static AtomTypePattern [ ] loadPatterns ( InputStream smaIn ) throws IOException { List < AtomTypePattern > matchers = new ArrayList < AtomTypePattern > ( ) ; BufferedReader br = new BufferedReader ( new InputStreamReader ( smaIn ) ) ; String line = null ; while ( ( line = br . readLine ( ) ) != null ) { if ( skipLine ( line ) ) continue ; String [ ] cols = line . split ( " " ) ; String sma = cols [ 0 ] ; String symb = cols [ 1 ] ; try { matchers . add ( new AtomTypePattern ( SmartsPattern . create ( sma ) . setPrepare ( false ) , symb ) ) ; } catch ( IllegalArgumentException ex ) { throw new IOException ( ex ) ; } } return matchers . toArray ( new AtomTypePattern [ matchers . size ( ) ] ) ; }
Internal - load the SMARTS patterns for each atom type from MMFFSYMB . sma .