Merge pull request #955 from papillot/v3000

V3000 support
nglviewer · Jan 20, 2023 · 3f0fd8e · 3f0fd8e
2 parents 29f89f7 + db6b3b5
commit 3f0fd8e
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Showing 3 changed files with 266 additions and 25 deletions.
diff --git a/src/parser/sdf-parser.ts b/src/parser/sdf-parser.ts
@@ -43,37 +43,74 @@ class SdfParser extends StructureParser {
     const ap2 = s.getAtomProxy()
 
     let idx = 0
-    let lineNo = 0
+    let lineNo = 0  // for V2000: current line number in currently parsed Mol file
     let modelIdx = 0
     let modelAtomIdxStart = 0
 
     const sdfData: {[k: string]: string[]}[] = []
     let currentItem: string|boolean = false
     let currentData: {[k: string]: string[]} = {}
-    let mItem
+    let mItem: RegExpMatchArray | null
     s.extraData.sdf = sdfData
 
-    let atomCount, bondCount, atomStart: number, atomEnd: number, bondStart: number, bondEnd: number
+    let atomCount, bondCount, atomStart: number, atomEnd: number, bondStart: number, bondEnd: number, x: number, y: number, z: number, atomname: string, element: string, atomindex: number, order: number
+    let isV3000 = false, isAtomBlock = false, isBondBlock = false
+    let tokens: string[] = [], acc: string[] = []
+    const atomindexToStoreindex = new Map<number, number>()
 
     function _parseChunkOfLines (_i: number, _n: number, lines: string[]) {
       for (let i = _i; i < _n; ++i) {
         const line = lines[ i ]
 
+        if (isV3000 && line) {
+          tokens = line.substring(7).split(' ')
+
+          // Entity properties may extend over multiple lines (hanging line finishes with '-')
+          // Tokens are accumulated to be processed at the same time for a given entity
+          if (acc.length) {
+            tokens = [...acc, ...tokens]
+            acc = []
+          }
+          if (tokens[tokens.length - 1] === '-') {
+            tokens.pop();
+            acc = tokens;
+            continue;
+          }
+        }
+
         if (line.substr(0, 4) === '$$$$') {
           lineNo = -1
           ++modelIdx
           modelAtomIdxStart = atomStore.count
           sdfData.push(currentData)
           currentData = {}
           currentItem = false
+          isV3000 = false
         } else if (lineNo === 3) {
-          atomCount = parseInt(line.substr(0, 3))
-          bondCount = parseInt(line.substr(3, 3))
+          isV3000 = line.indexOf(' V3000') > -1
+
+          if (isV3000) {
+            atomindexToStoreindex.clear()
+          } else {
+
+            atomCount = parseInt(line.substr(0, 3))
+            bondCount = parseInt(line.substr(3, 3))
 
-          atomStart = 4
-          atomEnd = atomStart + atomCount
-          bondStart = atomEnd
-          bondEnd = bondStart + bondCount
+            atomStart = 4
+            atomEnd = atomStart + atomCount
+            bondStart = atomEnd
+            bondEnd = bondStart + bondCount
+
+            if (asTrajectory) {
+              currentCoord = 0
+              currentFrame = new Float32Array(atomCount * 3)
+              frames.push(currentFrame)
+
+              if (modelIdx > 0) doFrames = true
+            }
+          }
+        } else if (isV3000 && tokens[0] === 'COUNTS') {
+          atomCount = parseInt(tokens[1]);
 
           if (asTrajectory) {
             currentCoord = 0
@@ -82,12 +119,45 @@ class SdfParser extends StructureParser {
 
             if (modelIdx > 0) doFrames = true
           }
-        } else if (lineNo >= atomStart && lineNo < atomEnd) {
+        } else if (isV3000 && tokens.length == 2) {
+          if (tokens[1] === 'ATOM') {
+            if (tokens[0] === 'BEGIN') isAtomBlock = true
+            else if (tokens[0] === 'END') isAtomBlock = false
+          } else if (tokens[1] === 'BOND') {
+            if (tokens[0] === 'BEGIN') isBondBlock = true
+            else if (tokens[0] === 'END') isBondBlock = false
+          }
+        } else if (
+          isAtomBlock 
+          || (!isV3000 && lineNo >= atomStart && lineNo < atomEnd)
+        ) {
           if (firstModelOnly && modelIdx > 0) continue
 
