parse PDB helices and sheets

src/mol-model-formats/structure/pdb/secondary-structure.ts

@@ -0,0 +1,262 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { CifCategory, CifField } from 'mol-io/reader/cif';
+import { mmCIF_Schema } from 'mol-io/reader/cif/schema/mmcif';
+import { Tokens } from 'mol-io/reader/common/text/tokenizer';
+
+const HelixTypes: {[k: string]: mmCIF_Schema['struct_conf']['conf_type_id']['T']} = {
+    // CLASS NUMBER
+    // TYPE OF  HELIX                     (COLUMNS 39 - 40)
+    // --------------------------------------------------------------
+    // Right-handed alpha (default)                1
+    // Right-handed omega                          2
+    // Right-handed pi                             3
+    // Right-handed gamma                          4
+    // Right-handed 3 - 10                         5
+    // Left-handed alpha                           6
+    // Left-handed omega                           7
+    // Left-handed gamma                           8
+    // 2 - 7 ribbon/helix                          9
+    // Polyproline                                10
+    1: 'HELX_RH_AL_P',
+    2: 'HELX_RH_OM_P',
+    3: 'HELX_RH_PI_P',
+    4: 'HELX_RH_GA_P',
+    5: 'HELX_RH_3T_P',
+    6: 'HELX_LH_AL_P',
+    7: 'HELX_LH_OM_P',
+    8: 'HELX_LH_GA_P',
+    9: 'HELX_RH_27_P', // TODO or left-handed???
+    10: 'HELX_RH_PP_P', // TODO or left-handed???
+}
+function getStructConfTypeId(type: string): mmCIF_Schema['struct_conf']['conf_type_id']['T'] {
+    return HelixTypes[type] || 'HELX_P'
+}
+
+interface PdbHelix {
+    serNum: string,
+    helixID: string,
+    initResName: string,
+    initChainID: string,
+    initSeqNum: string,
+    initICode: string,
+    endResName: string,
+    endChainID: string,
+    endSeqNum: string,
+    endICode: string,
+    helixClass: string,
+    comment: string,
+    length: string
+}
+
+export function parseHelix(lines: Tokens, lineStart: number, lineEnd: number): CifCategory {
+    const helices: PdbHelix[] = []
+    const getLine = (n: number) => lines.data.substring(lines.indices[2 * n], lines.indices[2 * n + 1]);
+
+    for (let i = lineStart; i < lineEnd; i++) {
+        let line = getLine(i);
+        // COLUMNS        DATA  TYPE     FIELD         DEFINITION
+        // -----------------------------------------------------------------------------------
+        // 1 -  6        Record name    "HELIX "
+        // 8 - 10        Integer        serNum        Serial number of the helix. This starts
+        //                                             at 1  and increases incrementally.
+        // 12 - 14        LString(3)     helixID       Helix  identifier. In addition to a serial
+        //                                             number, each helix is given an
+        //                                             alphanumeric character helix identifier.
+        // 16 - 18        Residue name   initResName   Name of the initial residue.
+        // 20             Character      initChainID   Chain identifier for the chain containing
+        //                                             this  helix.
+        // 22 - 25        Integer        initSeqNum    Sequence number of the initial residue.
+        // 26             AChar          initICode     Insertion code of the initial residue.
+        // 28 - 30        Residue  name  endResName    Name of the terminal residue of the helix.
+        // 32             Character      endChainID    Chain identifier for the chain containing
+        //                                             this  helix.
+        // 34 - 37        Integer        endSeqNum     Sequence number of the terminal residue.
+        // 38             AChar          endICode      Insertion code of the terminal residue.
+        // 39 - 40        Integer        helixClass    Helix class (see below).
+        // 41 - 70        String         comment       Comment about this helix.
+        // 72 - 76        Integer        length        Length of this helix.
+        helices.push({
+            serNum: line.substr(7, 3).trim(),
+            helixID: line.substr(11, 3).trim(),
+            initResName: line.substr(15, 3).trim(),
+            initChainID: line.substr(19, 1).trim(),
+            initSeqNum: line.substr(21, 4).trim(),
+            initICode: line.substr(25, 1).trim(),
+            endResName: line.substr(27, 3).trim(),
