feat: support RGROUPS in Molfile V3000 (#375)

Author: targos

__tests__/molfile_with_rgroups.test.ts

@@ -0,0 +1,188 @@
+import { expect, test } from 'vitest';
+
+import { Molecule } from '../lib';
+
+test('should parse molfile with RGROUPS 1', () => {
+  const molfile = `Spiramycin
+Actelion Java MolfileCreator 2.0
+
+  0  0  0  0  0  0              0 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 60 63 0 0 0
+M  V30 BEGIN ATOM
+M  V30 1 R# 0.0 0.0 0.0 0 RGROUPS=(1 0)
+M  V30 2 O -0.0157 1.5237 0.0 0
+M  V30 3 C -1.3666 2.3406 0.0 0 CFG=1
+M  V30 4 C -1.3823 3.8644 0.0 0 CFG=2
+M  V30 5 C -2.7176 1.6651 0.0 0
+M  V30 6 O -2.1521 5.2154 0.0 0
+M  V30 7 C -0.3455 4.964 0.0 0 CFG=1
+M  V30 8 C -4.0372 2.4663 0.0 0
+M  V30 9 C -2.9218 6.5663 0.0 0
+M  V30 10 O 0.8797 4.2571 0.0 0
+M  V30 11 C -0.377 6.4878 0.0 0 CFG=2
+M  V30 12 O -4.0529 3.9901 0.0 0
+M  V30 13 O -5.3882 1.8065 0.0 0
+M  V30 14 C 2.2778 3.9115 0.0 0
+M  V30 15 C -1.6965 7.289 0.0 0
+M  V30 16 C 0.8797 7.2575 0.0 0
+M  V30 17 C -6.7234 2.6234 0.0 0 CFG=1
+M  V30 18 O 3.1889 3.2674 0.0 0
+M  V30 19 C 3.723 4.0843 0.0 0
+M  V30 20 C -1.7122 8.8285 0.0 0 CFG=2
+M  V30 21 C 2.1207 6.5506 0.0 0
+M  V30 22 C -6.7391 4.1471 0.0 0
+M  V30 23 C -8.0901 1.9636 0.0 0
+M  V30 24 C 3.5659 1.6023 0.0 0
+M  V30 25 O 4.3985 5.4039 0.0 0
+M  V30 26 C 4.0529 2.482 0.0 0
+M  V30 27 C -3.0475 9.6139 0.0 0 CFG=1
+M  V30 28 C -0.4555 9.5825 0.0 0
+M  V30 29 O 3.3774 7.3047 0.0 0
+M  V30 30 C -5.4824 4.8855 0.0 0
+M  V30 31 C 5.0111 1.7594 0.0 0
+M  V30 32 C 2.7805 0.377 0.0 0
+M  V30 33 N 5.451 2.9218 0.0 0
+M  V30 34 O -3.0789 11.1534 0.0 0
+M  V30 35 C -4.4142 8.9541 0.0 0
+M  V30 36 C -5.5138 6.425 0.0 0
+M  V30 37 O 5.7023 0.5341 0.0 0
+M  V30 38 C 6.1265 4.2571 0.0 0
+M  V30 39 C 6.8491 2.5762 0.0 0
+M  V30 40 C -2.0421 12.253 0.0 0
+M  V30 41 C -4.477 7.5246 0.0 0
+M  V30 42 C 7.1476 0.5812 0.0 0
+M  V30 43 O -0.9268 12.6615 0.0 0
+M  V30 44 C -1.3509 13.5726 0.0 0
+M  V30 45 O 7.6189 -1.021 0.0 0
+M  V30 46 C 8.3886 -0.1099 0.0 0
+M  V30 47 C 0.6754 12.0959 0.0 0
+M  V30 48 C 0.1885 13.0071 0.0 0
+M  V30 49 C 9.5982 -0.6911 0.0 0
+M  V30 50 C 10.2737 0.2513 0.0 0
+M  V30 51 C 1.3666 13.4155 0.0 0
+M  V30 52 C 1.9007 11.4047 0.0 0
+M  V30 53 C 10.745 -1.3509 0.0 0
+M  V30 54 C 9.5354 -2.1207 0.0 0
+M  V30 55 O 10.2109 1.7751 0.0 0
+M  V30 56 C 11.7189 0.2827 0.0 0
+M  V30 57 N 2.6234 14.1695 0.0 0
+M  V30 58 O 12.1431 -0.9268 0.0 0
+M  V30 59 C 3.6602 15.2692 0.0 0
+M  V30 60 C 4.0215 13.8239 0.0 0
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 1 1 2
