@teselagen/ove 0.8.19 → 0.8.20

package/index.cjs.js

@@ -84349,6 +84349,160 @@ function calculateNebTm(sequence2, { monovalentCationConc = 0.05, primerConc = 5
   }
 }
 __name(calculateNebTm, "calculateNebTm");
+const PRIMER3_PARAMS = {
+  saltMonovalent: 50,
+  // mM
+  saltDivalent: 1.5,
+  // mM
+  dntpConc: 0.6,
+  // mM
+  dnaConc: 50,
+  // nM
+  R: 1.987
+  // Gas constant (cal/K·mol)
+};
+const SANTA_LUCIA_NN = {
+  AA: { dH: -7.9, dS: -22.2 },
+  TT: { dH: -7.9, dS: -22.2 },
+  AT: { dH: -7.2, dS: -20.4 },
+  TA: { dH: -7.2, dS: -21.3 },
+  CA: { dH: -8.5, dS: -22.7 },
+  TG: { dH: -8.5, dS: -22.7 },
+  GT: { dH: -8.4, dS: -22.4 },
+  AC: { dH: -8.4, dS: -22.4 },
+  CT: { dH: -7.8, dS: -21 },
+  AG: { dH: -7.8, dS: -21 },
+  GA: { dH: -8.2, dS: -22.2 },
+  TC: { dH: -8.2, dS: -22.2 },
+  CG: { dH: -10.6, dS: -27.2 },
+  GC: { dH: -9.8, dS: -24.4 },
+  GG: { dH: -8, dS: -19.9 },
+  CC: { dH: -8, dS: -19.9 }
+};
+const SANTA_LUCIA_INIT = {
+  GC: { dH: 0.1, dS: -2.8 },
+  // initiation with terminal GC
+  AT: { dH: 2.3, dS: 4.1 }
+  // initiation with terminal AT
+};
+function getEffectiveMonovalentConc() {
+  let effectiveMono = PRIMER3_PARAMS.saltMonovalent;
+  {
+    const freeMg = Math.max(
+      0,
+      PRIMER3_PARAMS.saltDivalent - PRIMER3_PARAMS.dntpConc
+    );
+    effectiveMono += 120 * Math.sqrt(freeMg);
+  }
+  return effectiveMono;
+}
+__name(getEffectiveMonovalentConc, "getEffectiveMonovalentConc");
+function applySaltCorrection(deltaS, nnPairs) {
+  const effectiveMono = getEffectiveMonovalentConc();
+  return deltaS + 0.368 * nnPairs * Math.log(effectiveMono / 1e3);
+}
+__name(applySaltCorrection, "applySaltCorrection");
+function isValidSequence(sequence2) {
+  return /^[ATGCN]+$/.test(sequence2);
+}
+__name(isValidSequence, "isValidSequence");
+function calculateSantaLuciaTm(sequence2) {
+  try {
+    sequence2 = sequence2 == null ? void 0 : sequence2.toUpperCase().trim();
+    if (!isValidSequence(sequence2)) {
+      throw new Error("Invalid sequence: contains non-DNA characters");
+    }
+    if (sequence2.length < 2) {
+      throw new Error("Sequence too short: minimum length is 2 bases");
+    }
+    let deltaH = 0;
+    let deltaS = 0;
+    for (let i = 0; i < sequence2.length - 1; i++) {
+      const dinucleotide = sequence2.substring(i, i + 2);
+      if (dinucleotide.includes("N")) {
+        continue;
+      }
+      const params = SANTA_LUCIA_NN[dinucleotide];
+      if (params) {
+        deltaH += params.dH;
+        deltaS += params.dS;
+      }
+    }
+    const firstBase = sequence2[0];
+    const lastBase = sequence2[sequence2.length - 1];
+    if (firstBase === "G" || firstBase === "C") {
+      deltaH += SANTA_LUCIA_INIT.GC.dH;
+      deltaS += SANTA_LUCIA_INIT.GC.dS;
+    } else {
+      deltaH += SANTA_LUCIA_INIT.AT.dH;
+      deltaS += SANTA_LUCIA_INIT.AT.dS;
+    }
+    if (lastBase === "G" || lastBase === "C") {
+      deltaH += SANTA_LUCIA_INIT.GC.dH;
+      deltaS += SANTA_LUCIA_INIT.GC.dS;
+    } else {
+      deltaH += SANTA_LUCIA_INIT.AT.dH;
+      deltaS += SANTA_LUCIA_INIT.AT.dS;
+    }
+    const nnPairs = sequence2.length - 1;
+    deltaS = applySaltCorrection(deltaS, nnPairs);
+    const C = PRIMER3_PARAMS.dnaConc * 1e-9;
+    const Tm = deltaH * 1e3 / (deltaS + PRIMER3_PARAMS.R * Math.log(C / 4));
+    return Tm - 273.15;
+  } catch (e) {
+    return `Error calculating Tm for sequence ${sequence2}. ${e}`;
+  }
+}
+__name(calculateSantaLuciaTm, "calculateSantaLuciaTm");
+function calculateEndStability(sequence2) {
+  try {
+    sequence2 = sequence2 == null ? void 0 : sequence2.toUpperCase().trim();
+    if (!isValidSequence(sequence2)) {
+      throw new Error("Invalid sequence: contains non-DNA characters");
+    }
+    if (sequence2.length < 5) {
+      throw new Error(
+        "Sequence too short: minimum length is 5 bases for end stability calculation"
+      );
+    }
+    const last5Bases = sequence2.substring(sequence2.length - 5);
+    let deltaH = 0;
+    let deltaS = 0;
+    for (let i = 0; i < 4; i++) {
+      const dinucleotide = last5Bases.substring(i, i + 2);
+      if (dinucleotide.includes("N")) {
+        continue;
+      }
+      const params = SANTA_LUCIA_NN[dinucleotide];
+      if (params) {
+        deltaH += params.dH;
+        deltaS += params.dS;
+      }
+    }
+    const firstBase = last5Bases[0];
+    const lastBase = last5Bases[last5Bases.length - 1];
