@i-vresse/haddock3-ui 0.1.5 → 0.1.6

package/README.md

@@ -12,6 +12,7 @@ The [haddock3 web application](https://github.com/i-VRESSE/haddock3-webapp) had
 
 - Components to render a 3D molecular structure from [PDB file](https://www.wwpdb.org/) using [NGL](https://nglviewer.org/)
 - Components to select residues in a molecule either passive or active
+- Components to handle files
 
 ## Installation
 
@@ -27,7 +28,7 @@ For your own webapp to pick up the classes in the components, you need to add th
 export default {
   content: [
     // Existing content goes here
-    './node_modules/@i-vresse/haddock3-ui/dist/index.js',
+    './node_modules/@i-vresse/haddock3-ui/dist/**/*.js',
   ],
   // Rest of the config goes here
 }
@@ -42,3 +43,5 @@ Once component is selected
 - interact with component
 - use `</>` button in footer to see the code.
 - use sliders icon button in footer to change props when available
+
+API documentation is available at [https://i-VRESSE.github.io/haddock3-ui/api/](https://i-VRESSE.github.io/haddock3-ui/api/)

package/dist/{src/CopyToClipBoardIcon.d.ts → CopyToClipBoardIcon.d.ts}

@@ -1 +1,2 @@
 export declare function CopyToClipBoardIcon(): import("react/jsx-runtime").JSX.Element;
+//# sourceMappingURL=CopyToClipBoardIcon.d.ts.map

package/dist/CopyToClipBoardIcon.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"CopyToClipBoardIcon.d.ts","sourceRoot":"","sources":["../src/CopyToClipBoardIcon.tsx"],"names":[],"mappings":"AAAA,wBAAgB,mBAAmB,4CAiBlC"}

package/dist/CopyToClipBoardIcon.js

@@ -0,0 +1,5 @@
+import { jsx as _jsx } from "react/jsx-runtime";
+export function CopyToClipBoardIcon() {
+    return (_jsx("svg", { width: "14", height: "14", viewBox: "0 0 14 15", fill: "none", xmlns: "http://www.w3.org/2000/svg", children: _jsx("path", { fillRule: "evenodd", clipRule: "evenodd", d: "M11.746.07A.5.5 0 0011.5.003h-6a.5.5 0 00-.5.5v2.5H.5a.5.5 0 00-.5.5v10a.5.5 0 00.5.5h8a.5.5 0 00.5-.5v-2.5h4.5a.5.5 0 00.5-.5v-8a.498.498 0 00-.15-.357L11.857.154a.506.506 0 00-.11-.085zM9 10.003h4v-7h-1.5a.5.5 0 01-.5-.5v-1.5H6v2h.5a.5.5 0 01.357.15L8.85 5.147c.093.09.15.217.15.357v4.5zm-8-6v9h7v-7H6.5a.5.5 0 01-.5-.5v-1.5H1z", fill: "currentColor" }) }));
+}
+//# sourceMappingURL=CopyToClipBoardIcon.js.map

package/dist/CopyToClipBoardIcon.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"CopyToClipBoardIcon.js","sourceRoot":"","sources":["../src/CopyToClipBoardIcon.tsx"],"names":[],"mappings":";AAAA,MAAM,UAAU,mBAAmB;IAClC,OAAO,CACN,cACC,KAAK,EAAC,IAAI,EACV,MAAM,EAAC,IAAI,EACX,OAAO,EAAC,WAAW,EACnB,IAAI,EAAC,MAAM,EACX,KAAK,EAAC,4BAA4B,YAElC,eACC,QAAQ,EAAC,SAAS,EAClB,QAAQ,EAAC,SAAS,EAClB,CAAC,EAAC,2UAA2U,EAC7U,IAAI,EAAC,cAAc,GACZ,GACH,CACN,CAAC;AACH,CAAC"}

package/dist/Hetero.d.ts

@@ -0,0 +1,17 @@
+export interface Hetero {
+    resno: number;
+    resname: string;
+    chain: string;
+    /**
+     * HETNAME record value from the PDB file.
+     */
+    description?: string;
+}
+/**
+ * Retrieve hetero residues from a PDB file.
+ *
+ * @param file PDB file to read from
+ * @returns
+ */
+export declare function heterosFromFile(file: File): Promise<Hetero[]>;
+//# sourceMappingURL=Hetero.d.ts.map

package/dist/Hetero.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"Hetero.d.ts","sourceRoot":"","sources":["../src/Hetero.tsx"],"names":[],"mappings":"AAEA,MAAM,WAAW,MAAM;IACtB,KAAK,EAAE,MAAM,CAAC;IACd,OAAO,EAAE,MAAM,CAAC;IAChB,KAAK,EAAE,MAAM,CAAC;IACd;;OAEG;IACH,WAAW,CAAC,EAAE,MAAM,CAAC;CACrB;AAED;;;;;GAKG;AACH,wBAAsB,eAAe,CAAC,IAAI,EAAE,IAAI,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC,CA0BnE"}

