cgsmiles package

Submodules

• cgsmiles.cgsmiles_utils module
  • find_complementary_bonding_descriptor()
  • find_open_bonds()
  • read_fragment_cgsmiles()
• cgsmiles.coordinates module
  • embedd_cg_molecule_via_rdkit()
  • forward_map_molecule()
• cgsmiles.dialects module
  • check_and_cast_types()
  • create_dialect()
  • parse_graph_base_node()
• cgsmiles.drawing module
  • draw_molecule()
• cgsmiles.drawing_utils module
  • angle_between()
  • angle_of_interest()
  • make_edge()
  • make_graph_edges()
  • make_mapped_edges()
  • make_node_pies()
  • rotate_2D()
  • rotation_from_x_axis()
• cgsmiles.graph_layout module
  • circular_layout()
  • vespr_layout()
  • vespr_refined_layout()
• cgsmiles.graph_layout_utils module
  • assign_angles()
  • assign_bonds()
  • assing_dihedral_angles()
  • check_and_fix_cis_trans()
  • find_triplets()
  • rotate_subgraph()
• cgsmiles.graph_utils module
  • annotate_fragments()
  • merge_graphs()
  • set_atom_names_atomistic()
  • sort_nodes_by_attr()
• cgsmiles.linalg_functions module
  • dihedral_angle_between()
  • rotate()
  • rotate_degrees()
  • rotate_to_axis()
  • u_vect()
  • vector_angle_degrees()
• cgsmiles.pysmiles_utils module
  • annotate_ez_isomers_cgsmiles()
  • compute_mass()
  • read_fragment_smiles()
  • rebuild_h_atoms()
• cgsmiles.rdkit module
  • embed_3d_via_rdkit()
  • networkx_to_rdkit()
  • rdkit_to_networkx()
• cgsmiles.read_cgsmiles module
  • read_cgsmiles()
• cgsmiles.read_fragments module
  • PeekIter
    • PeekIter.peek()
  • collect_ring_number()
  • fragment_iter()
  • read_fragments()
  • strip_bonding_descriptors()
• cgsmiles.resolve module
  • MoleculeResolver
    • MoleculeResolver.edges_from_bonding_descrpt()
    • MoleculeResolver.from_fragment_dicts()
    • MoleculeResolver.from_graph()
    • MoleculeResolver.from_string()
    • MoleculeResolver.read_fragment_strings()
    • MoleculeResolver.resolve()
    • MoleculeResolver.resolve_all()
    • MoleculeResolver.resolve_disconnected_molecule()
    • MoleculeResolver.resolve_iter()
    • MoleculeResolver.squash_atoms()
  • compatible()
  • match_bonding_descriptors()
• cgsmiles.sample module
  • MoleculeSampler
    • MoleculeSampler.add_fragment()
    • MoleculeSampler.from_fragment_string()
    • MoleculeSampler.sample()
• cgsmiles.test_utils module
• cgsmiles.write_cgsmiles module
  • format_bonding()
  • format_node()
  • write_cgsmiles()
  • write_cgsmiles_fragments()
  • write_cgsmiles_graph()
  • write_graph()

Module contents

CGsmiles: Coarse-Grained Smiles (CGsmiles) for representing abitrarily complex molecules using line notation.