+    if (firstBase === "G" || firstBase === "C") {
+      deltaH += SANTA_LUCIA_INIT.GC.dH;
+      deltaS += SANTA_LUCIA_INIT.GC.dS;
+    } else {
+      deltaH += SANTA_LUCIA_INIT.AT.dH;
+      deltaS += SANTA_LUCIA_INIT.AT.dS;
+    }
+    if (lastBase === "G" || lastBase === "C") {
+      deltaH += SANTA_LUCIA_INIT.GC.dH;
+      deltaS += SANTA_LUCIA_INIT.GC.dS;
+    } else {
+      deltaH += SANTA_LUCIA_INIT.AT.dH;
+      deltaS += SANTA_LUCIA_INIT.AT.dS;
+    }
+    const T2 = 310.15;
+    const deltaG = deltaH - T2 * deltaS / 1e3;
+    return Math.round(Math.abs(deltaG) * 100) / 100;
+  } catch (e) {
+    return `Error calculating end stability for sequence ${sequence2}. ${e}`;
+  }
+}
+__name(calculateEndStability, "calculateEndStability");
 function convertAACaretPositionOrRangeToDna(rangeOrCaret) {
   if (typeof rangeOrCaret === "object" && rangeOrCaret !== null) {
     return convertAARangeToDnaRange(__spreadProps(__spreadValues({}, rangeOrCaret), {
@@ -116654,7 +116808,7 @@ function showFileDialog({ multiple = false, onSelect }) {
   input.click();
 }
 __name(showFileDialog, "showFileDialog");
-const version = "0.8.18";
+const version = "0.8.19";
 const packageJson = {
   version
 };
@@ -137354,7 +137508,7 @@ function MeltingTemp({
     /* , setMonovalentCationConc */
   ] = React.useState(0.05);
   const [tmType, setTmType] = useTmType();
-  let tm = (tmType === "neb_tm" ? calculateNebTm : calculateTm)(sequence2, {
+  let tm = (tmType === "neb_tm" ? calculateNebTm : tmType === "default" ? calculateSantaLuciaTm : calculateTm)(sequence2, {
     monovalentCationConc,
     primerConc
   });
@@ -137379,8 +137533,9 @@ function MeltingTemp({
         {
           label: "Choose Tm Type:",
           options: [
-            { value: "default", label: "Default Tm (Breslauer)" },
-            { value: "neb_tm", label: "NEB Tm (SantaLucia)" }
+            { value: "default", label: "Santa Lucia (Default)" },
+            { value: "breslauer", label: "Breslauer" },
+            { value: "neb_tm", label: "NEB Tm" }
           ],
           onChange: /* @__PURE__ */ __name((e) => setTmType(e.target.value), "onChange"),
           selectedValue: tmType
@@ -137394,7 +137549,7 @@ function MeltingTemp({
         }
       ), hasWarning, /* @__PURE__ */ React.createElement("br", null), /* @__PURE__ */ React.createElement("br", null), "Try using the Default Tm"))
     },
-    /* @__PURE__ */ React.createElement(React.Fragment, null, /* @__PURE__ */ React.createElement(InnerWrapper, null, "Melting Temp: ", Number(tm) || 0, " "), hasWarning && /* @__PURE__ */ React.createElement(
+    /* @__PURE__ */ React.createElement(React.Fragment, null, /* @__PURE__ */ React.createElement(InnerWrapper, null, "Melting Temp: ", Number(tm) || 0, "°C"), hasWarning && /* @__PURE__ */ React.createElement(
       core.Icon,
       {
         style: { marginLeft: 5, marginRight: 5 },
@@ -137658,12 +137813,24 @@ const RenderBases = /* @__PURE__ */ __name((props) => {
     )), /* @__PURE__ */ React.createElement(
       MeltingTemp,
       {
-        InnerWrapper: InnerWrapperMeltingTemp,
+        InnerWrapper: TextInnerWrapper,
         sequence: bases
       }
-    ))
+    ), /* @__PURE__ */ React.createElement(TextInnerWrapper, null, "GC content: ", bases && calculatePercentGC(bases).toFixed(1), "%"), /* @__PURE__ */ React.createElement(TextInnerWrapper, null, "3' Stability: ", bases && calculateEndStability(bases), " kcal/mol"))
   );
 }, "RenderBases");
+const TextInnerWrapper = /* @__PURE__ */ __name((p2) => /* @__PURE__ */ React.createElement(
+  "div",
+  {
+    className: "bp3-text-muted bp3-text-small",
+    style: {
+      marginBottom: 15,
+      marginTop: -5,
+      fontStyle: "italic"
+    }
+  },
+  p2.children
+), "TextInnerWrapper");
 const AddOrEditPrimerDialog = AddOrEditAnnotationDialog$1({
   formName: "AddOrEditPrimerDialog",
   getProps: /* @__PURE__ */ __name((props) => ({
@@ -137672,14 +137839,6 @@ const AddOrEditPrimerDialog = AddOrEditAnnotationDialog$1({
     RenderBases
   }), "getProps")
 });
-const InnerWrapperMeltingTemp = /* @__PURE__ */ __name((p2) => /* @__PURE__ */ React.createElement(
-  "div",
-  {
-    className: "bp3-text-muted bp3-text-small",
-    style: { marginBottom: 15, marginTop: -5, fontStyle: "italic" }
-  },
-  p2.children
-), "InnerWrapperMeltingTemp");
 const Dialogs = {
   RenameSequenceDialog,
   PrintDialog: PrintDialog$1,

