@datagrok/bio 2.27.6 → 2.27.8

package/CREDITS.md

@@ -0,0 +1,246 @@
+# Bio — Third-Party Libraries
+
+The `@datagrok/bio` package is distributed under the MIT license that covers the
+rest of the `public/` repository (see [`../../LICENSE.md`](../../LICENSE.md)). It
+incorporates the open-source components listed below; this file reproduces the
+attribution and notices required by their respective licenses.
+
+All runtime JavaScript dependencies bundled into the published artifact are
+under permissive licenses (MIT, Apache-2.0, BSD-3-Clause). No copyleft
+(GPL/LGPL/MPL) component is bundled into the published Bio plugin.
+
+---
+
+## 1. Bundled in the published artifact (`dist/`)
+
+### immunum (1.1.0)
+
+ENPICOM's antibody/TCR numbering library, compiled to WebAssembly. The
+WASM binary is bundled into `dist/`; the wasm-bindgen JS glue is reused from
+[`src/utils/antibody-numbering/immunum-glue.js`](src/utils/antibody-numbering/immunum-glue.js),
+which is a port of the upstream `node_modules/immunum/immunum.js` modified
+only to replace the Node-only `require('fs').readFileSync` top-level loader
+with an explicit `initImmunum(bytes)` entry point so it works in browsers and
+web workers. The modification is noted in the file header per MIT terms.
+
+- Upstream: https://github.com/ENPICOM/immunum — https://immunum.enpicom.com
+- License: **MIT**
+
+```
+MIT License
+
+Copyright (c) 2026 ENPICOM
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+```
+
+### @biowasm/aioli (3.x)
+
+WebAssembly runtime that drives multiple sequence alignment (kalign). The
+aioli library itself is bundled; the kalign tool it loads is fetched at
+runtime — see Section 3 below.
+
+- Upstream: https://github.com/biowasm/aioli
+- License: **MIT**
+
+```
+MIT License
+
+Copyright (c) 2018 Robert Aboukhalil
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+```
+
+### Ajv (8.x) and ajv-errors (3.x)
+
+JSON-schema validator used for monomer-library JSON validation.
+
+- Upstream: https://ajv.js.org/ — https://github.com/ajv-validator/ajv-errors
+- License: **MIT**
+
+```
+The MIT License (MIT)
+
+Copyright (c) 2015-2021 Evgeny Poberezkin
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+```
+
+(`ajv-errors` carries an analogous MIT notice — *Copyright (c) 2017 Evgeny
+Poberezkin*.)
+
+### fastest-levenshtein (1.0.x)
+
+Levenshtein-distance implementation used in sequence comparison code paths.
+
+- Upstream: https://github.com/ka-weihe/fastest-levenshtein
+- License: **MIT**
+
+```
+MIT License
+
+Copyright (c) 2020 Kasper Unn Weihe
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+```
+
+### umap-js (1.4.x)
+
+UMAP dimensionality reduction used by sequence-space and similarity viewers.
+The npm package metadata declares MIT but the LICENSE file shipped in the
+tarball is **Apache-2.0**, so we comply with the more conservative Apache-2.0
+terms (preserve copyright/attribution; mark modifications, of which there are
+none).
+
+- Upstream: https://github.com/PAIR-code/umap-js
+- Author: Andy Coenen (Google PAIR)
+- License: **Apache-2.0**
+
+> Licensed under the Apache License, Version 2.0 (the "License"); you may not
+> use this file except in compliance with the License. You may obtain a copy of
+> the License at http://www.apache.org/licenses/LICENSE-2.0
+>
+> Unless required by applicable law or agreed to in writing, software
+> distributed under the License is distributed on an "AS IS" BASIS, WITHOUT
+> WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the
+> License for the specific language governing permissions and limitations
+> under the License.
+
+The full Apache-2.0 license text is available at the URL above and in
+`node_modules/umap-js/LICENSE`.
+
+---
+
+## 2. Linked at runtime via the Datagrok platform (webpack externals)
+
+These libraries are not bundled into Bio's `dist/` — they are provided once
+by the platform host and shared across all packages.
+
+| Component                        | Version | License      | Upstream                                          |
+|----------------------------------|---------|--------------|---------------------------------------------------|
+| OpenChemLib JS                   | 7.x     | BSD-3-Clause | https://github.com/cheminfo/openchemlib-js        |
+| RxJS                             | 6.x     | Apache-2.0   | https://github.com/ReactiveX/rxjs                 |
+| cash-dom                         | 8.x     | MIT          | https://github.com/fabiospampinato/cash           |
+| Day.js                           | 1.x     | MIT          | https://github.com/iamkun/dayjs                   |
+| wu.js                            | 2.x     | MIT          | https://github.com/fitzgen/wu.js                  |
+
+OpenChemLib JS is also referenced by Bio's `package.json` `sources`. The
+upstream `openchemlib-js` npm package is distributed under BSD-3-Clause:
+*Copyright (c) 2015-2017, cheminfo.*
+
+---
+
+## 3. Fetched at runtime from third-party CDNs (not bundled)
+
+### kalign (via @biowasm/aioli)
+
+`@biowasm/aioli` loads the **kalign** multiple-sequence-alignment tool from
+the public biowasm CDN (`https://biowasm.com/cdn/v3/...`) on demand. kalign
+itself is **not** bundled into Bio's `dist/` and is **not** redistributed by
+the Datagrok platform. Users that load it transitively are subject to
+kalign's upstream license (GPLv3).
+
+- Upstream: https://github.com/TimoLassmann/kalign
+- License: GPLv3 (used as a runtime-fetched, non-bundled dependency)
+
+---
+
+## 4. Docker container (`dockerfiles/`) — PepSeA service
+
+The Bio package ships a single Docker image (`dockerfiles/Dockerfile`) that
+provides a PepSeA-based MSA service for HELM peptide sequences. The image is
+built from `datagrok/python` and pulls third-party software at build time:
+
+| Component     | Source                                          | License                |
+|---------------|-------------------------------------------------|------------------------|
+| PepSeA        | https://github.com/Merck/PepSeA (main branch)   | MIT (Merck & Co.)      |
+| MAFFT         | https://mafft.cbrc.jp/ (`mafft_7.520-1` .deb)   | MAFFT license (BSD-style, free for any use with attribution) |
+| FastAPI       | https://github.com/tiangolo/fastapi             | MIT                    |
+| uvicorn       | https://www.uvicorn.org/                        | BSD-3-Clause           |
+| ujson         | https://github.com/ultrajson/ultrajson          | BSD-3-Clause           |
+| Python stdlib | https://www.python.org/                         | PSF License            |
+
+The `Dockerfile` patches a few lines of PepSeA's `api.py` at build time to
+add a `/distout` endpoint and JSON error-handling middleware; per MIT terms
+those modifications are noted here.
+
+---
+
+## 5. Development-only dependencies
+
+Tools used during the build/test cycle (not in the runtime tree, not bundled):
+the `datagrok-tools` CLI transitively pulls in `puppeteer-screen-recorder`,
+which references `@ffmpeg-installer/ffmpeg` (LGPL-2.1) and
+`@ffmpeg-installer/win32-x64` (GPLv3). These binaries are **not**
+redistributed as part of the published Bio plugin and impose no obligation on
+users of the plugin.
+
+The peer/devDependencies on other Datagrok plugins (`@datagrok/chem`,
+`@datagrok/dendrogram`, `@datagrok/eda`, `@datagrok/helm`,
+`@datagrok/peptides`) are MIT — covered by the repo-wide `LICENSE.md`. Each
+of those plugins maintains its own `CREDITS.md` (or will) for its own
+third-party content.

package/dist/455.js

@@ -1,2 +1,2 @@
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"+o.bonds.kwargs.get(s):"";n[e.bondShift+s]=t.V3K_BEGIN_DATA_LINE+i+" "+o.bonds.bondTypes[s]+" "+a+" "+l+h+r+"\n"}}function _(o){return Math.round(t.PRECISION_FACTOR*o)/t.PRECISION_FACTOR}new h(s.PT,r.fasta.peptide,.5),new h(s.DNA,r.fasta.dna,.55),new h(s.RNA,r.fasta.rna,.55),e.FASTA,e.SEPARATOR,e.HELM,e.BILN,function(t){t.BASE="HELM_BASE",t.SUGAR="HELM_SUGAR",t.LINKER="HELM_LINKER",t.AA="HELM_AA",t.CHEM="HELM_CHEM",t.BLOB="HELM_BLOB",t.NUCLEOTIDE="HELM_NUCLETIDE"}(c||(c={})),onmessage=t=>{const{seqList:o,rolesList:n,monomersDict:e,alphabet:s,polymerType:i,start:a,end:l}=t.data,h=new Array(l-a),r=new Array(0);for(let t=a;t<l;++t)try{const l=o[t],r=n?n[t]:void 0;h[t-a]=f(l,e,s,i,r)}catch(o){const n=`Cannot get molfile of row #${t}: ${o instanceof Error?o.message:o.toString()}.`;r.push(n)}postMessage({molfiles:h,warnings:r})},bio={}})();
+var bio;(()=>{"use strict";const t={V2K_RGP_SHIFT:8,V2K_RGP_LINE:"M  RGP",V2K_A_LINE:"A  ",V3K_COUNTS_SHIFT:14,V3K_IDX_SHIFT:7,V3K_HEADER_FIRST_LINE:"\nDatagrok macromolecule handler\n\n",V3K_HEADER_SECOND_LINE:"  0  0  0  0  0  0            999 V3000\n",V3K_BEGIN_CTAB_BLOCK:"M  V30 BEGIN CTAB\n",V3K_END_CTAB_BLOCK:"M  V30 END CTAB\n",V3K_BEGIN_COUNTS_LINE:"M  V30 COUNTS ",V3K_COUNTS_LINE_ENDING:" 0 0 0\n",V3K_BEGIN_ATOM_BLOCK:"M  V30 BEGIN ATOM\n",V3K_END_ATOM_BLOCK:"M  V30 END ATOM\n",V3K_BEGIN_BOND_BLOCK:"M  V30 BEGIN BOND\n",V3K_END_BOND_BLOCK:"M  V30 END BOND\n",V3K_BOND_CONFIG:" CFG=",V3K_BEGIN_DATA_LINE:"M  V30 ",V3K_END:"M  END",PRECISION_FACTOR:1e4,DEOXYRIBOSE:{polymerType:"RNA",symbol:"d"},RIBOSE:{polymerType:"RNA",symbol:"r"},PHOSPHATE:{polymerType:"RNA",symbol:"p"},OXYGEN:"O",HYDROGEN:"H"};function o(t,o){return t[o.polymerType]?.[o.symbol]}var n,e,s,i;!function(t){t[t.SUGAR=0]="SUGAR",t[t.BASE=1]="BASE",t[t.PHOSPHATE=2]="PHOSPHATE",t[t.TERMINAL_5P=3]="TERMINAL_5P",t[t.TERMINAL_3P=4]="TERMINAL_3P"}(n||(n={}));class a extends Map{constructor(t){super(t)}}class l{constructor(t,o){this.molfile=t,this.monomers=o}static createEmpty(){return new l("",new a(null))}}new RegExp("[rd]\\((\\w)\\)p?","g");class h{constructor(t,o,n){this.name=t,this.alphabet=o,this.cutoff=n}}!function(t){t.FASTA="fasta",t.SEPARATOR="separator",t.HELM="helm",t.CUSTOM="custom",t.BILN="biln"}(e||(e={})),function(t){t.DNA="DNA",t.RNA="RNA",t.PT="PT",t.UN="UN"}(s||(s={})),function(t){t.aligned="aligned",t.alphabet="alphabet",t.alphabetSize=".alphabetSize",t.alphabetIsMultichar=".alphabetIsMultichar",t.separator="separator",t.isHelmCompatible=".isHelmCompatible",t.positionNames=".positionNames",t.positionLabels=".positionLabels",t.regions=".regions",t.positionShift=".positionShift",t.selectedPosition=".selectedPosition",t.polymerTypeColumnName=".polymerTypeColumnName",t.annotations=".annotations",t.numberingScheme=".numberingScheme",t.annotationColumnName=".annotationColumnName"}(i||(i={}));const r=new class{constructor(){this.fasta={peptide:new Set(["G","L","Y","S","E","Q","D","N","F","A","K","R","H","C","V","P","W","I","M","T"]),dna:new Set(["A","C","G","T"]),rna:new Set(["A","C","G","U"])}}};var c;function b(t){let o;switch(t){case c.BASE:case c.SUGAR:case c.LINKER:case c.NUCLEOTIDE:case"nucleotide":o="RNA";break;case c.AA:o="PEPTIDE";break;case c.CHEM:o="CHEM";break;case c.BLOB:o="BLOB";break;default:o="PEPTIDE",console.warn(`Unexpected HelmType '${t}'`)}return o}function E(e,i,h,r,c){if(0===e.length)return l.createEmpty();const E="RNA"===r&&!!c&&c.length===e.length,{atomCount:A,bondCount:p,needsCapping:d}=function(e,i,a,l,h,r){let c=0,E=0,f=0,m=!0,N=null,_=null;for(let t=0;t<e.length;++t){const n=e[t];if(""!