, n_gaussians...
    method forward (line 185) | def forward(self, data_ligand, data_target, y=None):
    method compute_euclidean_distances_matrix (line 226) | def compute_euclidean_distances_matrix(self, X, Y):
  function mdn_loss_fn (line 236) | def mdn_loss_fn(pi, sigma, mu, y):

FILE: deepdock/prepare_target/computeAPBS.py
  function computeAPBS (line 16) | def computeAPBS(vertices, pdb_file, tmp_file_base):

FILE: deepdock/prepare_target/computeCharges.py
  function computeCharges (line 33) | def computeCharges(pdb_filename, vertices, names):
  function computeChargeHelper (line 73) | def computeChargeHelper(atom_name, res, v):
  function computeAngleDeviation (line 108) | def computeAngleDeviation(a, b, c, theta):
  function computePlaneDeviation (line 113) | def computePlaneDeviation(a, b, c, d):
  function computeAnglePenalty (line 121) | def computeAnglePenalty(angle_deviation):
  function isPolarHydrogen (line 126) | def isPolarHydrogen(atom_name, res):
  function isAcceptorAtom (line 133) | def isAcceptorAtom(atom_name, res):
  function computeSatisfied_CO_HN (line 146) | def computeSatisfied_CO_HN(atoms):
  function assignChargesToNewMesh (line 188) | def assignChargesToNewMesh(new_vertices, old_vertices, old_charges, seed...

FILE: deepdock/prepare_target/computeHydrophobicity.py
  function computeHydrophobicity (line 33) | def computeHydrophobicity(names):

FILE: deepdock/prepare_target/computeMSMS.py
  function computeMSMS (line 19) | def computeMSMS(pdb_file,  protonate=True, one_cavity=None):

FILE: deepdock/prepare_target/computeTargetMesh.py
  function compute_inp_surface (line 29) | def compute_inp_surface(target_filename, ligand_filename, dist_threshold...

FILE: deepdock/prepare_target/compute_normal.py
  function compute_normal (line 19) | def compute_normal(vertex, face):
  function crossp (line 71) | def crossp(x, y):

FILE: deepdock/prepare_target/fixmesh.py
  function fix_mesh (line 16) | def fix_mesh(mesh, resolution, detail="normal"):

FILE: deepdock/prepare_target/save_ply.py
  function save_ply (line 16) | def save_ply(

FILE: deepdock/utils/data.py
  function read_ply (line 18) | def read_ply(path):
  class PDBbind_protsurf_dataset (line 37) | class PDBbind_protsurf_dataset(Dataset):
    method __init__ (line 38) | def __init__(self, pdb_IDs, root, transform=None, pre_transform=None):
    method len (line 43) | def len(self):
    method get (line 46) | def get(self, idx):
  class PDBbind_complex_dataset (line 53) | class PDBbind_complex_dataset(Dataset):
    method __init__ (line 54) | def __init__(self, data_path, transform=None, pre_transform=None,
    method len (line 70) | def len(self):
    method get (line 73) | def get(self, idx):
  function compute_clusters (line 77) | def compute_clusters(data, n_clusters):
  function compute_cluster_batch_index (line 90) | def compute_cluster_batch_index(cluster, batch):
  function Mol2MolSupplier (line 98) | def Mol2MolSupplier (file=None, sanitize=True, cleanupSubstructures=True):

FILE: deepdock/utils/distributions.py
  class MixtureSameFamily (line 9) | class MixtureSameFamily(Distribution):
    method __init__ (line 48) | def __init__(self,
    method expand (line 87) | def expand(self, batch_shape, _instance=None):
    method support (line 105) | def support(self):
    method mixture_distribution (line 111) | def mixture_distribution(self):
    method component_distribution (line 115) | def component_distribution(self):
    method mean (line 119) | def mean(self):
    method variance (line 125) | def variance(self):
    method cdf (line 135) | def cdf(self, x):
    method log_prob (line 142) | def log_prob(self, x):
    method sample (line 149) | def sample(self, sample_shape=torch.Size()):
    method _pad (line 172) | def _pad(self, x):
    method _pad_mixture_dimensions (line 175) | def _pad_mixture_dimensions(self, x):
    method __repr__ (line 185) | def __repr__(self):

FILE: deepdock/utils/mol2graph.py
  function oneHotVector (line 14) | def oneHotVector(val, lst):
  function mol_to_nx (line 20) | def mol_to_nx(mol):
  function get_bonds (line 59) | def get_bonds(mol_list, bidirectional=True):
  function get_angles (line 75) | def get_angles(mol_list, bidirectional=True):
  function get_torsions (line 97) | def get_torsions(mol_list, bidirectional=True):
  function mol_with_atom_index (line 138) | def mol_with_atom_index( mol ):
  function atomenvironments (line 144) | def atomenvironments(mol, radius=3):