package/index.es.js

@@ -84331,6 +84331,160 @@ function calculateNebTm(sequence2, { monovalentCationConc = 0.05, primerConc = 5
   }
 }
 __name(calculateNebTm, "calculateNebTm");
+const PRIMER3_PARAMS = {
+  saltMonovalent: 50,
+  // mM
+  saltDivalent: 1.5,
+  // mM
+  dntpConc: 0.6,
+  // mM
+  dnaConc: 50,
+  // nM
+  R: 1.987
+  // Gas constant (cal/K·mol)
+};
+const SANTA_LUCIA_NN = {
+  AA: { dH: -7.9, dS: -22.2 },
+  TT: { dH: -7.9, dS: -22.2 },
+  AT: { dH: -7.2, dS: -20.4 },
+  TA: { dH: -7.2, dS: -21.3 },
+  CA: { dH: -8.5, dS: -22.7 },
+  TG: { dH: -8.5, dS: -22.7 },
+  GT: { dH: -8.4, dS: -22.4 },
+  AC: { dH: -8.4, dS: -22.4 },
+  CT: { dH: -7.8, dS: -21 },
+  AG: { dH: -7.8, dS: -21 },
+  GA: { dH: -8.2, dS: -22.2 },
+  TC: { dH: -8.2, dS: -22.2 },
+  CG: { dH: -10.6, dS: -27.2 },
+  GC: { dH: -9.8, dS: -24.4 },
+  GG: { dH: -8, dS: -19.9 },
+  CC: { dH: -8, dS: -19.9 }
+};
+const SANTA_LUCIA_INIT = {
+  GC: { dH: 0.1, dS: -2.8 },
+  // initiation with terminal GC
+  AT: { dH: 2.3, dS: 4.1 }
+  // initiation with terminal AT
+};
+function getEffectiveMonovalentConc() {
+  let effectiveMono = PRIMER3_PARAMS.saltMonovalent;
+  {
+    const freeMg = Math.max(
+      0,
+      PRIMER3_PARAMS.saltDivalent - PRIMER3_PARAMS.dntpConc
+    );
+    effectiveMono += 120 * Math.sqrt(freeMg);
+  }
+  return effectiveMono;
+}
+__name(getEffectiveMonovalentConc, "getEffectiveMonovalentConc");
+function applySaltCorrection(deltaS, nnPairs) {
+  const effectiveMono = getEffectiveMonovalentConc();
+  return deltaS + 0.368 * nnPairs * Math.log(effectiveMono / 1e3);
+}
+__name(applySaltCorrection, "applySaltCorrection");
+function isValidSequence(sequence2) {
+  return /^[ATGCN]+$/.test(sequence2);
+}
+__name(isValidSequence, "isValidSequence");
+function calculateSantaLuciaTm(sequence2) {
+  try {
+    sequence2 = sequence2 == null ? void 0 : sequence2.toUpperCase().trim();
+    if (!isValidSequence(sequence2)) {
+      throw new Error("Invalid sequence: contains non-DNA characters");
+    }
+    if (sequence2.length < 2) {
+      throw new Error("Sequence too short: minimum length is 2 bases");
+    }
+    let deltaH = 0;
+    let deltaS = 0;
+    for (let i = 0; i < sequence2.length - 1; i++) {
+      const dinucleotide = sequence2.substring(i, i + 2);
+      if (dinucleotide.includes("N")) {
+        continue;
+      }
+      const params = SANTA_LUCIA_NN[dinucleotide];
+      if (params) {
+        deltaH += params.dH;
+        deltaS += params.dS;
+      }
+    }
+    const firstBase = sequence2[0];
+    const lastBase = sequence2[sequence2.length - 1];
+    if (firstBase === "G" || firstBase === "C") {
+      deltaH += SANTA_LUCIA_INIT.GC.dH;
+      deltaS += SANTA_LUCIA_INIT.GC.dS;
+    } else {
+      deltaH += SANTA_LUCIA_INIT.AT.dH;
+      deltaS += SANTA_LUCIA_INIT.AT.dS;
+    }
+    if (lastBase === "G" || lastBase === "C") {
+      deltaH += SANTA_LUCIA_INIT.GC.dH;
+      deltaS += SANTA_LUCIA_INIT.GC.dS;
+    } else {
+      deltaH += SANTA_LUCIA_INIT.AT.dH;
+      deltaS += SANTA_LUCIA_INIT.AT.dS;
+    }
+    const nnPairs = sequence2.length - 1;
+    deltaS = applySaltCorrection(deltaS, nnPairs);
+    const C = PRIMER3_PARAMS.dnaConc * 1e-9;
+    const Tm = deltaH * 1e3 / (deltaS + PRIMER3_PARAMS.R * Math.log(C / 4));
+    return Tm - 273.15;
+  } catch (e) {
+    return `Error calculating Tm for sequence ${sequence2}. ${e}`;
+  }
+}
+__name(calculateSantaLuciaTm, "calculateSantaLuciaTm");
+function calculateEndStability(sequence2) {
+  try {
+    sequence2 = sequence2 == null ? void 0 : sequence2.toUpperCase().trim();
+    if (!isValidSequence(sequence2)) {
+      throw new Error("Invalid sequence: contains non-DNA characters");
+    }
+    if (sequence2.length < 5) {
+      throw new Error(
+        "Sequence too short: minimum length is 5 bases for end stability calculation"
+      );
+    }
+    const last5Bases = sequence2.substring(sequence2.length - 5);
+    let deltaH = 0;
+    let deltaS = 0;
+    for (let i = 0; i < 4; i++) {
+      const dinucleotide = last5Bases.substring(i, i + 2);
+      if (dinucleotide.includes("N")) {
+        continue;
+      }
+      const params = SANTA_LUCIA_NN[dinucleotide];
+      if (params) {
+        deltaH += params.dH;
+        deltaS += params.dS;
+      }
+    }
+    const firstBase = last5Bases[0];
+    const lastBase = last5Bases[last5Bases.length - 1];
+    if (firstBase === "G" || firstBase === "C") {
+      deltaH += SANTA_LUCIA_INIT.GC.dH;
