@platforma-open/milaboratories.sequence-properties.workflow 1.2.0 → 1.2.1

package/.turbo/turbo-build.log

@@ -1,15 +1,17 @@
  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@1.2.0 build /home/runner/work/sequence-properties/sequence-properties/workflow
+> @platforma-open/milaboratories.sequence-properties.workflow@1.2.1 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
+Processing "src/columns.lib.tengo"...
 Processing "src/main.tpl.tengo"...
 Processing "src/messages.lib.tengo"...
 Processing "src/process.tpl.tengo"...
 No syntax errors found.
   info: Skipping unknown file type: wf.test.ts
   info: Compiling 'dist'...
+  info:   - writing /home/runner/work/sequence-properties/sequence-properties/workflow/dist/tengo/lib/columns.lib.tengo
   info:   - writing /home/runner/work/sequence-properties/sequence-properties/workflow/dist/tengo/lib/messages.lib.tengo
   info:   - writing /home/runner/work/sequence-properties/sequence-properties/workflow/dist/tengo/tpl/process.plj.gz
   info:   - writing /home/runner/work/sequence-properties/sequence-properties/workflow/dist/tengo/tpl/main.plj.gz

package/CHANGELOG.md

@@ -1,5 +1,11 @@
 # @platforma-open/MiLaboratories.sequence-properties.workflow
 
+## 1.2.1
+
+### Patch Changes
+
+- 73b4e4d: Enable linker usage to show plot options
+
 ## 1.2.0
 
