Merge pull request #80 from cdk/more-h-options

More hydrogen options
cdk · Jan 23, 2024 · bed0ac2 · bed0ac2
2 parents 008bea5 + d1dbad0
commit bed0ac2
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Showing 3 changed files with 42 additions and 24 deletions.
diff --git a/cdkdepict-lib/src/main/java/org/openscience/cdk/app/DepictController.java b/cdkdepict-lib/src/main/java/org/openscience/cdk/app/DepictController.java
@@ -249,21 +249,7 @@ private HydrogenDisplayType getHydrogenDisplay(Map<String, String> params) {
  if (!getBoolean(Param.SUPRESSH, params)) {
  return HydrogenDisplayType.Provided;
  } else {
- switch (getString(Param.HDISPLAY, params)) {
- case "suppressed":
- return HydrogenDisplayType.Minimal;
- case "provided":
- return HydrogenDisplayType.Provided;
- case "stereo":
- return HydrogenDisplayType.Stereo;
- case "bridgeheadtetrahedral":
- case "bridgehead":
- case "default":
- case "smart":
- return HydrogenDisplayType.Smart;
- default:
- return HydrogenDisplayType.Smart;
- }
+ return HydrogenDisplayType.parse(getString(Param.HDISPLAY, params));
  }
  }
 
@@ -694,6 +680,9 @@ private void setHydrogenDisplay(IAtomContainer mol, HydrogenDisplayType hDisplay
  case Minimal:
  AtomContainerManipulator.suppressHydrogens(mol);
  break;
+ case Explicit:
+ AtomContainerManipulator.convertImplicitToExplicitHydrogens(mol);
+ break;
  case Stereo: {
  AtomContainerManipulator.suppressHydrogens(mol);
  List<IStereoElement> ses = new ArrayList<>();

diff --git a/cdkdepict-lib/src/main/java/org/openscience/cdk/app/HydrogenDisplayType.java b/cdkdepict-lib/src/main/java/org/openscience/cdk/app/HydrogenDisplayType.java
@@ -4,9 +4,37 @@
 
 package org.openscience.cdk.app;
 
+import java.util.HashMap;
+import java.util.Locale;
+import java.util.Map;
+
 enum HydrogenDisplayType {
- Provided,
- Minimal,
- Stereo,
- Smart;
+ Provided('P'),
+ Minimal('M'),
+ Stereo('C'),
+ Smart('S'),
+ Explicit('X');
+
+ private final char ch;
+ private static Map<String, HydrogenDisplayType> map = new HashMap<>();
+
+ static {
+ for (HydrogenDisplayType hdisp : values()) {
+ map.put(hdisp.name(), hdisp);
+ map.put(hdisp.name().toLowerCase(Locale.ROOT), hdisp);
+ map.put(Character.toString(hdisp.ch), hdisp);
+ }
+ map.put("suppressed", HydrogenDisplayType.Minimal);
+ map.put("bridgeheadtetrahedral", HydrogenDisplayType.Smart);
+ map.put("bridgehead", HydrogenDisplayType.Smart);
+ map.put("default", HydrogenDisplayType.Smart);
+ }
+
+ HydrogenDisplayType(char ch) {
+ this.ch = ch;
+ }
+
+ static HydrogenDisplayType parse(String key) {
+ return map.getOrDefault(key, HydrogenDisplayType.Smart);
+ }
 }
diff --git a/cdkdepict-webapp/src/main/webapp/WEB-INF/static/depict.html b/cdkdepict-webapp/src/main/webapp/WEB-INF/static/depict.html
@@ -56,11 +56,12 @@
  <option value="atomvalue">Atom Value</option>
  <option value="cip">CIP Stereo Label</option>
  </select>
- <select name="hdisp" onchange="update()">
- <option value="minimal">Minimal Hydrogens</option>
- <option value="stereo">Chiral Hydrogens</option>
- <option value="bridgehead" selected>Chiral Hydrogens (smart)</option>
- <option value="provided">Default Hydrogens</option>
+ <select id="hdisp" name="hdisp" onchange="update()">
+ <option value="M">Minimal Hydrogens</option>
+ <option value="P">Input Hydrogens</option>
+ <option value="S" selected>Smart Hydrogens</option>
+ <option value="C">Chiral Hydrogens</option>
+ <option value="X">Explicit Hydrogens</option>
  </select>
  <select name="abbr" onchange="update()">
  <option value="on" selected>Abbreviate Reagents and Groups</option>