+      deltaS += SANTA_LUCIA_INIT.GC.dS;
+    } else {
+      deltaH += SANTA_LUCIA_INIT.AT.dH;
+      deltaS += SANTA_LUCIA_INIT.AT.dS;
+    }
+    if (lastBase === "G" || lastBase === "C") {
+      deltaH += SANTA_LUCIA_INIT.GC.dH;
+      deltaS += SANTA_LUCIA_INIT.GC.dS;
+    } else {
+      deltaH += SANTA_LUCIA_INIT.AT.dH;
+      deltaS += SANTA_LUCIA_INIT.AT.dS;
+    }
+    const T2 = 310.15;
+    const deltaG = deltaH - T2 * deltaS / 1e3;
+    return Math.round(Math.abs(deltaG) * 100) / 100;
+  } catch (e) {
+    return `Error calculating end stability for sequence ${sequence2}. ${e}`;
+  }
+}
+__name(calculateEndStability, "calculateEndStability");
 function convertAACaretPositionOrRangeToDna(rangeOrCaret) {
   if (typeof rangeOrCaret === "object" && rangeOrCaret !== null) {
     return convertAARangeToDnaRange(__spreadProps(__spreadValues({}, rangeOrCaret), {
@@ -116636,7 +116790,7 @@ function showFileDialog({ multiple = false, onSelect }) {
   input.click();
 }
 __name(showFileDialog, "showFileDialog");
-const version = "0.8.18";
+const version = "0.8.19";
 const packageJson = {
   version
 };
@@ -137336,7 +137490,7 @@ function MeltingTemp({
     /* , setMonovalentCationConc */
   ] = React__default.useState(0.05);
   const [tmType, setTmType] = useTmType();
-  let tm = (tmType === "neb_tm" ? calculateNebTm : calculateTm)(sequence2, {
+  let tm = (tmType === "neb_tm" ? calculateNebTm : tmType === "default" ? calculateSantaLuciaTm : calculateTm)(sequence2, {
     monovalentCationConc,
     primerConc
   });
@@ -137361,8 +137515,9 @@ function MeltingTemp({
         {
           label: "Choose Tm Type:",
           options: [
-            { value: "default", label: "Default Tm (Breslauer)" },
-            { value: "neb_tm", label: "NEB Tm (SantaLucia)" }
+            { value: "default", label: "Santa Lucia (Default)" },
+            { value: "breslauer", label: "Breslauer" },
+            { value: "neb_tm", label: "NEB Tm" }
           ],
           onChange: /* @__PURE__ */ __name((e) => setTmType(e.target.value), "onChange"),
           selectedValue: tmType
@@ -137376,7 +137531,7 @@ function MeltingTemp({
         }
       ), hasWarning, /* @__PURE__ */ React__default.createElement("br", null), /* @__PURE__ */ React__default.createElement("br", null), "Try using the Default Tm"))
     },
-    /* @__PURE__ */ React__default.createElement(React__default.Fragment, null, /* @__PURE__ */ React__default.createElement(InnerWrapper, null, "Melting Temp: ", Number(tm) || 0, " "), hasWarning && /* @__PURE__ */ React__default.createElement(
+    /* @__PURE__ */ React__default.createElement(React__default.Fragment, null, /* @__PURE__ */ React__default.createElement(InnerWrapper, null, "Melting Temp: ", Number(tm) || 0, "°C"), hasWarning && /* @__PURE__ */ React__default.createElement(
       Icon,
       {
         style: { marginLeft: 5, marginRight: 5 },
@@ -137640,12 +137795,24 @@ const RenderBases = /* @__PURE__ */ __name((props) => {
     )), /* @__PURE__ */ React__default.createElement(
       MeltingTemp,
       {
-        InnerWrapper: InnerWrapperMeltingTemp,
+        InnerWrapper: TextInnerWrapper,
         sequence: bases
       }
-    ))
+    ), /* @__PURE__ */ React__default.createElement(TextInnerWrapper, null, "GC content: ", bases && calculatePercentGC(bases).toFixed(1), "%"), /* @__PURE__ */ React__default.createElement(TextInnerWrapper, null, "3' Stability: ", bases && calculateEndStability(bases), " kcal/mol"))
   );
 }, "RenderBases");
+const TextInnerWrapper = /* @__PURE__ */ __name((p2) => /* @__PURE__ */ React__default.createElement(
+  "div",
+  {
+    className: "bp3-text-muted bp3-text-small",
+    style: {
+      marginBottom: 15,
+      marginTop: -5,
+      fontStyle: "italic"
+    }
+  },
+  p2.children
+), "TextInnerWrapper");
 const AddOrEditPrimerDialog = AddOrEditAnnotationDialog$1({
   formName: "AddOrEditPrimerDialog",
   getProps: /* @__PURE__ */ __name((props) => ({
@@ -137654,14 +137821,6 @@ const AddOrEditPrimerDialog = AddOrEditAnnotationDialog$1({
     RenderBases
   }), "getProps")
 });
-const InnerWrapperMeltingTemp = /* @__PURE__ */ __name((p2) => /* @__PURE__ */ React__default.createElement(
-  "div",
-  {
-    className: "bp3-text-muted bp3-text-small",
-    style: { marginBottom: 15, marginTop: -5, fontStyle: "italic" }
-  },
-  p2.children
-), "InnerWrapperMeltingTemp");
 const Dialogs = {
   RenameSequenceDialog,
   PrintDialog: PrintDialog$1,

