Table of Contents

Class: molecule bkchem/oasa/oasa/molecule.py
Base Classes   
graph.graph
Methods   
__init__
__str__
_get_atom_distance_matrix
_get_atoms_possible_aromatic_electrons
_read_file
add_missing_bond_orders
add_missing_hydrogens
create_graph
find_longest_mostly_carbon_chain
get_symmetry_unique_atoms
localize_aromatic_bonds
localize_fake_aromatic_bonds
mark_aromatic_bonds
number_atoms_uniquely
remove_all_hydrogens
  __init__ 
__init__ ( self,  vertices=[] )

  __str__ 
__str__ ( self )

  _get_atom_distance_matrix 
_get_atom_distance_matrix ( self,  a )

  _get_atoms_possible_aromatic_electrons 
_get_atoms_possible_aromatic_electrons (
        self,
        at,
        ring,
        )

  _read_file 
_read_file ( self,  name="/home/beda/oasa/oasa/mol.graph" )

  add_missing_bond_orders 
add_missing_bond_orders ( self )

  add_missing_hydrogens 
add_missing_hydrogens ( self )

  create_graph 
create_graph ( self )

  find_longest_mostly_carbon_chain 
find_longest_mostly_carbon_chain ( 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 )

  number_atoms_uniquely 
number_atoms_uniquely ( self )

  remove_all_hydrogens 
remove_all_hydrogens ( self )

removes all H atoms


Table of Contents

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