Count the number of atoms in mol with atomic number atomic_num Parameters: mol (rdkit.Chem.rdchem.Mol) : Molecule in which search is

Obtain a list of all selfie characters in string selfies Parameters: selfie (string) : A selfie string - representing a molecule

Return the number of consequtive double bonds in an entire molecule including rings Examples >>> count_conseq_double(Chem.MolFromSmil

Given a list of SMILES (smiles_back), tanimoto similarities are calculated (using Morgan fingerprints) to SMILES (target_smi). Paramet

Given a list of SELFIES alphabets, make random changes to the molecule using alphabet. Opertations to molecules are character replacements,

Compare with value in memory. If there is an improvement, reset the checkpoint and save the model weights. Return True if stopping cr

Featurize smiles and train classifier network. Return trained network.

Obtain network Parameters: n_hidden (list) : Intermediate discrm layers (e.g. [100, 10]) device (str) : D

Do steps for training. Set batch_size to -1 for full batch training, and 1 for SGD.

Get all the bond indices with Rotatable bonds atoms (generated from 'get_rot_bonds_posn')

Given a list of SMILES (smiles_back), tanimoto similarities are calculated (using Morgan fingerprints) to SMILES (target_smi). Paramete

Create fragments from smi with some radius. Remove duplicates and any fragments that are blank molecules.

Given fitness values of all SMILES in population, and the generation size, this function smplits the population into two lists: kee

Get joint similarity values for all smiles in all_smiles, calculated with refernce to starting_smile & target_smile. Parameters --

Calculate a set of 51 RdKit properties, collected from above helper functions. Parameters: smi (string) : SMILE string of molecule

Calculate the ratio of total number of (single, double, triple, aromatic) bonds to the total number of bonds. Parameters: mol (

Return atom indices with Rotatable bonds Examples: >>> get_rot_bonds_posn('CC1=CC=CC=C1') # Toluene (Rotatable Bonds At: CH3 & Benzene

Create a single path between molecules starting_smile and target_smile. Parameters ---------- starting_smile : (str) Valid

Obtain a list of all rings present in SMILE string smi Examples: >>> obtain_rings('CCC1=CC=CC=C1') ['c1ccccc1'] >>> obtain_rings(

Create multiple paths between SMILES in comb_smi to obtain median molecules, representing the crossover structure. Parameters ----

Run optimization based on hyperparameters initialized

Return a canonical smile representation of smi Parameters ---------- smi : str smile string to be canonicalized Retur

Get the number of rings of sizes 3 to 20 and the number of consequtive double bonds in a ring Parameters: ring_ls (list) : list of rings

Return a random split of training and validation data. Ratio determines the size of training set. Avoids use of sklearn.

Return a list of smiles (crossover molecules) that are ordered (highest to lowest) by joint similarity scores. Parameters ---------

Function that takes in a smile and returns a boolean. True indicates the smiles PASSES the filter.

User-defined function that takes in individual smiles and outputs a fitness value.

Create fragments of certain radius. Returns a list of fragments using SELFIES characters.

Given a SMILES string (smi), a user needs to provide code for creating descriptors for the molecules. This will be used as features for the (

Given an input smile, perform mutations to the strucutre using provided SELFIE alphabet list. 'num_random_samples' number of different SMILES

Return a canonical smile representation of smi Parameters: smi (string) : smile string to be canonicalized Returns: mol (rdkit.Chem.r