private static void createIDsForAtomContainerSet ( IAtomContainerSet containerSet , List < String > tabuList ) { if ( tabuList == null ) tabuList = AtomContainerSetManipulator . getAllIDs ( containerSet ) ; if ( null == containerSet . getID ( ) ) { atomContainerSetCount = setID ( ATOMCONTAINERSET_PREFIX , atomContainerSetCount , containerSet , tabuList ) ; } if ( policy == OBJECT_UNIQUE_POLICY ) { // start atom and bond indices within a container set always from 1 atomCount = 0 ; bondCount = 0 ; } Iterator < IAtomContainer > acs = containerSet . atomContainers ( ) . iterator ( ) ; while ( acs . hasNext ( ) ) { createIDsForAtomContainer ( ( IAtomContainer ) acs . next ( ) , tabuList ) ; } }
Labels the Atom s and Bond s in each AtomContainer using the a1 a2 b1 b2 scheme often used in CML . It will also set id s for all AtomContainers naming them m1 m2 etc . It will not the AtomContainerSet itself .