==n.symbol){if("*"==n.symbol)throw new Error("Gap canonical symbol is '', not '*");N=o(i,{symbol:n.symbol,polymerType:b(n.biotype)}),c+=N.atoms.x.length,E+=N.bonds.bondTypes.length,f++,h&&t%3==2&&(_=N)}}if("PEPTIDE"===l)c+=1,E+=f,f>0&&((N?.meta?.rNodes?.length??0)<2||N?.terminalR2Atom?.toLowerCase()===t.HYDROGEN.toLowerCase())&&(m=!1,c-=1,E-=1);else if(h)E+=f,r&&r.length>0&&r[r.length-1]===n.TERMINAL_3P?m=!1:c+=1;else{const n=a===s.DNA?o(i,t.DEOXYRIBOSE):o(i,t.RIBOSE),l=o(i,t.PHOSPHATE);c+=(e.length-1)*l.atoms.x.length,c+=e.length*n.atoms.x.length,c+=1,E+=(e.length-1)*l.bonds.bondTypes.length,E+=e.length*n.bonds.bondTypes.length,E-=1,E+=3*e.length}return{atomCount:c,bondCount:E,needsCapping:m}}(e,i,h,r,E,c),T=new Array(A),y=new Array(p);let u,I=null,O=null;"PEPTIDE"===r?u=f:(u=N,E||(I=h===s.DNA?o(i,t.DEOXYRIBOSE):o(i,t.RIBOSE),O=o(i,t.PHOSPHATE)));const g={i:0,nodeShift:0,bondShift:0,backbonePositionShift:new Array(2).fill(0),branchPositionShift:new Array(2).fill(0),backboneAttachNode:0,branchAttachNode:0,flipFactor:1},L={sugar:I,phosphate:O,seqLength:E?Math.ceil(e.length/3):e.length,atomCount:A,bondCount:p},C=new a,B=[];let D,P=0;if(E)!function(t,e,s,i,a,l,h,r,c,E,f){const N=e.length>0&&e[0]===n.TERMINAL_5P,A=e.length>0&&e[e.length-1]===n.TERMINAL_3P,S=N?1:0,p=(A?e.length-1:e.length)-S,d=Math.ceil(p/3),T=p===3*d,y=(t,n)=>{const e=o(s,{symbol:t.symbol,polymerType:b(t.biotype)}),h=l.nodeShift,N=l.bondShift;m(e,i,a,l),e.stereoAtoms?.forEach(t=>c.push(t+f())),E(e.atoms.x.length);const _=[];for(let t=h;t<l.nodeShift;++t)_.push(t);const A=[];for(let t=N;t<l.bondShift;++t)A.push(t);r.set(n,{biotype:t.biotype,symbol:t.symbol,atoms:_,bonds:A})};N&&(l.i=0,y(t[0],0));for(let n=0;n<d;++n){l.i=n+(N?1:0);const e=S+3*n,h=e+1,A=t[e],p=t[h],d=o(s,{symbol:A.symbol,polymerType:b(A.biotype)}),T=o(s,{symbol:p.symbol,polymerType:b(p.biotype)});if(n>=1){const o=S+3*(n-1)+2;y(t[o],o)}const u=l.nodeShift,I=l.bondShift;m(d,i,a,l),d.stereoAtoms?.forEach(t=>c.push(t+f())),E(d.atoms.x.length);const O=[];for(let t=u;t<l.nodeShift;++t)O.push(t);const g=[];for(let t=I;t<l.bondShift;++t)g.push(t);r.set(e,{biotype:A.biotype,symbol:A.symbol,atoms:O,bonds:g});const L=l.nodeShift,C=l.bondShift;_(T,i,a,l),T.stereoAtoms?.forEach(t=>c.push(t+f())),E(T.atoms.x.length);const B=[];for(let t=L;t<l.nodeShift;++t)B.push(t);const D=[];for(let t=C;t<l.bondShift;++t)D.push(t);r.set(h,{biotype:p.biotype,symbol:p.symbol,atoms:B,bonds:D})}if(T){const o=S+3*(d-1)+2;y(t[o],o)}A&&(l.i=d+(N?1:0),y(t[e.length-1],e.length-1))}(e,c,i,T,y,g,0,C,B,t=>{P+=t},()=>P);else for(g.i=0;g.i<L.seqLength;++g.i){const t=e[g.i];if(""===t.symbol)continue;const n=o(i,{symbol:t.symbol,polymerType:b(t.biotype)});D=n.terminalR2Atom;const s=g.nodeShift,a=g.bondShift;u(n,T,y,g,L),n.stereoAtoms?.forEach(t=>B.push(t+P)),P+=n.atoms.x.length;const l=g.nodeShift-s,h=new Array(l);for(let t=0;t<l;++t)h[t]=s+t;const r=g.bondShift-a,c=new Array(r);for(let t=0;t<r;++t)c[t]=a+t;C.set(g.i,{biotype:t.biotype,symbol:t.symbol,atoms:h,bonds:c})}d&&function(o,n,e,s,i=t.OXYGEN){const a=e.nodeShift+1;o[s.atomCount]=t.V3K_BEGIN_DATA_LINE+a+" "+(i??t.OXYGEN)+" "+S(e.backbonePositionShift[0])+" "+e.flipFactor*S(e.backbonePositionShift[1])+" 0.000000 0\n";const l=e.backboneAttachNode,h=a;n[s.bondCount]=t.V3K_BEGIN_DATA_LINE+e.bondShift+" 1 "+l+" "+h+"\n"}(T,y,g,L,D??t.OXYGEN);const R=t.V3K_BEGIN_COUNTS_LINE+A+" "+p+t.V3K_COUNTS_LINE_ENDING;let K="";return K+=t.V3K_HEADER_FIRST_LINE,K+=t.V3K_HEADER_SECOND_LINE,K+=t.V3K_BEGIN_CTAB_BLOCK,K+=R,K+=t.V3K_BEGIN_ATOM_BLOCK,K+=T.join(""),K+=t.V3K_END_ATOM_BLOCK,K+=t.V3K_BEGIN_BOND_BLOCK,K+=y.join(""),K+=t.V3K_END_BOND_BLOCK,B.length>0&&(K+=function(t){const o=[];let n=`M  V30 MDLV30/STEABS ATOMS=(${t.length}`;for(let e=0;e<t.length;e++){const s=`${n} ${t[e]}`;s.length>76?(o.push(`${n} -\n`),n=`M  V30 ${t[e]}`):n=s,e===t.length-1&&o.push(`${n})\n`)}return`M  V30 BEGIN COLLECTION\n${o.join("")}M  V30 END COLLECTION\n`}(B)),K+=t.V3K_END_CTAB_BLOCK,K+=t.V3K_END,{molfile:K,monomers:C}}function f(t,o,n,e){e.flipFactor=(-1)**(e.i%2),m(t,o,n,e)}function m(o,n,e,s){!function(o,n,e){for(let s=0;s<o.atoms.atomTypes.length;++s){const i=e.nodeShift+s+1;n[e.nodeShift+s]=t.V3K_BEGIN_DATA_LINE+i+" "+o.atoms.atomTypes[s]+" "+S(e.backbonePositionShift[0]+o.atoms.x[s])+" "+S(e.backbonePositionShift[1]+e.flipFactor*o.atoms.y[s])+" "+o.atoms.kwargs[s]}}(o,n,s),A(o,e,s),function(o,n,e){if(0!==e.backboneAttachNode){const s=e.bondShift,i=e.backboneAttachNode,a=o.meta.terminalNodes[0]+e.nodeShift;n[e.bondShift-1]=t.V3K_BEGIN_DATA_LINE+s+" 1 "+i+" "+a+"\n"}}(o,e,s),null!==o.meta.branchShift&&o.meta.terminalNodes.length>2&&function(t,o){o.branchAttachNode=o.nodeShift+t.meta.terminalNodes[2];for(let n=0;n<2;++n)o.branchPositionShift[n]=o.backbonePositionShift[n]+t.meta.branchShift[n]}(o,s),function(t,o){o.backboneAttachNode=o.nodeShift+t.meta.terminalNodes[1],o.bondShift+=t.bonds.atomPairs.length+1,o.nodeShift+=t.atoms.atomTypes.length,o.backbonePositionShift[0]+=t.meta.backboneShift?.[0]??0,o.backbonePositionShift[1]+=o.flipFactor*(t.meta.backboneShift?.[1]??0)}(o,s)}function N(t,o,n,e,s){if(0===e.i)m(s.sugar,o,n,e);else for(const t of[s.phosphate,s.sugar])m(t,o,n,e);_(t,o,n,e)}function _(o,n,e,s){!function(o,n,e){for(let s=0;s<o.atoms.atomTypes.length;++s){const i=e.nodeShift+s+1;n[e.nodeShift+s]=t.V3K_BEGIN_DATA_LINE+i+" "+o.atoms.atomTypes[s]+" "+S(e.branchPositionShift[0]+o.atoms.x[s])+" "+S(e.branchPositionShift[1]+e.flipFactor*o.atoms.y[s])+" "+o.atoms.kwargs[s]}}(o,n,s),A(o,e,s),function(o,n,e){const s=e.bondShift,i=e.branchAttachNode,a=o.meta.terminalNodes[0]+e.nodeShift;n[s-1]=t.V3K_BEGIN_DATA_LINE+s+" 1 "+i+" "+a+"\n"}(o,e,s);const i=s.bondShift,a=s.branchAttachNode,l=o.meta.terminalNodes[0]+s.nodeShift;e[i-1]=t.V3K_BEGIN_DATA_LINE+i+" 1 "+a+" "+l+"\n",s.bondShift+=o.bonds.atomPairs.length+1,s.nodeShift+=o.atoms.atomTypes.length}function A(o,n,e){for(let s=0;s<o.bonds.atomPairs.length;++s){const i=e.bondShift+s+1,a=o.bonds.atomPairs[s][0]+e.nodeShift,l=o.bonds.atomPairs[s][1]+e.nodeShift;let h="";if(o.bonds.bondConfiguration.has(s)){let t=o.bonds.bondConfiguration.get(s);e.flipFactor<0&&(t=1===t?3:1),h=" CFG="+t}const r=o.bonds.kwargs.has(s)?" "+o.bonds.kwargs.get(s):"";n[e.bondShift+s]=t.V3K_BEGIN_DATA_LINE+i+" "+o.bonds.bondTypes[s]+" "+a+" "+l+h+r+"\n"}}function S(o){return Math.round(t.PRECISION_FACTOR*o)/t.PRECISION_FACTOR}new h(s.PT,r.fasta.peptide,.5),new h(s.DNA,r.fasta.dna,.55),new h(s.RNA,r.fasta.rna,.55),e.FASTA,e.SEPARATOR,e.HELM,e.BILN,function(t){t.BASE="HELM_BASE",t.SUGAR="HELM_SUGAR",t.LINKER="HELM_LINKER",t.AA="HELM_AA",t.CHEM="HELM_CHEM",t.BLOB="HELM_BLOB",t.NUCLEOTIDE="HELM_NUCLETIDE"}(c||(c={})),onmessage=t=>{const{seqList:o,rolesList:n,monomersDict:e,alphabet:s,polymerType:i,start:a,end:l}=t.data,h=new Array(l-a),r=new Array(0);for(let t=a;t<l;++t)try{const l=o[t],r=n?n[t]:void 0;h[t-a]=E(l,e,s,i,r)}catch(o){const n=`Cannot get molfile of row #${t}: ${o instanceof Error?o.message:o.toString()}.`;r.push(n)}postMessage({molfiles:h,warnings:r})},bio={}})();
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package/dist/455.js.map

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const monomerWorksConsts = {\n    // constants for parsing molfile V2000\n    V2K_RGP_SHIFT: 8,\n    V2K_RGP_LINE: 'M  RGP',\n    V2K_A_LINE: 'A  ',\n    // constants for parsing/reconstruction of molfile V3000\n    V3K_COUNTS_SHIFT: 14,\n    V3K_IDX_SHIFT: 7,\n    V3K_HEADER_FIRST_LINE: '\\nDatagrok macromolecule handler\\n\\n',\n    V3K_HEADER_SECOND_LINE: '  0  0  0  0  0  0            999 V3000\\n',\n    V3K_BEGIN_CTAB_BLOCK: 'M  V30 BEGIN CTAB\\n',\n    V3K_END_CTAB_BLOCK: 'M  V30 END CTAB\\n',\n    V3K_BEGIN_COUNTS_LINE: 'M  V30 COUNTS ',\n    V3K_COUNTS_LINE_ENDING: ' 0 0 0\\n',\n    V3K_BEGIN_ATOM_BLOCK: 'M  V30 BEGIN ATOM\\n',\n    V3K_END_ATOM_BLOCK: 'M  V30 END ATOM\\n',\n    V3K_BEGIN_BOND_BLOCK: 'M  V30 BEGIN BOND\\n',\n    V3K_END_BOND_BLOCK: 'M  V30 END BOND\\n',\n    V3K_BOND_CONFIG: ' CFG=',\n    V3K_BEGIN_DATA_LINE: 'M  V30 ',\n    V3K_END: 'M  END',\n    PRECISION_FACTOR: 10000, // HELMCoreLibrary has 4 significant digits after decimal point in atom coordinates\n    // symbols for the corresponding monomers in HELM library\n    DEOXYRIBOSE: { polymerType: \"RNA\" /* PolymerTypes.RNA */, symbol: 'd' },\n    RIBOSE: { polymerType: \"RNA\" /* PolymerTypes.RNA */, symbol: 'r' },\n    PHOSPHATE: { polymerType: \"RNA\" /* PolymerTypes.RNA */, symbol: 'p' },\n    OXYGEN: 'O',\n    HYDROGEN: 'H',\n};\n//# sourceMappingURL=consts.js.map","export function getMolGraph(dict, libKey) {\n    return dict[libKey.polymerType]?.[libKey.symbol];\n}\nexport function hasMolGraph(dict, libKey) {\n    return !!dict[libKey.polymerType]?.[libKey.symbol];\n}\nexport function setMolGraph(dict, libKey, value) {\n    let pt = dict[libKey.polymerType];\n    if (!pt)\n        pt = dict[libKey.polymerType] = {};\n    pt[libKey.symbol] = value;\n}\n/** Role of an entry in a HELM RNA splitted sequence (sugar, base, phosphate). */\nexport var NucleotideRole;\n(function (NucleotideRole) {\n    NucleotideRole[NucleotideRole[\"SUGAR\"] = 0] = \"SUGAR\";\n    NucleotideRole[NucleotideRole[\"BASE\"] = 1] = \"BASE\";\n    NucleotideRole[NucleotideRole[\"PHOSPHATE\"] = 2] = \"PHOSPHATE\";\n})(NucleotideRole || (NucleotideRole = {}));\nexport class MonomerMap extends Map {\n    constructor(entries) {\n        super(entries);\n    }\n}\n/** @property monomers key - helm seq position, */\nexport class MolfileWithMap {\n    constructor(molfile, monomers) {\n        this.molfile = molfile;\n        this.monomers = monomers;\n    }\n    static createEmpty() { return new MolfileWithMap('', new MonomerMap(null)); }\n}\n//# sourceMappingURL=types.js.map","import { CandidateType } from './types';\n/** enum type to simplify setting \"user-friendly\" notation if necessary */\nexport var NOTATION;\n(function (NOTATION) {\n    NOTATION[\"FASTA\"] = \"fasta\";\n    NOTATION[\"SEPARATOR\"] = \"separator\";\n    NOTATION[\"HELM\"] = \"helm\";\n    /* Requires notation handler */ NOTATION[\"CUSTOM\"] = \"custom\";\n    /* Requires notation handler */ NOTATION[\"BILN\"] = \"biln\";\n})(NOTATION || (NOTATION = {}));\nexport var ALPHABET;\n(function (ALPHABET) {\n    ALPHABET[\"DNA\"] = \"DNA\";\n    ALPHABET[\"RNA\"] = \"RNA\";\n    ALPHABET[\"PT\"] = \"PT\";\n    /** Unknown */\n    ALPHABET[\"UN\"] = \"UN\";\n})(ALPHABET || (ALPHABET = {}));\nexport var TAGS;\n(function (TAGS) {\n    TAGS[\"aligned\"] = \"aligned\";\n    TAGS[\"alphabet\"] = \"alphabet\";\n    TAGS[\"alphabetSize\"] = \".alphabetSize\";\n    TAGS[\"alphabetIsMultichar\"] = \".alphabetIsMultichar\";\n    TAGS[\"separator\"] = \"separator\";\n    TAGS[\"isHelmCompatible\"] = \".isHelmCompatible\";\n    TAGS[\"positionNames\"] = \".positionNames\";\n    TAGS[\"positionLabels\"] = \".positionLabels\";\n    TAGS[\"regions\"] = \".regions\";\n    TAGS[\"positionShift\"] = \".positionShift\";\n    TAGS[\"selectedPosition\"] = \".selectedPosition\";\n    TAGS[\"polymerTypeColumnName\"] = \".polymerTypeColumnName\";\n    TAGS[\"annotations\"] = \".annotations\";\n    TAGS[\"numberingScheme\"] = \".numberingScheme\";\n    TAGS[\"annotationColumnName\"] = \".annotationColumnName\";\n})(TAGS || (TAGS = {}));\nexport { TAGS as BioTags };\nexport const positionSeparator = ', ';\nexport const monomerRe = /(?:\\[([A-Za-z0-9_\\-,()]+)\\])|([A-Za-z\\-])/g;\nexport const helmRe = /(PEPTIDE1|DNA1|RNA1)\\{([^}]+)}/g;\nexport const helmPp1Re = /\\[([^\\[\\]]+)]/g;\nexport const Alphabets = new class {\n    constructor() {\n        this.fasta = {\n            peptide: new Set([\n                'G', 'L', 'Y', 'S', 'E', 'Q', 'D', 'N', 'F', 'A',\n                'K', 'R', 'H', 'C', 'V', 'P', 'W', 'I', 'M', 'T',\n            ]),\n            dna: new Set(['A', 'C', 'G', 'T']),\n            rna: new Set(['A', 'C', 'G', 'U']),\n        };\n    }\n}();\nexport const candidateAlphabets = [\n    new CandidateType(ALPHABET.PT, Alphabets.fasta.peptide, 0.50),\n    new CandidateType(ALPHABET.DNA, Alphabets.fasta.dna, 0.55),\n    new CandidateType(ALPHABET.RNA, Alphabets.fasta.rna, 0.55),\n];\n/** Canonical gap symbol */\nexport const GAP_SYMBOL = '';\nexport const GapOriginals = {\n    [NOTATION.FASTA]: '-',\n    [NOTATION.SEPARATOR]: '',\n    [NOTATION.HELM]: '*',\n    [NOTATION.BILN]: '',\n};\nexport const MONOMER_MOTIF_SPLITTER = ' , ';\n/** Tag on Monomer columns storing the nqName of a function that returns an IMonomerCanonicalizer.\n *  The `.%` prefix ensures this tag is persisted with projects. */\nexport const MONOMER_CANONICALIZER_FUNC_TAG = '.