+M  V30 2 1 3 2 CFG=3
+M  V30 3 1 3 4
+M  V30 4 1 3 5
+M  V30 5 1 4 6 CFG=3
+M  V30 6 1 4 7
+M  V30 7 1 5 8
+M  V30 8 1 6 9
+M  V30 9 1 7 10 CFG=3
+M  V30 10 1 7 11
+M  V30 11 2 8 12
+M  V30 12 1 8 13
+M  V30 13 1 10 14
+M  V30 14 1 11 15
+M  V30 15 1 11 16 CFG=3
+M  V30 16 1 13 17
+M  V30 17 1 14 18
+M  V30 18 1 14 19
+M  V30 19 1 15 20
+M  V30 20 1 16 21
+M  V30 21 1 17 22
+M  V30 22 1 17 23 CFG=3
+M  V30 23 1 18 24
+M  V30 24 1 19 25
+M  V30 25 1 19 26
+M  V30 26 1 20 27
+M  V30 27 1 20 28 CFG=3
+M  V30 28 2 21 29
+M  V30 29 1 22 30
+M  V30 30 1 24 31
+M  V30 31 1 24 32
+M  V30 32 1 26 33
+M  V30 33 1 27 34 CFG=3
+M  V30 34 1 27 35
+M  V30 35 2 30 36
+M  V30 36 1 31 37
+M  V30 37 1 33 38
+M  V30 38 1 33 39
+M  V30 39 1 34 40
+M  V30 40 2 35 41
+M  V30 41 1 37 42
+M  V30 42 1 40 43
+M  V30 43 1 40 44
+M  V30 44 1 42 45
+M  V30 45 1 42 46
+M  V30 46 1 43 47
+M  V30 47 1 44 48
+M  V30 48 1 45 49
+M  V30 49 1 46 50
+M  V30 50 1 47 51
+M  V30 51 1 47 52
+M  V30 52 1 49 53
+M  V30 53 1 49 54
+M  V30 54 1 50 55
+M  V30 55 1 50 56
+M  V30 56 1 51 57
+M  V30 57 1 53 58
+M  V30 58 1 57 59
+M  V30 59 1 57 60
+M  V30 60 1 26 31
+M  V30 61 1 36 41
+M  V30 62 1 48 51
+M  V30 63 1 50 53
+M  V30 END BOND
+M  V30 BEGIN COLLECTION
+M  V30 MDLV30/STEABS ATOMS=(7 3 4 7 11 17 20 27)
+M  V30 END COLLECTION
+M  V30 END CTAB
+M  END
+`;
+
+  const molecule = Molecule.fromMolfile(molfile);
+  expect(molecule.getAllAtoms()).toBe(60);
+
+  expect(molecule.getAtomCustomLabel(0)).toBe('R0');
+  expect(molecule.getAtomicNo(0)).toBe(0);
+  expect(molecule.getAtomLabel(0)).toBe('?');
+});
+
+test('should parse molfile with RGROUPS 2', () => {
+  const molfile = `
+  Mrv2308 02172612172D          
+
+  0  0  0     0  0            999 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 7 7 0 0 0
+M  V30 BEGIN ATOM
+M  V30 1 C -1.3959 1.7901 0 0
+M  V30 2 C -2.7295 1.0201 0 0
+M  V30 3 C -2.7295 -0.5201 0 0
+M  V30 4 C -1.3959 -1.2901 0 0
+M  V30 5 C -0.0622 -0.5201 0 0
+M  V30 6 C -0.0622 1.0201 0 0
+M  V30 7 R# -1.396 3.3301 0 0 RGROUPS=(1 1)
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 2 1 2
+M  V30 2 1 2 3
+M  V30 3 2 3 4
+M  V30 4 1 4 5
+M  V30 5 2 5 6
+M  V30 6 1 6 1
+M  V30 7 1 1 7
+M  V30 END BOND
+M  V30 END CTAB
+M  END`;
+
+  const molecule = Molecule.fromMolfile(molfile);
+  expect(molecule.getAllAtoms()).toBe(7);
+
+  expect(molecule.getAtomCustomLabel(6)).toBe('R1');
+  expect(molecule.getAtomicNo(6)).toBe(0);
+  expect(molecule.getAtomLabel(6)).toBe('?');
+});

