Skip to content

Commit

Permalink
added support for prostaglandins in goslin grammar
Browse files Browse the repository at this point in the history
  • Loading branch information
@dominik-kopczynski
dominik-kopczynski committed May 14, 2024
1 parent cb8e49a commit 8bea8ab
Show file tree
Hide file tree
Showing 2 changed files with 194 additions and 4 deletions.
197 changes: 194 additions & 3 deletions parsers/src/main/java/org/lifstools/jgoslin/parser/GoslinParserEventHandler.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -31,11 +31,15 @@
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import static java.util.Map.entry;
import java.util.TreeMap;
import org.lifstools.jgoslin.domain.Element;
import org.lifstools.jgoslin.domain.HeadgroupDecorator;
import static org.lifstools.jgoslin.parser.Parser.EOF_SIGN;

/**
Expand All @@ -55,6 +59,8 @@ public class GoslinParserEventHandler extends LipidBaseParserEventHandler {
private Element heavyElement;
private int heavyElementNumber;
private boolean trivialMediator;
private String prostaglandinType;
private String prostaglandinNumber;

private final static Map<String, Integer> MEDIATOR_FA = Map.of(
"H", 17, "O", 18, "E", 20, "Do", 22);
Expand Down Expand Up @@ -137,7 +143,11 @@ public GoslinParserEventHandler(KnownFunctionalGroups knownFunctionalGroups) {
entry("heavy_pre_event", this::newAdduct),
entry("adduct_heavy_element_pre_event", this::setHeavyElement),
entry("adduct_heavy_number_pre_event", this::setHeavyNumber),
entry("adduct_heavy_component_post_event", this::addHeavyComponent)
entry("adduct_heavy_component_post_event", this::addHeavyComponent),

entry("prostaglandin_number_pre_event", this::setProstaglandinNumber),
entry("prostaglandin_type_pre_event", this::setProstaglandinType),
entry("prostaglandin_post_event", this::addProstaglandin)
);

} catch (Exception e) {
Expand All @@ -148,7 +158,7 @@ public GoslinParserEventHandler(KnownFunctionalGroups knownFunctionalGroups) {
@Override
protected void resetParser(TreeNode node) {
content = null;
level = LipidLevel.FULL_STRUCTURE;
level = LipidLevel.COMPLETE_STRUCTURE;
headGroup = "";
lcb = null;
faList.clear();
Expand All @@ -165,6 +175,8 @@ protected void resetParser(TreeNode node) {
heavyElement = Element.C;
heavyElementNumber = 0;
trivialMediator = false;
prostaglandinType = "";
prostaglandinNumber = "";
}

private void setHeadGroupName(TreeNode node) {
Expand Down Expand Up @@ -236,6 +248,7 @@ private void appendFa(TreeNode node) {
throw new LipidException("Double bond count does not match with number of double bond positions");
}

removeDeoxy(currentFa.getFunctionalGroupsInternal());
faList.add(currentFa);
if (headGroup.compareTo("Sa") == 0 || headGroup.compareTo("So") == 0 || headGroup.compareTo("S1P") == 0 || headGroup.compareTo("Sa1P") == 0){
FunctionalGroup functional_group = knownFunctionalGroups.get("OH");
Expand Down Expand Up @@ -451,6 +464,80 @@ private void addMediatorFunction(TreeNode node) {
currentFa.getFunctionalGroupsInternal().get(fg).add(functionalGroup);
}


private boolean recursiveDeletion(String fgName, FunctionalGroup fg, Map<String, ArrayList<FunctionalGroup>> functionalGroups){
ArrayList<String> delFunctions = new ArrayList<>();
boolean returnValue = false;
for (Entry<String, ArrayList<FunctionalGroup>> kv : functionalGroups.entrySet()){
ArrayList<Integer> delFg = new ArrayList<>();
for (int i = 0; i < kv.getValue().size(); ++i){
if (kv.getValue().get(i).getPosition() == fg.getPosition()) delFg.add(i);
}
if (!delFg.isEmpty()){
for (int i = delFg.size() - 1; i >= 0; --i){
kv.getValue().remove(i);
if (kv.getValue().isEmpty()) delFunctions.add(kv.getKey());
}
if (!functionalGroups.containsKey(fgName)){
functionalGroups.put(fgName, new ArrayList<>());
}
functionalGroups.get(fgName).add(fg);
returnValue = true;
}
for (FunctionalGroup fgCurr : kv.getValue()){
if (returnValue) break;
if (recursiveDeletion(fgName, fg, fgCurr.getFunctionalGroupsInternal())) returnValue = true;
}
}
for (String delFgName : delFunctions) functionalGroups.remove(delFgName);
return returnValue;
}


private void cleanMediator(FattyAcid fa){
if (!fa.getFunctionalGroups().isEmpty()){
for (Entry<String, ArrayList<FunctionalGroup>> kv : fa.getFunctionalGroupsInternal().entrySet()){