%monomer-canonicalizer-func';\n/** Column temp key for the cached IMonomerCanonicalizer instance */\nexport const MONOMER_CANONICALIZER_TEMP = 'monomer-canonicalizer';\nexport const NOTATION_PROVIDER_CONSTRUCTOR_ROLE = 'notationProviderConstructor';\n//# sourceMappingURL=consts.js.map","// core fields of HELM library object used in toAtomicLevel function\nexport const HELM_CORE_FIELDS = [\n    \"symbol\" /* HELM_FIELDS.SYMBOL */,\n    \"molfile\" /* HELM_FIELDS.MOLFILE */,\n    \"rgroups\" /* HELM_FIELDS.RGROUPS */,\n    \"name\" /* HELM_FIELDS.NAME */,\n    // HELM_FIELDS.MONOMER_TYPE, // add if terminal monomers for PEPTIDEs to be\n    // supported\n];\nexport const SDF_MONOMER_NAME = 'MonomerName';\n// todo: ideally, keys should be expressed via constants\nexport const jsonSdfMonomerLibDict = {\n    'monomerType': null, // -> Backbone\n    'smiles': null,\n    'name': 'Name',\n    'author': null,\n    'molfile': 'molecule',\n    'naturalAnalog': 'MonomerNaturalAnalogCode',\n    'rgroups': 'MonomerCaps',\n    'createDate': null,\n    'id': null,\n    'polymerType': 'MonomerType',\n    'symbol': 'MonomerName'\n};\nexport const DUMMY_MONOMER = {\n    'monomerType': 'Backbone',\n    'smiles': '',\n    'name': '',\n    'author': 'Datagrok',\n    'molfile': '',\n    'naturalAnalog': '',\n    'rgroups': [],\n    'createDate': null,\n    'id': 0,\n    'polymerType': 'PEPTIDE',\n    'symbol': ''\n};\n// range of hex nubers used in PepSea library to endode monomers\nexport const MONOMER_ENCODE_MIN = 0x100;\nexport const MONOMER_ENCODE_MAX = 0x40A;\nexport const RIBOSE_SYMBOL = 'r';\nexport const DEOXYRIBOSE_SYMBOL = 'd';\nexport const PHOSPHATE_SYMBOL = 'p';\nexport const HELM_WRAPPERS_REGEXP = new RegExp(`[${RIBOSE_SYMBOL}${DEOXYRIBOSE_SYMBOL}]\\\\((\\\\w)\\\\)${PHOSPHATE_SYMBOL}?`, 'g');\n//# sourceMappingURL=const.js.map","import { NOTATION_PROVIDER_CONSTRUCTOR_ROLE } from './consts';\nexport class NotationProviderBase {\n    /** Name of the custom notation */\n    static get notationName() {\n        return 'Custom';\n    }\n    ;\n    /** flag to let bio know if this provider implements method for converting helm to it */\n    static get implementsFromHelm() {\n        return false;\n    }\n    ;\n    /** Method for converting HELM to this notation */\n    static convertFromHelm(helm, options) {\n        throw new Error(`Method convertFromHelm not implemented for this notation provider`);\n    }\n    ;\n    static async getProviderConstructors() {\n        // this is terrible, I know, but otherwise this gets put in webworkers and fails due to DG resolution)))\n        // @ts-ignore\n        if (window?.DG) {\n            // @ts-ignore\n            const constFuncs = window.DG.Func.find({ meta: { role: NOTATION_PROVIDER_CONSTRUCTOR_ROLE } });\n            return Promise.all(constFuncs.map((f) => f.apply({})));\n        }\n        return [];\n    }\n}\n/** Alphabet candidate type */\nexport class CandidateType {\n    constructor(name, alphabet, cutoff) {\n        this.name = name;\n        this.alphabet = alphabet;\n        this.cutoff = cutoff;\n    }\n}\n/** Alphabet candidate similarity type */\nexport class CandidateSimType extends CandidateType {\n    constructor(candidate, freq, similarity) {\n        super(candidate.name, candidate.alphabet, candidate.cutoff);\n        this.freq = freq;\n        this.similarity = similarity;\n    }\n}\n//# sourceMappingURL=types.js.map","export var HelmTypes;\n(function (HelmTypes) {\n    HelmTypes[\"BASE\"] = \"HELM_BASE\";\n    HelmTypes[\"SUGAR\"] = \"HELM_SUGAR\";\n    HelmTypes[\"LINKER\"] = \"HELM_LINKER\";\n    HelmTypes[\"AA\"] = \"HELM_AA\";\n    HelmTypes[\"CHEM\"] = \"HELM_CHEM\";\n    HelmTypes[\"BLOB\"] = \"HELM_BLOB\";\n    HelmTypes[\"NUCLEOTIDE\"] = \"HELM_NUCLETIDE\";\n})(HelmTypes || (HelmTypes = {}));\n//# sourceMappingURL=org.js.map","import { HelmTypes } from '../helm/consts';\nexport class MonomerWorks {\n    //private molfileConverter: IMolfileConverter;\n    constructor(monomerLib /*, molfileConverter: IMolfileConverter*/) {\n        this.monomerLib = monomerLib;\n        //this.molfileConverter = molfileConverter;\n    }\n    //types according to Monomer possible\n    getCappedRotatedMonomer(monomerType, monomerName) {\n        // TODO: Check type of monomerType arg\n        const monomer = this.monomerLib.getMonomer(monomerType, monomerName);\n        if (monomer)\n            return monomer.molfile; //TODO cap\n        return null;\n    }\n}\nexport function helmTypeToPolymerType(helmType) {\n    let polymerType = undefined;\n    switch (helmType) {\n        case HelmTypes.BASE:\n        case HelmTypes.SUGAR: // r - ribose, d - deoxyribose\n        case HelmTypes.LINKER: // p - phosphate\n        case HelmTypes.NUCLEOTIDE:\n        // @ts-ignore\n        case 'nucleotide':\n            polymerType = \"RNA\" /* PolymerTypes.RNA */;\n            break;\n        case HelmTypes.AA:\n            polymerType = \"PEPTIDE\" /* PolymerTypes.PEPTIDE */;\n            break;\n        case HelmTypes.CHEM:\n            polymerType = \"CHEM\" /* PolymerTypes.CHEM */;\n            break;\n        case HelmTypes.BLOB:\n            polymerType = \"BLOB\" /* PolymerTypes.BLOB */;\n            break;\n        default:\n            polymerType = \"PEPTIDE\" /* PolymerTypes.PEPTIDE */;\n            console.warn(`Unexpected HelmType '${helmType}'`);\n    }\n    return polymerType;\n}\n//# sourceMappingURL=monomer-works.js.map","/* eslint-disable max-len */\nimport { monomerWorksConsts as C } from './consts';\nimport { getMolGraph, MolfileWithMap, MonomerMap } from './types';\nimport { HELM_CORE_FIELDS, } from '../utils/const';\nimport { ALPHABET, GAP_SYMBOL } from '../utils/macromolecule/consts';\nimport { helmTypeToPolymerType } from './monomer-works';\n/** Get a mapping of peptide symbols to HELM monomer library objects with selected fields.\n * @param {IMonomerLib} monomerLib - Monomer library\n * @param {HELM_POLYMER_TYPE} polymerType - Polymer type\n * @param {ALPHABET} alphabet - Alphabet of the column\n * @return {Map<string, any>} - Mapping of peptide symbols to HELM monomer library objects with selected fields*/\nexport function getFormattedMonomerLib(monomerLib, polymerType, alphabet) {\n    const map = new Map();\n    for (const monomerSymbol of monomerLib.getMonomerSymbolsByType(polymerType)) {\n        const it = monomerLib.getMonomer(polymerType, monomerSymbol);\n        if (\n        // RNA: all branch monomers (bases) and all backbone monomers (sugars +\n        // phosphates, including modified ones). Modifications are looked up by\n        // symbol at assembly time, so they MUST be present in the formatted lib.\n        polymerType === \"RNA\" /* HELM_POLYMER_TYPE.RNA */ &&\n            (it[\"monomerType\" /* HELM_FIELDS.MONOMER_TYPE */] === \"Branch\" /* HELM_MONOMER_TYPE.BRANCH */ ||\n                it[\"monomerType\" /* HELM_FIELDS.MONOMER_TYPE */] === \"Backbone\" /* HELM_MONOMER_TYPE.BACKBONE */) ||\n            polymerType === \"PEPTIDE\" /* HELM_POLYMER_TYPE.PEPTIDE */ &&\n                it[\"monomerType\" /* HELM_FIELDS.MONOMER_TYPE */] !== \"Branch\" /* HELM_MONOMER_TYPE.BRANCH */) {\n            const monomerObject = {};\n            HELM_CORE_FIELDS.forEach((field) => {\n                //@ts-ignore\n                monomerObject[field] = it[field];\n            });\n            map.set(monomerSymbol, monomerObject);\n        }\n    }\n    return map;\n}\n/** Translate a sequence of monomer symbols into Molfile V3000\n * @param {ISeqMonomer[]} monomerSeq - Sequence of monomer symbols (canonical)\n * @param {MonomerMolGraphMap} monomersDict - Mapping of monomer symbols to MolGraph objects\n * @param {ALPHABET} alphabet - Alphabet of the column\n * @param {PolymerType} polymerType - Polymer type\n * @param {Array} roles - Optional per-position NucleotideRole tags. When set, RNA assembly\n *   uses per-position sugars/phosphates from monomerSeq directly (HELM triples mode).\n * @return {MolfileWithMap} - Molfile V3000 + per-position monomer index map */\nexport function monomerSeqToMolfile(monomerSeq, monomersDict, alphabet, polymerType, roles) {\n    if (monomerSeq.length === 0) {\n        // throw new Error('monomerSeq is empty');\n        return MolfileWithMap.createEmpty();\n    }\n    // Triples mode is on only when (a) caller flagged the row with roles, and\n    // (b) the row's length is a positive multiple of 3 (sugar/base/phosphate triples).\n    // in edge cases, terminal phosphate may be missing, so we also allow length % 3 === 2, but only if roles are present to disambiguate the monomers.\n    const triplesMode = polymerType === \"RNA\" /* HELM_POLYMER_TYPE.RNA */ && !!roles &&\n        roles.length === monomerSeq.length && (monomerSeq.length % 3 === 0 || monomerSeq.length % 3 === 2);\n    // define atom and bond counts, taking into account the bond type\n    const { atomCount, bondCount, needsCapping } = getResultingAtomBondCounts(monomerSeq, monomersDict, alphabet, polymerType, triplesMode);\n    // create arrays to store lines of the resulting molfile\n    const molfileAtomBlock = new Array(atomCount);\n    const molfileBondBlock = new Array(bondCount);\n    let addMonomerToMolblock;\n    let sugar = null;\n    let phosphate = null;\n    if (polymerType === \"PEPTIDE\" /* HELM_POLYMER_TYPE.PEPTIDE */)\n        addMonomerToMolblock = addAminoAcidToMolblock;\n    else { // nucleotides\n        addMonomerToMolblock = addNucleotideToMolblock;\n        // Default sugar/phosphate are only consulted in bases-only mode. In\n        // triples mode, every nucleotide carries its own.\n        if (!triplesMode) {\n            sugar = (alphabet === ALPHABET.DNA) ? getMolGraph(monomersDict, C.DEOXYRIBOSE) : getMolGraph(monomersDict, C.RIBOSE);\n            phosphate = getMolGraph(monomersDict, C.PHOSPHATE);\n        }\n    }\n    const v = {\n        i: 0,\n        nodeShift: 0,\n        bondShift: 0,\n        backbonePositionShift: new Array(2).fill(0),\n        branchPositionShift: new Array(2).fill(0),\n        backboneAttachNode: 0,\n        branchAttachNode: 0,\n        flipFactor: 1,\n    };\n    const LC = {\n        sugar: sugar,\n        phosphate: phosphate,\n        // In triples mode, the \"logical\" sequence length is the nucleotide count.\n        seqLength: triplesMode ? Math.ceil(monomerSeq.length / 3) : monomerSeq.length,\n        atomCount: atomCount,\n        bondCount: bondCount,\n    };\n    const monomers = new MonomerMap();\n    const steabsCollection = [];\n    let nAtoms = 0;\n    let lastMonomerCappingAtom = undefined;\n    if (triplesMode) {\n        runTriplesAssembly(monomerSeq, monomersDict, molfileAtomBlock, molfileBondBlock, v, LC, monomers, steabsCollection, (a) => { nAtoms += a; }, () => nAtoms);\n    }\n    else {\n        for (v.i = 0; v.i < LC.seqLength; ++v.i) {\n            const seqMonomer = monomerSeq[v.i];\n            if (seqMonomer.symbol === GAP_SYMBOL)\n                continue;\n            const monomer = getMolGraph(monomersDict, { symbol: seqMonomer.symbol, polymerType: helmTypeToPolymerType(seqMonomer.biotype) });\n            lastMonomerCappingAtom = monomer.terminalR2Atom;\n            const mAtomFirst = v.nodeShift;\n            const mBondFirst = v.bondShift;\n            addMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v, LC);\n            //adding stereo atoms to array for further STEABS block generation\n            monomer.stereoAtoms?.forEach((i) => steabsCollection.push(i + nAtoms));\n            nAtoms += monomer.atoms.x.length;\n            const mAtomCount = v.nodeShift - mAtomFirst;\n            const mAtomList = new Array(mAtomCount);\n            for (let maI = 0; maI < mAtomCount; ++maI)\n                mAtomList[maI] = mAtomFirst + maI;\n            const mBondCount = v.bondShift - mBondFirst;\n            const mBondList = new Array(mBondCount);\n            for (let mbI = 0; mbI < mBondCount; ++mbI)\n                mBondList[mbI] = mBondFirst + mbI;\n            monomers.set(v.i, {\n                biotype: seqMonomer.biotype,\n                symbol: seqMonomer.symbol,\n                atoms: mAtomList, bonds: mBondList\n            });\n        }\n    }\n    // if the last monomer needs to be capped, add the terminal OH to the resulting molfile\n    if (needsCapping)\n        capResultingMolblock(molfileAtomBlock, molfileBondBlock, v, LC, lastMonomerCappingAtom ?? C.OXYGEN);\n    const molfileCountsLine = C.V3K_BEGIN_COUNTS_LINE + atomCount + ' ' + bondCount + C.V3K_COUNTS_LINE_ENDING;\n    // todo: possible optimization may be achieved by replacing .join('') with +=\n    // since counterintuitively joining an array into a new string is reportedly\n    // slower than using += as below\n    let result = '';\n    result += C.V3K_HEADER_FIRST_LINE;\n    result += C.V3K_HEADER_SECOND_LINE;\n    result += C.V3K_BEGIN_CTAB_BLOCK;\n    result += molfileCountsLine;\n    result += C.V3K_BEGIN_ATOM_BLOCK;\n    result += molfileAtomBlock.join('');\n    result += C.V3K_END_ATOM_BLOCK;\n    result += C.V3K_BEGIN_BOND_BLOCK;\n    result += molfileBondBlock.join('');\n    result += C.V3K_END_BOND_BLOCK;\n    