src/com/actelion/research/gwt/jre/java/util/regex/Matcher.java

@@ -1,11 +1,28 @@
 package java.util.regex;
 
 import org.cheminfo.utils.JSException;
+import org.cheminfo.utils.JSRegexMatcher;
+import org.cheminfo.utils.JSRegexMatchResult;
 
 public class Matcher {
+  private JSRegexMatcher jsMatcher;
+  // To simplify emulation for now, `find` can only be called once.
+  private boolean wasCalled = false;
+  private JSRegexMatchResult matchResult = null;
+
+  public Matcher(JSRegexMatcher matcher) {
+    this.jsMatcher = matcher;
+  }
+
   public boolean find() {
-    JSException.throwUnimplemented();
-    return false;
+    if (wasCalled) {
+      JSException.throwError("find was already called on this matcher");
+      return false;
+    } else {
+      wasCalled = true;
+      matchResult = this.jsMatcher.find();
+      return matchResult != null;
+    }
   }
 
   public boolean find(int start) {
@@ -19,7 +36,6 @@ public MatchResult toMatchResult() {
   }
 
   public String group(int group) {
-    JSException.throwUnimplemented();
-    return null;
+    return matchResult.group(group);
   }
 }

src/com/actelion/research/gwt/jre/java/util/regex/Pattern.java

@@ -1,17 +1,27 @@
 package java.util.regex;
 
 import org.cheminfo.utils.JSException;
+import org.cheminfo.utils.JSRegexMatcher;
+import org.cheminfo.utils.JSRegexPattern;
 
 public class Pattern {
-  public Pattern() {}
+  private JSRegexPattern jsPattern;
 
-  public static Pattern compile(String p) {
-    JSException.throwUnimplemented();
-    return null;
+  private Pattern(JSRegexPattern jsPattern) {
+    this.jsPattern = jsPattern;
+  }
+
+  public static Pattern compile(String p) throws PatternSyntaxException {
+    JSRegexPattern jsPattern = JSRegexPattern.compile(p);
+    if (jsPattern == null) {
+      throw new PatternSyntaxException("invalid JS RegExp: " + p);
+    } else {
+      return new Pattern(jsPattern);
+    }
   }
 
   public Matcher matcher(String input) {
-    JSException.throwUnimplemented();
-    return null;
+    JSRegexMatcher jsMatcher = this.jsPattern.getMatcher(input);
+    return new Matcher(jsMatcher);
   }
 }

src/com/actelion/research/gwt/jre/java/util/regex/PatternSyntaxException.java

@@ -0,0 +1,9 @@
+package java.util.regex;
+
+import java.lang.IllegalArgumentException;
+
+public class PatternSyntaxException extends IllegalArgumentException {
+  public PatternSyntaxException(String desc) {
+    super(desc);
+  }
+}

src/com/actelion/research/gwt/utils/org/cheminfo/utils/JSRegexMatchResult.java

@@ -0,0 +1,20 @@
+package org.cheminfo.utils;
+
+import com.google.gwt.core.client.JavaScriptObject;
+
+public class JSRegexMatchResult {
+  private JavaScriptObject jsResult;
+
+  public JSRegexMatchResult(JavaScriptObject jsResult) {
+    this.jsResult = jsResult;
+  }
+
+  public String group(int group) {
+    return groupNative(jsResult, group);
+  }
+
+  public native String groupNative(JavaScriptObject result, int group)
+  /*-{
+    return result[group] || null;
+  }-*/;
+}

src/com/actelion/research/gwt/utils/org/cheminfo/utils/JSRegexMatcher.java

@@ -0,0 +1,27 @@
+package org.cheminfo.utils;
+
+import com.google.gwt.core.client.JavaScriptObject;
+
+public class JSRegexMatcher {
+  private JavaScriptObject regex;
+  private String input;
+
+  public JSRegexMatcher(JavaScriptObject regex, String input) {
+    this.regex = regex;
+    this.input = input;
+  }
+
+  public JSRegexMatchResult find() {
+    JavaScriptObject result = findNative(regex, input);
+    if (result == null) {
+      return null;
+    } else {
+      return new JSRegexMatchResult(result);
+    }
+  }
+
+  public native JavaScriptObject findNative(JavaScriptObject regex, String input)
+  /*-{
+    return regex.exec(input);
+  }-*/;
+}

src/com/actelion/research/gwt/utils/org/cheminfo/utils/JSRegexPattern.java

@@ -0,0 +1,33 @@
+package org.cheminfo.utils;
+
+import com.google.gwt.core.client.JavaScriptObject;
+
+public class JSRegexPattern {
+  private JavaScriptObject regex;
+
+  private JSRegexPattern(JavaScriptObject regex) {
+    this.regex = regex;
+  }
+
+  public static JSRegexPattern compile(String pattern)  {
+    JavaScriptObject regex = compileNative(pattern);
+    if (regex == null) {
+      return null;
+    } else {
+      return new JSRegexPattern(regex);
+    }
+  }
+
+  private native static JavaScriptObject compileNative(String pattern)
+  /*-{
+    try {
+      return new RegExp(pattern);
+    } catch (err) {
+      return null;
+    }
+  }-*/;
+
+  public JSRegexMatcher getMatcher(String input) {
+    return new JSRegexMatcher(this.regex, input);
+  }
+}