feat: update OCL to v2023.4.0

cheminfo · Apr 5, 2023 · a886ff4 · a886ff4
1 parent 9da9811
commit a886ff4
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Showing 45 changed files with 2,453 additions and 1,736 deletions.
diff --git a/__tests__/__snapshots__/conformers.js.snap b/__tests__/__snapshots__/conformers.js.snap
@@ -1,25 +1,25 @@
 // Jest Snapshot v1, https://goo.gl/fbAQLP
 
 exports[`ConformerGenerator should generate conformers 1`] = `
-"
+"#1
 Actelion Java MolfileCreator 1.0
 
  15 14  0  0  0  0  0  0  0  0999 V2000
-    0.0209   -2.5358    6.9912 C   0  0  0  0  0  0  0  0  0  0  0  0
-    0.4019   -1.6934    5.6364 O   0  0  0  0  0  0  0  0  0  0  0  0
-    0.2666   -0.0439    5.7657 C   0  0  0  0  0  0  0  0  0  0  0  0
-    0.7123    0.7908    4.2081 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -0.4234    0.4480    3.0453 O   0  0  0  0  0  0  0  0  0  0  0  0
-   -0.1832    1.1036    1.6138 N   0  0  0  0  0  0  0  0  0  0  0  0
-   -0.9350   -2.1387    7.5082 H   0  0  0  0  0  0  0  0  0  0  0  0
-    0.8873   -2.5457    7.7647 H   0  0  0  0  0  0  0  0  0  0  0  0
-   -0.1686   -3.6460    6.6492 H   0  0  0  0  0  0  0  0  0  0  0  0
-   -0.8241    0.2442    6.0545 H   0  0  0  0  0  0  0  0  0  0  0  0
-    0.9037    0.3671    6.6327 H   0  0  0  0  0  0  0  0  0  0  0  0
-    0.7892    1.9248    4.3812 H   0  0  0  0  0  0  0  0  0  0  0  0
-    1.7629    0.4125    3.8524 H   0  0  0  0  0  0  0  0  0  0  0  0
-    0.7009    0.8284    1.1579 H   0  0  0  0  0  0  0  0  0  0  0  0
-   -0.9561    0.8636    0.9815 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -4.5770    2.5000   -2.1185 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.9333    3.2322   -3.4776 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.8935    2.1799   -4.2575 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.2507    2.2660   -3.4812 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.3324    1.6314   -1.9352 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.4253   -0.0302   -2.0151 N   0  0  0  0  0  0  0  0  0  0  0  0
+   -5.2007    1.5768   -2.4320 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.7235    2.1678   -1.4110 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -5.2609    3.2524   -1.5646 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.8052    2.4732   -5.3736 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.3008    1.1001   -4.1756 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.9084    3.3711   -3.4304 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.4952    1.6598   -4.1123 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.7255   -0.4000   -1.1042 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.5034   -0.4157   -2.2514 H   0  0  0  0  0  0  0  0  0  0  0  0
   1  2  1  0  0  0  0
   2  3  1  0  0  0  0
   3  4  1  0  0  0  0
@@ -39,25 +39,25 @@ M  END
 `;
 
 exports[`ConformerGenerator should generate conformers 2`] = `
-"
+"#2
 Actelion Java MolfileCreator 1.0
 