+            endChainID: line.substr(31, 3).trim(),
+            endSeqNum: line.substr(33, 4).trim(),
+            endICode: line.substr(37, 1).trim(),
+            helixClass: line.substr(38, 2).trim(),
+            comment: line.substr(40, 30).trim(),
+            length: line.substr(71, 5).trim()
+        })
+    }
+
+    const beg_auth_asym_id = CifField.ofStrings(helices.map(h => h.initChainID))
+    const beg_auth_comp_id = CifField.ofStrings(helices.map(h => h.initResName))
+    const beg_auth_seq_id = CifField.ofStrings(helices.map(h => h.initSeqNum))
+
+    const end_auth_asym_id = CifField.ofStrings(helices.map(h => h.endChainID))
+    const end_auth_comp_id = CifField.ofStrings(helices.map(h => h.endResName))
+    const end_auth_seq_id = CifField.ofStrings(helices.map(h => h.endSeqNum))
+
+    const struct_conf: CifCategory.Fields<mmCIF_Schema['struct_conf']> = {
+        beg_label_asym_id: beg_auth_asym_id,
+        beg_label_comp_id: beg_auth_comp_id,
+        beg_label_seq_id: beg_auth_seq_id,
+        beg_auth_asym_id,
+        beg_auth_comp_id,
+        beg_auth_seq_id,
+
+        conf_type_id: CifField.ofStrings(helices.map(h => getStructConfTypeId(h.helixClass))),
+        details: CifField.ofStrings(helices.map(h => h.comment)),
+
+        end_label_asym_id: end_auth_asym_id,
+        end_label_comp_id: end_auth_asym_id,
+        end_label_seq_id: end_auth_seq_id,
+        end_auth_asym_id,
+        end_auth_comp_id,
+        end_auth_seq_id,
+
+        id: CifField.ofStrings(helices.map(h => h.serNum)),
+        pdbx_beg_PDB_ins_code: CifField.ofStrings(helices.map(h => h.initICode)),
+        pdbx_end_PDB_ins_code: CifField.ofStrings(helices.map(h => h.endICode)),
+        pdbx_PDB_helix_class: CifField.ofStrings(helices.map(h => h.helixClass)),
+        pdbx_PDB_helix_length: CifField.ofStrings(helices.map(h => h.length)),
+        pdbx_PDB_helix_id: CifField.ofStrings(helices.map(h => h.helixID)),
+    };
+    return CifCategory.ofFields('struct_conf', struct_conf);
+}
+
+//
+
+interface PdbSheet {
+    strand: string,
+    sheetID: string,
+    numStrands: string,
+    initResName: string,
+    initChainID: string,
+    initSeqNum: string,
+    initICode: string,
+    endResName: string,
+    endChainID: string,
+    endSeqNum: string,
+    endICode: string,
+    sense: string,
+    curAtom: string,
+    curResName: string,
+    curChainId: string,
+    curResSeq: string,
+    curICode: string,
+    prevAtom: string,
+    prevResName: string,
+    prevChainId: string,
+    prevResSeq: string,
+    prevICode: string,
+}
+
+export function parseSheet(lines: Tokens, lineStart: number, lineEnd: number): CifCategory {
+    const sheets: PdbSheet[] = []
+    const getLine = (n: number) => lines.data.substring(lines.indices[2 * n], lines.indices[2 * n + 1]);
+
+    for (let i = lineStart; i < lineEnd; i++) {
+        let line = getLine(i);
+        // COLUMNS       DATA  TYPE     FIELD          DEFINITION
+        // -------------------------------------------------------------------------------------
+        // 1 -  6        Record name   "SHEET "
+        // 8 - 10        Integer       strand         Strand  number which starts at 1 for each
+        //                                             strand within a sheet and increases by one.
+        // 12 - 14        LString(3)    sheetID        Sheet  identifier.
+        // 15 - 16        Integer       numStrands     Number  of strands in sheet.
+        // 18 - 20        Residue name  initResName    Residue  name of initial residue.
+        // 22             Character     initChainID    Chain identifier of initial residue
+        //                                             in strand.
+        // 23 - 26        Integer       initSeqNum     Sequence number of initial residue
+        //                                             in strand.
+        // 27             AChar         initICode      Insertion code of initial residue
+        //                                             in  strand.
+        // 29 - 31        Residue name  endResName     Residue name of terminal residue.
+        // 33             Character     endChainID     Chain identifier of terminal residue.
+        // 34 - 37        Integer       endSeqNum      Sequence number of terminal residue.