 ### Minor Changes

package/dist/tengo/lib/columns.lib.tengo

@@ -0,0 +1,446 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ll := import("@platforma-sdk/workflow-tengo:ll")
+
+
+
+CHARGE_SHIFT_PH_FROM := "7.4"
+CHARGE_SHIFT_PH_TO := "6.0"
+
+
+
+
+
+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)."
+
+
+
+labelFragments := func(receptor, chain) {
+	if receptor == "TCRAB" {
+		if chain == "A" { return { cdr3: "CDR-α3", fullChain: "Vα" } }
+		if chain == "B" { return { cdr3: "CDR-β3", fullChain: "Vβ" } }
+	}
+	if receptor == "TCRGD" {
+		if chain == "A" { return { cdr3: "CDR-γ3", fullChain: "Vγ" } }
+		if chain == "B" { return { cdr3: "CDR-δ3", fullChain: "Vδ" } }
+	}
+
+	if chain == "A" { return { cdr3: "CDR-H3", fullChain: "VH" } }
+	return { cdr3: "CDR-L3", fullChain: "VL" }
+}
+
+
+
+
+
+makeCol := func(tsvCol, valName, valueType, label, domain, annotations) {
+	newAnnotations := {}
+	if annotations {
+		for k, v in annotations {
+			newAnnotations[k] = v
+		}
+	}
+	newAnnotations["pl7.app/label"] = label
+	spec := {
+		name: valName,
+		valueType: valueType,
+		domain: domain,
+		annotations: newAnnotations
+	}
+	return { column: tsvCol, id: tsvCol, naRegex: "", allowNA: true, spec: spec }
+}
+
+
+
+
+
+
+buildPeptideColumns := func() {
+	dom := { "pl7.app/feature": "peptide" }
+	cols := []
+
+	cols += [makeCol("charge_peptide", "pl7.app/charge", "Double",
+		"Net Charge (pH 7)", dom, {
+			"pl7.app/format": ".2f",
+			"pl7.app/isScore": "true",
+			"pl7.app/description": "Net charge at pH 7 (Henderson-Hasselbalch, IPC 2.0 peptide pKa set). Positive = net basic (Arg, Lys, His dominate); negative = net acidic (Asp, Glu dominate). No universal preferred direction.",
+			"pl7.app/table/visibility": "default",
+			"pl7.app/table/orderPriority": "70000"
+		})]
+
+	cols += [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"
+		})]
+
+	cols += [makeCol("gravy_peptide", "pl7.app/hydrophobicity", "Double",
+		"Hydrophobicity (GRAVY)", dom, {
+			"pl7.app/format": ".3f",
+			"pl7.app/isScore": "true",
+			"pl7.app/score/rankingOrder": "increasing",
+			"pl7.app/description": "rankingOrder: increasing reflects preference for lower hydrophobicity. Invert direction in Lead Selection for hydrophobic-target applications.",
+			"pl7.app/table/visibility": "default",
+			"pl7.app/table/orderPriority": "69900"
+		})]
+
+	cols += [makeCol("mw_peptide", "pl7.app/molecularWeight", "Double",
+		"Molecular Weight (Da, average masses)", dom, {
+			"pl7.app/format": ".1f",
+			"pl7.app/min": "0",
+			"pl7.app/table/visibility": "default",
+			"pl7.app/table/orderPriority": "69800"
+		})]
+
+	cols += [makeCol("pi_peptide", "pl7.app/isoelectricPoint", "Double",
+		"Isoelectric Point (pI)", dom, {
+			"pl7.app/format": ".2f",
+			"pl7.app/min": "0",
+			"pl7.app/max": "14",
+			"pl7.app/table/visibility": "default",
+			"pl7.app/table/orderPriority": "69700"
+		})]
+
+	cols += [makeCol("eox_peptide", "pl7.app/extinctionCoefficientOx", "Double",
+		"Extinction Coeff., Oxidized (M⁻¹cm⁻¹)", dom, {
+			"pl7.app/format": ".0f",
+			"pl7.app/min": "0",
+			"pl7.app/description": "Assumes all Cys are in disulfide bonds. For unprotected linear peptides use the reduced form.",
+			"pl7.app/table/visibility": "optional",
+			"pl7.app/table/orderPriority": "69600"
+		})]
+
+	cols += [makeCol("ered_peptide", "pl7.app/extinctionCoefficientRed", "Double",
+		"Extinction Coeff., Reduced (M⁻¹cm⁻¹)", dom, {
+			"pl7.app/format": ".0f",
+			"pl7.app/min": "0",
+			"pl7.app/description": "Extinction coefficient at 280 nm, disulfide bonds reduced (Cys contribution omitted). A value of 0 means no Tyr or Trp — A280-based quantification is not possible.",
+			"pl7.app/table/visibility": "optional",
+			"pl7.app/table/orderPriority": "69500"
+		})]
+
+	cols += [makeCol("instability_peptide", "pl7.app/instabilityIndex", "Double",
+		"Instability Index", dom, {
+			"pl7.app/format": ".2f",