if (steabsCollection.length > 0)\n        result += getCollectionBlock(steabsCollection);\n    result += C.V3K_END_CTAB_BLOCK;\n    result += C.V3K_END;\n    // return molfileParts.join('');\n    return { molfile: result, monomers: monomers };\n}\nfunction getCollectionBlock(collection) {\n    //one row in STEABS block can be no longer than 80 symbols\n    //maxSymbols = 80 symbols minus ' -\\n' (4 symbols)\n    const maxSymbols = 76;\n    const rowsArray = [];\n    let newCollectionRow = `M  V30 MDLV30/STEABS ATOMS=(${collection.length}`;\n    for (let i = 0; i < collection.length; i++) {\n        const updatedRow = `${newCollectionRow} ${collection[i]}`;\n        if (updatedRow.length > maxSymbols) {\n            rowsArray.push(`${newCollectionRow} -\\n`);\n            newCollectionRow = `M  V30 ${collection[i]}`;\n        }\n        else\n            newCollectionRow = updatedRow;\n        //in case last atom was added - close the block\n        if (i === collection.length - 1)\n            rowsArray.push(`${newCollectionRow})\\n`);\n    }\n    return `M  V30 BEGIN COLLECTION\\n${rowsArray.join('')}M  V30 END COLLECTION\\n`;\n}\n/** Cap the resulting (after sewing up all the monomers) molfile with 'O'\n * @param {string[]} molfileAtomBlock - Array of lines of the resulting molfile atom block\n * @param {string[]} molfileBondBlock - Array of lines of the resulting molfile bond block\n * @param {LoopVariables} v - Loop variables\n * @param {LoopConstants} LC - Loop constants*/\nfunction capResultingMolblock(molfileAtomBlock, molfileBondBlock, v, LC, cappingAtomType = C.OXYGEN) {\n    // add terminal oxygen\n    const atomIdx = v.nodeShift + 1;\n    molfileAtomBlock[LC.atomCount] = C.V3K_BEGIN_DATA_LINE + atomIdx + ' ' +\n        (cappingAtomType ?? C.OXYGEN) + ' ' + keepPrecision(v.backbonePositionShift[0]) + ' ' +\n        v.flipFactor * keepPrecision(v.backbonePositionShift[1]) + ' ' + '0.000000 0' + '\\n';\n    // add terminal bond\n    const firstAtom = v.backboneAttachNode;\n    const secondAtom = atomIdx;\n    molfileBondBlock[LC.bondCount] = C.V3K_BEGIN_DATA_LINE + v.bondShift + ' ' +\n        1 + ' ' + firstAtom + ' ' + secondAtom + '\\n';\n}\nfunction addAminoAcidToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v) {\n    v.flipFactor = (-1) ** (v.i % 2); // to flip every even monomer over OX\n    addBackboneMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v);\n}\nfunction addBackboneMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v) {\n    // todo: remove these comments to the docstrings of the corr. functions\n    // construnct the lines of V3K molfile atom block\n    fillAtomLines(monomer, molfileAtomBlock, v);\n    // construct the lines of V3K molfile bond block\n    fillBondLines(monomer, molfileBondBlock, v);\n    // peptide bond\n    fillChainExtendingBond(monomer, molfileBondBlock, v);\n    // update branch variables if necessary\n    if (monomer.meta.branchShift !== null && monomer.meta.terminalNodes.length > 2)\n        updateBranchVariables(monomer, v);\n    // update loop variables\n    updateChainExtendingVariables(monomer, v);\n}\nfunction addNucleotideToMolblock(nucleobase, molfileAtomBlock, molfileBondBlock, v, LC) {\n    // construnct the lines of V3K molfile atom block corresponding to phosphate\n    // and sugar\n    if (v.i === 0)\n        addBackboneMonomerToMolblock(LC.sugar, molfileAtomBlock, molfileBondBlock, v);\n    else {\n        for (const monomer of [LC.phosphate, LC.sugar])\n            addBackboneMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v);\n    }\n    addBranchMonomerToMolblock(nucleobase, molfileAtomBlock, molfileBondBlock, v);\n}\nfunction addBranchMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v) {\n    fillBranchAtomLines(monomer, molfileAtomBlock, v);\n    fillBondLines(monomer, molfileBondBlock, v);\n    fillBackboneToBranchBond(monomer, molfileBondBlock, v);\n    // C-N bond\n    const bondIdx = v.bondShift;\n    const firstAtom = v.branchAttachNode;\n    const secondAtom = monomer.meta.terminalNodes[0] + v.nodeShift;\n    molfileBondBlock[bondIdx - 1] = C.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +\n        1 + ' ' + firstAtom + ' ' + secondAtom + '\\n';\n    // update loop variables\n    v.bondShift += monomer.bonds.atomPairs.length + 1;\n    v.nodeShift += monomer.atoms.atomTypes.length;\n}\nfunction updateChainExtendingVariables(monomer, v) {\n    v.backboneAttachNode = v.nodeShift + monomer.meta.terminalNodes[1];\n    v.bondShift += monomer.bonds.atomPairs.length + 1;\n    v.nodeShift += monomer.atoms.atomTypes.length;\n    v.backbonePositionShift[0] += monomer.meta.backboneShift?.[0] ?? 0; // todo: non-null check\n    v.backbonePositionShift[1] += v.flipFactor * (monomer.meta.backboneShift?.[1] ?? 0);\n}\nfunction updateBranchVariables(monomer, v) {\n    v.branchAttachNode = v.nodeShift + monomer.meta.terminalNodes[2];\n    for (let i = 0; i < 2; ++i)\n        v.branchPositionShift[i] = v.backbonePositionShift[i] + monomer.meta.branchShift[i];\n}\nfunction fillAtomLines(monomer, molfileAtomBlock, v) {\n    for (let j = 0; j < monomer.atoms.atomTypes.length; ++j) {\n        const atomIdx = v.nodeShift + j + 1;\n        molfileAtomBlock[v.nodeShift + j] = C.V3K_BEGIN_DATA_LINE + atomIdx + ' ' +\n            monomer.atoms.atomTypes[j] + ' ' +\n            keepPrecision(v.backbonePositionShift[0] + monomer.atoms.x[j]) + ' ' +\n            keepPrecision(v.backbonePositionShift[1] + v.flipFactor * monomer.atoms.y[j]) +\n            ' ' + monomer.atoms.kwargs[j];\n    }\n}\n// todo: remove as quickfix\nfunction fillBranchAtomLines(monomer, molfileAtomBlock, v) {\n    for (let j = 0; j < monomer.atoms.atomTypes.length; ++j) {\n        const atomIdx = v.nodeShift + j + 1;\n        molfileAtomBlock[v.nodeShift + j] = C.V3K_BEGIN_DATA_LINE + atomIdx + ' ' +\n            monomer.atoms.atomTypes[j] + ' ' +\n            keepPrecision(v.branchPositionShift[0] + monomer.atoms.x[j]) + ' ' +\n            keepPrecision(v.branchPositionShift[1] + v.flipFactor * monomer.atoms.y[j]) +\n            ' ' + monomer.atoms.kwargs[j];\n    }\n}\nfunction fillBondLines(monomer, molfileBondBlock, v) {\n    // construct the lines of V3K molfile bond block\n    for (let j = 0; j < monomer.bonds.atomPairs.length; ++j) {\n        const bondIdx = v.bondShift + j + 1;\n        const firstAtom = monomer.bonds.atomPairs[j][0] + v.nodeShift;\n        const secondAtom = monomer.bonds.atomPairs[j][1] + v.nodeShift;\n        let bondCfg = '';\n        if (monomer.bonds.bondConfiguration.has(j)) {\n            // flip orientation when necessary\n            let orientation = monomer.bonds.bondConfiguration.get(j);\n            if (v.flipFactor < 0)\n                orientation = (orientation === 1) ? 3 : 1;\n            bondCfg = ' CFG=' + orientation;\n        }\n        const kwargs = monomer.bonds.kwargs.has(j) ?\n            ' ' + monomer.bonds.kwargs.get(j) : '';\n        molfileBondBlock[v.bondShift + j] = C.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +\n            monomer.bonds.bondTypes[j] + ' ' +\n            firstAtom + ' ' + secondAtom + bondCfg + kwargs + '\\n';\n    }\n}\nfunction fillChainExtendingBond(monomer, molfileBondBlock, v) {\n    if (v.backboneAttachNode !== 0) {\n        const bondIdx = v.bondShift;\n        const firstAtom = v.backboneAttachNode;\n        const secondAtom = monomer.meta.terminalNodes[0] + v.nodeShift;\n        molfileBondBlock[v.bondShift - 1] = C.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +\n            1 + ' ' + firstAtom + ' ' + secondAtom + '\\n';\n    }\n}\n// todo: remove\nfunction fillBackboneToBranchBond(branchMonomer, molfileBondBlock, v) {\n    const bondIdx = v.bondShift;\n    const firstAtom = v.branchAttachNode;\n    const secondAtom = branchMonomer.meta.terminalNodes[0] + v.nodeShift;\n    molfileBondBlock[bondIdx - 1] = C.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +\n        1 + ' ' + firstAtom + ' ' + secondAtom + '\\n';\n}\n/** Compute the atom/bond counts for the resulting molfile, depending on the\n * type of polymer (peptide/nucleotide)\n * @param {ISeqMonomer[]} monomerSeq - the sequence of monomers\n * @param {MonomerMolGraphMap} monomersDict - the dictionary of monomers\n * @param {ALPHABET} alphabet - the alphabet of the monomers\n * @param {PolymerType} polymerType - the type of polymer\n * @param {boolean} triplesMode - true when monomerSeq is a flat list of HELM RNA triples\n * @return {Object} the atom/bond counts plus needsCapping flag */\nfunction getResultingAtomBondCounts(monomerSeq, monomersDict, alphabet, polymerType, triplesMode) {\n    let atomCount = 0;\n    let bondCount = 0;\n    let monomerCount = 0;\n    let needsCapping = true;\n    let lastMonomerGraph = null;\n    let lastPhosphateGraph = null;\n    // sum up all the atoms/nodes provided by the sequence\n    for (let i = 0; i < monomerSeq.length; ++i) {\n        const seqMonomer = monomerSeq[i];\n        if (seqMonomer.symbol === GAP_SYMBOL)\n            continue; // Skip for gap/empty monomer in MSA\n        if (seqMonomer.symbol == '*')\n            throw new Error(`Gap canonical symbol is '', not '*`);\n        lastMonomerGraph = getMolGraph(monomersDict, { symbol: seqMonomer.symbol, polymerType: helmTypeToPolymerType(seqMonomer.biotype) });\n        atomCount += lastMonomerGraph.atoms.x.length;\n        bondCount += lastMonomerGraph.bonds.bondTypes.length;\n        monomerCount++;\n        // In triples mode, every 3rd entry (index 2 mod 3) is a phosphate. Track\n        // the LAST one — its atoms/bonds are dropped at the 3'-terminus.\n        if (triplesMode && i % 3 === 2)\n            lastPhosphateGraph = lastMonomerGraph;\n    }\n    // add extra values depending on the polymer type\n    if (polymerType === \"PEPTIDE\" /* HELM_POLYMER_TYPE.PEPTIDE */) {\n        // add the rightmost/terminating cap group 'OH' (i.e. 'O')\n        atomCount += 1;\n        // add chain-extending bonds (C-NH per each monomer pair and terminal C-OH)\n        bondCount += monomerCount;\n        // if the last monomer is something like NH2, which only has R1, there is no need to cap it\n        // although, this should never happen, but hey... in other bits of code, there is a chunk that adds pseudo-R2 as hydrogen\n        // we should also check, if the R2 of the last monomer is not hydrogen, that case should also be omitted\n        if (monomerCount > 0) {\n            if ((lastMonomerGraph?.meta?.rNodes?.length ?? 0) < 2 || lastMonomerGraph?.terminalR2Atom?.toLowerCase() === C.HYDROGEN.toLowerCase()) {\n                needsCapping = false;\n                atomCount -= 1; // remove the last atom (the terminal 'O')\n                bondCount -= 1; // remove the last bond (the terminal C-OH)\n            }\n        }\n    }\n    else if (triplesMode) { // nucleotides — HELM triples (per-position sugar/base/phosphate)\n        void lastPhosphateGraph; // kept for symmetry; trailing P is now retained when HELM wrote it\n        // Per-monomer-loop already summed sugars + bases + phosphates for every\n        // entry in monomerSeq. Reservation: each backbone (sugar/phosphate)\n        // reserves +1 bond slot for the chain-extending bond, each branch (base)\n        // reserves +1 for its branch bond. Total reservations = monomerCount.\n        //   length === 3N      → trailing P emitted, monomerCount = 3N.\n        //   length === 3N - 1  → trailing P absent, monomerCount = 3N - 1.\n        // Either way, bondCount = sum_bonds + monomerCount.\n        atomCount += 1; // OH cap atom (rides on trailing P or on last sugar's R2)\n        bondCount += monomerCount;\n    }\n    else { // nucleotides — bases-only legacy path with default sugar/phosphate\n        const sugar = (alphabet === ALPHABET.DNA) ?\n            getMolGraph(monomersDict, C.DEOXYRIBOSE) : getMolGraph(monomersDict, C.RIBOSE);\n        const phosphate = getMolGraph(monomersDict, C.PHOSPHATE);\n        // add phosphate per each pair of nucleobase symbols\n        atomCount += (monomerSeq.length - 1) * phosphate.atoms.x.length;\n        // add sugar per each nucleobase symbol\n        atomCount += monomerSeq.length * sugar.atoms.x.length;\n        // add the leftmost cap group 'OH' (i.e. 