-          const x = parseFloat(line.substr(0, 10))
-          const y = parseFloat(line.substr(10, 10))
-          const z = parseFloat(line.substr(20, 10))
+          let charge = 0
+          if (isV3000) {
+            x = parseFloat(tokens[2])
+            y = parseFloat(tokens[3])
+            z = parseFloat(tokens[4])
+
+            element = tokens[1]
+            atomindex = parseInt(tokens[0])
+            atomindexToStoreindex.set(atomindex, idx)
+            atomname = element + atomindex
+
+            if (tokens.length > 6) {
+              let chgTok = tokens.slice(6).find(t => t.indexOf('CHG=') === 0);
+              if (chgTok) {
+                charge = parseInt(chgTok.substring(4))
+              }
+            }
+          } else {
+            x = parseFloat(line.substr(0, 10))
+            y = parseFloat(line.substr(10, 10))
+            z = parseFloat(line.substr(20, 10))
+
+            element = line.substr(31, 3).trim()
+            atomname = element + (idx - modelAtomIdxStart + 1)
+          }
 
           if (asTrajectory) {
             const j = currentCoord * 3
@@ -101,31 +171,37 @@ class SdfParser extends StructureParser {
             if (doFrames) continue
           }
 
-          const element = line.substr(31, 3).trim()
-          const atomname = element + (idx - modelAtomIdxStart + 1)
-
           atomStore.growIfFull()
           atomStore.atomTypeId[ idx ] = atomMap.add(atomname, element)
 
           atomStore.x[ idx ] = x
           atomStore.y[ idx ] = y
           atomStore.z[ idx ] = z
-          atomStore.serial[ idx ] = idx
-          atomStore.formalCharge[ idx ] = 0
+          atomStore.serial[ idx ] = isV3000 ? atomindex : idx
+          atomStore.formalCharge[ idx ] = charge
 
           sb.addAtom(modelIdx, '', '', 'HET', 1, 1)
 
           idx += 1
-        } else if (lineNo >= bondStart && lineNo < bondEnd) {
+        } else if (
+          isBondBlock 
+          || (!isV3000 && lineNo >= bondStart && lineNo < bondEnd)
+        ) {
           if (firstModelOnly && modelIdx > 0) continue
           if (asTrajectory && modelIdx > 0) continue
 
-          ap1.index = parseInt(line.substr(0, 3)) - 1 + modelAtomIdxStart
-          ap2.index = parseInt(line.substr(3, 3)) - 1 + modelAtomIdxStart
-          const order = parseInt(line.substr(6, 3))
+          if (isV3000) {
+            ap1.index = atomindexToStoreindex.get(parseInt(tokens[2]))
+            ap2.index = atomindexToStoreindex.get(parseInt(tokens[3]))
+            order = parseInt(tokens[1])
+          } else {
+            ap1.index = parseInt(line.substr(0, 3)) - 1 + modelAtomIdxStart
+            ap2.index = parseInt(line.substr(3, 3)) - 1 + modelAtomIdxStart
+            order = parseInt(line.substr(6, 3))
+          }
 
           s.bondStore.addBond(ap1, ap2, order)
-        } else if (line.match(/M {2}CHG/)) {
+        } else if (line.substr(0, 6) === 'M  CHG') {
           const chargeCount = parseInt(line.substr(6, 3))
           for (let ci = 0, coffset = 10; ci < chargeCount; ++ci, coffset += 8) {
             const aToken = parseInt(line.substr(coffset, 3))
@@ -134,7 +210,7 @@ class SdfParser extends StructureParser {
             atomStore.formalCharge[ atomIdx ] = cToken
           }
         // eslint-disable-next-line no-cond-assign
-        } else if (mItem = line.match(reItem)) {
+        } else if (line.charAt(0) === '>' && (mItem = line.match(reItem))) {
           currentItem = mItem[ 1 ]
           currentData[ currentItem ] = []
         } else if (currentItem !== false && line) {

