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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