+			"pl7.app/description": "Guruprasad index — derived from globular proteins. The II > 40 threshold does not apply to short linear peptides; use as a relative composition ranking aid only.",
+			"pl7.app/table/visibility": "default",
+			"pl7.app/table/orderPriority": "69400"
+		})]
+
+	cols += [makeCol("aliphatic_peptide", "pl7.app/aliphaticIndex", "Double",
+		"Aliphatic Index", dom, {
+			"pl7.app/format": ".1f",
+			"pl7.app/min": "0",
+			"pl7.app/description": "Measures fraction of nonpolar aliphatic residues (Ala, Val, Ile, Leu). For short linear peptides, thermostability interpretation does not apply — the Ikai index was derived for globular mesophilic enzymes, and thermostability is not a meaningful concept for unstructured peptides. Useful as a composition indicator and a proxy for hydrophobic character alongside GRAVY — both metrics increase with Ala/Val/Ile/Leu content, but neither has a universal preferred direction for therapeutic peptides.",
+			"pl7.app/table/visibility": "optional",
+			"pl7.app/table/orderPriority": "69300"
+		})]
+
+	cols += [makeCol("aromaticity_peptide", "pl7.app/aromaticity", "Double",
+		"Aromaticity", dom, {
+			"pl7.app/format": ".3f",
+			"pl7.app/min": "0",
+			"pl7.app/max": "1",
+			"pl7.app/description": "Fraction of aromatic residues (Phe, Trp, Tyr).",
+			"pl7.app/table/visibility": "optional",
+			"pl7.app/table/orderPriority": "69200"
+		})]
+
+	return cols
+}
+
+
+
+CDR3_CHARGE_DESC := {
+	A: "Strongly positive CDR3 charge correlates with polyreactivity via electrostatic interactions. No universal preferred direction in Lead Selection. IPC 2.0 peptide pKa set.",
+	B: "Strongly positive CDR-L3 charge contributes to paratope polyreactivity. Strongly negative charge is primarily a PK concern. No universal preferred direction. IPC 2.0 peptide pKa set."
+}
+CDR3_GRAVY_DESC := {
+	A: "Lower hydrophobicity preferred for developability. CDR3 GRAVY > 0 is an informal aggregation/polyreactivity heuristic.",
+	B: "Same aggregation and polyreactivity signal as CDR-H3 hydrophobicity; lower independent predictive weight. The TAP score uses combined 6-CDR GRAVY — CDR-L3 alone has limited independent validation."
+}
+
+buildCdr3Columns := func(receptor, chains) {
+	cols := []
+	cdr3OrderA := 68000
+	cdr3OrderB := 67700
+	for chain in chains {
+		frag := labelFragments(receptor, chain)
+		cdr3Dom := { "pl7.app/feature": "CDR3", "pl7.app/vdj/scClonotypeChain": chain }
+		chargeOrder := (chain == "A" ? cdr3OrderA : cdr3OrderB)
+		gravyOrder := chargeOrder - 100
+
+		cols += [makeCol("charge_" + chain + "_CDR3", "pl7.app/charge", "Double",
+			frag.cdr3 + " Net Charge (pH 7)", cdr3Dom, {
+				"pl7.app/format": ".2f",
+				"pl7.app/isScore": "true",
+				"pl7.app/description": CDR3_CHARGE_DESC[chain],
+				"pl7.app/table/visibility": "default",
+				"pl7.app/table/orderPriority": string(chargeOrder)
+			})]
+		cols += [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)
+			})]
+		cols += [makeCol("gravy_" + chain + "_CDR3", "pl7.app/hydrophobicity", "Double",
+			frag.cdr3 + " Hydrophobicity (GRAVY)", cdr3Dom, {
+				"pl7.app/format": ".3f",
+				"pl7.app/isScore": "true",
+				"pl7.app/score/rankingOrder": "increasing",
+				"pl7.app/description": CDR3_GRAVY_DESC[chain],
+				"pl7.app/table/visibility": "default",
+				"pl7.app/table/orderPriority": string(gravyOrder)
+			})]
+	}
+	return cols
+}
+
+buildFullChainColumns := func(receptor, fullChains) {
+	cols := []
+	fcOrderBaseA := 67000
+	fcOrderBaseB := 66000
+	for chain in fullChains {
+		frag := labelFragments(receptor, chain)
+		fcDom := { "pl7.app/feature": "VDJRegion", "pl7.app/vdj/scClonotypeChain": chain }
+		base := (chain == "A" ? fcOrderBaseA : fcOrderBaseB)
+		fcLabel := frag.fullChain
+
+		cols += [makeCol("charge_" + chain + "_VDJRegion", "pl7.app/charge", "Double",
+			fcLabel + " Net Charge (pH 7)", fcDom, {
+				"pl7.app/format": ".2f",
+				"pl7.app/isScore": "true",
+				"pl7.app/description": "Non-monotonic vs developability: strongly positive correlates with polyreactivity; strongly negative with rapid clearance.",
