@platforma-open/milaboratories.sequence-properties.workflow 1.1.2 → 1.2.0

package/.turbo/turbo-build.log

@@ -1,6 +1,6 @@
  WARN  Issue while reading "/home/runner/work/sequence-properties/sequence-properties/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
 
-> @platforma-open/milaboratories.sequence-properties.workflow@1.1.2 build /home/runner/work/sequence-properties/sequence-properties/workflow
+> @platforma-open/milaboratories.sequence-properties.workflow@1.2.0 build /home/runner/work/sequence-properties/sequence-properties/workflow
 > shx rm -rf dist && pl-tengo check && pl-tengo build
 
   info: Skipping unknown file type: wf.test.ts

package/CHANGELOG.md

@@ -1,5 +1,18 @@
 # @platforma-open/MiLaboratories.sequence-properties.workflow
 
+## 1.2.0
+
+### Minor Changes
+
+- a3eaf4b: Add ΔCharge (pH 7.4 → 6.0) metric — `pl7.app/chargeShift` — emitted at peptide, CDR3 (per chain), and Fv scopes. Captures pH-switching capacity (FcRn recycling, endosomal release); negative values mean the molecule gains positive charge on acidification, the productive direction for histidine-driven pH switching. Histidine dominates the metric (~−0.46 per His; pKa ~6.0 sits in the window). Domain carries the pH endpoints (`pl7.app/pH/from`, `pl7.app/pH/to`) so additional pH pairs can land later without breaking the v1 column identity. Default-visible alongside the static charge column at each scope; not marked `isScore` (interpretive, not a Lead Selection ranking criterion).
+
+  Performance: cache per-sequence `_prepare`, `ProteinAnalysis`, and `IsoelectricPoint` via a `SequenceContext` so each sequence does the BioPython setup work once instead of per-property. Pipeline reuses the full-chain context for the Fv pass (one `IsoelectricPoint(IPC2_PROTEIN, include_cys=False)` shared between `charge_at_pH(7.0)` and pI bisection per chain). DataFrames are built columnarly (dict-of-lists) instead of via list-of-dicts. Output is byte-identical to pre-refactor on the corpus tests; ~1.7× faster on per-property micro-bench, end-to-end ~40k peptides/s and ~10k antibody-clones/s with full-chain + Fv. CDR3 chain-mode byte-stability tests added.
+
+### Patch Changes
+
+- Updated dependencies [a3eaf4b]
+  - @platforma-open/milaboratories.sequence-properties.software@1.2.0
+
 ## 1.1.2
 
 ### Patch Changes

package/dist/tengo/lib/messages.lib.tengo

@@ -47,6 +47,12 @@ vhh := func() {
 		"disregard these thresholds for nanobody libraries."
 }
 
+
+
+peptidesShortInstability := func() {
+	return "Instability Index applies only to peptides ≥10 aa; shorter peptides show blank values."
+}
+
 export ll.toStrict({
 	partialChainMissingFullChain: partialChainMissingFullChain,
 	partialChainNoCdr3: partialChainNoCdr3,
@@ -54,5 +60,6 @@ export ll.toStrict({
 	cdr3OnlyInput: cdr3OnlyInput,
 	gammaDeltaTcr: gammaDeltaTcr,
 	receptorNotDetected: receptorNotDetected,
-	vhh: vhh
+	vhh: vhh,
+	peptidesShortInstability: peptidesShortInstability
 })

package/package.json

@@ -1,11 +1,11 @@
 {
   "name": "@platforma-open/milaboratories.sequence-properties.workflow",
-  "version": "1.1.2",
+  "version": "1.2.0",
   "description": "Block Workflow",
   "type": "module",
   "dependencies": {
     "@platforma-sdk/workflow-tengo": "5.16.0",
-    "@platforma-open/milaboratories.sequence-properties.software": "1.1.1"
+    "@platforma-open/milaboratories.sequence-properties.software": "1.2.0"
   },
   "devDependencies": {
     "@platforma-sdk/tengo-builder": "2.5.17",

package/src/messages.lib.tengo

@@ -47,6 +47,12 @@ vhh := func() {
 		"disregard these thresholds for nanobody libraries."
 }
 
+// R9 — Guruprasad instability index is undefined for sequences shorter than
+// 10 residues; emitted in peptide mode whenever any peptide falls below the floor.
+peptidesShortInstability := func() {
+	return "Instability Index applies only to peptides ≥10 aa; shorter peptides show blank values."
+}
+
 export ll.toStrict({
 	partialChainMissingFullChain: partialChainMissingFullChain,
 	partialChainNoCdr3: partialChainNoCdr3,
@@ -54,5 +60,6 @@ export ll.toStrict({
 	cdr3OnlyInput: cdr3OnlyInput,
 	gammaDeltaTcr: gammaDeltaTcr,
 	receptorNotDetected: receptorNotDetected,
-	vhh: vhh
+	vhh: vhh,
+	peptidesShortInstability: peptidesShortInstability
 })

package/src/process.tpl.tengo

@@ -14,6 +14,17 @@ messages := import(":messages")
 
 self.defineOutputs("propertiesPf", "exportPframe", "info")
 