String fgName = kv.getKey();
for (FunctionalGroup fg : kv.getValue()){

if (fg.getPosition() >= -1){
// erase prevously added functional group, if findable
if (!recursiveDeletion(fgName, fg, currentFa.getFunctionalGroupsInternal())){
if (!currentFa.getFunctionalGroupsInternal().containsKey(fgName)){
currentFa.getFunctionalGroupsInternal().put(fgName, new ArrayList<>());
}
currentFa.getFunctionalGroupsInternal().get(fgName).add(fg);
}
}
else {
if (!currentFa.getFunctionalGroupsInternal().containsKey(fgName)){
currentFa.getFunctionalGroupsInternal().put(fgName, new ArrayList<>());
}
currentFa.getFunctionalGroupsInternal().get(fgName).add(fg);
}
}
}
fa.getFunctionalGroupsInternal().clear();
}
removeDeoxy(currentFa.getFunctionalGroupsInternal());

}


private void removeDeoxy(Map<String, ArrayList<FunctionalGroup>> functionalGroups){
if (functionalGroups.containsKey("d")){
functionalGroups.remove("d");
}
for (Entry<String, ArrayList<FunctionalGroup>> kv : functionalGroups.entrySet()){
for (FunctionalGroup fg : kv.getValue()){
removeDeoxy(fg.getFunctionalGroupsInternal());
}
}
}


private void setTrivialMediator(TreeNode node) {
headGroup = "FA";

Expand Down Expand Up @@ -501,5 +588,109 @@ private void setHeavyNumber(TreeNode node) {
private void addHeavyComponent(TreeNode node) {
adduct.getHeavyElements().put(heavyElement, adduct.getHeavyElements().get(heavyElement) + heavyElementNumber);
}



private void setProstaglandinType(TreeNode node){
prostaglandinType = node.getText();
}



private void setProstaglandinNumber(TreeNode node){
prostaglandinNumber = node.getText();
}



private void addProstaglandin(TreeNode node){
HashSet<String> pgTypes = new HashSet<>(Arrays.asList("B", "D", "E", "F", "J", "K"));
HashSet<String> pgNumbers = new HashSet<>(Arrays.asList("1", "2", "3"));
if (!pgTypes.contains(prostaglandinType) || !pgNumbers.contains(prostaglandinNumber)) return;

DoubleBonds db = null;
FattyAcid tmpFa = currentFa;

if (prostaglandinNumber == "1") db = new DoubleBonds(new TreeMap<>(Map.of(13, "E")));
else if (prostaglandinNumber == "2") db = new DoubleBonds(new TreeMap<>(Map.of(5, "Z", 13, "E")));
else if (prostaglandinNumber == "3") db = new DoubleBonds(new TreeMap<>(Map.of(5, "Z", 13, "E", 17, "Z")));

