@datagrok-libraries/bio 5.65.3 → 5.65.4

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Files changed (4) hide show
  1. package/package.json +1 -1
  2. package/src/monomer-works/to-atomic-level-utils.d.ts.map +1 -1
  3. package/src/monomer-works/to-atomic-level-utils.js +12 -1
  4. package/src/monomer-works/to-atomic-level-utils.js.map +1 -1
package/package.json CHANGED
@@ -8,7 +8,7 @@
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  "access": "public"
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  },
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  "friendlyName": "Datagrok bio library",
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- "version": "5.65.3",
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+ "version": "5.65.4",
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  "description": "Bio utilities, types supporting Macromolecule, Molecule3D data",
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  "dependencies": {
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  "@datagrok-libraries/chem-meta": "^1.2.7",
package/src/monomer-works/to-atomic-level-utils.d.ts.map CHANGED
@@ -1 +1 @@
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+ {"version":3,"file":"to-atomic-level-utils.d.ts","sourceRoot":"","sources":["to-atomic-level-utils.ts"],"names":[],"mappings":"AAEA,OAAO,EAA4C,cAAc,EAAwB,kBAAkB,EACzG,cAAc,EAAC,MAAM,SAAS,CAAC;AAEjC,OAAO,EAAC,QAAQ,EAAa,MAAM,+BAA+B,CAAC;AACnE,OAAO,EAAC,eAAe,EAAU,MAAM,0BAA0B,CAAC;AAClE,OAAO,EAAC,WAAW,EAAE,WAAW,EAAC,MAAM,eAAe,CAAC;AAIvD;;;;iHAIiH;AACjH,wBAAgB,sBAAsB,CACpC,UAAU,EAAE,eAAe,EAAE,WAAW,EAAE,WAAW,EAAE,QAAQ,EAAE,QAAQ,GACxE,GAAG,CAAC,MAAM,EAAE,GAAG,CAAC,CAqBlB;AAED;;;;;;;+EAO+E;AAC/E,wBAAgB,mBAAmB,CACjC,UAAU,EAAE,WAAW,EAAE,EAAE,YAAY,EAAE,kBAAkB,EAC3D,QAAQ,EAAE,QAAQ,EAAE,WAAW,EAAE,WAAW,EAC5C,KAAK,CAAC,EAAE,cAAc,EAAE,GACvB,cAAc,CA6HhB;AAmWD;;;GAGG;AACH,wBAAgB,aAAa,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,CAE/C"}
package/src/monomer-works/to-atomic-level-utils.js CHANGED
@@ -358,8 +358,19 @@ function getResultingAtomBondCounts(monomerSeq, monomersDict, alphabet, polymerT
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  // 3'-terminal modifier (e.g. GalNAc) that IS the chain end.
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  const has3pTerm = !!roles && roles.length > 0 &&
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  roles[roles.length - 1] === NucleotideRole.TERMINAL_3P;
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- if (has3pTerm)
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+ if (has3pTerm) {
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  needsCapping = false;
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+ // Mirror the peptide branch (which does both atomCount-- and bondCount--
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+ // when it skips the terminal cap). `bondCount += monomerCount` above
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+ // reserves one chain-extending slot per monomer; the LAST monomer's slot
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+ // is normally filled by the terminal OH cap bond. With a 3'-terminal
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+ // modifier there is no cap, so that last reserved slot stays empty —
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+ // leaving the declared bond count one higher than the emitted bond
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+ // lines. Drop it so the V3000 COUNTS line matches the bond block exactly
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+ // (otherwise the pre-OCL molfile is malformed and only survives because
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+ // the OCL chirality pass re-derives the counts).
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+ bondCount -= 1;
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+ }
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  else
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  atomCount += 1; // OH cap atom (rides on trailing P or on last sugar's R2)
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  }
package/src/monomer-works/to-atomic-level-utils.js.map CHANGED
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