+        // 38             AChar         endICode       Insertion code of terminal residue.
+        // 39 - 40        Integer       sense          Sense of strand with respect to previous
+        //                                             strand in the sheet. 0 if first strand,
+        //                                             1 if  parallel,and -1 if anti-parallel.
+        // 42 - 45        Atom          curAtom        Registration.  Atom name in current strand.
+        // 46 - 48        Residue name  curResName     Registration.  Residue name in current strand
+        // 50             Character     curChainId     Registration. Chain identifier in
+        //                                             current strand.
+        // 51 - 54        Integer       curResSeq      Registration.  Residue sequence number
+        //                                             in current strand.
+        // 55             AChar         curICode       Registration. Insertion code in
+        //                                             current strand.
+        // 57 - 60        Atom          prevAtom       Registration.  Atom name in previous strand.
+        // 61 - 63        Residue name  prevResName    Registration.  Residue name in
+        //                                             previous strand.
+        // 65             Character     prevChainId    Registration.  Chain identifier in
+        //                                             previous  strand.
+        // 66 - 69        Integer       prevResSeq     Registration. Residue sequence number
+        //                                             in previous strand.
+        // 70             AChar         prevICode      Registration.  Insertion code in
+        //                                             previous strand.
+        sheets.push({
+            strand: line.substr(7, 3).trim(),
+            sheetID: line.substr(11, 3).trim(),
+            numStrands: line.substr(14, 2).trim(),
+            initResName: line.substr(17, 3).trim(),
+            initChainID: line.substr(21, 1).trim(),
+            initSeqNum: line.substr(22, 4).trim(),
+            initICode: line.substr(26, 1).trim(),
+            endResName: line.substr(28, 3).trim(),
+            endChainID: line.substr(32, 1).trim(),
+            endSeqNum: line.substr(33, 4).trim(),
+            endICode: line.substr(37, 1).trim(),
+            sense: line.substr(38, 2).trim(),
+            curAtom: line.substr(41, 4).trim(),
+            curResName: line.substr(45, 3).trim(),
+            curChainId: line.substr(49, 1).trim(),
+            curResSeq: line.substr(50, 4).trim(),
+            curICode: line.substr(54, 1).trim(),
+            prevAtom: line.substr(56, 4).trim(),
+            prevResName: line.substr(60, 3).trim(),
+            prevChainId: line.substr(64, 1).trim(),
+            prevResSeq: line.substr(65, 4).trim(),
+            prevICode: line.substr(69, 1).trim(),
+        })
+    }
+
+    const beg_auth_asym_id = CifField.ofStrings(sheets.map(s => s.initChainID))
+    const beg_auth_comp_id = CifField.ofStrings(sheets.map(s => s.initResName))
+    const beg_auth_seq_id = CifField.ofStrings(sheets.map(s => s.initSeqNum))
+
+    const end_auth_asym_id = CifField.ofStrings(sheets.map(s => s.endChainID))
+    const end_auth_comp_id = CifField.ofStrings(sheets.map(s => s.endResName))
+    const end_auth_seq_id = CifField.ofStrings(sheets.map(s => s.endSeqNum))
+
+    const struct_sheet_range: CifCategory.Fields<mmCIF_Schema['struct_sheet_range']> = {
+        beg_label_asym_id: beg_auth_asym_id,
+        beg_label_comp_id: beg_auth_comp_id,
+        beg_label_seq_id: beg_auth_seq_id,
+        beg_auth_asym_id,
+        beg_auth_comp_id,
+        beg_auth_seq_id,
+
+        end_label_asym_id: end_auth_asym_id,
+        end_label_comp_id: end_auth_asym_id,
+        end_label_seq_id: end_auth_seq_id,
+        end_auth_asym_id,
+        end_auth_comp_id,
+        end_auth_seq_id,
+
+        id: CifField.ofStrings(sheets.map(s => s.strand)),
+        sheet_id: CifField.ofStrings(sheets.map(s => s.sheetID)), // TODO wrong, needs to point to _struct_sheet.id
+        pdbx_beg_PDB_ins_code: CifField.ofStrings(sheets.map(s => s.initICode)),
+        pdbx_end_PDB_ins_code: CifField.ofStrings(sheets.map(s => s.endICode)),
+    };
+    return CifCategory.ofFields('struct_sheet_range', struct_sheet_range);
+}