diff --git a/test/data/v3000.sdf b/test/data/v3000.sdf
@@ -0,0 +1,130 @@
+
+  SciTegic04161911273D
+
+  0  0  0  0  0  0            999 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 23 24 0 0 0
+M  V30 BEGIN ATOM
+M  V30 1 C 3.69653 -0.53111 -0.07569 0
+M  V30 2 N 4.83107 -1.1738 0.63455 0
+M  V30 3 O 2.48284 -1.4333 -0.00289 0
+M  V30 4 C 4.08798 -0.11703 -1.56721 0
+M  V30 5 C 4.71272 -2.28965 1.40283 0
+M  V30 6 N 6.07017 -0.66124 0.69861 0
+M  V30 7 C 1.20743 -0.69735 -0.00008 0
+M  V30 8 C 4.42492 -1.30971 -2.54228 0
+M  V30 9 O 2.98159 0.67208 -2.19303 0
+M  V30 10 N 5.94489 -2.48273 1.97545 0
+M  V30 11 C 6.77991 -1.48028 1.54171 0
+M  V30 12 C 1.20809 0.69256 0.00012 0
+M  V30 13 C 0.00395 -1.39238 -0.00028 0
+M  V30 14 C 4.79438 -0.70993 -3.90963 0
+M  V30 15 C 3.20101 -2.22546 -2.73765 0
+M  V30 16 C 5.61846 -2.15207 -2.05702 0
+M  V30 17 C 0.00465 1.38756 0.00012 0
+M  V30 18 C -1.19951 -0.69741 -0.00028 0
+M  V30 19 C -1.19887 0.69232 -0.00008 0
+M  V30 20 C -2.5099 1.45264 -0.00006 0
+M  V30 21 N -2.74496 2.76473 -0.00015 0 -
+M  V30 CHG=1
+M  V30 22 C -1.69103 3.82223 -0.00033 0
+M  V30 23 O -4.08697 3.18583 -0.0001 0 CHG=-1
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 1 1 2
+M  V30 2 1 1 3
+M  V30 3 1 1 4
+M  V30 4 1 2 5
+M  V30 5 1 2 6
+M  V30 6 1 3 7
+M  V30 7 1 4 8
+M  V30 8 1 4 9
+M  V30 9 2 5 10
+M  V30 10 2 6 11
+M  V30 11 1 7 12
+M  V30 12 2 7 13
+M  V30 13 1 8 14
+M  V30 14 1 8 15
+M  V30 15 1 8 16
+M  V30 16 2 12 17
+M  V30 17 1 13 18
+M  V30 18 1 17 19
+M  V30 19 1 19 20
+M  V30 20 2 20 21
+M  V30 21 1 21 22
+M  V30 22 1 21 23
+M  V30 23 1 10 11
+M  V30 24 2 18 19
+M  V30 END BOND
+M  V30 END CTAB
+M  END
+> <IDNUMBER>
+BAS 0003964
+
+> <CLUSTER>
+19849
+
+> <CL_SIZE>
+1
+
+> <CL_VAR>
+0.0000
+
+$$$$
+CHEBI:57262
+     RDKit          3D
+
+  0  0  0  0  0  0  0  0  0  0999 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 22 21 0 0 0
+M  V30 BEGIN ATOM
+M  V30 1 P 18.2567 -5.6825 0 0
+M  V30 2 O 18.0395 -6.6275 0 0 CHG=-1
+M  V30 3 O 18.255 -4.7415 0 0
+M  V30 4 O 18.9453 -6.0633 0 0
+M  V30 5 O 17.4245 -5.9341 0 0
+M  V30 6 C 15.2886 -5.4953 0 0
+M  V30 7 C 15.9989 -5.9147 0 0
+M  V30 8 C 16.7174 -5.5091 0 0
+M  V30 9 O 14.5702 -5.9009 0 0
+M  V30 10 C 13.8556 -5.4886 0 0
+M  V30 11 O 13.8553 -4.6636 0 0
+M  V30 12 O 15.9909 -6.7396 0 0
+M  V30 13 O 21.0888 -4.8258 0 0
+M  V30 14 C 21.0888 -5.6508 0 0
+M  V30 15 C 20.3743 -6.0633 0 0
+M  V30 16 N 20.3743 -6.8883 0 0 CHG=1
+M  V30 17 C 19.6598 -5.6508 0 0
+M  V30 18 O 21.8033 -6.0633 0 0 CHG=-1
+M  V30 19 R1 13.1411 -5.9011 0 0
+M  V30 20 C 15.2764 -7.1521 0 0
+M  V30 21 O 15.2764 -7.9771 0 0
+M  V30 22 R2 14.562 -6.7396 0 0
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 1 1 2
+M  V30 2 2 1 3
+M  V30 3 1 1 4
+M  V30 4 1 6 9
+M  V30 5 1 7 6 -
+M  V30 CFG=3
+M  V30 6 1 8 7
+M  V30 7 1 5 8
+M  V30 8 1 10 9
+M  V30 9 2 10 11
+M  V30 10 1 7 12
+M  V30 11 1 1 5
+M  V30 12 1 15 14 CFG=1
+M  V30 13 2 14 13
+M  V30 14 1 15 16
+M  V30 15 1 15 17
+M  V30 16 1 17 4
+M  V30 17 1 18 14
+M  V30 18 1 10 19
+M  V30 19 1 12 20
+M  V30 20 2 20 21
+M  V30 21 1 20 22
+M  V30 END BOND
+M  V30 END CTAB
+M  END
+$$$$
diff --git a/test/parser/tests-sdf-parser.spec.ts b/test/parser/tests-sdf-parser.spec.ts
@@ -7,7 +7,7 @@ import { join } from 'path'
 import * as fs from 'fs'
 
