Fix, read SDF multi-line values

src/mol-io/reader/_spec/sdf.spec.ts

@@ -2,7 +2,7 @@
 import { parseSdf } from '../sdf/parser';
 
 const SdfString = `
-  Mrv1718007121815122D          
+  Mrv1718007121815122D
 
   5  4  0  0  0  0            999 V2000
     0.0000    0.8250    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
@@ -129,7 +129,208 @@ Comp 2
 M  CHG  3   1  -1   3  -1   5  -1
 M  END
 > <DATABASE_ID>
-1`;
+1
+
+$$$$
+
+2244
+  -OEChem-04122119123D
+
+ 21 21  0     0  0  0  0  0  0999 V2000
+    1.2333    0.5540    0.7792 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.6952   -2.7148   -0.7502 O   0  0  0  0  0  0  0  0  0  0  0  0
+    0.7958   -2.1843    0.8685 O   0  0  0  0  0  0  0  0  0  0  0  0
+    1.7813    0.8105   -1.4821 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.0857    0.6088    0.4403 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.7927   -0.5515    0.1244 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.7288    1.8464    0.4133 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.1426   -0.4741   -0.2184 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.0787    1.9238    0.0706 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.7855    0.7636   -0.2453 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.1409   -1.8536    0.1477 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.1094    0.6715   -0.3113 C   0  0  0  0  0  0  0  0  0  0  0  0
+    3.5305    0.5996    0.1635 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.1851    2.7545    0.6593 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.7247   -1.3605   -0.4564 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.5797    2.8872    0.0506 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.8374    0.8238   -0.5090 H   0  0  0  0  0  0  0  0  0  0  0  0
+    3.7290    1.4184    0.8593 H   0  0  0  0  0  0  0  0  0  0  0  0
+    4.2045    0.6969   -0.6924 H   0  0  0  0  0  0  0  0  0  0  0  0
+    3.7105   -0.3659    0.6426 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.2555   -3.5916   -0.7337 H   0  0  0  0  0  0  0  0  0  0  0  0
+  1  5  1  0  0  0  0
+  1 12  1  0  0  0  0
+  2 11  1  0  0  0  0
+  2 21  1  0  0  0  0
+  3 11  2  0  0  0  0
+  4 12  2  0  0  0  0
+  5  6  1  0  0  0  0
+  5  7  2  0  0  0  0
+  6  8  2  0  0  0  0
+  6 11  1  0  0  0  0
+  7  9  1  0  0  0  0
+  7 14  1  0  0  0  0
+  8 10  1  0  0  0  0
+  8 15  1  0  0  0  0
+  9 10  2  0  0  0  0
+  9 16  1  0  0  0  0
+ 10 17  1  0  0  0  0
+ 12 13  1  0  0  0  0
+ 13 18  1  0  0  0  0
+ 13 19  1  0  0  0  0
+ 13 20  1  0  0  0  0
+M  END
+> <PUBCHEM_COMPOUND_CID>
+2244
+
+> <PUBCHEM_CONFORMER_RMSD>
+0.6
+
+> <PUBCHEM_CONFORMER_DIVERSEORDER>
+1
+11
+10
+3
+15
+17
+13
+5
+16
+7
+14
+9
+8
+4
+18
+6
+12
+2
+
+> <PUBCHEM_MMFF94_PARTIAL_CHARGES>
+18
+1 -0.23
+10 -0.15
+11 0.63
+12 0.66
+13 0.06
+14 0.15
+15 0.15
+16 0.15
+17 0.15
+2 -0.65
+21 0.5
+3 -0.57
+4 -0.57
+5 0.08
+6 0.09
+7 -0.15
+8 -0.15
+9 -0.15
+
+> <PUBCHEM_EFFECTIVE_ROTOR_COUNT>
+3
+
+> <PUBCHEM_PHARMACOPHORE_FEATURES>
+5
+1 2 acceptor
+1 3 acceptor
+1 4 acceptor
+3 2 3 11 anion
+6 5 6 7 8 9 10 rings
+
+> <PUBCHEM_HEAVY_ATOM_COUNT>
+13
+
+> <PUBCHEM_ATOM_DEF_STEREO_COUNT>
+0
+
+> <PUBCHEM_ATOM_UDEF_STEREO_COUNT>
+0
+
+> <PUBCHEM_BOND_DEF_STEREO_COUNT>
+0
+
+> <PUBCHEM_BOND_UDEF_STEREO_COUNT>
+0
+
+> <PUBCHEM_ISOTOPIC_ATOM_COUNT>
+0
+
+> <PUBCHEM_COMPONENT_COUNT>
+1
+
+> <PUBCHEM_CACTVS_TAUTO_COUNT>
+1
+
+> <PUBCHEM_CONFORMER_ID>
+000008C400000001
+
+> <PUBCHEM_MMFF94_ENERGY>
+39.5952
+
+> <PUBCHEM_FEATURE_SELFOVERLAP>
+25.432
+
+> <PUBCHEM_SHAPE_FINGERPRINT>
+1 1 18265615372930943622
+100427 49 16967750034970055351
+12138202 97 18271247217817981012
+12423570 1 16692715976000295083
+12524768 44 16753525617747228747
+12716758 59 18341332292274886536
+13024252 1 17968377969333732145
+14181834 199 17830728755827362645
+14614273 12 18262232214645093005
+15207287 21 17703787037639964108
+15775835 57 18340488876329928641
+16945 1 18271533103414939405
+193761 8 17907860604865584321
+20645476 183 17677348215414174190
+20871998 184 18198632231250704846
+21040471 1 18411412921197846465
+21501502 16 18123463883164380929
+23402539 116 18271795865171824860
+23419403 2 13539898140662769886
+23552423 10 18048876295495619569
+23559900 14 18272369794190581304
+241688 4 16179044415907240795
+257057 1 17478316999871287486
+2748010 2 18339085878070479087
+305870 269 18263645056784260212
+528862 383 18117272558388284091
+53812653 8 18410289211719108569
+7364860 26 17910392788380644719
+81228 2 18050568744116491203
+
+> <PUBCHEM_SHAPE_MULTIPOLES>
+244.06
+3.86
+2.45
+0.89
+1.95
+1.58
+0.15
+-1.85
+0.38
+-0.61
+-0.02
+0.29
+0.01
+-0.33
+
+> <PUBCHEM_SHAPE_SELFOVERLAP>
+513.037
+
+> <PUBCHEM_SHAPE_VOLUME>
+136
+
+> <PUBCHEM_COORDINATE_TYPE>
+2
+5
+10
+
+$$$$
+`;
 