src/mol-model-formats/structure/pdb/to-cif.ts

@@ -2,6 +2,7 @@
  * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
 import { substringStartsWith } from 'mol-util/string';
@@ -11,6 +12,7 @@ import { TokenBuilder, Tokenizer } from 'mol-io/reader/common/text/tokenizer';
 import { PdbFile } from 'mol-io/reader/pdb/schema';
 import { parseCryst1, parseRemark350, parseMtrix } from './assembly';
 import { WaterNames } from 'mol-model/structure/model/types';
+import { parseHelix, parseSheet } from './secondary-structure';
 
 function _entity(): { [K in keyof mmCIF_Schema['entity']]?: CifField } {
     return {
@@ -215,8 +217,16 @@ export async function pdbToMmCif(pdb: PdbFile): Promise<CifFrame> {
                 if (substringStartsWith(data, s, e, 'HETATM')) {
                     if (!modelNum) { modelNum++; modelStr = '' + modelNum; }
                     addAtom(atom_site, modelStr, tokenizer, s, e, true);
+                } else if (substringStartsWith(data, s, e, 'HELIX')) {
+                    let j = i + 1;
+                    while (true) {
+                        s = indices[2 * j]; e = indices[2 * j + 1];
+                        if (!substringStartsWith(data, s, e, 'HELIX')) break;
+                        j++;
+                    }
+                    helperCategories.push(parseHelix(lines, i, j));
+                    i = j - 1;
                 }
-                // TODO: HELIX
                 break;
             case 'M':
                 if (substringStartsWith(data, s, e, 'MODEL ')) {
@@ -251,8 +261,16 @@ export async function pdbToMmCif(pdb: PdbFile): Promise<CifFrame> {
                 }
                 break;
             case 'S':
-                // TODO
-                // SHEET
+                if (substringStartsWith(data, s, e, 'SHEET')) {
+                    let j = i + 1;
+                    while (true) {
+                        s = indices[2 * j]; e = indices[2 * j + 1];
+                        if (!substringStartsWith(data, s, e, 'SHEET')) break;
+                        j++;
+                    }
+                    helperCategories.push(parseSheet(lines, i, j));
+                    i = j - 1;
+                }
                 break;
         }
     }

src/mol-state/state.ts

@@ -529,6 +529,7 @@ async function updateSubtree(ctx: UpdateContext, root: Ref) {
         ctx.changed = true;
         if (!ctx.hadError) ctx.newCurrent = root;
         doError(ctx, root, '' + e, false);
+        console.error(e);
         return;
     }