'O')\n        atomCount += 1;\n        // add bonds from phosphate monomers\n        bondCount += (monomerSeq.length - 1) * phosphate.bonds.bondTypes.length;\n        // add bonds from sugar monomers\n        bondCount += monomerSeq.length * sugar.bonds.bondTypes.length;\n        // exclude the first chain-extending bond O-P (absent, no 'leftmost' phosphate)\n        bondCount -= 1;\n        // add chain-extending and branch bonds (O-P, C-O and C-N per each nucleotide)\n        bondCount += monomerSeq.length * 3;\n    }\n    return { atomCount, bondCount, needsCapping };\n}\n/** Triples-mode RNA assembly. Iterate by NUCLEOTIDE; each nucleotide normally\n * contributes 3 entries from monomerSeq in order [sugar, base, phosphate].\n * The LAST nucleotide may omit its trailing phosphate (length === 3N - 1) —\n * in that case HELM specified an unphosphorylated 3'-end and we cap on the\n * last sugar's R2 instead of on a final phosphate.\n *\n * @param {ISeqMonomer[]} monomerSeq - flat sugar/base/[phosphate] entries\n * @param {MonomerMolGraphMap} monomersDict - monomer dictionary\n * @param {string[]} molfileAtomBlock - output atom block buffer\n * @param {string[]} molfileBondBlock - output bond block buffer\n * @param {LoopVariables} v - mutable loop variables\n * @param {LoopConstants} LC - loop constants (seqLength = nucleotide count)\n * @param {MonomerMap} monomers - per-position monomer index map (filled in)\n * @param {number[]} steabsCollection - stereo atoms collected for STEABS block\n * @param {Function} addAtoms - callback to bump per-row atom counter for stereo offsets\n * @param {Function} getAtoms - callback to read current atom counter */\nfunction runTriplesAssembly(monomerSeq, monomersDict, molfileAtomBlock, molfileBondBlock, v, LC, monomers, steabsCollection, addAtoms, getAtoms) {\n    const N = LC.seqLength;\n    // length === 3N → trailing P present. length === 3N-1 → trailing P absent.\n    const hasTrailingP = monomerSeq.length === 3 * N;\n    for (let n = 0; n < N; ++n) {\n        v.i = n;\n        const sugarSm = monomerSeq[3 * n];\n        const baseSm = monomerSeq[3 * n + 1];\n        const sugarG = getMolGraph(monomersDict, { symbol: sugarSm.symbol, polymerType: helmTypeToPolymerType(sugarSm.biotype) });\n        const baseG = getMolGraph(monomersDict, { symbol: baseSm.symbol, polymerType: helmTypeToPolymerType(baseSm.biotype) });\n        // The previous nucleotide's trailing phosphate is the linker into THIS\n        // nucleotide's sugar. It always exists for n >= 1 because only the\n        // very LAST nucleotide is permitted to omit its phosphate.\n        const prevPhosG = (n === 0) ? null :\n            getMolGraph(monomersDict, { symbol: monomerSeq[3 * (n - 1) + 2].symbol,\n                polymerType: helmTypeToPolymerType(monomerSeq[3 * (n - 1) + 2].biotype) });\n        // emit prevPhosphate (chain linker), then sugar, then base\n        const seqStartIdx = 3 * n; // for keying the per-row monomer map by HELM splitter index\n        if (prevPhosG) {\n            const prevAtomFirst = v.nodeShift;\n            const prevBondFirst = v.bondShift;\n            addBackboneMonomerToMolblock(prevPhosG, molfileAtomBlock, molfileBondBlock, v);\n            prevPhosG.stereoAtoms?.forEach((i) => steabsCollection.push(i + getAtoms()));\n            addAtoms(prevPhosG.atoms.x.length);\n            // The phosphate \"belongs to\" nucleotide n-1's HELM index (3*(n-1)+2).\n            const prevPhosKey = 3 * (n - 1) + 2;\n            const aList = [];\n            for (let a = prevAtomFirst; a < v.nodeShift; ++a)\n                aList.push(a);\n            const bList = [];\n            for (let b = prevBondFirst; b < v.bondShift; ++b)\n                bList.push(b);\n            monomers.set(prevPhosKey, {\n                biotype: monomerSeq[prevPhosKey].biotype,\n                symbol: monomerSeq[prevPhosKey].symbol,\n                atoms: aList, bonds: bList,\n            });\n        }\n        const sugarAtomFirst = v.nodeShift;\n        const sugarBondFirst = v.bondShift;\n        addBackboneMonomerToMolblock(sugarG, molfileAtomBlock, molfileBondBlock, v);\n        sugarG.stereoAtoms?.forEach((i) => steabsCollection.push(i + getAtoms()));\n        addAtoms(sugarG.atoms.x.length);\n        const sAList = [];\n        for (let a = sugarAtomFirst; a < v.nodeShift; ++a)\n            sAList.push(a);\n        const sBList = [];\n        for (let b = sugarBondFirst; b < v.bondShift; ++b)\n            sBList.push(b);\n        monomers.set(seqStartIdx, {\n            biotype: sugarSm.biotype, symbol: sugarSm.symbol,\n            atoms: sAList, bonds: sBList,\n        });\n        const baseAtomFirst = v.nodeShift;\n        const baseBondFirst = v.bondShift;\n        addBranchMonomerToMolblock(baseG, molfileAtomBlock, molfileBondBlock, v);\n        baseG.stereoAtoms?.forEach((i) => steabsCollection.push(i + getAtoms()));\n        addAtoms(baseG.atoms.x.length);\n        const bAList = [];\n        for (let a = baseAtomFirst; a < v.nodeShift; ++a)\n            bAList.push(a);\n        const bBList = [];\n        for (let b = baseBondFirst; b < v.bondShift; ++b)\n            bBList.push(b);\n        monomers.set(seqStartIdx + 1, {\n            biotype: baseSm.biotype, symbol: baseSm.symbol,\n            atoms: bAList, bonds: bBList,\n        });\n    }\n    // Emit the trailing phosphate (the LAST nucleotide's P) as the final\n    // backbone monomer ONLY if HELM explicitly wrote it. The OH cap then\n    // rides on its free oxygen (3'-phosphate-OH terminus). If HELM omitted\n    // the trailing phosphate, the cap rides on the last sugar's R2 — that\n    // requires no extra emission here, since v.backboneAttachNode already\n    // points at the last sugar's R2 attach.\n    if (hasTrailingP) {\n        const lastPhosKey = 3 * (N - 1) + 2;\n        const lastPhosSm = monomerSeq[lastPhosKey];\n        const lastPhosG = getMolGraph(monomersDict, { symbol: lastPhosSm.symbol, polymerType: helmTypeToPolymerType(lastPhosSm.biotype) });\n        const trailAtomFirst = v.nodeShift;\n        const trailBondFirst = v.bondShift;\n        addBackboneMonomerToMolblock(lastPhosG, molfileAtomBlock, molfileBondBlock, v);\n        lastPhosG.stereoAtoms?.forEach((i) => steabsCollection.push(i + getAtoms()));\n        addAtoms(lastPhosG.atoms.x.length);\n        const tAList = [];\n        for (let a = trailAtomFirst; a < v.nodeShift; ++a)\n            tAList.push(a);\n        const tBList = [];\n        for (let b = trailBondFirst; b < v.bondShift; ++b)\n            tBList.push(b);\n        monomers.set(lastPhosKey, {\n            biotype: lastPhosSm.biotype, symbol: lastPhosSm.symbol,\n            atoms: tAList, bonds: tBList,\n        });\n    }\n}\n/** Keep precision upon floating point operations over atom coordinates\n * @param {number}x - the floating point number\n * @return {number} - the floating point number with the same precision\n */\nexport function keepPrecision(x) {\n    return Math.round(C.PRECISION_FACTOR * x) / C.PRECISION_FACTOR;\n}\n//# sourceMappingURL=to-atomic-level-utils.js.map","import { monomerSeqToMolfile } from './to-atomic-level-utils';\nonmessage = (event) => {\n    const { seqList, rolesList, monomersDict, alphabet, polymerType, start, end } = event.data;\n    const resMolList = new Array(end - start);\n    const molfileWarningList = new Array(0);\n    for (let rowI = start; rowI < end; ++rowI) {\n        try {\n            const seq = seqList[rowI];\n            const roles = rolesList ? 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const monomerWorksConsts = {\n    // constants for parsing molfile V2000\n    V2K_RGP_SHIFT: 8,\n    V2K_RGP_LINE: 'M  RGP',\n    V2K_A_LINE: 'A  ',\n    // constants for parsing/reconstruction of molfile V3000\n    V3K_COUNTS_SHIFT: 14,\n    V3K_IDX_SHIFT: 7,\n    V3K_HEADER_FIRST_LINE: '\\nDatagrok macromolecule handler\\n\\n',\n    V3K_HEADER_SECOND_LINE: '  0  0  0  0  0  0            999 V3000\\n',\n    V3K_BEGIN_CTAB_BLOCK: 'M  V30 BEGIN CTAB\\n',\n    V3K_END_CTAB_BLOCK: 'M  V30 END CTAB\\n',\n    V3K_BEGIN_COUNTS_LINE: 'M  V30 COUNTS ',\n    V3K_COUNTS_LINE_ENDING: ' 0 0 0\\n',\n    V3K_BEGIN_ATOM_BLOCK: 'M  V30 BEGIN ATOM\\n',\n    V3K_END_ATOM_BLOCK: 'M  V30 END ATOM\\n',\n    V3K_BEGIN_BOND_BLOCK: 'M  V30 BEGIN BOND\\n',\n    V3K_END_BOND_BLOCK: 'M  V30 END BOND\\n',\n    V3K_BOND_CONFIG: ' CFG=',\n    V3K_BEGIN_DATA_LINE: 'M  V30 ',\n    V3K_END: 'M  END',\n    PRECISION_FACTOR: 10000, // HELMCoreLibrary has 4 significant digits after decimal point in atom coordinates\n    // symbols for the corresponding monomers in HELM library\n    DEOXYRIBOSE: { polymerType: \"RNA\" /* PolymerTypes.RNA */, symbol: 'd' },\n    RIBOSE: { polymerType: \"RNA\" /* PolymerTypes.RNA */, symbol: 'r' },\n    PHOSPHATE: { polymerType: \"RNA\" /* PolymerTypes.RNA */, symbol: 'p' },\n    OXYGEN: 'O',\n    HYDROGEN: 'H',\n};\n//# sourceMappingURL=consts.js.map","export function getMolGraph(dict, libKey) {\n    return dict[libKey.polymerType]?.[libKey.symbol];\n}\nexport function hasMolGraph(dict, libKey) {\n    return !!dict[libKey.polymerType]?.[libKey.symbol];\n}\nexport function setMolGraph(dict, libKey, value) {\n    let pt = dict[libKey.polymerType];\n    if (!pt)\n        pt = dict[libKey.polymerType] = {};\n    pt[libKey.symbol] = value;\n}\n/** Role of an entry in a HELM RNA splitted sequence.\n * SUGAR/BASE/PHOSPHATE are the standard triple positions.\n * TERMINAL_5P marks a 5'-end terminal modifier (e.g. Chol) — a monomer\n * with R2 only that takes the place of the leading sugar.\n * TERMINAL_3P marks a 3'-end terminal modifier (e.g. GalNAc) — a monomer\n * with R1 only that takes the place of the trailing phosphate. The OH cap\n * MUST be omitted when a TERMINAL_3P is present. */\nexport var NucleotideRole;\n(function (NucleotideRole) {\n    NucleotideRole[NucleotideRole[\"SUGAR\"] = 0] = \"SUGAR\";\n    NucleotideRole[NucleotideRole[\"BASE\"] = 1] = \"BASE\";\n    NucleotideRole[NucleotideRole[\"PHOSPHATE\"] = 2] = \"PHOSPHATE\";\n    NucleotideRole[NucleotideRole[\"TERMINAL_5P\"] = 3] = \"TERMINAL_5P\";\n    NucleotideRole[NucleotideRole[\"TERMINAL_3P\"] = 4] = \"TERMINAL_3P\";\n})(NucleotideRole || (NucleotideRole = {}));\nexport class MonomerMap extends Map {\n    constructor(entries) {\n        super(entries);\n    }\n}\n/** @property monomers key - helm seq position, */\nexport class MolfileWithMap {\n    constructor(molfile, monomers) {\n        this.molfile = molfile;\n        this.monomers = monomers;\n    }\n    static createEmpty() { return new MolfileWithMap('', new MonomerMap(null)); }\n}\n//# sourceMappingURL=types.js.map","import { CandidateType } from './types';\n/** enum type to simplify setting \"user-friendly\" notation if necessary */\nexport var NOTATION;\n(function (NOTATION) {\n    NOTATION[\"FASTA\"] = \"fasta\";\n    NOTATION[\"SEPARATOR\"] = \"separator\";\n    NOTATION[\"HELM\"] = \"helm\";\n    /* Requires notation handler */ NOTATION[\"CUSTOM\"] = \"custom\";\n    /* Requires notation handler */ NOTATION[\"BILN\"] = \"biln\";\n})(NOTATION || (NOTATION = {}));\nexport var ALPHABET;\n(function (ALPHABET) {\n    ALPHABET[\"DNA\"] = \"DNA\";\n    ALPHABET[\"RNA\"] = \"RNA\";\n    ALPHABET[\"PT\"] = \"PT\";\n    /** Unknown */\n    ALPHABET[\"UN\"] = \"UN\";\n})(ALPHABET || (ALPHABET = {}));\nexport var TAGS;\n(function (TAGS) {\n    TAGS[\"aligned\"] = \"aligned\";\n    TAGS[\"alphabet\"] = \"alphabet\";\n    TAGS[\"alphabetSize\"] = \".alphabetSize\";\n    TAGS[\"alphabetIsMultichar\"] = \".alphabetIsMultichar\";\n    TAGS[\"separator\"] = \"separator\";\n    TAGS[\"isHelmCompatible\"] = \".isHelmCompatible\";\n    TAGS[\"positionNames\"] = \".positionNames\";\n    TAGS[\"positionLabels\"] = \".positionLabels\";\n    TAGS[\"regions\"] = \".regions\";\n    TAGS[\"positionShift\"] = \".positionShift\";\n    TAGS[\"selectedPosition\"] = \".selectedPosition\";\n    TAGS[\"polymerTypeColumnName\"] = \".polymerTypeColumnName\";\n    TAGS[\"annotations\"] = \".annotations\";\n    TAGS[\"numberingScheme\"] = \".numberingScheme\";\n    TAGS[\"annotationColumnName\"] = \".annotationColumnName\";\n})(TAGS || (TAGS = {}));\nexport { TAGS as BioTags };\nexport const positionSeparator = ', ';\nexport const monomerRe = /(?:\\[([A-Za-z0-9_\\-,()]+)\\])|([A-Za-z\\-])/g;\nexport const helmRe = /(PEPTIDE1|DNA1|RNA1)\\{([^}]+)}/g;\nexport const helmPp1Re = /\\[([^\\[\\]]+)]/g;\nexport const Alphabets = new class {\n    constructor() {\n        this.fasta = {\n            peptide: new Set([\n                'G', 'L', 'Y', 'S', 'E', 'Q', 'D', 'N', 'F', 'A',\n                'K', 'R', 'H', 'C', 'V', 'P', 'W', 'I', 'M', 'T',\n            ]),\n            dna: new Set(['A', 'C', 'G', 'T']),\n            rna: new Set(['A', 'C', 'G', 'U']),\n        };\n    }\n}();\nexport const candidateAlphabets = [\n    new CandidateType(ALPHABET.PT, Alphabets.fasta.peptide, 0.50),\n    new CandidateType(ALPHABET.DNA, Alphabets.fasta.dna, 0.55),\n    new CandidateType(ALPHABET.RNA, Alphabets.fasta.rna, 0.55),\n];\n/** Canonical gap symbol */\nexport const GAP_SYMBOL = '';\nexport const GapOriginals = {\n    [NOTATION.FASTA]: '-',\n    [NOTATION.SEPARATOR]: '',\n    [NOTATION.HELM]: '*',\n    [NOTATION.BILN]: '',\n};\nexport const MONOMER_MOTIF_SPLITTER = ' , ';\n/** Tag on Monomer columns storing the nqName of a function that returns an IMonomerCanonicalizer.