E/nMT tailoring of PARAS predictions

gui/src/client/src/components/MotifName.tsx

@@ -2,10 +2,15 @@ import React from "react";
 import Box from "@mui/material/Box";
 import { isLinkToken } from "../features/reconstruction/types";
 
-// Renders a monomer name like "A2^R" or "C^E2", superscripting the trailing stereo marker.
-// The link token (joining two merged primary sequence paths, see LINK_TOKEN) isn't a real
-// building block -- render it as a muted glyph instead of a name, everywhere a monomer
-// name would otherwise be rendered (sequence chips, alignment grid cells, ...).
+// Stereo markers mxn.yml appends after "^": R/S (PK alpha/beta carbons), E/Z (PK
+// alkene geometry), L/D (NRPS amino acid alpha carbons, e.g. "alanine^L").
+const STEREO_MARKER = /^\^[A-Za-z]+$/;
+
+// Renders a monomer name like "A2^R" or "C^E2" or "alanine^L", superscripting the
+// trailing stereo marker(s). The link token (joining two merged primary sequence
+// paths, see LINK_TOKEN) isn't a real building block -- render it as a muted glyph
+// instead of a name, everywhere a monomer name would otherwise be rendered (sequence
+// chips, alignment grid cells, ...).
 export function MotifName({ name }: { name: string }) {
   if (isLinkToken(name)) {
     return (
@@ -15,12 +20,12 @@ export function MotifName({ name }: { name: string }) {
     );
   }
 
-  const parts = name.split(/(\^[SREZ])/g);
+  const parts = name.split(/(\^[A-Za-z]+)/g);
 
   return (
     <>
       {parts.map((part, i) => {
-        if (part === "^S" || part === "^R" || part === "^E" || part === "^Z") {
+        if (STEREO_MARKER.test(part)) {
           return (
             <Box
               key={i}

gui/src/client/src/components/workspace/alignmentSvgExport.ts

@@ -50,20 +50,23 @@ function escapeXml(value: string): string {
     .replace(/'/g, "'");
 }
 
-// Splits a name like "A2^R" or "C^E2" into plain/superscript runs, matching MotifName's convention.
-// The link token renders as the same muted glyph MotifName uses instead of its literal text.
+// Stereo markers mxn.yml appends after "^": R/S (PK alpha/beta carbons), E/Z (PK
+// alkene geometry), L/D (NRPS amino acid alpha carbons, e.g. "alanine^L").
+const STEREO_MARKER = /^\^[A-Za-z]+$/;
+
+// Splits a name like "A2^R" or "C^E2" or "alanine^L" into plain/superscript runs,
+// matching MotifName's convention. The link token renders as the same muted glyph
+// MotifName uses instead of its literal text.
 function splitStereoMarkers(name: string): { text: string; sup: boolean }[] {
   if (name === LINK_TOKEN) {
     return [{ text: "⋮", sup: false }];
   }
 
   return name
-    .split(/(\^[SREZ])/g)
+    .split(/(\^[A-Za-z]+)/g)
     .filter((part) => part !== "")
     .map((part) =>
-      part === "^S" || part === "^R" || part === "^E" || part === "^Z"
-        ? { text: part.slice(1), sup: true }
-        : { text: part, sup: false }
+      STEREO_MARKER.test(part) ? { text: part.slice(1), sup: true } : { text: part, sup: false }
     );
 }