package/index.umd.js

@@ -113252,6 +113252,160 @@ ${latestSubscriptionCallbackError.current.stack}
     }
   }
   __name(calculateNebTm, "calculateNebTm");
+  const PRIMER3_PARAMS = {
+    saltMonovalent: 50,
+    // mM
+    saltDivalent: 1.5,
+    // mM
+    dntpConc: 0.6,
+    // mM
+    dnaConc: 50,
+    // nM
+    R: 1.987
+    // Gas constant (cal/K·mol)
+  };
+  const SANTA_LUCIA_NN = {
+    AA: { dH: -7.9, dS: -22.2 },
+    TT: { dH: -7.9, dS: -22.2 },
+    AT: { dH: -7.2, dS: -20.4 },
+    TA: { dH: -7.2, dS: -21.3 },
+    CA: { dH: -8.5, dS: -22.7 },
+    TG: { dH: -8.5, dS: -22.7 },
+    GT: { dH: -8.4, dS: -22.4 },
+    AC: { dH: -8.4, dS: -22.4 },
+    CT: { dH: -7.8, dS: -21 },
+    AG: { dH: -7.8, dS: -21 },
+    GA: { dH: -8.2, dS: -22.2 },
+    TC: { dH: -8.2, dS: -22.2 },
+    CG: { dH: -10.6, dS: -27.2 },
+    GC: { dH: -9.8, dS: -24.4 },
+    GG: { dH: -8, dS: -19.9 },
+    CC: { dH: -8, dS: -19.9 }
+  };
+  const SANTA_LUCIA_INIT = {
+    GC: { dH: 0.1, dS: -2.8 },
+    // initiation with terminal GC
+    AT: { dH: 2.3, dS: 4.1 }
+    // initiation with terminal AT
+  };
+  function getEffectiveMonovalentConc() {
+    let effectiveMono = PRIMER3_PARAMS.saltMonovalent;
+    {
+      const freeMg = Math.max(
+        0,
+        PRIMER3_PARAMS.saltDivalent - PRIMER3_PARAMS.dntpConc
+      );
+      effectiveMono += 120 * Math.sqrt(freeMg);
+    }
+    return effectiveMono;
+  }
+  __name(getEffectiveMonovalentConc, "getEffectiveMonovalentConc");
+  function applySaltCorrection(deltaS, nnPairs) {
+    const effectiveMono = getEffectiveMonovalentConc();
+    return deltaS + 0.368 * nnPairs * Math.log(effectiveMono / 1e3);
+  }
+  __name(applySaltCorrection, "applySaltCorrection");
+  function isValidSequence(sequence2) {
+    return /^[ATGCN]+$/.test(sequence2);
+  }
+  __name(isValidSequence, "isValidSequence");
+  function calculateSantaLuciaTm(sequence2) {
+    try {
+      sequence2 = sequence2 == null ? void 0 : sequence2.toUpperCase().trim();
+      if (!isValidSequence(sequence2)) {
+        throw new Error("Invalid sequence: contains non-DNA characters");
+      }
+      if (sequence2.length < 2) {
+        throw new Error("Sequence too short: minimum length is 2 bases");
+      }
+      let deltaH = 0;
+      let deltaS = 0;
+      for (let i2 = 0; i2 < sequence2.length - 1; i2++) {
+        const dinucleotide = sequence2.substring(i2, i2 + 2);
+        if (dinucleotide.includes("N")) {
+          continue;
+        }
+        const params = SANTA_LUCIA_NN[dinucleotide];
+        if (params) {
+          deltaH += params.dH;
+          deltaS += params.dS;
+        }
+      }
+      const firstBase = sequence2[0];
+      const lastBase = sequence2[sequence2.length - 1];
+      if (firstBase === "G" || firstBase === "C") {
+        deltaH += SANTA_LUCIA_INIT.GC.dH;
+        deltaS += SANTA_LUCIA_INIT.GC.dS;
+      } else {
+        deltaH += SANTA_LUCIA_INIT.AT.dH;
+        deltaS += SANTA_LUCIA_INIT.AT.dS;
+      }
+      if (lastBase === "G" || lastBase === "C") {
+        deltaH += SANTA_LUCIA_INIT.GC.dH;
+        deltaS += SANTA_LUCIA_INIT.GC.dS;
+      } else {
+        deltaH += SANTA_LUCIA_INIT.AT.dH;
+        deltaS += SANTA_LUCIA_INIT.AT.dS;
+      }
+      const nnPairs = sequence2.length - 1;