 describe('parser/sdf-parser', function () {
-  describe('parsing', function () {
+  describe('parsing V2000', function () {
     it('basic', function () {
       var file = join(__dirname, '/../data/01W_ideal.sdf')
       var str = fs.readFileSync(file, 'utf-8')
@@ -23,4 +23,39 @@ describe('parser/sdf-parser', function () {
       })
     })
   })
+
+  describe('parsing V3000', function () {
+    it('basic', function () {
+      var file = join(__dirname, '/../data/v3000.sdf')
+      var str = fs.readFileSync(file, 'utf-8')
+      var streamer = new StringStreamer(str)
+      var sdfParser = new SdfParser(streamer)
+      return sdfParser.parse().then(function (structure) {
+        expect(structure.modelStore.count).toBe(2)
+        expect(structure.atomCount).toBe(45)
+        expect(structure.bondCount).toBe(45)
+        expect(structure.atomStore.count).toBe(45)
+        expect(structure.atomStore.formalCharge).toBeTruthy()
+        expect(structure.bondStore.count).toBe(45)
+        expect(structure.atomStore.formalCharge[20]).toBe(1)
+        expect(structure.atomStore.formalCharge[22]).toBe(-1)
+        expect(structure.atomStore.formalCharge[24]).toBe(-1)
+        expect(structure.atomStore.formalCharge[25]).toBe(0)
+      })
+    })
+  })
+
+  describe('parsing mixed V2000/V3000 sdf file', function () {
+    it('basic', function () {
+      var file = join(__dirname, '/../data/v3000.sdf')
+      var str = fs.readFileSync(file, 'utf-8')
+      file = join(__dirname, '/../data/01W_ideal.sdf')
+      str = str.trimRight() + '\n' + fs.readFileSync(file, 'utf-8')
+      var streamer = new StringStreamer(str)
+      var sdfParser = new SdfParser(streamer)
+      return sdfParser.parse().then(function (structure) {
+        expect(structure.modelStore.count).toBe(3)
+      })
+    })
+  })
 })