fix with some tests for issue #4, #3, #7, needs evaluation

src/main/java/lychi/LyChIStandardizer.java

@@ -1166,7 +1166,129 @@ else if (chiral != 0) {
             int i = m.indexOf(me.getKey());
             m.setChirality(i, me.getValue());
         }
-
+        try{
+
+        	Map<MolAtom,MolBond> nonChiralStereo = new LinkedHashMap<>();
+
+        	for(int k=0;k<m.getBondCount();k++){
+	            MolBond b = m.getBond(k);
+	            int parity = b.getFlags() & MolBond.STEREO1_MASK;
+	            MolAtom ma1=b.getAtom1();
+	            if(chirality.get(ma1)==null){
+	            	if(parity!=0){
+	            		//some other parity assigned here
+//	            		if(parity==MolBond.UP)System.out.println("UP");	
+//	            		if(parity==MolBond.DOWN)System.out.println("DOWN");
+	            		nonChiralStereo.put(ma1, b);
+	            	}
+	            }
+	        }
+
+        	if(!nonChiralStereo.isEmpty()){
+        		String igprop=m.getProperty("IGNORE_COMPLEX");
+
+        		if(!"true".equals(igprop)){
+	        		m.setProperty("IGNORE_COMPLEX", "true");
+
+        			Set<int[]> rings = new HashSet<int[]>();
+
+        			int[][] sssr=m.getSSSR();
+	        		for(MolAtom ma:nonChiralStereo.keySet()){
+	        			//need to find all atoms in the ring
+	        			int im=m.indexOf(ma);
+	        			for(int[] ir:sssr){	        				
+	        				for(int i=0;i<ir.length;i++){
+	        					if(ir[i]==im){
+	        						rings.add(ir);
+	        					}
+	        				}
+
+	        			}
+	        		}
+
+	        		for(int[] rr:rings){
+	        			Set<MolAtom> ratoms=Arrays.stream(rr)
+	        									   .mapToObj(i->m.getAtom(i))
+	        									   .collect(Collectors.toSet());
+
+	        			MolBond[] bonds=ratoms.stream()
+	        				  .filter(a->!chirality.containsKey(a))
+	        			      .flatMap(a->IntStream.range(0, a.getEdgeCount()).mapToObj(i->a.getEdge(i)))
+	        			      .filter(e->!ratoms.contains(e.getNode1()) || !ratoms.contains(e.getNode2()))
+	        			      .map(b->(MolBond)b)
+	        			      .filter(b->b.getType()==1)
+	        			      .peek(b->{
+	        			    	  if(ratoms.contains(b.getAtom1()))b.swap();  
+	        			      })
+	        			      .toArray(i->new MolBond[i]);
+
+	        			BitSet bs = new BitSet(bonds.length*2);
+	        			for(int i=0;i<bonds.length;i++){
+	        				  MolBond b=bonds[i];
+	        				  int parity = b.getFlags() & MolBond.STEREO1_MASK;
+	        				  if(parity==MolBond.UP){
+	        					  bs.set(i*2);
+	        				  }else if(parity==MolBond.DOWN){
+	        					  bs.set(i*2+1);
+	        				  }else{
+	        					  bs.set(i*2);
+	        					  bs.set(i*2+1);
+	        				  }
+	        			}
+
+	        			Set<String> allPossible = new HashSet<String>();
+	        			Set<String> currentPossible = new HashSet<String>();
+
+	        			for(int i=0;i<Math.pow(2, bonds.length);i++){
+	        				BitSet onOff = new BitSet(bonds.length*2);
+	        				for(int j=0;j<bonds.length;j++){
+	        					if((i>>j&1)==1){
+	        						onOff.set(j*2);
+	        						bonds[j].setFlags(MolBond.UP, MolBond.STEREO1_MASK);
+	        					}else{
+	        						onOff.set(j*2+1);
+	        						bonds[j].setFlags(MolBond.DOWN, MolBond.STEREO1_MASK);
+	        					}
+	        				}
+	        				Molecule mclone=m.cloneMolecule();
+		        			//(new LyChIStandardizer()).standardize(mclone);
+		        			String hash1=LyChIStandardizer.hashKey(mclone);
+		        			allPossible.add(hash1);
+		        			onOff.or(bs);
+
+		        			if(onOff.cardinality() == bs.cardinality()){
+		        				currentPossible.add(hash1);
+		        			}
+	        			}
+	        			if(allPossible.size()==currentPossible.size()){
+	        				for(int j=0;j<bonds.length;j++){
+	        					bonds[j].setFlags(0, MolBond.STEREO1_MASK);
+	        				}
+	        			}else{
+	        				for(int j=0;j<bonds.length;j++){
+	        					boolean isUp=bs.get(j*2);
+	        					boolean isDown=bs.get(j*2+1);
+
+	        					if(isUp && ! isDown){
+	        						bonds[j].setFlags(MolBond.UP, MolBond.STEREO1_MASK);
+	        					}else if(!isUp && isDown){
+	        						bonds[j].setFlags(MolBond.DOWN, MolBond.STEREO1_MASK);
+	        					}else{
+	        						bonds[j].setFlags(0, MolBond.STEREO1_MASK);
+	        					}
+	        				}
+	        			}	        			
+	        		}
+
+
+
+	        		m.setProperty("IGNORE_COMPLEX", null);
+        		}
+        	}
+
+        }catch(Exception e){
+
+        }
 
 
         for (Map.Entry<MolAtom, Integer> me : chirality.entrySet()) {