 describe('sdf reader', () => {
     it('basic', async () => {
@@ -139,10 +340,11 @@ describe('sdf reader', () => {
         }
         const compound1 = parsed.result.compounds[0];
         const compound2 = parsed.result.compounds[1];
+        const compound3 = parsed.result.compounds[2];
         const { molFile, dataItems } = compound1;
         const { atoms, bonds } = molFile;
 
-        expect(parsed.result.compounds.length).toBe(2);
+        expect(parsed.result.compounds.length).toBe(3);
 
         // number of structures
         expect(atoms.count).toBe(5);
@@ -171,5 +373,11 @@ describe('sdf reader', () => {
 
         expect(compound1.dataItems.data.value(0)).toBe('0');
         expect(compound2.dataItems.data.value(0)).toBe('1');
+
+        expect(compound3.dataItems.dataHeader.value(2)).toBe('PUBCHEM_CONFORMER_DIVERSEORDER');
+        expect(compound3.dataItems.data.value(2)).toBe('1\n11\n10\n3\n15\n17\n13\n5\n16\n7\n14\n9\n8\n4\n18\n6\n12\n2');
+
+        expect(compound3.dataItems.dataHeader.value(21)).toBe('PUBCHEM_COORDINATE_TYPE');
+        expect(compound3.dataItems.data.value(21)).toBe('2\n5\n10');
     });
 });

src/mol-io/reader/sdf/parser.ts

@@ -1,7 +1,8 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
 import { Column } from '../../../mol-data/db';
@@ -27,21 +28,31 @@ function handleDataItems(tokenizer: Tokenizer): { dataHeader: Column<string>, da
     const dataHeader = TokenBuilder.create(tokenizer.data, 32);
     const data = TokenBuilder.create(tokenizer.data, 32);
 
-    let sawHeaderToken = false;
     while (tokenizer.position < tokenizer.length) {
         const line = Tokenizer.readLine(tokenizer);
         if (line.startsWith(delimiter)) break;
-        if (!!line) {
-            if (line.startsWith('> <')) {
-                TokenBuilder.add(dataHeader, tokenizer.tokenStart + 3, tokenizer.tokenEnd - 1);
-                sawHeaderToken = true;
-            } else if (sawHeaderToken) {
-                TokenBuilder.add(data, tokenizer.tokenStart, tokenizer.tokenEnd);
-                sawHeaderToken = false;
-                // TODO can there be multiline values?
+        if (!line) continue;
+
+        if (line.startsWith('> <')) {
+            TokenBuilder.add(dataHeader, tokenizer.tokenStart + 3, tokenizer.tokenEnd - 1);
+
+            Tokenizer.markLine(tokenizer);
+            const start = tokenizer.tokenStart;
+            let end = tokenizer.tokenEnd;
+            let added = false;
+            while (tokenizer.position < tokenizer.length) {
+                const line2 = Tokenizer.readLine(tokenizer);
+                if (!line2 || line2.startsWith(delimiter) || line2.startsWith('> <')) {
+                    TokenBuilder.add(data, start, end);
+                    added = true;
+                    break;
+                }
+                end = tokenizer.tokenEnd;
+            }
+
+            if (!added) {
+                TokenBuilder.add(data, start, end);
             }
-        } else {
-            sawHeaderToken = false;
         }
     }