\n *  The `.%` prefix ensures this tag is persisted with projects. */\nexport const MONOMER_CANONICALIZER_FUNC_TAG = '.%monomer-canonicalizer-func';\n/** Column temp key for the cached IMonomerCanonicalizer instance */\nexport const MONOMER_CANONICALIZER_TEMP = 'monomer-canonicalizer';\nexport const NOTATION_PROVIDER_CONSTRUCTOR_ROLE = 'notationProviderConstructor';\n//# sourceMappingURL=consts.js.map","// core fields of HELM library object used in toAtomicLevel function\nexport const HELM_CORE_FIELDS = [\n    \"symbol\" /* HELM_FIELDS.SYMBOL */,\n    \"molfile\" /* HELM_FIELDS.MOLFILE */,\n    \"rgroups\" /* HELM_FIELDS.RGROUPS */,\n    \"name\" /* HELM_FIELDS.NAME */,\n    // HELM_FIELDS.MONOMER_TYPE, // add if terminal monomers for PEPTIDEs to be\n    // supported\n];\nexport const SDF_MONOMER_NAME = 'MonomerName';\n// todo: ideally, keys should be expressed via constants\nexport const jsonSdfMonomerLibDict = {\n    'monomerType': null, // -> Backbone\n    'smiles': null,\n    'name': 'Name',\n    'author': null,\n    'molfile': 'molecule',\n    'naturalAnalog': 'MonomerNaturalAnalogCode',\n    'rgroups': 'MonomerCaps',\n    'createDate': null,\n    'id': null,\n    'polymerType': 'MonomerType',\n    'symbol': 'MonomerName'\n};\nexport const DUMMY_MONOMER = {\n    'monomerType': 'Backbone',\n    'smiles': '',\n    'name': '',\n    'author': 'Datagrok',\n    'molfile': '',\n    'naturalAnalog': '',\n    'rgroups': [],\n    'createDate': null,\n    'id': 0,\n    'polymerType': 'PEPTIDE',\n    'symbol': ''\n};\n// range of hex nubers used in PepSea library to endode monomers\nexport const MONOMER_ENCODE_MIN = 0x100;\nexport const MONOMER_ENCODE_MAX = 0x40A;\nexport const RIBOSE_SYMBOL = 'r';\nexport const DEOXYRIBOSE_SYMBOL = 'd';\nexport const PHOSPHATE_SYMBOL = 'p';\nexport const HELM_WRAPPERS_REGEXP = new RegExp(`[${RIBOSE_SYMBOL}${DEOXYRIBOSE_SYMBOL}]\\\\((\\\\w)\\\\)${PHOSPHATE_SYMBOL}?`, 'g');\n//# sourceMappingURL=const.js.map","import { NOTATION_PROVIDER_CONSTRUCTOR_ROLE } from './consts';\nexport class NotationProviderBase {\n    /** Name of the custom notation */\n    static get notationName() {\n        return 'Custom';\n    }\n    ;\n    /** flag to let bio know if this provider implements method for converting helm to it */\n    static get implementsFromHelm() {\n        return false;\n    }\n    ;\n    /** Method for converting HELM to this notation */\n    static convertFromHelm(helm, options) {\n        throw new Error(`Method convertFromHelm not implemented for this notation provider`);\n    }\n    ;\n    static async getProviderConstructors() {\n        // this is terrible, I know, but otherwise this gets put in webworkers and fails due to DG resolution)))\n        // @ts-ignore\n        if (window?.DG) {\n            // @ts-ignore\n            const constFuncs = window.DG.Func.find({ meta: { role: NOTATION_PROVIDER_CONSTRUCTOR_ROLE } });\n            return Promise.all(constFuncs.map((f) => f.apply({})));\n        }\n        return [];\n    }\n}\n/** Alphabet candidate type */\nexport class CandidateType {\n    constructor(name, alphabet, cutoff) {\n        this.name = name;\n        this.alphabet = alphabet;\n        this.cutoff = cutoff;\n    }\n}\n/** Alphabet candidate similarity type */\nexport class CandidateSimType extends CandidateType {\n    constructor(candidate, freq, similarity) {\n        super(candidate.name, candidate.alphabet, candidate.cutoff);\n        this.freq = freq;\n        this.similarity = similarity;\n    }\n}\n//# sourceMappingURL=types.js.map","export var HelmTypes;\n(function (HelmTypes) {\n    HelmTypes[\"BASE\"] = \"HELM_BASE\";\n    HelmTypes[\"SUGAR\"] = \"HELM_SUGAR\";\n    HelmTypes[\"LINKER\"] = \"HELM_LINKER\";\n    HelmTypes[\"AA\"] = \"HELM_AA\";\n    HelmTypes[\"CHEM\"] = \"HELM_CHEM\";\n    HelmTypes[\"BLOB\"] = \"HELM_BLOB\";\n    HelmTypes[\"NUCLEOTIDE\"] = \"HELM_NUCLETIDE\";\n})(HelmTypes || (HelmTypes = {}));\n//# sourceMappingURL=org.js.map","import { HelmTypes } from '../helm/consts';\nexport class MonomerWorks {\n    //private molfileConverter: IMolfileConverter;\n    constructor(monomerLib /*, molfileConverter: IMolfileConverter*/) {\n        this.monomerLib = monomerLib;\n        //this.molfileConverter = molfileConverter;\n    }\n    //types according to Monomer possible\n    getCappedRotatedMonomer(monomerType, monomerName) {\n        // TODO: Check type of monomerType arg\n        const monomer = this.monomerLib.getMonomer(monomerType, monomerName);\n        if (monomer)\n            return monomer.molfile; //TODO cap\n        return null;\n    }\n}\nexport function helmTypeToPolymerType(helmType) {\n    let polymerType = undefined;\n    switch (helmType) {\n        case HelmTypes.BASE:\n        case HelmTypes.SUGAR: // r - ribose, d - deoxyribose\n        case HelmTypes.LINKER: // p - phosphate\n        case HelmTypes.NUCLEOTIDE:\n        // @ts-ignore\n        case 'nucleotide':\n            polymerType = \"RNA\" /* PolymerTypes.RNA */;\n            break;\n        case HelmTypes.AA:\n            polymerType = \"PEPTIDE\" /* PolymerTypes.PEPTIDE */;\n            break;\n        case HelmTypes.CHEM:\n            polymerType = \"CHEM\" /* PolymerTypes.CHEM */;\n            break;\n        case HelmTypes.BLOB:\n            polymerType = \"BLOB\" /* PolymerTypes.BLOB */;\n            break;\n        default:\n            polymerType = \"PEPTIDE\" /* PolymerTypes.PEPTIDE */;\n            console.warn(`Unexpected HelmType '${helmType}'`);\n    }\n    return polymerType;\n}\n//# sourceMappingURL=monomer-works.js.map","/* eslint-disable max-len */\nimport { monomerWorksConsts as C } from './consts';\nimport { getMolGraph, MolfileWithMap, MonomerMap, NucleotideRole } from './types';\nimport { HELM_CORE_FIELDS, } from '../utils/const';\nimport { ALPHABET, GAP_SYMBOL } from '../utils/macromolecule/consts';\nimport { helmTypeToPolymerType } from './monomer-works';\n/** Get a mapping of peptide symbols to HELM monomer library objects with selected fields.\n * @param {IMonomerLib} monomerLib - Monomer library\n * @param {HELM_POLYMER_TYPE} polymerType - Polymer type\n * @param {ALPHABET} alphabet - Alphabet of the column\n * @return {Map<string, any>} - Mapping of peptide symbols to HELM monomer library objects with selected fields*/\nexport function getFormattedMonomerLib(monomerLib, polymerType, alphabet) {\n    const map = new Map();\n    for (const monomerSymbol of monomerLib.getMonomerSymbolsByType(polymerType)) {\n        const it = monomerLib.getMonomer(polymerType, monomerSymbol);\n        if (\n        // RNA: all branch monomers (bases) and all backbone monomers (sugars +\n        // phosphates, including modified ones). Modifications are looked up by\n        // symbol at assembly time, so they MUST be present in the formatted lib.\n        polymerType === \"RNA\" /* HELM_POLYMER_TYPE.RNA */ || (polymerType === \"PEPTIDE\" /* HELM_POLYMER_TYPE.PEPTIDE */ &&\n            it[\"monomerType\" /* HELM_FIELDS.MONOMER_TYPE */] !== \"Branch\" /* HELM_MONOMER_TYPE.BRANCH */)) {\n            const monomerObject = {};\n            HELM_CORE_FIELDS.forEach((field) => {\n                //@ts-ignore\n                monomerObject[field] = it[field];\n            });\n            map.set(monomerSymbol, monomerObject);\n        }\n    }\n    return map;\n}\n/** Translate a sequence of monomer symbols into Molfile V3000\n * @param {ISeqMonomer[]} monomerSeq - Sequence of monomer symbols (canonical)\n * @param {MonomerMolGraphMap} monomersDict - Mapping of monomer symbols to MolGraph objects\n * @param {ALPHABET} alphabet - Alphabet of the column\n * @param {PolymerType} polymerType - Polymer type\n * @param {Array} roles - Optional per-position NucleotideRole tags. When set, RNA assembly\n *   uses per-position sugars/phosphates from monomerSeq directly (HELM triples mode).\n * @return {MolfileWithMap} - Molfile V3000 + per-position monomer index map */\nexport function monomerSeqToMolfile(monomerSeq, monomersDict, alphabet, polymerType, roles) {\n    if (monomerSeq.length === 0) {\n        // throw new Error('monomerSeq is empty');\n        return MolfileWithMap.createEmpty();\n    }\n    // Triples mode is on only when the caller flagged the row with roles\n    // (built and validated by `buildRolesForHelmRna` in to-atomic-level.ts).\n    // The roles array carries the per-position semantics — including\n    // TERMINAL_5P / TERMINAL_3P for non-canonical chain ends — so we don't\n    // re-validate the length here.\n    const triplesMode = polymerType === \"RNA\" /* HELM_POLYMER_TYPE.RNA */ && !!roles &&\n        roles.length === monomerSeq.length;\n    // define atom and bond counts, taking into account the bond type\n    const { atomCount, bondCount, needsCapping } = getResultingAtomBondCounts(monomerSeq, monomersDict, alphabet, polymerType, triplesMode, roles);\n    // create arrays to store lines of the resulting molfile\n    const molfileAtomBlock = new Array(atomCount);\n    const molfileBondBlock = new Array(bondCount);\n    let addMonomerToMolblock;\n    let sugar = null;\n    let phosphate = null;\n    if (polymerType === \"PEPTIDE\" /* HELM_POLYMER_TYPE.PEPTIDE */)\n        addMonomerToMolblock = addAminoAcidToMolblock;\n    else { // nucleotides\n        addMonomerToMolblock = addNucleotideToMolblock;\n        // Default sugar/phosphate are only consulted in bases-only mode. In\n        // triples mode, every nucleotide carries its own.\n        if (!triplesMode) {\n            sugar = (alphabet === ALPHABET.DNA) ? getMolGraph(monomersDict, C.DEOXYRIBOSE) : getMolGraph(monomersDict, C.RIBOSE);\n            phosphate = getMolGraph(monomersDict, C.PHOSPHATE);\n        }\n    }\n    const v = {\n        i: 0,\n        nodeShift: 0,\n        bondShift: 0,\n        backbonePositionShift: new Array(2).fill(0),\n        branchPositionShift: new Array(2).fill(0),\n        backboneAttachNode: 0,\n        branchAttachNode: 0,\n        flipFactor: 1,\n    };\n    const LC = {\n        sugar: sugar,\n        phosphate: phosphate,\n        // In triples mode, the \"logical\" sequence length is the nucleotide count.