  15 14  0  0  0  0  0  0  0  0999 V2000
-    1.9089   -2.2937    5.8792 C   0  0  0  0  0  0  0  0  0  0  0  0
-    0.4019   -1.6934    5.6364 O   0  0  0  0  0  0  0  0  0  0  0  0
-    0.2666   -0.0439    5.7657 C   0  0  0  0  0  0  0  0  0  0  0  0
-    0.7123    0.7908    4.2081 C   0  0  0  0  0  0  0  0  0  0  0  0
-    0.5603    2.4347    4.3914 O   0  0  0  0  0  0  0  0  0  0  0  0
-    1.7021    3.1562    5.2356 N   0  0  0  0  0  0  0  0  0  0  0  0
-    2.4428   -1.8047    6.7817 H   0  0  0  0  0  0  0  0  0  0  0  0
-    2.5852   -2.1850    4.9413 H   0  0  0  0  0  0  0  0  0  0  0  0
-    1.7771   -3.4431    6.0962 H   0  0  0  0  0  0  0  0  0  0  0  0
-   -0.8241    0.2442    6.0545 H   0  0  0  0  0  0  0  0  0  0  0  0
-    0.9037    0.3671    6.6327 H   0  0  0  0  0  0  0  0  0  0  0  0
-    1.7868    0.5114    3.9093 H   0  0  0  0  0  0  0  0  0  0  0  0
-   -0.0017    0.4248    3.3540 H   0  0  0  0  0  0  0  0  0  0  0  0
-    2.6525    3.0566    4.8460 H   0  0  0  0  0  0  0  0  0  0  0  0
-    1.4966    4.1586    5.3228 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -5.4499    3.1652   -4.1799 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.9333    3.2322   -3.4776 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.8935    2.1799   -4.2575 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.2507    2.2660   -3.4812 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.5676    3.7618   -3.7899 O   0  0  0  0  0  0  0  0  0  0  0  0
+    0.9379    3.8478   -3.0815 N   0  0  0  0  0  0  0  0  0  0  0  0
+   -5.3836    3.5091   -5.2830 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -5.8544    2.0819   -4.1363 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -6.1706    3.8654   -3.6045 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.8052    2.4732   -5.3736 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.3008    1.1001   -4.1756 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.5761    1.4326   -3.9186 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.3564    2.1134   -2.3401 H   0  0  0  0  0  0  0  0  0  0  0  0
+    1.2462    4.8280   -3.0515 H   0  0  0  0  0  0  0  0  0  0  0  0
+    1.6088    3.2972   -3.6302 H   0  0  0  0  0  0  0  0  0  0  0  0
   1  2  1  0  0  0  0
   2  3  1  0  0  0  0
   3  4  1  0  0  0  0

diff --git a/__tests__/__snapshots__/force-field-mmff94.js.snap b/__tests__/__snapshots__/force-field-mmff94.js.snap
@@ -1,25 +1,25 @@
 // Jest Snapshot v1, https://goo.gl/fbAQLP
 
 exports[`ForceFieldMMFF94 should generate force field 1`] = `
-"
+"#1
 Actelion Java MolfileCreator 1.0
 
  15 14  0  0  0  0  0  0  0  0999 V2000
-    0.3531   -2.1287    6.8340 C   0  0  0  0  0  0  0  0  0  0  0  0
-    0.6562   -1.5101    5.5910 O   0  0  0  0  0  0  0  0  0  0  0  0
-    0.2639   -0.1332    5.5764 C   0  0  0  0  0  0  0  0  0  0  0  0
-    0.6454    0.4978    4.2405 C   0  0  0  0  0  0  0  0  0  0  0  0
-    2.0674    0.6836    4.2007 O   0  0  0  0  0  0  0  0  0  0  0  0
-    2.4060    1.3845    2.9656 N   0  0  0  0  0  0  0  0  0  0  0  0
-   -0.7236   -2.0955    7.0261 H   0  0  0  0  0  0  0  0  0  0  0  0
-    0.8967   -1.6395    7.6479 H   0  0  0  0  0  0  0  0  0  0  0  0
-    0.6670   -3.1747    6.7838 H   0  0  0  0  0  0  0  0  0  0  0  0
-   -0.8220   -0.0770    5.7099 H   0  0  0  0  0  0  0  0  0  0  0  0
-    0.7633    0.3915    6.3988 H   0  0  0  0  0  0  0  0  0  0  0  0
-    0.3480   -0.1520    3.4095 H   0  0  0  0  0  0  0  0  0  0  0  0
-    0.1551    1.4736    4.1458 H   0  0  0  0  0  0  0  0  0  0  0  0
-    3.0103    2.1262    3.3223 H   0  0  0  0  0  0  0  0  0  0  0  0
-    3.0309    0.7055    2.5268 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -4.3423    2.6153   -2.3397 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.8783    2.9630   -3.6364 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.8566    2.0874   -4.1292 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.4746    2.4010   -3.5536 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.0233    3.6899   -3.9928 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.2808    3.5370   -5.2408 N   0  0  0  0  0  0  0  0  0  0  0  0
+   -4.7361    1.5945   -2.3324 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.5480    2.7187   -1.5962 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -5.1522    3.2997   -2.0724 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.8395    2.2197   -5.2160 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.1330    1.0464   -3.9263 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.7528    1.6241   -3.8346 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.5055    2.4375   -2.4612 H   0  0  0  0  0  0  0  0  0  0  0  0
+    0.5834    4.0318   -5.0129 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.8047    4.1683   -5.8509 H   0  0  0  0  0  0  0  0  0  0  0  0
   1  2  1  0  0  0  0
   2  3  1  0  0  0  0
   3  4  1  0  0  0  0