+// ΔCharge (pH 7.4 → 6.0) endpoints — fixed in v1 per spec; schema accepts
+// additional pH pairs without breaking existing column identities.
+CHARGE_SHIFT_PH_FROM := "7.4"
+CHARGE_SHIFT_PH_TO := "6.0"
+
+// Spec R6b — same description on every chargeShift column (peptide / CDR3 / Fv).
+// Trimmed to ~30 words for the column-header tooltip; PlAgDataTableV2 clips the
+// top edge against the page header. Magnitude rule and scope-exclusion caveats
+// live in pcolumn-spec.md / the spec, not in the tooltip.
+CHARGE_SHIFT_DESC := "Net charge change from pH 7.4 (blood) to pH 6.0 (endosome). Negative values mean the molecule gains positive charge on acidification — the productive direction for histidine-driven pH switching. Histidine dominates (~−0.46 per His)."
+
 // Receptor + chain → human label fragments (CDR3 / full-chain).
 // Spec R13a: PColumn name and chain domain are unchanged; only the label varies.
 labelFragments := func(receptor, chain) {
@@ -81,6 +92,13 @@ self.body(func(args) {
 		}
 	}
 
+	// R9 — Instability Index is NA for peptides shorter than 10 aa. Surface a
+	// banner in peptide mode whenever any row falls below the floor so the
+	// user understands why the Instability Index column is blank.
+	if mode == "peptide" && stats.hasPeptideBelowInstabilityFloor == true {
+		infoMessages += [messages.peptidesShortInstability()]
+	}
+
 	infoBlob := smart.createValueResource(constants.RTYPE_JSON, canonical.encode({
 		mode: mode,
 		receptor: receptor,
@@ -106,6 +124,18 @@ self.body(func(args) {
 				"pl7.app/table/orderPriority": "70000"
 			})]
 
+		columns += [makeCol("chargeShift_peptide", "pl7.app/chargeShift", "Double",
+			"Peptide ΔCharge (pH 7.4 → 6.0)", {
+				"pl7.app/feature": "peptide",
+				"pl7.app/pH/from": CHARGE_SHIFT_PH_FROM,
+				"pl7.app/pH/to": CHARGE_SHIFT_PH_TO
+			}, {
+				"pl7.app/format": ".2f",
+				"pl7.app/description": CHARGE_SHIFT_DESC,
+				"pl7.app/table/visibility": "default",
+				"pl7.app/table/orderPriority": "69950"
+			})]
+
 		columns += [makeCol("gravy_peptide", "pl7.app/hydrophobicity", "Double",
 			"Hydrophobicity (GRAVY)", dom, {
 				"pl7.app/format": ".3f",
@@ -206,6 +236,18 @@ self.body(func(args) {
 					"pl7.app/table/visibility": "default",
 					"pl7.app/table/orderPriority": string(chargeOrder)
 				})]
+			columns += [makeCol("chargeShift_" + chain + "_CDR3", "pl7.app/chargeShift", "Double",
+				frag.cdr3 + " ΔCharge (pH 7.4 → 6.0)", {
+					"pl7.app/feature": "CDR3",
+					"pl7.app/vdj/scClonotypeChain": chain,
+					"pl7.app/pH/from": CHARGE_SHIFT_PH_FROM,
+					"pl7.app/pH/to": CHARGE_SHIFT_PH_TO
+				}, {
+					"pl7.app/format": ".2f",
+					"pl7.app/description": CHARGE_SHIFT_DESC,
+					"pl7.app/table/visibility": "default",
+					"pl7.app/table/orderPriority": string(chargeOrder - 50)
+				})]
 			columns += [makeCol("gravy_" + chain + "_CDR3", "pl7.app/hydrophobicity", "Double",
 				frag.cdr3 + " Hydrophobicity (GRAVY)", cdr3Dom, {
 					"pl7.app/format": ".3f",
@@ -308,6 +350,17 @@ self.body(func(args) {
 					"pl7.app/table/visibility": "default",
 					"pl7.app/table/orderPriority": "65100"
 				})]
+			columns += [makeCol("chargeShift_Fv", "pl7.app/chargeShift", "Double",
+				"Fv ΔCharge (pH 7.4 → 6.0)", {
+					"pl7.app/feature": "Fv",
+					"pl7.app/pH/from": CHARGE_SHIFT_PH_FROM,
+					"pl7.app/pH/to": CHARGE_SHIFT_PH_TO
+				}, {
+					"pl7.app/format": ".2f",
+					"pl7.app/description": CHARGE_SHIFT_DESC,
+					"pl7.app/table/visibility": "default",
+					"pl7.app/table/orderPriority": "65050"
+				})]
 			columns += [makeCol("pi_Fv", "pl7.app/isoelectricPoint", "Double",
 				"Fv Isoelectric Point (pI)", fvDom, {
 					"pl7.app/format": ".2f",