Table of Contents

Class: inchi ../bkchem/oasa/oasa/inchi.py
Base Classes   
plugin
Methods   
__init__
cleanup
compensate_for_forced_charges
deal_with_da_bonds
get_layer
get_number_of_hydrogens_in_hydrogen_layer
get_structure
process_forced_charges
read_charge_layer
read_connectivity_layer
read_hydrogen_layer
read_inchi
read_p_layer
read_sum_layer
set_structure
split_layers
  __init__ 
__init__ ( self,  structure=None )

  cleanup 
cleanup ( self )

  compensate_for_forced_charges 
compensate_for_forced_charges ( self )

if there were foced charges and they the molecule should not have any charge, we have to take care of it here

  deal_with_da_bonds 
deal_with_da_bonds ( self )

deal with donor-acceptor bonds, this fixes mostly boron containing compounds

  get_layer 
get_layer ( self,  prefix )

  get_number_of_hydrogens_in_hydrogen_layer 
get_number_of_hydrogens_in_hydrogen_layer ( self )

Exceptions   
oasa_not_implemented_error( "INChI", "multiple compound systems are not supported by the library" )
  get_structure 
get_structure ( self )

  process_forced_charges 
process_forced_charges ( self )

this marks the charges that are forced by the connectivity and thus helps process zwitrions

  read_charge_layer 
read_charge_layer ( self )

Exceptions   
oasa_exceptions.oasa_inchi_error( "The molecular charge could not be allocated to any atom (%d)." % charge )
  read_connectivity_layer 
read_connectivity_layer ( self )

Exceptions   
ValueError, "unexpected character %s in the connectivity layer" % c
  read_hydrogen_layer 
read_hydrogen_layer ( self,  run=0 )

  read_inchi 
read_inchi ( self,  text )

Exceptions   
oasa_inchi_error( "Localization of bonds, charges or movable hydrogens failed" )
  read_p_layer 
read_p_layer ( self )

  read_sum_layer 
read_sum_layer ( self )

Exceptions   
oasa_not_implemented_error( "INChI", "multiple compound systems are not supported by the library" )
  set_structure 
set_structure ( self,  structure )

  split_layers 
split_layers ( self,  text )

Exceptions   
"no '%s' tag found in xml string" % name
"no structures found in xml string %s" % text

Table of Contents

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