Table of Contents

Class: molecule | ../bkchem/oasa/oasa/molecule.py
--- | ---
Base Classes |
--- | ---
graph.graph
Methods |
--- | ---
__init__ __str__ add_missing_bond_orders add_missing_hydrogens clean_after_search create_edge create_graph create_vertex | find_longest_mostly_carbon_chain get_mean_bond_length get_mol_weight get_symmetry_unique_atoms localize_aromatic_bonds localize_fake_aromatic_bonds mark_aromatic_bonds mark_morgan | normalize_bond_length number_atoms_uniquely remove_all_hydrogens select_matching_substructures
| __init__
    __init__ ( self,  vertices=[] )
| __str__
    __str__ ( self )
| add_missing_bond_orders
    add_missing_bond_orders ( self,  retry=False )
retry means to try a different approach because the last one was not successful
| add_missing_hydrogens
    add_missing_hydrogens ( self )
| clean_after_search
    clean_after_search ( self,  other )
| create_edge
    create_edge ( self )
| create_graph
    create_graph ( self )
| create_vertex
    create_vertex ( self,  vertex_class=None )
| find_longest_mostly_carbon_chain
    find_longest_mostly_carbon_chain ( self )
| get_mean_bond_length
    get_mean_bond_length ( self )
returns the mean bond length of bonds in the molecule
| get_mol_weight
    get_mol_weight ( self )
| get_symmetry_unique_atoms
    get_symmetry_unique_atoms ( self )
| localize_aromatic_bonds
    localize_aromatic_bonds ( self )
localizes aromatic bonds (does not relocalize already localized ones), for those that are not aromatic but marked so (it is for instance possible to misuse `cccc` in smiles to create butadiene) they will be properly localized but marked as non-aromatic
| localize_fake_aromatic_bonds
    localize_fake_aromatic_bonds ( self )
| mark_aromatic_bonds
    mark_aromatic_bonds ( self )
| mark_morgan
    mark_morgan ( self )
| normalize_bond_length
    normalize_bond_length ( self,  bond_length=30 )
make the average bond-length be bond_length by scaling the structure up
| number_atoms_uniquely
    number_atoms_uniquely ( self )
| remove_all_hydrogens
    remove_all_hydrogens ( self )
removes all H atoms
| select_matching_substructures
    select_matching_substructures (
            self,
            other,
            implicit_freesites=False,
            auto_cleanup=True,
            )
select fragments that match the complete molecule `other` and yield them as lists of atoms in the order of other.vertices; however when other has explicit hydrogens that match implicit hydrogens on self the length of the returned fragment might be shorter of the matched implicit hydrogens; IF YOU DON'T LET THE GENERATOR RUN TO THE END OR SET THE auto_cleanup TO FALSE, YOU HAVE TO RUN clean_after_search MANUALLY NOT TO CLUTTER THE STRUCTURE

Table of Contents

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