LACAN Documentation

LACAN (Leveraging Adjacent Co-occurrence of Atomic Neighborhoods) is a statistical filter and generative cheminformatics toolkit for scoring, mutating, and generating drug-like molecules using a model of bond environments learned from ChEMBL.

Contents

• Installation
  • PyPI
  • From source
  • Requirements
  • Development install
• Overview
  • Scoring model
  • Module overview
  • Quick start
  • Genetic algorithm
• lacan.lacan
  • Scoring model
  • CLI usage
  • hash_invariants()
  • mol_to_pairs()
  • get_neighbors()
  • get_atom_invariants()
  • get_profile_for_mols()
  • assess_per_bond()
  • load_profile()
  • get_default_profile()
  • score_mol()
• lacan.gen
  • Random generation
  • Corpus biasing
  • Adaptive GA
  • GA design
  • load_corpus()
  • generate_random_molecule()
  • generate_filtered_molecule()
  • generate_filtered_molecules()
  • get_corpus_from_mols()
  • bias_corpus()
  • ThompsonBandit
  • HallOfFame
  • generate_optimized_molecules()
  • GAReporter
  • optimize_from_mol()
  • next_population()
• lacan.replace
  • Reaction conventions
  • rxn1
  • rxn2
  • htodummy
  • decompose1
  • singledummy
  • doubledummy
  • load_corpus()
  • decorate_scaffold()
  • replace_substituent()
  • replace_linker()
  • replace_ring()
• lacan.mutate
  • Protection
  • Multiprocessing
  • mutate_smarts
  • mutate_ops
  • apply_mutations_mols()
  • apply_mutations()
• lacan.protect
  • PROP
  • get_protected_atoms()
  • reaction_touches_protected()
  • protect_bonds_for_idx()
  • protect_rejected_bonds()
  • get_protected_bond_indices()
  • bond_is_protected()
  • score_mol_ignoring_protected_bonds()
  • mol_cleaner()
• lacan.breed
  • Algorithm
  • Fallback
  • combine_frags
  • fragment_molecule()
  • crossover_fragments()
  • breed()
  • cross_breed_mols()
• lacan.decompose
  • Fragment taxonomy
  • Reaction SMARTS
  • Corpus format
  • decompose1
  • decompose2
  • ringdummy
  • nonringdummy
  • singledummy
  • doubledummy
  • get_bonds_string()
  • decompose_molecule()
  • get_all_decompositions()
  • save_frags()
  • get_corpus()

Indices and tables

• Index

• Module Index

• Search Page