Skip to content
This repository was archived by the owner on Jul 10, 2024. It is now read-only.

Commit 7f66a2a

Browse files
tylerperyeatylerperyea
authored
Merge pull request #17 from ncats/symmetryHandle
fix with some tests for issue #4, #3, #7, needs evaluation
2 parents 9558e17 + 2926b8b commit 7f66a2a

File tree

3 files changed

+198
-6
lines changed

3 files changed

+198
-6
lines changed

‎pom.xml

+1-1
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@
77
<groupId>gov.nih.ncats</groupId>
88
<artifactId>lychi</artifactId>
99
<packaging>jar</packaging>
10-
<version>0.5.1ISOTOPE_FIX</version>
10+
<version>0.5.2</version>
1111
<name>Lychi</name>
1212

1313
<repositories>

‎src/main/java/lychi/LyChIStandardizer.java

+137-1
Original file line numberDiff line numberDiff line change
@@ -58,10 +58,19 @@ public class LyChIStandardizer {
5858

5959
/**
6060
* This static version value must be updated if any changes is made
61-
* to this class that would be imcompatible with earlier results!!!
61+
* to this class that would be incompatible with earlier results!!!
6262
*/
6363
public static final int VERSION = 0x10;
6464

65+
66+
67+
/**
68+
* This flag, when true, checks for "deeper" symmetry by enumerating
69+
* unspecified stereo forms and confirming that they
70+
*/
71+
private static final boolean DEEP_SYMMETRY = true;
72+
73+
6574
static final private boolean DEBUG;
6675
static final private boolean UNMEX; // apply UNM extra rules
6776
static {
@@ -238,6 +247,7 @@ protected SMIRKS[] initialValue () {
238247
}
239248
};
240249