\n        seqLength: triplesMode ? Math.ceil(monomerSeq.length / 3) : monomerSeq.length,\n        atomCount: atomCount,\n        bondCount: bondCount,\n    };\n    const monomers = new MonomerMap();\n    const steabsCollection = [];\n    let nAtoms = 0;\n    let lastMonomerCappingAtom = undefined;\n    if (triplesMode) {\n        runTriplesAssembly(monomerSeq, roles, monomersDict, molfileAtomBlock, molfileBondBlock, v, LC, monomers, steabsCollection, (a) => { nAtoms += a; }, () => nAtoms);\n    }\n    else {\n        for (v.i = 0; v.i < LC.seqLength; ++v.i) {\n            const seqMonomer = monomerSeq[v.i];\n            if (seqMonomer.symbol === GAP_SYMBOL)\n                continue;\n            const monomer = getMolGraph(monomersDict, { symbol: seqMonomer.symbol, polymerType: helmTypeToPolymerType(seqMonomer.biotype) });\n            lastMonomerCappingAtom = monomer.terminalR2Atom;\n            const mAtomFirst = v.nodeShift;\n            const mBondFirst = v.bondShift;\n            addMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v, LC);\n            //adding stereo atoms to array for further STEABS block generation\n            monomer.stereoAtoms?.forEach((i) => steabsCollection.push(i + nAtoms));\n            nAtoms += monomer.atoms.x.length;\n            const mAtomCount = v.nodeShift - mAtomFirst;\n            const mAtomList = new Array(mAtomCount);\n            for (let maI = 0; maI < mAtomCount; ++maI)\n                mAtomList[maI] = mAtomFirst + maI;\n            const mBondCount = v.bondShift - mBondFirst;\n            const mBondList = new Array(mBondCount);\n            for (let mbI = 0; mbI < mBondCount; ++mbI)\n                mBondList[mbI] = mBondFirst + mbI;\n            monomers.set(v.i, {\n                biotype: seqMonomer.biotype,\n                symbol: seqMonomer.symbol,\n                atoms: mAtomList, bonds: mBondList\n            });\n        }\n    }\n    // if the last monomer needs to be capped, add the terminal OH to the resulting molfile\n    if (needsCapping)\n        capResultingMolblock(molfileAtomBlock, molfileBondBlock, v, LC, lastMonomerCappingAtom ?? C.OXYGEN);\n    const molfileCountsLine = C.V3K_BEGIN_COUNTS_LINE + atomCount + ' ' + bondCount + C.V3K_COUNTS_LINE_ENDING;\n    // todo: possible optimization may be achieved by replacing .join('') with +=\n    // since counterintuitively joining an array into a new string is reportedly\n    // slower than using += as below\n    let result = '';\n    result += C.V3K_HEADER_FIRST_LINE;\n    result += C.V3K_HEADER_SECOND_LINE;\n    result += C.V3K_BEGIN_CTAB_BLOCK;\n    result += molfileCountsLine;\n    result += C.V3K_BEGIN_ATOM_BLOCK;\n    result += molfileAtomBlock.join('');\n    result += C.V3K_END_ATOM_BLOCK;\n    result += C.V3K_BEGIN_BOND_BLOCK;\n    result += molfileBondBlock.join('');\n    result += C.V3K_END_BOND_BLOCK;\n    if (steabsCollection.length > 0)\n        result += getCollectionBlock(steabsCollection);\n    result += C.V3K_END_CTAB_BLOCK;\n    result += C.V3K_END;\n    // return molfileParts.join('');\n    return { molfile: result, monomers: monomers };\n}\nfunction getCollectionBlock(collection) {\n    //one row in STEABS block can be no longer than 80 symbols\n    //maxSymbols = 80 symbols minus ' -\\n' (4 symbols)\n    const maxSymbols = 76;\n    const rowsArray = [];\n    let newCollectionRow = `M  V30 MDLV30/STEABS ATOMS=(${collection.length}`;\n    for (let i = 0; i < collection.length; i++) {\n        const updatedRow = `${newCollectionRow} ${collection[i]}`;\n        if (updatedRow.length > maxSymbols) {\n            rowsArray.push(`${newCollectionRow} -\\n`);\n            newCollectionRow = `M  V30 ${collection[i]}`;\n        }\n        else\n            newCollectionRow = updatedRow;\n        //in case last atom was added - close the block\n        if (i === collection.length - 1)\n            rowsArray.push(`${newCollectionRow})\\n`);\n    }\n    return `M  V30 BEGIN COLLECTION\\n${rowsArray.join('')}M  V30 END COLLECTION\\n`;\n}\n/** Cap the resulting (after sewing up all the monomers) molfile with 'O'\n * @param {string[]} molfileAtomBlock - Array of lines of the resulting molfile atom block\n * @param {string[]} molfileBondBlock - Array of lines of the resulting molfile bond block\n * @param {LoopVariables} v - Loop variables\n * @param {LoopConstants} LC - Loop constants*/\nfunction capResultingMolblock(molfileAtomBlock, molfileBondBlock, v, LC, cappingAtomType = C.OXYGEN) {\n    // add terminal oxygen\n    const atomIdx = v.nodeShift + 1;\n    molfileAtomBlock[LC.atomCount] = C.V3K_BEGIN_DATA_LINE + atomIdx + ' ' +\n        (cappingAtomType ?? C.OXYGEN) + ' ' + keepPrecision(v.backbonePositionShift[0]) + ' ' +\n        v.flipFactor * keepPrecision(v.backbonePositionShift[1]) + ' ' + '0.000000 0' + '\\n';\n    // add terminal bond\n    const firstAtom = v.backboneAttachNode;\n    const secondAtom = atomIdx;\n    molfileBondBlock[LC.bondCount] = C.V3K_BEGIN_DATA_LINE + v.bondShift + ' ' +\n        1 + ' ' + firstAtom + ' ' + secondAtom + '\\n';\n}\nfunction addAminoAcidToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v) {\n    v.flipFactor = (-1) ** (v.i % 2); // to flip every even monomer over OX\n    addBackboneMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v);\n}\nfunction addBackboneMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v) {\n    // todo: remove these comments to the docstrings of the corr. functions\n    // construnct the lines of V3K molfile atom block\n    fillAtomLines(monomer, molfileAtomBlock, v);\n    // construct the lines of V3K molfile bond block\n    fillBondLines(monomer, molfileBondBlock, v);\n    // peptide bond\n    fillChainExtendingBond(monomer, molfileBondBlock, v);\n    // update branch variables if necessary\n    if (monomer.meta.branchShift !== null && monomer.meta.terminalNodes.length > 2)\n        updateBranchVariables(monomer, v);\n    // update loop variables\n    updateChainExtendingVariables(monomer, v);\n}\nfunction addNucleotideToMolblock(nucleobase, molfileAtomBlock, molfileBondBlock, v, LC) {\n    // construnct the lines of V3K molfile atom block corresponding to phosphate\n    // and sugar\n    if (v.i === 0)\n        addBackboneMonomerToMolblock(LC.sugar, molfileAtomBlock, molfileBondBlock, v);\n    else {\n        for (const monomer of [LC.phosphate, LC.sugar])\n            addBackboneMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v);\n    }\n    addBranchMonomerToMolblock(nucleobase, molfileAtomBlock, molfileBondBlock, v);\n}\nfunction addBranchMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v) {\n    fillBranchAtomLines(monomer, molfileAtomBlock, v);\n    fillBondLines(monomer, molfileBondBlock, v);\n    fillBackboneToBranchBond(monomer, molfileBondBlock, v);\n    // C-N bond\n    const bondIdx = v.bondShift;\n    const firstAtom = v.branchAttachNode;\n    const secondAtom = monomer.meta.terminalNodes[0] + v.nodeShift;\n    molfileBondBlock[bondIdx - 1] = C.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +\n        1 + ' ' + firstAtom + ' ' + secondAtom + '\\n';\n    // update loop variables\n    v.bondShift += monomer.bonds.atomPairs.length + 1;\n    v.nodeShift += monomer.atoms.atomTypes.length;\n}\nfunction updateChainExtendingVariables(monomer, v) {\n    v.backboneAttachNode = v.nodeShift + monomer.meta.terminalNodes[1];\n    v.bondShift += monomer.bonds.atomPairs.length + 1;\n    v.nodeShift += monomer.atoms.atomTypes.length;\n    v.backbonePositionShift[0] += monomer.meta.backboneShift?.[0] ?? 0; // todo: non-null check\n    v.backbonePositionShift[1] += v.flipFactor * (monomer.meta.backboneShift?.[1] ?? 0);\n}\nfunction updateBranchVariables(monomer, v) {\n    v.branchAttachNode = v.nodeShift + monomer.meta.terminalNodes[2];\n    for (let i = 0; i < 2; ++i)\n        v.branchPositionShift[i] = v.backbonePositionShift[i] + monomer.meta.branchShift[i];\n}\nfunction fillAtomLines(monomer, molfileAtomBlock, v) {\n    for (let j = 0; j < monomer.atoms.atomTypes.length; ++j) {\n        const atomIdx = v.nodeShift + j + 1;\n        molfileAtomBlock[v.nodeShift + j] = C.V3K_BEGIN_DATA_LINE + atomIdx + ' ' +\n            monomer.atoms.atomTypes[j] + ' ' +\n            keepPrecision(v.backbonePositionShift[0] + monomer.atoms.x[j]) + ' ' +\n            keepPrecision(v.backbonePositionShift[1] + v.flipFactor * monomer.atoms.y[j]) +\n            ' ' + monomer.atoms.kwargs[j];\n    }\n}\n// todo: remove as quickfix\nfunction fillBranchAtomLines(monomer, molfileAtomBlock, v) {\n    for (let j = 0; j < monomer.atoms.atomTypes.length; ++j) {\n        const atomIdx = v.nodeShift + j + 1;\n        molfileAtomBlock[v.nodeShift + j] = C.V3K_BEGIN_DATA_LINE + atomIdx + ' ' +\n            monomer.atoms.atomTypes[j] + ' ' +\n            keepPrecision(v.branchPositionShift[0] + monomer.atoms.x[j]) + ' ' +\n            keepPrecision(v.branchPositionShift[1] + v.flipFactor * monomer.atoms.y[j]) +\n            ' ' + monomer.atoms.kwargs[j];\n    }\n}\nfunction fillBondLines(monomer, molfileBondBlock, v) {\n    // construct the lines of V3K molfile bond block\n    for (let j = 0; j < monomer.bonds.atomPairs.length; ++j) {\n        const bondIdx = v.bondShift + j + 1;\n        const firstAtom = monomer.bonds.atomPairs[j][0] + v.nodeShift;\n        const secondAtom = monomer.bonds.atomPairs[j][1] + v.nodeShift;\n        let bondCfg = '';\n        if (monomer.bonds.bondConfiguration.has(j)) {\n            // flip orientation when necessary\n            let orientation = monomer.bonds.bondConfiguration.get(j);\n            if (v.flipFactor < 0)\n                orientation = (orientation === 1) ? 3 : 1;\n            bondCfg = ' CFG=' + orientation;\n        }\n        const kwargs = monomer.bonds.kwargs.has(j) ?\n            ' ' + monomer.bonds.kwargs.get(j) : '';\n        molfileBondBlock[v.bondShift + j] = C.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +\n            monomer.bonds.bondTypes[j] + ' ' +\n            firstAtom + ' ' + secondAtom + bondCfg + kwargs + '\\n';\n    }\n}\nfunction fillChainExtendingBond(monomer, molfileBondBlock, v) {\n    if (v.backboneAttachNode !== 0) {\n        const bondIdx = v.bondShift;\n        const firstAtom = v.backboneAttachNode;\n        const secondAtom = monomer.meta.terminalNodes[0] + v.nodeShift;\n        molfileBondBlock[v.bondShift - 1] = C.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +\n            1 + ' ' + firstAtom + ' ' + secondAtom + '\\n';\n    }\n}\n// todo: remove\nfunction fillBackboneToBranchBond(branchMonomer, molfileBondBlock, v) {\n    const bondIdx = v.bondShift;\n    const firstAtom = v.branchAttachNode;\n    const secondAtom = branchMonomer.meta.terminalNodes[0] + v.nodeShift;\n    molfileBondBlock[bondIdx - 1] = C.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +\n        1 + ' ' + firstAtom + ' ' + secondAtom + '\\n';\n}\n/** Compute the atom/bond counts for the resulting molfile, depending on the\n * type of polymer (peptide/nucleotide)\n * @param {ISeqMonomer[]} monomerSeq - the sequence of monomers\n * @param {MonomerMolGraphMap} monomersDict - the dictionary of monomers\n * @param {ALPHABET} alphabet - the alphabet of the monomers\n * @param {PolymerType} polymerType - the type of polymer\n * @param {boolean} triplesMode - true when monomerSeq is a flat list of HELM RNA triples\n * @param {Array} roles - per-position role tags (only meaningful when triplesMode is true)\n * @return {Object} the atom/bond counts plus needsCapping flag */\nfunction getResultingAtomBondCounts(monomerSeq, monomersDict, alphabet, polymerType, triplesMode, roles) {\n    let atomCount = 0;\n    let bondCount = 0;\n    let monomerCount = 0;\n    let needsCapping = true;\n    let lastMonomerGraph = null;\n    let lastPhosphateGraph = null;\n    // sum up all the atoms/nodes provided by the sequence\n    for (let i = 0; i < monomerSeq.length; ++i) {\n        const seqMonomer = monomerSeq[i];\n        if (seqMonomer.symbol === GAP_SYMBOL)\n            continue; // Skip for gap/empty monomer in MSA\n        if (seqMonomer.symbol == '*')\n            throw new Error(`Gap canonical symbol is '', not '*`);\n        lastMonomerGraph = getMolGraph(monomersDict, { symbol: seqMonomer.symbol, polymerType: helmTypeToPolymerType(seqMonomer.biotype) });\n        atomCount += lastMonomerGraph.atoms.x.length;\n        bondCount += lastMonomerGraph.bonds.bondTypes.length;\n        monomerCount++;\n        // In triples mode, every 3rd entry (index 2 mod 3) is a phosphate. Track\n        // the LAST one — its atoms/bonds are dropped at the 3'-terminus.\n        if (triplesMode && i % 3 === 2)\n            lastPhosphateGraph = lastMonomerGraph;\n    }\n    // add extra values depending on the polymer type\n    if (polymerType === \"PEPTIDE\" /* HELM_POLYMER_TYPE.PEPTIDE */) {\n        // add the rightmost/terminating cap group 'OH' (i.e. 'O')\n        atomCount += 1;\n        // add chain-extending bonds (C-NH per each monomer pair and terminal C-OH)\n        bondCount += monomerCount;\n        // if the last monomer is something like NH2, which only has R1, there is no need to cap it\n        // although, this should never happen, but hey... in other bits of code, there is a chunk that adds pseudo-R2 as hydrogen\n        // we should also check, if the R2 of the last monomer is not hydrogen, that case should also be omitted\n        if (monomerCount > 0) {\n            if ((lastMonomerGraph?.meta?.rNodes?.length ?? 