diff --git a/__tests__/__snapshots__/library.js.snap b/__tests__/__snapshots__/library.js.snap
@@ -9,7 +9,6 @@ exports[`prototype properties of ConformerGenerator 1`] = `
   "getOCL",
   "getOneConformerAsMolecule",
   "getPotentialConformerCount",
-  "getPreviousConformerContribution",
   "initializeConformers",
   "molecules",
 ]

diff --git a/__tests__/__snapshots__/reaction.js.snap b/__tests__/__snapshots__/reaction.js.snap
@@ -4,7 +4,7 @@ exports[`Reaction class should load and create RXN files 1`] = `
 "$RXN
 
 
-OCL_RXN_V1.0:gJX@@eKU@@ gGQHDHaInfh@!gJX@@eKU@@ fHdP@@##!ROvp@[C}c@FNZz@@ !R_\`CW?Hc|_\`BH_Ykh@@ !ROvp@[C}c@FNZz@@ !RGP@@##
+OCL_RXN_V1.0:gGQHDHaInfh@ gJX@@eKU@@!gJX@@eKU@@ fHdP@@##!R_\`CW?Hc|_\`BH_Ykh@@ !ROvp@[C}c@FNZz@@ !ROvp@[C}c@FNZz@@ !RGP@@##
   2  2
 $MOL
 CC(C)C(=O)Cl.CCNCC>>CCNCC.Cl

diff --git a/__tests__/conformers.js b/__tests__/conformers.js
@@ -24,13 +24,11 @@ describe('ConformerGenerator', () => {
     const gen = new ConformerGenerator(1);
     expect(gen.getPotentialConformerCount()).toBe(1);
     expect(gen.getConformerCount()).toBe(0);
-    expect(gen.getPreviousConformerContribution()).toBe(1);
     gen.initializeConformers(mol);
     expect(gen.getPotentialConformerCount()).toBeGreaterThan(1);
 
     const conf1 = gen.getNextConformerAsMolecule();
     expect(gen.getConformerCount()).toBe(1);
-    expect(gen.getPreviousConformerContribution()).toBeCloseTo(0.17, 2);
     const conf1Molfile = conf1.toMolfile();
     expect(conf1Molfile).toMatchSnapshot();
 