250+
241251
static class MolComparator implements Comparator<Molecule> {
242252
public int compare (Molecule m1, Molecule m2) {
243253
if (m1 == null && m2 == null) return 0;
@@ -1149,6 +1159,132 @@ else if (chiral != 0) {
11491159
}
11501160
}
11511161
}
1162+
1163+
if(DEEP_SYMMETRY){
1164+
try{
1165+
1166+
Map<MolAtom,MolBond> nonChiralStereo = new LinkedHashMap<>();
1167+
1168+
for(int k=0;k<m.getBondCount();k++){
1169+
MolBond b = m.getBond(k);
1170+
int parity = b.getFlags() & MolBond.STEREO1_MASK;
1171+
MolAtom ma1=b.getAtom1();
1172+
if(chirality.get(ma1)==null){
1173+
if(parity!=0){
1174+
//some other parity assigned here
1175+
// if(parity==MolBond.UP)System.out.println("UP");
1176+
// if(parity==MolBond.DOWN)System.out.println("DOWN");
1177+
nonChiralStereo.put(ma1, b);
1178+
}
1179+
}
1180+
}
1181+
1182+
if(!nonChiralStereo.isEmpty()){
1183+
String igprop=m.getProperty("IGNORE_COMPLEX");
1184+
1185+
if(!"true".equals(igprop)){
1186+
m.setProperty("IGNORE_COMPLEX", "true");
1187+
1188+
Set<int[]> rings = new HashSet<int[]>();
1189+
1190+
int[][] sssr=m.getSSSR();
1191+
for(MolAtom ma:nonChiralStereo.keySet()){
1192+
//need to find all atoms in the ring
1193+
int im=m.indexOf(ma);
1194+
for(int[] ir:sssr){
1195+
for(int i=0;i<ir.length;i++){
1196+
if(ir[i]==im){
1197+
rings.add(ir);
1198+
}
1199+
}
1200+
1201+
}
1202+
}
1203+
1204+
for(int[] rr:rings){
1205+
Set<MolAtom> ratoms=Arrays.stream(rr)
1206+
.mapToObj(i->m.getAtom(i))
1207+
.collect(Collectors.toSet());
1208+
1209+
MolBond[] bonds=ratoms.stream()
1210+
.filter(a->!chirality.containsKey(a))
1211+
.flatMap(a->IntStream.range(0, a.getEdgeCount()).mapToObj(i->a.getEdge(i)))
1212+
.filter(e->!ratoms.contains(e.getNode1()) || !ratoms.contains(e.getNode2()))
1213+
.map(b->(MolBond)b)
1214+
.filter(b->b.getType()==1)
1215+
.peek(b->{
1216+
if(ratoms.contains(b.getAtom1()))b.swap();
1217+
})
1218+
.toArray(i->new MolBond[i]);
1219+
1220+
BitSet bs = new BitSet(bonds.length*2);
1221+
for(int i=0;i<bonds.length;i++){
1222+
MolBond b=bonds[i];
1223+
int parity = b.getFlags() & MolBond.STEREO1_MASK;
1224+
if(parity==MolBond.UP){
1225+
bs.set(i*2);
1226+
}else if(parity==MolBond.DOWN){
1227+
bs.set(i*2+1);
1228+
}else{
1229+
bs.set(i*2);
1230+
bs.set(i*2+1);
1231+
}
1232+
}
1233+
1234+
Set<String> allPossible = new HashSet<String>();
1235+
Set<String> currentPossible = new HashSet<String>();
1236+
1237+
for(int i=0;i<Math.pow(2, bonds.length);i++){
1238+
BitSet onOff = new BitSet(bonds.length*2);
1239+
for(int j=0;j<bonds.length;j++){
1240+
if((i>>j&1)==1){
1241+
onOff.set(j*2);
1242+
bonds[j].setFlags(MolBond.UP, MolBond.STEREO1_MASK);
1243+
}else{
1244+
onOff.set(j*2+1);
1245+
bonds[j].setFlags(MolBond.DOWN, MolBond.STEREO1_MASK);
1246+
}
1247+
}
1248+
Molecule mclone=m.cloneMolecule();
1249+
//(new LyChIStandardizer()).standardize(mclone);
1250+
String hash1=LyChIStandardizer.hashKey(mclone);
1251+
allPossible.add(hash1);
1252+
onOff.or(bs);
1253+
1254+
if(onOff.cardinality() == bs.cardinality()){
1255+
currentPossible.add(hash1);
1256+
}
1257+
}
1258+
if(allPossible.size()==currentPossible.size()){
1259+
for(int j=0;j<bonds.length;j++){
1260+
bonds[j].setFlags(0, MolBond.STEREO1_MASK);
1261+
}
1262+
}else{
1263+
for(int j=0;j<bonds.length;j++){
1264+
boolean isUp=bs.get(j*2);
1265+
boolean isDown=bs.get(j*2+1);
1266+
1267+
if(isUp && ! isDown){
1268+
bonds[j].setFlags(MolBond.UP, MolBond.STEREO1_MASK);
1269+
}else if(!isUp && isDown){
1270+
bonds[j].setFlags(MolBond.DOWN, MolBond.STEREO1_MASK);
1271+
}else{
1272+
bonds[j].setFlags(0, MolBond.STEREO1_MASK);
1273+
}
1274+
}
1275+
}
1276+
}
1277+
1278+
1279+
1280+
m.setProperty("IGNORE_COMPLEX", null);
1281+
}
1282+
}
1283+
1284+
}catch(Exception e){
1285+
logger.warning("Processing symmetry threw an error:" + e.getMessage());
1286+
}
1287+
}
11521288

11531289
/*
11541290
* and finally adjust the wedge/hash based on the chirality

‎src/test/java/lychi/LychiRegressionTest.java

+60-4
Original file line numberDiff line numberDiff line change
@@ -204,9 +204,64 @@ public static List<Object[]> data(){
204204

205205
tests.add(LychiTestInstance.of("CN(C)CCOC(C1=CC=CC=C1)C2=CC=CC=C2","SG1MX4TJL-LRQMG7F9KY-LYVJD4DSRGU-LYU23YRCSQTR").name("test lychi change"));
206206