+				"pl7.app/table/visibility": "default",
+				"pl7.app/table/orderPriority": string(base)
+			})]
+		cols += [makeCol("pi_" + chain + "_VDJRegion", "pl7.app/isoelectricPoint", "Double",
+			fcLabel + " Isoelectric Point (pI)", fcDom, {
+				"pl7.app/format": ".2f",
+				"pl7.app/isScore": "true",
+				"pl7.app/min": "0",
+				"pl7.app/max": "14",
+				"pl7.app/table/visibility": "default",
+				"pl7.app/table/orderPriority": string(base - 100)
+			})]
+		cols += [makeCol("gravy_" + chain + "_VDJRegion", "pl7.app/hydrophobicity", "Double",
+			fcLabel + " Hydrophobicity (GRAVY)", fcDom, {
+				"pl7.app/format": ".3f",
+				"pl7.app/description": "Framework regions dominate; weak developability signal at chain level — CDR3 hydrophobicity is more discriminating.",
+				"pl7.app/table/visibility": "default",
+				"pl7.app/table/orderPriority": string(base - 200)
+			})]
+		cols += [makeCol("mw_" + chain + "_VDJRegion", "pl7.app/molecularWeight", "Double",
+			fcLabel + " Molecular Weight (Da, average masses)", fcDom, {
+				"pl7.app/format": ".1f",
+				"pl7.app/min": "0",
+				"pl7.app/description": "Unglycosylated sequence mass — does not include N-glycan contributions from any NXS/NXT sequons in the variable region.",
+				"pl7.app/table/visibility": "optional",
+				"pl7.app/table/orderPriority": string(base - 300)
+			})]
+		cols += [makeCol("eox_" + chain + "_VDJRegion", "pl7.app/extinctionCoefficientOx", "Double",
+			fcLabel + " Extinction Coeff., Oxidized (M⁻¹cm⁻¹)", fcDom, {
+				"pl7.app/format": ".0f",
+				"pl7.app/min": "0",
+				"pl7.app/table/visibility": "optional",
+				"pl7.app/table/orderPriority": string(base - 400)
+			})]
+		cols += [makeCol("ered_" + chain + "_VDJRegion", "pl7.app/extinctionCoefficientRed", "Double",
+			fcLabel + " Extinction Coeff., Reduced (M⁻¹cm⁻¹)", fcDom, {
+				"pl7.app/format": ".0f",
+				"pl7.app/min": "0",
+				"pl7.app/table/visibility": "optional",
+				"pl7.app/table/orderPriority": string(base - 500)
+			})]
+		cols += [makeCol("instability_" + chain + "_VDJRegion", "pl7.app/instabilityIndex", "Double",
+			fcLabel + " Instability Index", fcDom, {
+				"pl7.app/format": ".2f",
+				"pl7.app/description": "Guruprasad index, calibrated for in-vitro stability of soluble globular proteins via dipeptide composition. Weak predictor of antibody Tm — use as supplementary ranking aid.",
+				"pl7.app/table/visibility": "optional",
+				"pl7.app/table/orderPriority": string(base - 600)
+			})]
+		cols += [makeCol("aliphatic_" + chain + "_VDJRegion", "pl7.app/aliphaticIndex", "Double",
+			fcLabel + " Aliphatic Index", fcDom, {
+				"pl7.app/format": ".1f",
+				"pl7.app/min": "0",
+				"pl7.app/description": "Ikai aliphatic index, derived from globular mesophilic enzymes. Weak correlation with antibody Tm. No rankingOrder — high values can correlate with aggregation propensity.",
+				"pl7.app/table/visibility": "optional",
+				"pl7.app/table/orderPriority": string(base - 700)
+			})]
+		cols += [makeCol("aromaticity_" + chain + "_VDJRegion", "pl7.app/aromaticity", "Double",
+			fcLabel + " Aromaticity", fcDom, {
+				"pl7.app/format": ".3f",
+				"pl7.app/min": "0",
+				"pl7.app/max": "1",
+				"pl7.app/description": "Fraction of aromatic residues (Phe, Trp, Tyr) over the full chain. Framework dominates; CDR-specific aromaticity is a stronger predictor (Phase 2).",
+				"pl7.app/table/visibility": "optional",
+				"pl7.app/table/orderPriority": string(base - 800)
+			})]
+	}
+	return cols
+}
+
+buildFvColumns := func() {
+	cols := []
+	fvDom := { "pl7.app/feature": "Fv" }
+
+	cols += [makeCol("charge_Fv", "pl7.app/charge", "Double",
+		"Fv Net Charge (pH 7)", fvDom, {
+			"pl7.app/format": ".2f",
+			"pl7.app/isScore": "true",
+			"pl7.app/table/visibility": "default",
+			"pl7.app/table/orderPriority": "65100"
+		})]
+	cols += [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"
+		})]