if (prostaglandinType == "B"){
FunctionalGroup f1 = knownFunctionalGroups.get("OH");
FunctionalGroup f2 = knownFunctionalGroups.get("OH");
f1.setPosition(15);
f2.setPosition(9);
HashMap<String, ArrayList<FunctionalGroup>> fgCy = new HashMap<>(Map.of("OH", new ArrayList<>(Arrays.asList(f2))));
Cycle cy = new Cycle(5, 8, 12, new DoubleBonds(new TreeMap<>(Map.of(8, ""))), fgCy, knownFunctionalGroups);
HashMap<String, ArrayList<FunctionalGroup>> fg = new HashMap<>(Map.of("OH", new ArrayList<>(Arrays.asList(f1)), "cy", new ArrayList<>(Arrays.asList(cy))));
currentFa = new FattyAcid("FA", 20, db, fg, knownFunctionalGroups);
}
else if (prostaglandinType == "D"){
FunctionalGroup f1 = knownFunctionalGroups.get("OH");
FunctionalGroup f2 = knownFunctionalGroups.get("OH");
FunctionalGroup f3 = knownFunctionalGroups.get("oxo");
f1.setPosition(15);
f2.setPosition(9);
f3.setPosition(11);
HashMap<String, ArrayList<FunctionalGroup>> fgCy = new HashMap<>(Map.of("OH", new ArrayList<>(Arrays.asList(f2)), "oxo", new ArrayList<>(Arrays.asList(f3))));
Cycle cy = new Cycle(5, 8, 12, null, fgCy, knownFunctionalGroups);
HashMap<String, ArrayList<FunctionalGroup>> fg = new HashMap<>(Map.of("OH", new ArrayList<>(Arrays.asList(f1)), "cy", new ArrayList<>(Arrays.asList(cy))));
currentFa = new FattyAcid("FA", 20, db, fg, knownFunctionalGroups);
}
else if (prostaglandinType == "E"){
FunctionalGroup f1 = knownFunctionalGroups.get("OH");
FunctionalGroup f2 = knownFunctionalGroups.get("oxo");
FunctionalGroup f3 = knownFunctionalGroups.get("OH");
f1.setPosition(15);
f2.setPosition(9);
f3.setPosition(11);
HashMap<String, ArrayList<FunctionalGroup>> fgCy = new HashMap<>(Map.of("OH", new ArrayList<>(Arrays.asList(f3)), "oxo", new ArrayList<>(Arrays.asList(f3))));
Cycle cy = new Cycle(5, 8, 12, null, fgCy, knownFunctionalGroups);
HashMap<String, ArrayList<FunctionalGroup>> fg = new HashMap<>(Map.of("OH", new ArrayList<>(Arrays.asList(f1)), "cy", new ArrayList<>(Arrays.asList(cy))));
currentFa = new FattyAcid("FA", 20, db, fg, knownFunctionalGroups);
}
else if (prostaglandinType == "F"){
FunctionalGroup f1 = knownFunctionalGroups.get("OH");
FunctionalGroup f2 = knownFunctionalGroups.get("OH");
FunctionalGroup f3 = knownFunctionalGroups.get("OH");
f1.setPosition(15);
f2.setPosition(9);
f3.setPosition(11);
HashMap<String, ArrayList<FunctionalGroup>> fgCy = new HashMap<>(Map.of("OH", new ArrayList<>(Arrays.asList(f2, f3))));
Cycle cy = new Cycle(5, 8, 12, null, fgCy, knownFunctionalGroups);
HashMap<String, ArrayList<FunctionalGroup>> fg = new HashMap<>(Map.of("OH", new ArrayList<>(Arrays.asList(f1)), "cy", new ArrayList<>(Arrays.asList(cy))));
currentFa = new FattyAcid("FA", 20, db, fg, knownFunctionalGroups);
}
else if (prostaglandinType == "J"){
FunctionalGroup f1 = knownFunctionalGroups.get("OH");
FunctionalGroup f2 = knownFunctionalGroups.get("oxo");
f1.setPosition(15);
f2.setPosition(11);
HashMap<String, ArrayList<FunctionalGroup>> fgCy = new HashMap<>(Map.of("oxo", new ArrayList<>(Arrays.asList(f2))));
Cycle cy = new Cycle(5, 8, 12, new DoubleBonds(new TreeMap<>(Map.of(9, ""))), fgCy, knownFunctionalGroups);
HashMap<String, ArrayList<FunctionalGroup>> fg = new HashMap<>(Map.of("OH", new ArrayList<>(Arrays.asList(f1)), "cy", new ArrayList<>(Arrays.asList(cy))));
currentFa = new FattyAcid("FA", 20, db, fg, knownFunctionalGroups);
}
else if (prostaglandinType == "K"){
FunctionalGroup f1 = knownFunctionalGroups.get("OH");
FunctionalGroup f2 = knownFunctionalGroups.get("oxo");
FunctionalGroup f3 = knownFunctionalGroups.get("oxo");
f1.setPosition(15);
f2.setPosition(9);
f3.setPosition(11);
HashMap<String, ArrayList<FunctionalGroup>> fgCy = new HashMap<>(Map.of("oxo", new ArrayList<>(Arrays.asList(f2, f3))));
Cycle cy = new Cycle(5, 8, 12, null, fgCy, knownFunctionalGroups);
HashMap<String, ArrayList<FunctionalGroup>> fg = new HashMap<>(Map.of("OH", new ArrayList<>(Arrays.asList(f1)), "cy", new ArrayList<>(Arrays.asList(cy))));
currentFa = new FattyAcid("FA", 20, db, fg, knownFunctionalGroups);
}
else {
return;
}

cleanMediator(tmpFa);
faList.clear();
faList.add(currentFa);
mediatorSuffix = true;
prostaglandinType = "";
prostaglandinNumber = "";
}
}
1 change: 0 additions & 1 deletion parsers/src/main/java/org/lifstools/jgoslin/parser/ShorthandParserEventHandler.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -242,7 +242,6 @@ private void buildLipid(TreeNode node) {

private void setSterolDefinition(TreeNode node) {
headGroup += " " + node.getText();
faList.remove(0);

}

Expand Down

0 comments on commit 8bea8ab

Please sign in to comment.