+      deltaS = applySaltCorrection(deltaS, nnPairs);
+      const C = PRIMER3_PARAMS.dnaConc * 1e-9;
+      const Tm = deltaH * 1e3 / (deltaS + PRIMER3_PARAMS.R * Math.log(C / 4));
+      return Tm - 273.15;
+    } catch (e2) {
+      return `Error calculating Tm for sequence ${sequence2}. ${e2}`;
+    }
+  }
+  __name(calculateSantaLuciaTm, "calculateSantaLuciaTm");
+  function calculateEndStability(sequence2) {
+    try {
+      sequence2 = sequence2 == null ? void 0 : sequence2.toUpperCase().trim();
+      if (!isValidSequence(sequence2)) {
+        throw new Error("Invalid sequence: contains non-DNA characters");
+      }
+      if (sequence2.length < 5) {
+        throw new Error(
+          "Sequence too short: minimum length is 5 bases for end stability calculation"
+        );
+      }
+      const last5Bases = sequence2.substring(sequence2.length - 5);
+      let deltaH = 0;
+      let deltaS = 0;
+      for (let i2 = 0; i2 < 4; i2++) {
+        const dinucleotide = last5Bases.substring(i2, i2 + 2);
+        if (dinucleotide.includes("N")) {
+          continue;
+        }
+        const params = SANTA_LUCIA_NN[dinucleotide];
+        if (params) {
+          deltaH += params.dH;
+          deltaS += params.dS;
+        }
+      }
+      const firstBase = last5Bases[0];
+      const lastBase = last5Bases[last5Bases.length - 1];
+      if (firstBase === "G" || firstBase === "C") {
+        deltaH += SANTA_LUCIA_INIT.GC.dH;
+        deltaS += SANTA_LUCIA_INIT.GC.dS;
+      } else {
+        deltaH += SANTA_LUCIA_INIT.AT.dH;
+        deltaS += SANTA_LUCIA_INIT.AT.dS;
+      }
+      if (lastBase === "G" || lastBase === "C") {
+        deltaH += SANTA_LUCIA_INIT.GC.dH;
+        deltaS += SANTA_LUCIA_INIT.GC.dS;
+      } else {
+        deltaH += SANTA_LUCIA_INIT.AT.dH;
+        deltaS += SANTA_LUCIA_INIT.AT.dS;
+      }
+      const T2 = 310.15;
+      const deltaG = deltaH - T2 * deltaS / 1e3;
+      return Math.round(Math.abs(deltaG) * 100) / 100;
+    } catch (e2) {
+      return `Error calculating end stability for sequence ${sequence2}. ${e2}`;
+    }
+  }
+  __name(calculateEndStability, "calculateEndStability");
   function convertAACaretPositionOrRangeToDna(rangeOrCaret) {
     if (typeof rangeOrCaret === "object" && rangeOrCaret !== null) {
       return convertAARangeToDnaRange(__spreadProps(__spreadValues({}, rangeOrCaret), {
@@ -144752,7 +144906,7 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
     input.click();
   }
   __name(showFileDialog, "showFileDialog");
-  const version = "0.8.18";
+  const version = "0.8.19";
   const packageJson = {
     version
   };
@@ -163850,7 +164004,7 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
       /* , setMonovalentCationConc */
     ] = React.useState(0.05);
     const [tmType, setTmType] = useTmType();
-    let tm = (tmType === "neb_tm" ? calculateNebTm : calculateTm)(sequence2, {
+    let tm = (tmType === "neb_tm" ? calculateNebTm : tmType === "default" ? calculateSantaLuciaTm : calculateTm)(sequence2, {
       monovalentCationConc,
       primerConc
     });
@@ -163875,8 +164029,9 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
           {
             label: "Choose Tm Type:",
             options: [
