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Data Structures used to represented molecules for convolutions.
from __future__ import division
from __future__ import unicode_literals
__author__ = "Han Altae-Tran and Bharath Ramsundar"
__copyright__ = "Copyright 2016, Stanford University"
__license__ = "MIT"
import csv
import random
import numpy as np
def cumulative_sum_minus_last(l, offset=0):
"""Returns cumulative sums for set of counts, removing last entry.
Returns the cumulative sums for a set of counts with the first returned value
starting at 0. I.e [3,2,4] -> [0, 3, 5]. Note last sum element 9 is missing.
Useful for reindexing
l: list
List of integers. Typically small counts.
return np.delete(np.insert(np.cumsum(l), 0, 0), -1) + offset
def cumulative_sum(l, offset=0):
"""Returns cumulative sums for set of counts.
Returns the cumulative sums for a set of counts with the first returned value
starting at 0. I.e [3,2,4] -> [0, 3, 5, 9]. Keeps final sum for searching.
Useful for reindexing.
l: list
List of integers. Typically small counts.
return np.insert(np.cumsum(l), 0, 0) + offset
class ConvMol(object):
"""Holds information about a molecules.
Resorts order of atoms internally to be in order of increasing degree. Note
that only heavy atoms (hydrogens excluded) are considered here.
def __init__(self, atom_features, adj_list, max_deg=10, min_deg=0):
atom_features: np.ndarray
Has shape (n_atoms, n_feat)
canon_ad_list: list
List of length n_atoms, with neighor indices of each atom.
max_deg: int, optional
Maximum degree of any atom.
min_deg: int, optional
Minimum degree of any atom.
self.atom_features = atom_features
self.n_atoms, self.n_feat = atom_features.shape
self.deg_list = np.array([len(nbrs) for nbrs in adj_list], dtype=np.int32)
self.canon_adj_list = adj_list
self.deg_adj_lists = []
self.deg_slice = []
self.max_deg = max_deg
self.min_deg = min_deg
self.membership = self.get_num_atoms() * [0]
# Get the degree id list (which corrects for min_deg)
self.deg_id_list = np.array(self.deg_list) - min_deg
# Get the size of each degree block
deg_size = [
for deg in range(self.min_deg, self.max_deg + 1)
self.degree_list = []
for i, deg in enumerate(range(self.min_deg, self.max_deg + 1)):
self.degree_list.extend([deg] * deg_size[i])
# Get the the start indices for items in each block
self.deg_start = cumulative_sum(deg_size)
# Get the node indices when they are reset when the degree changes
deg_block_indices = [
i - self.deg_start[self.deg_list[i]] for i in range(self.n_atoms)
# Convert to numpy array
self.deg_block_indices = np.array(deg_block_indices)
def get_atoms_with_deg(self, deg):
"""Retrieves atom_features with the specific degree"""
start_ind = self.deg_slice[deg - self.min_deg, 0]
size = self.deg_slice[deg - self.min_deg, 1]
return self.atom_features[start_ind:(start_ind + size), :]
def get_num_atoms_with_deg(self, deg):
"""Returns the number of atoms with the given degree"""
return self.deg_slice[deg - self.min_deg, 1]
def get_num_atoms(self):
return self.n_atoms
def _deg_sort(self):
"""Sorts atoms by degree and reorders internal data structures.
Sort the order of the atom_features by degree, maintaining original order
whenever two atom_features have the same degree.