+	cols += [makeCol("pi_Fv", "pl7.app/isoelectricPoint", "Double",
+		"Fv Isoelectric Point (pI)", fvDom, {
+			"pl7.app/format": ".2f",
+			"pl7.app/isScore": "true",
+			"pl7.app/min": "0",
+			"pl7.app/max": "14",
+			"pl7.app/description": "Variable region (VH+VL) only. Fv pI is typically 2–4 pH units higher than whole-IgG cIEF measurements, which include constant regions (IgG1 Fc pI ≈ 5–6).",
+			"pl7.app/table/visibility": "default",
+			"pl7.app/table/orderPriority": "65000"
+		})]
+	cols += [makeCol("eox_Fv", "pl7.app/extinctionCoefficientOx", "Double",
+		"Fv Extinction Coeff., Oxidized (M⁻¹cm⁻¹)", fvDom, {
+			"pl7.app/format": ".0f",
+			"pl7.app/min": "0",
+			"pl7.app/description": "Variable region (VH+VL) only — does not include constant regions. For whole-IgG A280 quantification, use the full-antibody ε.",
+			"pl7.app/table/visibility": "optional",
+			"pl7.app/table/orderPriority": "64900"
+		})]
+	cols += [makeCol("ered_Fv", "pl7.app/extinctionCoefficientRed", "Double",
+		"Fv Extinction Coeff., Reduced (M⁻¹cm⁻¹)", fvDom, {
+			"pl7.app/format": ".0f",
+			"pl7.app/min": "0",
+			"pl7.app/description": "Variable region (VH+VL) only, disulfide bonds reduced (Cys contribution omitted). A value of 0 means no Tyr or Trp — A280-based quantification is not possible.",
+			"pl7.app/table/visibility": "optional",
+			"pl7.app/table/orderPriority": "64800"
+		})]
+	cols += [makeCol("mw_Fv", "pl7.app/molecularWeight", "Double",
+		"Fv Molecular Weight (Da, average masses)", fvDom, {
+			"pl7.app/format": ".1f",
+			"pl7.app/min": "0",
+			"pl7.app/description": "Unglycosylated sequence mass (VH + VL).",
+			"pl7.app/table/visibility": "optional",
+			"pl7.app/table/orderPriority": "64700"
+		})]
+	return cols
+}
+
+buildColumns := func(args) {
+	if args.mode == "peptide" {
+		return buildPeptideColumns()
+	}
+	cols := buildCdr3Columns(args.receptor, args.chains)
+	cols += buildFullChainColumns(args.receptor, args.fullChains)
+	if args.hasFv {
+		cols += buildFvColumns()
+	}
+	return cols
+}
+
+
+
+
+
+
+
+cloneSpec := func(spec, domainExtras, annotationExtras) {
+	newDomain := {}
+	if spec.domain {
+		for k, v in spec.domain { newDomain[k] = v }
+	}
+	if domainExtras {
+		for k, v in domainExtras { newDomain[k] = v }
+	}
+	newAnnotations := {}
+	if spec.annotations {
+		for k, v in spec.annotations { newAnnotations[k] = v }
+	}
+	if annotationExtras {
+		for k, v in annotationExtras { newAnnotations[k] = v }
+	}
+	return {
+		name: spec.name,
+		valueType: spec.valueType,
+		domain: newDomain,
+		annotations: newAnnotations
+	}
+}
+
+wrap := func(col, newSpec) {
+	return {
+		column: col.column,
+		id: col.id,
+		naRegex: col.naRegex,
+		allowNA: col.allowNA,
+		spec: newSpec
+	}
+}
+
+
+
+
+
+forPropertiesPf := func(args) {
+	cols := buildColumns(args)
+	out := []
+	for col in cols {
+		out += [wrap(col, cloneSpec(col.spec, undefined, { "pl7.app/isOutput": "true" }))]
+	}
+	return out
+}
+
+forExport := func(args, blockId) {
+	cols := buildColumns(args)
+	out := []
+	for col in cols {
+		if !col.spec.annotations { continue }
+		if col.spec.annotations["pl7.app/isScore"] != "true" { continue }
+		out += [wrap(col, cloneSpec(col.spec, { "pl7.app/blockId": blockId }, undefined))]
+	}
+	return out
+}
+
+export ll.toStrict({
+	forPropertiesPf: forPropertiesPf,
+	forExport: forExport
+})

package/package.json

@@ -1,15 +1,15 @@
 {
   "name": "@platforma-open/milaboratories.sequence-properties.workflow",
-  "version": "1.2.0",
+  "version": "1.2.1",
   "description": "Block Workflow",
   "type": "module",
   "dependencies": {
-    "@platforma-sdk/workflow-tengo": "5.16.0",
+    "@platforma-sdk/workflow-tengo": "5.21.0",
     "@platforma-open/milaboratories.sequence-properties.software": "1.2.0"
   },
   "devDependencies": {
-    "@platforma-sdk/tengo-builder": "2.5.17",
-    "@platforma-sdk/test": "1.69.0"
+    "@platforma-sdk/tengo-builder": "2.5.26",
+    "@platforma-sdk/test": "1.75.6"
   },
   "peerDependencies": {
     "vitest": "*"