-              { value: "default", label: "Default Tm (Breslauer)" },
-              { value: "neb_tm", label: "NEB Tm (SantaLucia)" }
+              { value: "default", label: "Santa Lucia (Default)" },
+              { value: "breslauer", label: "Breslauer" },
+              { value: "neb_tm", label: "NEB Tm" }
             ],
             onChange: /* @__PURE__ */ __name((e2) => setTmType(e2.target.value), "onChange"),
             selectedValue: tmType
@@ -163890,7 +164045,7 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
           }
         ), hasWarning, /* @__PURE__ */ React.createElement("br", null), /* @__PURE__ */ React.createElement("br", null), "Try using the Default Tm"))
       },
-      /* @__PURE__ */ React.createElement(React.Fragment, null, /* @__PURE__ */ React.createElement(InnerWrapper, null, "Melting Temp: ", Number(tm) || 0, " "), hasWarning && /* @__PURE__ */ React.createElement(
+      /* @__PURE__ */ React.createElement(React.Fragment, null, /* @__PURE__ */ React.createElement(InnerWrapper, null, "Melting Temp: ", Number(tm) || 0, "°C"), hasWarning && /* @__PURE__ */ React.createElement(
         Icon,
         {
           style: { marginLeft: 5, marginRight: 5 },
@@ -164154,12 +164309,24 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
       )), /* @__PURE__ */ React.createElement(
         MeltingTemp,
         {
-          InnerWrapper: InnerWrapperMeltingTemp,
+          InnerWrapper: TextInnerWrapper,
           sequence: bases
         }
-      ))
+      ), /* @__PURE__ */ React.createElement(TextInnerWrapper, null, "GC content: ", bases && calculatePercentGC(bases).toFixed(1), "%"), /* @__PURE__ */ React.createElement(TextInnerWrapper, null, "3' Stability: ", bases && calculateEndStability(bases), " kcal/mol"))
     );
   }, "RenderBases");
+  const TextInnerWrapper = /* @__PURE__ */ __name((p2) => /* @__PURE__ */ React.createElement(
+    "div",
+    {
+      className: "bp3-text-muted bp3-text-small",
+      style: {
+        marginBottom: 15,
+        marginTop: -5,
+        fontStyle: "italic"
+      }
+    },
+    p2.children
+  ), "TextInnerWrapper");
   const AddOrEditPrimerDialog = AddOrEditAnnotationDialog$1({
     formName: "AddOrEditPrimerDialog",
     getProps: /* @__PURE__ */ __name((props) => ({
@@ -164168,14 +164335,6 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
       RenderBases
     }), "getProps")
   });
-  const InnerWrapperMeltingTemp = /* @__PURE__ */ __name((p2) => /* @__PURE__ */ React.createElement(
-    "div",
-    {
-      className: "bp3-text-muted bp3-text-small",
-      style: { marginBottom: 15, marginTop: -5, fontStyle: "italic" }
-    },
-    p2.children
-  ), "InnerWrapperMeltingTemp");
   const Dialogs = {
     RenameSequenceDialog,
     PrintDialog: PrintDialog$1,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@teselagen/ove",
-  "version": "0.8.19",
+  "version": "0.8.20",
   "main": "./src/index.js",
   "type": "module",
   "exports": {
@@ -18,7 +18,7 @@
     "@teselagen/file-utils": "0.3.20",
     "@teselagen/range-utils": "0.3.13",
     "@teselagen/react-list": "0.8.18",
-    "@teselagen/sequence-utils": "0.3.35",
+    "@teselagen/sequence-utils": "0.3.36",
     "@teselagen/ui": "0.10.9",
     "@use-gesture/react": "10.3.0",
     "biomsa": "^0.2.4",