old_ind = range(self.get_num_atoms())
deg_list = self.deg_list
new_ind = list(np.lexsort((old_ind, deg_list)))
num_atoms = self.get_num_atoms()
# Reorder old atom_features
self.atom_features = self.atom_features[new_ind, :]
# Reorder old deg lists
self.deg_list = [self.deg_list[i] for i in new_ind]
# Sort membership
self.membership = [self.membership[i] for i in new_ind]
# Create old to new dictionary. not exactly intuitive
old_to_new = dict(zip(new_ind, old_ind))
# Reorder adjacency lists
self.canon_adj_list = [self.canon_adj_list[i] for i in new_ind]
self.canon_adj_list = [[old_to_new[k]
for k in self.canon_adj_list[i]]
for i in range(len(new_ind))]
# Get numpy version of degree list for indexing
deg_array = np.array(self.deg_list)
# Initialize adj_lists, which supports min_deg = 1 only
self.deg_adj_lists = (self.max_deg + 1 - self.min_deg) * [0]
# Parse as deg separated
for deg in range(self.min_deg, self.max_deg + 1):
# Get indices corresponding to the current degree
rng = np.array(range(num_atoms))
indices = rng[deg_array == deg]
# Extract and save adjacency list for the current degree
to_cat = [self.canon_adj_list[i] for i in indices]
if len(to_cat) > 0:
adj_list = np.vstack([self.canon_adj_list[i] for i in indices])
self.deg_adj_lists[deg - self.min_deg] = adj_list
self.deg_adj_lists[deg - self.min_deg] = np.zeros(
[0, deg], dtype=np.int32)
# Construct the slice information
deg_slice = np.zeros([self.max_deg + 1 - self.min_deg, 2], dtype=np.int32)
for deg in range(self.min_deg, self.max_deg + 1):
if deg == 0:
deg_size = np.sum(deg_array == deg)
deg_size = self.deg_adj_lists[deg - self.min_deg].shape[0]
deg_slice[deg - self.min_deg, 1] = deg_size
# Get the cumulative indices after the first index
if deg > self.min_deg:
deg_slice[deg - self.min_deg, 0] = (
deg_slice[deg - self.min_deg - 1, 0] +
deg_slice[deg - self.min_deg - 1, 1])
# Set indices with zero sized slices to zero to avoid indexing errors
deg_slice[:, 0] *= (deg_slice[:, 1] != 0)
self.deg_slice = deg_slice
def get_atom_features(self):
"""Returns canonicalized version of atom features.
Features are sorted by atom degree, with original order maintained when
degrees are same.
return self.atom_features
def get_adjacency_list(self):
"""Returns a canonicalized adjacency list.
Canonicalized means that the atoms are re-ordered by degree.
Canonicalized form of adjacency list.
return self.canon_adj_list
def get_deg_adjacency_lists(self):
"""Returns adjacency lists grouped by atom degree.
Has length (max_deg+1-min_deg). The element at position deg is
itself a list of the neighbor-lists for atoms with degree deg.
return self.deg_adj_lists
def get_deg_slice(self):
"""Returns degree-slice tensor.
The deg_slice tensor allows indexing into a flattened version of the
molecule's atoms. Assume atoms are sorted in order of degree. Then
deg_slice[deg][0] is the starting position for atoms of degree deg in
flattened list, and deg_slice[deg][1] is the number of atoms with degree deg.
Note deg_slice has shape (max_deg+1-min_deg, 2).
deg_slice: np.ndarray
Shape (max_deg+1-min_deg, 2)
return self.deg_slice
# TODO(rbharath): Can this be removed?
def get_null_mol(n_feat, max_deg=10, min_deg=0):
"""Constructs a null molecules
Get one molecule with one atom of each degree, with all the atoms
connected to themselves, and containing n_feat features.
n_feat : int
number of features for the nodes in the null molecule
# Use random insted of zeros to prevent weird issues with summing to zero
atom_features = np.random.uniform(0, 1, [max_deg + 1 - min_deg, n_feat])
canon_adj_list = [
deg * [deg - min_deg] for deg in range(min_deg, max_deg + 1)
return ConvMol(atom_features, canon_adj_list)
def agglomerate_mols(mols, max_deg=10, min_deg=0):
"""Concatenates list of ConvMol's into one mol object that can be used to feed
into tensorflow placeholders. The indexing of the molecules are preseved during the
combination, but the indexing of the atoms are greatly changed.
mols: list
ConvMol objects to be combined into one molecule."""
num_mols = len(mols)
# Results should be sorted by (atom_degree, mol_index)
atoms_by_deg = np.concatenate([x.atom_features for x in mols])
degree_vector = np.concatenate([x.degree_list for x in mols], axis=0)
# Mergesort is a "stable" sort, so the array maintains it's secondary sort of mol_index
all_atoms = atoms_by_deg[degree_vector.argsort(kind='mergesort')]