diff --git a/openchemlib b/openchemlib
diff --git a/scripts/openchemlib/classes.js b/scripts/openchemlib/classes.js
@@ -25,6 +25,15 @@ const changed = [
     '@org/openmolecules/chem/conf/gen/ConformerSetDiagnostics',
     changeConformerSetDiagnostics,
   ],
+  ['@org/openmolecules/chem/conf/gen/BaseConformer', changeBaseConformer],
+  [
+    '@org/openmolecules/chem/conf/gen/ConformerGenerator',
+    changeConformerGenerator,
+  ],
+  [
+    '@org/openmolecules/chem/conf/so/SelfOrganizedConformer',
+    changeSelfOrganizedConformer,
+  ],
   ['@org/openmolecules/chem/conf/gen/RigidFragmentCache', removeCacheIO],
   ['chem/ChemistryHelper', removePrintf],
   ['chem/Coordinates', removeToStringSpaceDelimited],
@@ -244,38 +253,63 @@ function removeToStringSpaceDelimited(code) {
   return code.replaceAll(methodRegExp('toStringSpaceDelimited'), '');
 }
 
+function replaceChecked(code, from, to) {
+  if (code.indexOf(from) === -1) {
+    throw new Error(`Cannot find ${from} in code`);
+  }
+  return code.replace(from, to);
+}
+
+function removeSlice(code, start, end) {
+  const startIdx = code.indexOf(start);
+  if (startIdx === -1) {
+    throw new Error(`did not find index for: ${start}`);
+  }
+  const endIdx = code.indexOf(end, startIdx + start.length);
+  if (endIdx === -1) {
+    throw new Error(`did not find index for: ${end}`);
+  }
+  return code.substr(0, startIdx) + code.substr(endIdx + end.length);
+}
+
 function changeInventorFragment(code) {
-  return code.replace(
+  return replaceChecked(
+    code,
     'mGlobalAtom.clone();',
     'Arrays.copyOf(mGlobalAtom, mGlobalAtom.length);',
   );
 }
 
 function removeCloneInfos(code) {
-  return code.replace(
+  return replaceChecked(
+    code,
     'infos[a] = m.infos[i].clone();',
     '// infos[a] = m.infos[i].clone();',
   );
 }
 
 function changeTautomerHelper(code) {
-  code = code.replace(
+  code = replaceChecked(
+    code,
     'import java.util',
     'import java.util.Arrays;\nimport java.util',
   );
-  code = code.replace(
+  code = replaceChecked(
+    code,
     'mRegionDCount.clone();',
     'Arrays.copyOf(mRegionDCount, mRegionDCount.length);',
   );
-  code = code.replace(
+  code = replaceChecked(
+    code,
     'mRegionTCount.clone();',
     'Arrays.copyOf(mRegionTCount, mRegionTCount.length);',
   );
   return code;
 }
 
 function changeTextDrawingObject(code) {
-  return code.replace(
+  return replaceChecked(
+    code,
     'detail.append(String.format(" size=\\"%.4f\\"", new Double(mSize)));',
     'detail.append(" size=\\""+mSize+"\\"");',
   );
@@ -296,7 +330,7 @@ function changeGenericEditorArea(code) {
 }
 
 function changeCustomAtomDialogBuilder(code) {
-  code = code.replace('e.getSource() instanceof JTextField', 'false');
+  code = replaceChecked(code, 'e.getSource() instanceof JTextField', 'false');
   return code;
 }
 
@@ -314,28 +348,25 @@ function changeIntVec(code) {
   return code;
 }
 
-function removeSlice(code, start, end) {
-  const startIdx = code.indexOf(start);
-  if (startIdx === -1) {
-    throw new Error(`did not find index for: ${start}`);
-  }
-  const endIdx = code.indexOf(end, startIdx + start.length);
-  if (endIdx === -1) {
-    throw new Error(`did not find index for: ${end}`);
-  }
-  return code.substr(0, startIdx) + code.substr(endIdx + end.length);
-}
-
 function removeRXNStringFormat(code) {
-  return code.replace(
+  return replaceChecked(
+    code,
     'theWriter.write(String.format("M  V30 COUNTS %d %d"+NL,rcnt,pcnt));',
     'theWriter.write("M  V30 COUNTS "+rcnt+" "+pcnt+NL,rcnt,pcnt);',
   );
 }
 
 function changeMolecule(code) {
-  code = code.replace('stream.writeLong(mAtomQueryFeatures[atom]);', '');
-  code = code.replace('mAtomQueryFeatures[atom] = stream.readLong();', '');
+  code = replaceChecked(
+    code,
+    'stream.writeLong(mAtomQueryFeatures[atom]);',
+    '',
+  );
+  code = replaceChecked(
+    code,
+    'mAtomQueryFeatures[atom] = stream.readLong();',
+    '',
+  );
   return code;
 }
 