package/src/StatusBar/MeltingTemp.js

@@ -1,7 +1,11 @@
 import React from "react";
 import { Button, Icon, Popover, RadioGroup } from "@blueprintjs/core";
 
-import { calculateTm, calculateNebTm } from "@teselagen/sequence-utils";
+import {
+  calculateTm,
+  calculateNebTm,
+  calculateSantaLuciaTm
+} from "@teselagen/sequence-utils";
 
 import { isNumber, isString } from "lodash-es";
 import { popoverOverflowModifiers } from "@teselagen/ui";
@@ -20,7 +24,13 @@ export default function MeltingTemp({
   const [monovalentCationConc /* , setMonovalentCationConc */] =
     React.useState(0.05);
   const [tmType, setTmType] = useTmType();
-  let tm = (tmType === "neb_tm" ? calculateNebTm : calculateTm)(sequence, {
+  let tm = (
+    tmType === "neb_tm"
+      ? calculateNebTm
+      : tmType === "default"
+        ? calculateSantaLuciaTm
+        : calculateTm
+  )(sequence, {
     monovalentCationConc,
     primerConc
   });
@@ -47,8 +57,9 @@ export default function MeltingTemp({
             <RadioGroup
               label="Choose Tm Type:"
               options={[
-                { value: "default", label: "Default Tm (Breslauer)" },
-                { value: "neb_tm", label: "NEB Tm (SantaLucia)" }
+                { value: "default", label: "Santa Lucia (Default)" },
+                { value: "breslauer", label: "Breslauer" },
+                { value: "neb_tm", label: "NEB Tm" }
               ]}
               onChange={e => setTmType(e.target.value)}
               selectedValue={tmType}
@@ -70,7 +81,7 @@ export default function MeltingTemp({
         }
       >
         <React.Fragment>
-          <InnerWrapper>Melting Temp: {Number(tm) || 0} </InnerWrapper>
+          <InnerWrapper>Melting Temp: {Number(tm) || 0}°C</InnerWrapper>
           {hasWarning && (
             <Icon
               style={{ marginLeft: 5, marginRight: 5 }}

package/src/helperComponents/AddOrEditPrimerDialog/index.js

@@ -8,7 +8,9 @@ import {
 } from "@teselagen/ui";
 import {
   filterSequenceString,
-  getReverseComplementSequenceString
+  getReverseComplementSequenceString,
+  calculatePercentGC,
+  calculateEndStability
 } from "@teselagen/sequence-utils";
 
 import AddOrEditAnnotationDialog from "../AddOrEditAnnotationDialog";
@@ -294,15 +296,34 @@ const RenderBases = props => {
           </AdvancedOptions>
 
           <MeltingTemp
-            InnerWrapper={InnerWrapperMeltingTemp}
+            InnerWrapper={TextInnerWrapper}
             sequence={bases}
           ></MeltingTemp>
+          <TextInnerWrapper>
+            GC content: {bases && calculatePercentGC(bases).toFixed(1)}%
+          </TextInnerWrapper>
+          <TextInnerWrapper>
+            3' Stability: {bases && calculateEndStability(bases)} kcal/mol
+          </TextInnerWrapper>
         </div>
       )}
     </div>
   );
 };
 
+const TextInnerWrapper = p => (
+  <div
+    className="bp3-text-muted bp3-text-small"
+    style={{
+      marginBottom: 15,
+      marginTop: -5,
+      fontStyle: "italic"
+    }}
+  >
+    {p.children}
+  </div>
+);
+
 export default AddOrEditAnnotationDialog({
   formName: "AddOrEditPrimerDialog",
   getProps: props => ({
@@ -311,12 +332,3 @@ export default AddOrEditAnnotationDialog({
     RenderBases
   })
 });
-
-const InnerWrapperMeltingTemp = p => (
-  <div
-    className="bp3-text-muted bp3-text-small"
-    style={{ marginBottom: 15, marginTop: -5, fontStyle: "italic" }}
-  >
-    {p.children}
-  </div>
-);