# Sort all atoms by degree.
# Get the size of each atom list separated by molecule id, then by degree
mol_deg_sz = [[mol.get_num_atoms_with_deg(deg)
for mol in mols]
for deg in range(min_deg, max_deg + 1)]
# Get the final size of each degree block
deg_sizes = list(map(np.sum, mol_deg_sz))
# Get the index at which each degree starts, not resetting after each degree
# And not stopping at any speciic molecule
deg_start = cumulative_sum_minus_last(deg_sizes)
# Get the tensorflow object required for slicing (deg x 2) matrix, with the
# first column telling the start indices of each degree block and the
# second colum telling the size of each degree block
# Input for tensorflow
deg_slice = np.array(list(zip(deg_start, deg_sizes)))
# Determines the membership (atom i belongs to membership[i] molecule)
membership = [
k for deg in range(min_deg, max_deg + 1) for k in range(num_mols)
for i in range(mol_deg_sz[deg][k])
# Get the index at which each deg starts, resetting after each degree
# (deg x num_mols) matrix describing the start indices when you count up the atoms
# in the final representation, stopping at each molecule,
# resetting every time the degree changes
start_by_deg = np.vstack([cumulative_sum_minus_last(l) for l in mol_deg_sz])
# Gets the degree resetting block indices for the atoms in each molecule
# Here, the indices reset when the molecules change, and reset when the
# degree changes
deg_block_indices = [mol.deg_block_indices for mol in mols]
# Get the degree id lookup list. It allows us to search for the degree of a
# molecule mol_id with corresponding atom mol_atom_id using
# deg_id_lists[mol_id,mol_atom_id]
deg_id_lists = [mol.deg_id_list for mol in mols]
# This is used for convience in the following function (explained below)
start_per_mol = deg_start[:, np.newaxis] + start_by_deg
def to_final_id(mol_atom_id, mol_id):
# Get the degree id (corrected for min_deg) of the considered atom
deg_id = deg_id_lists[mol_id][mol_atom_id]
# Return the final index of atom mol_atom_id in molecule mol_id. Using
# the degree of this atom, must find the index in the molecule's original
# degree block corresponding to degree id deg_id (second term), and then
# calculate which index this degree block ends up in the final
# representation (first term). The sum of the two is the final indexn
return start_per_mol[deg_id,
mol_id] + deg_block_indices[mol_id][mol_atom_id]
# Initialize the new degree separated adjacency lists
deg_adj_lists = [
np.zeros([deg_sizes[deg], deg], dtype=np.int32)
for deg in range(min_deg, max_deg + 1)
# Update the old adjcency lists with the new atom indices and then combine
# all together
for deg in range(min_deg, max_deg + 1):
row = 0 # Initialize counter
deg_id = deg - min_deg # Get corresponding degree id
# Iterate through all the molecules
for mol_id in range(num_mols):
# Get the adjacency lists for this molecule and current degree id
nbr_list = mols[mol_id].deg_adj_lists[deg_id]
# Correct all atom indices to the final indices, and then save the
# results into the new adjacency lists
for i in range(nbr_list.shape[0]):
for j in range(nbr_list.shape[1]):
deg_adj_lists[deg_id][row, j] = to_final_id(nbr_list[i, j], mol_id)
# Increment once row is done
row += 1
# Get the final aggregated molecule
concat_mol = MultiConvMol(all_atoms, deg_adj_lists, deg_slice, membership,
return concat_mol
class MultiConvMol(object):
"""Holds information about multiple molecules, for use in feeding information
into tensorflow. Generated using the agglomerate_mols function
def __init__(self, nodes, deg_adj_lists, deg_slice, membership, num_mols):
self.nodes = nodes
self.deg_adj_lists = deg_adj_lists
self.deg_slice = deg_slice
self.membership = membership
self.num_mols = num_mols
self.num_atoms = nodes.shape[0]
def get_deg_adjacency_lists(self):
return self.deg_adj_lists
def get_atom_features(self):
return self.nodes
def get_num_atoms(self):
return self.num_atoms
def get_num_molecules(self):
return self.num_mols
class WeaveMol(object):
"""Holds information about a molecule
Molecule struct used in weave models
def __init__(self, nodes, pairs):
self.nodes = nodes
self.pairs = pairs
self.num_atoms = self.nodes.shape[0]
self.n_features = self.nodes.shape[1]
def get_pair_features(self):
return self.pairs
def get_atom_features(self):
return self.nodes
def get_num_atoms(self):
return self.num_atoms
def get_num_features(self):
return self.n_features