0) < 2 || lastMonomerGraph?.terminalR2Atom?.toLowerCase() === C.HYDROGEN.toLowerCase()) {\n                needsCapping = false;\n                atomCount -= 1; // remove the last atom (the terminal 'O')\n                bondCount -= 1; // remove the last bond (the terminal C-OH)\n            }\n        }\n    }\n    else if (triplesMode) { // nucleotides — HELM triples (per-position sugar/base/phosphate)\n        void lastPhosphateGraph; // kept for symmetry; trailing P is now retained when HELM wrote it\n        // Per-monomer-loop already summed sugars + bases + phosphates for every\n        // entry in monomerSeq (terminals included). Reservation: each backbone\n        // emit (sugar / phosphate / terminal) reserves +1 bond slot for the\n        // chain-extending bond, each branch (base) reserves +1 for its branch\n        // bond. Total reservations = monomerCount.\n        bondCount += monomerCount;\n        // OH cap atom rides on the 3'-end. Skip it when HELM specified a\n        // 3'-terminal modifier (e.g. GalNAc) that IS the chain end.\n        const has3pTerm = !!roles && roles.length > 0 &&\n            roles[roles.length - 1] === NucleotideRole.TERMINAL_3P;\n        if (has3pTerm)\n            needsCapping = false;\n        else\n            atomCount += 1; // OH cap atom (rides on trailing P or on last sugar's R2)\n    }\n    else { // nucleotides — bases-only legacy path with default sugar/phosphate\n        const sugar = (alphabet === ALPHABET.DNA) ?\n            getMolGraph(monomersDict, C.DEOXYRIBOSE) : getMolGraph(monomersDict, C.RIBOSE);\n        const phosphate = getMolGraph(monomersDict, C.PHOSPHATE);\n        // add phosphate per each pair of nucleobase symbols\n        atomCount += (monomerSeq.length - 1) * phosphate.atoms.x.length;\n        // add sugar per each nucleobase symbol\n        atomCount += monomerSeq.length * sugar.atoms.x.length;\n        // add the leftmost cap group 'OH' (i.e. 'O')\n        atomCount += 1;\n        // add bonds from phosphate monomers\n        bondCount += (monomerSeq.length - 1) * phosphate.bonds.bondTypes.length;\n        // add bonds from sugar monomers\n        bondCount += monomerSeq.length * sugar.bonds.bondTypes.length;\n        // exclude the first chain-extending bond O-P (absent, no 'leftmost' phosphate)\n        bondCount -= 1;\n        // add chain-extending and branch bonds (O-P, C-O and C-N per each nucleotide)\n        bondCount += monomerSeq.length * 3;\n    }\n    return { atomCount, bondCount, needsCapping };\n}\n// Triples-mode RNA assembly. Iterates by NUCLEOTIDE over the row's \"core\"\n// positions (those tagged SUGAR/BASE/PHOSPHATE), and emits at most one\n// TERMINAL_5P at the head and one TERMINAL_3P at the tail.\n//\n// Layout permutations the function handles:\n//   roles = [SUGAR, BASE, PHOSPHATE, ...]                     // standard RNA\n//   roles = [..., SUGAR, BASE]                                // no trailing P\n//   roles = [TERMINAL_5P, SUGAR, BASE, PHOSPHATE, ...]        // 5' modifier\n//   roles = [..., SUGAR, BASE, TERMINAL_3P]                   // 3' modifier (replaces last P)\n//   roles = [TERMINAL_5P, ..., TERMINAL_3P]                   // both\n//\n// When a TERMINAL_3P is present the OH cap MUST be skipped (the last\n// monomer is the chain end, period); the caller takes responsibility for\n// needsCapping=false in `getResultingAtomBondCounts`.\nfunction runTriplesAssembly(monomerSeq, roles, monomersDict, molfileAtomBlock, molfileBondBlock, v, LC, monomers, steabsCollection, addAtoms, getAtoms) {\n    const has5pTerm = roles.length > 0 && roles[0] === NucleotideRole.TERMINAL_5P;\n    const has3pTerm = roles.length > 0 && roles[roles.length - 1] === NucleotideRole.TERMINAL_3P;\n    const coreStart = has5pTerm ? 1 : 0;\n    const coreEnd = has3pTerm ? roles.length - 1 : roles.length;\n    const coreLen = coreEnd - coreStart;\n    const N = Math.ceil(coreLen / 3); // nucleotide count in the core\n    // coreLen === 3N → trailing P present.  coreLen === 3N - 1 → no trailing P.\n    const hasTrailingP = coreLen === 3 * N;\n    // Helper: emit one monomer as a backbone unit and record its atom/bond\n    // ranges in the per-row monomer map.\n    const emitBackbone = (sm, mapKey) => {\n        const mG = getMolGraph(monomersDict, { symbol: sm.symbol, polymerType: helmTypeToPolymerType(sm.biotype) });\n        const aFirst = v.nodeShift;\n        const bFirst = v.bondShift;\n        addBackboneMonomerToMolblock(mG, molfileAtomBlock, molfileBondBlock, v);\n        mG.stereoAtoms?.forEach((i) => steabsCollection.push(i + getAtoms()));\n        addAtoms(mG.atoms.x.length);\n        const aList = [];\n        for (let a = aFirst; a < v.nodeShift; ++a)\n            aList.push(a);\n        const bList = [];\n        for (let b = bFirst; b < v.bondShift; ++b)\n            bList.push(b);\n        monomers.set(mapKey, { biotype: sm.biotype, symbol: sm.symbol, atoms: aList, bonds: bList });\n    };\n    // 1. 5'-end terminal modifier (e.g. Chol).\n    if (has5pTerm) {\n        v.i = 0;\n        emitBackbone(monomerSeq[0], 0);\n    }\n    // 2. Core triples loop: each iteration emits [prev-P (if n>=1)] + sugar + base.\n    for (let n = 0; n < N; ++n) {\n        v.i = n + (has5pTerm ? 1 : 0); // keep v.i monotone across emits\n        const sugarSeqIdx = coreStart + 3 * n;\n        const baseSeqIdx = sugarSeqIdx + 1;\n        const sugarSm = monomerSeq[sugarSeqIdx];\n        const baseSm = monomerSeq[baseSeqIdx];\n        const sugarG = getMolGraph(monomersDict, { symbol: sugarSm.symbol, polymerType: helmTypeToPolymerType(sugarSm.biotype) });\n        const baseG = getMolGraph(monomersDict, { symbol: baseSm.symbol, polymerType: helmTypeToPolymerType(baseSm.biotype) });\n        // Inter-nucleotide phosphate sits at coreStart + 3*(n-1) + 2 for n >= 1.\n        if (n >= 1) {\n            const prevPhosKey = coreStart + 3 * (n - 1) + 2;\n            emitBackbone(monomerSeq[prevPhosKey], prevPhosKey);\n        }\n        // Sugar (backbone)\n        const sugarAtomFirst = v.nodeShift;\n        const sugarBondFirst = v.bondShift;\n        addBackboneMonomerToMolblock(sugarG, molfileAtomBlock, molfileBondBlock, v);\n        sugarG.stereoAtoms?.forEach((i) => steabsCollection.push(i + getAtoms()));\n        addAtoms(sugarG.atoms.x.length);\n        const sAList = [];\n        for (let a = sugarAtomFirst; a < v.nodeShift; ++a)\n            sAList.push(a);\n        const sBList = [];\n        for (let b = sugarBondFirst; b < v.bondShift; ++b)\n            sBList.push(b);\n        monomers.set(sugarSeqIdx, {\n            biotype: sugarSm.biotype, symbol: sugarSm.symbol,\n            atoms: sAList, bonds: sBList,\n        });\n        // Base (branch)\n        const baseAtomFirst = v.nodeShift;\n        const baseBondFirst = v.bondShift;\n        addBranchMonomerToMolblock(baseG, molfileAtomBlock, molfileBondBlock, v);\n        baseG.stereoAtoms?.forEach((i) => steabsCollection.push(i + getAtoms()));\n        addAtoms(baseG.atoms.x.length);\n        const bAList = [];\n        for (let a = baseAtomFirst; a < v.nodeShift; ++a)\n            bAList.push(a);\n        const bBList = [];\n        for (let b = baseBondFirst; b < v.bondShift; ++b)\n            bBList.push(b);\n        monomers.set(baseSeqIdx, {\n            biotype: baseSm.biotype, symbol: baseSm.symbol,\n            atoms: bAList, bonds: bBList,\n        });\n    }\n    // 3. Trailing phosphate (the LAST nucleotide's P) — only if HELM wrote\n    // one AND there is no 3'-terminal modifier replacing it.\n    if (hasTrailingP) {\n        const lastPhosKey = coreStart + 3 * (N - 1) + 2;\n        emitBackbone(monomerSeq[lastPhosKey], lastPhosKey);\n    }\n    // 4. 3'-end terminal modifier (e.g. GalNAc).\n    if (has3pTerm) {\n        v.i = N + (has5pTerm ? 1 : 0);\n        emitBackbone(monomerSeq[roles.length - 1], roles.length - 1);\n    }\n}\n/** Keep precision upon floating point operations over atom coordinates\n * @param {number}x - the floating point number\n * @return {number} - the floating point number with the same precision\n */\nexport function keepPrecision(x) {\n    return Math.round(C.PRECISION_FACTOR * x) / C.PRECISION_FACTOR;\n}\n//# sourceMappingURL=to-atomic-level-utils.js.map","import { monomerSeqToMolfile } from './to-atomic-level-utils';\nonmessage = (event) => {\n    const { seqList, rolesList, monomersDict, alphabet, polymerType, start, end } = event.data;\n    const resMolList = new Array(end - start);\n    const molfileWarningList = new Array(0);\n    for (let rowI = start; rowI < end; ++rowI) {\n        try {\n            const seq = seqList[rowI];\n            const roles = rolesList ? rolesList[rowI] : undefined;\n            resMolList[rowI - start] = monomerSeqToMolfile(seq, monomersDict, alphabet, polymerType, roles);\n        }\n        catch (err) {\n            const errMsg = err instanceof Error ? err.message : err.toString();\n            const msg = `Cannot get molfile of row #${rowI}: ${errMsg}.`;\n            molfileWarningList.push(msg);\n        }\n    }\n    postMessage({ molfiles: resMolList, warnings: molfileWarningList });\n};\n//# sourceMappingURL=seq-to-molfile-worker.js.map"],"names":["monomerWorksConsts","V2K_RGP_SHIFT","V2K_RGP_LINE","V2K_A_LINE","V3K_COUNTS_SHIFT","V3K_IDX_SHIFT","V3K_HEADER_FIRST_LINE","V3K_HEADER_SECOND_LINE","V3K_BEGIN_CTAB_BLOCK","V3K_END_CTAB_BLOCK","V3K_BEGIN_COUNTS_LINE","V3K_COUNTS_LINE_ENDING","V3K_BEGIN_ATOM_BLOCK","V3K_END_ATOM_BLOCK","V3K_BEGIN_BOND_BLOCK","V3K_END_BOND_BLOCK","V3K_BOND_CONFIG","V3K_BEGIN_DATA_LINE","V3K_END","PRECISION_FACTOR","DEOXYRIBOSE","polymerType","symbol","RIBOSE","PHOSPHATE","OXYGEN","HYDROGEN","getMolGraph","dict","libKey","NucleotideRole","NOTATION","ALPHABET","TAGS","MonomerMap","Map","constructor","entries","super","MolfileWithMap","molfile","monomers","this","createEmpty","RegExp","CandidateType","name","alphabet","cutoff","Alphabets","fasta","peptide","Set","dna","rna","HelmTypes","helmTypeToPolymerType","helmType","BASE","SUGAR","LINKER","NUCLEOTIDE","AA","CHEM","BLOB","console","warn","monomerSeqToMolfile","monomerSeq","monomersDict","roles","length","triplesMode","atomCount","bondCount","needsCapping","monomerCount","lastMonomerGraph","lastPhosphateGraph","i","seqMonomer","Error","biotype","atoms","x","bonds","bondTypes","meta","rNodes","terminalR2Atom","toLowerCase","TERMINAL_3P","sugar","DNA","phosphate","getResultingAtomBondCounts","molfileAtomBlock","Array","molfileBondBlock","addMonomerToMolblock","addAminoAcidToMolblock","addNucleotideToMolblock","v","nodeShift","bondShift","backbonePositionShift","fill","branchPositionShift","backboneAttachNode","branchAttachNode","flipFactor","LC","seqLength","Math","ceil","steabsCollection","lastMonomerCappingAtom","nAtoms","addAtoms","getAtoms","has5pTerm","TERMINAL_5P","has3pTerm","coreStart","coreLen","N","hasTrailingP","emitBackbone","sm","mapKey","mG","aFirst","bFirst","addBackboneMonomerToMolblock","stereoAtoms","forEach","push","aList","a","bList","b","set","n","sugarSeqIdx","baseSeqIdx","sugarSm","baseSm","sugarG","baseG","prevPhosKey","sugarAtomFirst","sugarBondFirst","sAList","sBList","baseAtomFirst","baseBondFirst","addBranchMonomerToMolblock","bAList","bBList","lastPhosKey","runTriplesAssembly","monomer","mAtomFirst","mBondFirst","mAtomCount","mAtomList","maI","mBondCount","mBondList","mbI","cappingAtomType","atomIdx","keepPrecision","firstAtom","secondAtom","capResultingMolblock","molfileCountsLine","result","join","collection","rowsArray","newCollectionRow","updatedRow","getCollectionBlock","j","atomTypes","y","kwargs","fillAtomLines","fillBondLines","bondIdx","terminalNodes","fillChainExtendingBond","branchShift","updateBranchVariables","atomPairs","backboneShift","updateChainExtendingVariables","nucleobase","fillBranchAtomLines","branchMonomer","fillBackboneToBranchBond","bondCfg","bondConfiguration","has","orientation","get","round","PT","RNA","FASTA","SEPARATOR","HELM","BILN","onmessage","event","seqList","rolesList","start","end","data","resMolList","molfileWarningList","rowI","seq","undefined","err","msg","message","toString","postMessage","molfiles","warnings"],"sourceRoot":""}