@@ -393,7 +424,8 @@ private void init(int mode) {
 `;
 
 function changeTorsionDB(code) {
-  code = code.replace(
+  code = replaceChecked(
+    code,
     'util.TreeMap;',
     'util.TreeMap;\nimport com.actelion.research.chem.conf.TorsionDBData;',
   );
@@ -442,7 +474,8 @@ private static void initialize() {
 `;
 
 function changeBondLengthSet(code) {
-  code = code.replace(
+  code = replaceChecked(
+    code,
     'chem.StereoMolecule;',
     'chem.StereoMolecule;\nimport com.actelion.research.chem.conf.TorsionDBData;',
   );
@@ -466,6 +499,58 @@ function changeConformerSetDiagnostics(code) {
   return code;
 }
 
+function changeBaseConformer(code) {
+  code = replaceChecked(
+    code,
+    'import java.util.ArrayList;',
+    'import java.util.Arrays;\nimport java.util.ArrayList;',
+  );
+  code = replaceChecked(
+    code,
+    'mTorsion[bondIndex] = rotatableBond[bondIndex].getDefaultTorsions().clone();',
+    'short[] torsions = rotatableBond[bondIndex].getDefaultTorsions();\n			mTorsion[bondIndex] = Arrays.copyOf(torsions, torsions.length);',
+  );
+  code = replaceChecked(
+    code,
+    'mFrequency[bondIndex] = rotatableBond[bondIndex].getDefaultFrequencies().clone();',
+    'short[] frequencies = rotatableBond[bondIndex].getDefaultFrequencies();\n			mFrequency[bondIndex] = Arrays.copyOf(frequencies, frequencies.length);',
+  );
+  code = replaceChecked(
+    code,
+    '\n			mTorsion[bondIndex] = rotatableBond[bondIndex].getDefaultTorsions().clone();',
+    '',
+  );
+  return code;
+}
+
+function changeConformerGenerator(code) {
+  code = replaceChecked(
+    code,
+    'fragmentPermutation.clone()',
+    'Arrays.copyOf(fragmentPermutation, fragmentPermutation.length)',
+  );
+  return code;
+}
+
+function changeSelfOrganizedConformer(code) {
+  code = replaceChecked(
+    code,
+    'import java.util.ArrayList;',
+    'import java.util.Arrays;\nimport java.util.ArrayList;',
+  );
+  code = replaceChecked(
+    code,
+    'conformer.mAtomStrain.clone()',
+    'Arrays.copyOf(conformer.mAtomStrain, conformer.mAtomStrain.length)',
+  );
+  code = replaceChecked(
+    code,
+    'conformer.mRuleStrain.clone()',
+    'Arrays.copyOf(conformer.mRuleStrain, conformer.mRuleStrain.length)',
+  );
+  return code;
+}
+
 function removeCacheIO(code) {
   code = removeSlice(
     code,
@@ -503,8 +588,13 @@ function removeCacheIO(code) {
 }
 
 function changeCsv(code) {
-  code = code.replace('java.io.InputStreamReader;', 'java.io.StringReader;');
-  code = code.replace(
+  code = replaceChecked(
+    code,
+    'java.io.InputStreamReader;',
+    'java.io.StringReader;',
+  );
+  code = replaceChecked(
+    code,
     'br = new BufferedReader(new InputStreamReader(Csv.class.getResourceAsStream(path)));',
     'br = new BufferedReader(new StringReader(path));',
   );