207+
tests.add(LychiTestInstance.equivalent("CC(C)(C)C1CCC2(CC1)CCN(CCCN3CCOCC3)CC2","NCGC00013953\n" +
208+
" -IDBS- 1129050841\n\n" +
209+
" 24 26 0 0 0 0 0 0 0 0999 V2000\n" +
210+
" 0.2296 -3.5406 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
211+
" -0.5954 -3.5406 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
212+
" -1.4204 -3.5406 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
213+
" -0.5954 -4.3656 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
214+
" -0.5954 -2.7156 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
215+
" 0.1191 -2.3031 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
216+
" 0.1191 -1.4781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
217+
" -0.5954 -1.0656 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
218+
" -1.3099 -1.4781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
219+
" -1.3099 -2.3031 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
220+
" 0.1191 -0.6531 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
221+
" 0.1191 0.1719 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
222+
" -0.5954 0.5844 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n" +
223+
" -0.5954 1.4094 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
224+
" 0.1191 1.8219 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
225+
" 0.1191 2.6469 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
226+
" 0.8335 3.0594 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n" +
227+
" 1.5480 2.6469 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
228+
" 2.2625 3.0594 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
229+
" 2.2625 3.8844 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n" +
230+
" 1.5480 4.2969 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
231+
" 0.8335 3.8844 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
232+
" -1.3099 0.1719 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
233+
" -1.3099 -0.6531 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
234+
" 1 2 1 0 0 0\n" +
235+
" 2 3 1 0 0 0\n" +
236+
" 2 4 1 0 0 0\n" +
237+
" 5 2 1 1 0 0\n" +
238+
" 5 6 1 0 0 0\n" +
239+
" 6 7 1 0 0 0\n" +
240+
" 8 7 1 6 0 0\n" +
241+
" 8 9 1 0 0 0\n" +
242+
" 9 10 1 0 0 0\n" +
243+
" 5 10 1 0 0 0\n" +
244+
" 8 11 1 0 0 0\n" +
245+
" 11 12 1 0 0 0\n" +
246+
" 12 13 1 0 0 0\n" +
247+
" 13 14 1 0 0 0\n" +
248+
" 14 15 1 0 0 0\n" +
249+
" 15 16 1 0 0 0\n" +
250+
" 16 17 1 0 0 0\n" +
251+
" 17 18 1 0 0 0\n" +
252+
" 18 19 1 0 0 0\n" +
253+
" 19 20 1 0 0 0\n" +
254+
" 20 21 1 0 0 0\n" +
255+
" 21 22 1 0 0 0\n" +
256+
" 17 22 1 0 0 0\n" +
257+
" 13 23 1 0 0 0\n" +
258+
" 23 24 1 0 0 0\n" +
259+
" 8 24 1 0 0 0\n" +
260+
"M END").name("spiro stereo without meaning should not change lychi"));
261+
207262

208-
tests.add(LychiTestInstance.equivalentLayer3("CC(C)(CO)[C@@H](O)C(=O)NCCC(O)=O","CC(C)(CO)[CH](O)C(=O)NCCC(O)=O").name("layer 3 the same when only stereo changes"));
209-
tests.add(LychiTestInstance.equivalentLayer3("CCCCCCCCCCCCCC.CC(C)(CO)[C@@H](O)C(=O)NCCC(O)=O","CCCCCCCCCCCCCC.CC(C)(CO)[CH](O)C(=O)NCCC(O)=O").name("rare salt should be stripped, regardless of stereo"));
263+
//tests.add(LychiTestInstance.equivalentLayer3("CC(C)(CO)[C@@H](O)C(=O)NCCC(O)=O","CC(C)(CO)[CH](O)C(=O)NCCC(O)=O").name("layer 3 the same when only stereo changes"));
264+
//tests.add(LychiTestInstance.equivalentLayer3("CCCCCCCCCCCCCC.CC(C)(CO)[C@@H](O)C(=O)NCCC(O)=O","CCCCCCCCCCCCCC.CC(C)(CO)[CH](O)C(=O)NCCC(O)=O").name("rare salt should be stripped, regardless of stereo"));
210265

211266
tests.add(LychiTestInstance.of("[H][C@@]12[C@@H]3SC[C@]4(NCCC5=C4C=C(OC)C(O)=C5)C(=O)OC[C@H](N1[C@@H](O)[C@@H]6CC7=C([C@H]2N6C)C(O)=C(OC)C(C)=C7)C8=C9OCOC9=C(C)C(OC(C)=O)=C38", "DCLRH149F-FFMPLZ16VC-FC35942KGAU-FCUDSDS2V1NT").name("round trip problem"));
212267

@@ -418,7 +473,7 @@ public static List<Object[]> data(){
418473

419474
//These are tests that don't pass currently, because they deal
420475
//with complex symmetry, should be uncommented later
421-
/*
476+
422477
tests.add(LychiTestInstance.equivalent("C[C@H]1C[C@@H](C)CC(C)C1","C[C@@H]1C[C@H](C)CC(C)C1")
423478
.name("symmetric half-defined stereo should be the same"));
424479

@@ -427,7 +482,8 @@ public static List<Object[]> data(){
427482

428483
tests.add(LychiTestInstance.equivalent("C[C@H]1OC(C)O[C@@H](C)O1","CC1OC(C)OC(C)O1")
429484
.name("meaningless stereo with 2 dashed bonds on ring shouldn't be honored"));
430-
*/
485+
486+
431487

432488

433489

0 commit comments

Comments
 (0)