package/dist/Hetero.js

@@ -0,0 +1,36 @@
+import { autoLoad } from "ngl";
+/**
+ * Retrieve hetero residues from a PDB file.
+ *
+ * @param file PDB file to read from
+ * @returns
+ */
+export async function heterosFromFile(file) {
+    const structure = await autoLoad(file);
+    const heteros = [];
+    structure.eachResidue((r) => {
+        if (r.isHetero() && !r.isWater() && !r.isIon()) {
+            const hetero = {
+                resno: r.resno,
+                resname: r.resname,
+                chain: r.chain.chainname,
+            };
+            if (r.entity) {
+                hetero.description = r.entity.description;
+            }
+            heteros.push(hetero);
+        }
+    });
+    heteros.sort((a, b) => {
+        if (a.resname !== b.resname) {
+            return a.resname.localeCompare(b.resname);
+        }
+        if (a.chain !== b.chain) {
+            return a.chain.localeCompare(b.chain);
+        }
+        return a.resno - b.resno;
+    });
+    return heteros;
+}
+// TODO write e2e test. Unit test not possible because ngl does not work in nodejs.
+//# sourceMappingURL=Hetero.js.map

package/dist/Hetero.js.map

@@ -0,0 +1 @@
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package/dist/HiddenFileInput.d.ts

@@ -0,0 +1,5 @@
+export declare function HiddenFileInput({ name, file }: {
+    name: string;
+    file: File;
+}): import("react/jsx-runtime").JSX.Element;
+//# sourceMappingURL=HiddenFileInput.d.ts.map

package/dist/HiddenFileInput.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"HiddenFileInput.d.ts","sourceRoot":"","sources":["../src/HiddenFileInput.tsx"],"names":[],"mappings":"AAEA,wBAAgB,eAAe,CAAC,EAAE,IAAI,EAAE,IAAI,EAAE,EAAE;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,IAAI,CAAA;CAAE,2CAY3E"}

package/dist/HiddenFileInput.js

@@ -0,0 +1,14 @@
+import { jsx as _jsx } from "react/jsx-runtime";
+import { useEffect, useRef } from "react";
+export function HiddenFileInput({ name, file }) {
+    const ref = useRef(null);
+    useEffect(() => {
+        if (ref.current) {
+            const dataTransfer = new DataTransfer();
+            dataTransfer.items.add(file);
+            ref.current.files = dataTransfer.files;
+        }
+    }, [file]);
+    return _jsx("input", { ref: ref, type: "file", name: name, className: "hidden" });
+}
+//# sourceMappingURL=HiddenFileInput.js.map

package/dist/HiddenFileInput.js.map

@@ -0,0 +1 @@
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package/dist/LinkToFile.d.ts

@@ -0,0 +1,7 @@
+import { type ReactNode } from "react";
+export declare function LinkToFile({ file, children, className, }: {
+    file: File;
+    children: ReactNode;
+    className?: string;
+}): import("react/jsx-runtime").JSX.Element;
+//# sourceMappingURL=LinkToFile.d.ts.map

package/dist/LinkToFile.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"LinkToFile.d.ts","sourceRoot":"","sources":["../src/LinkToFile.tsx"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,SAAS,EAAuB,MAAM,OAAO,CAAC;AAK5D,wBAAgB,UAAU,CAAC,EAC1B,IAAI,EACJ,QAAQ,EACR,SAAqB,GACrB,EAAE;IACF,IAAI,EAAE,IAAI,CAAC;IACX,QAAQ,EAAE,SAAS,CAAC;IACpB,SAAS,CAAC,EAAE,MAAM,CAAC;CACnB,2CAmBA"}

package/dist/LinkToFile.js

@@ -0,0 +1,14 @@
+import { jsx as _jsx } from "react/jsx-runtime";
+import { useEffect, useState } from "react";
+import { cn } from "./cn.js";
+// TODO allow other a tag attributes like title or target to be passed in
+export function LinkToFile({ file, children, className = undefined, }) {
+    const [url, setUrl] = useState("#");
+    useEffect(() => {
+        const url = URL.createObjectURL(file);
+        setUrl(url);
+        return () => URL.revokeObjectURL(url);
+    }, [file]);
+    return (_jsx("a", { className: cn("underline", className), download: file.name, href: url, type: file.type, children: children }));
+}
+//# sourceMappingURL=LinkToFile.js.map

package/dist/LinkToFile.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"LinkToFile.js","sourceRoot":"","sources":["../src/LinkToFile.tsx"],"names":[],"mappings":";AAAA,OAAO,EAAkB,SAAS,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAC;AAC5D,OAAO,EAAE,EAAE,EAAE,MAAM,SAAS,CAAC;AAE7B,yEAAyE;AAEzE,MAAM,UAAU,UAAU,CAAC,EAC1B,IAAI,EACJ,QAAQ,EACR,SAAS,GAAG,SAAS,GAKrB;IACA,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAC;IAEpC,SAAS,CAAC,GAAG,EAAE;QACd,MAAM,GAAG,GAAG,GAAG,CAAC,eAAe,CAAC,IAAI,CAAC,CAAC;QACtC,MAAM,CAAC,GAAG,CAAC,CAAC;QACZ,OAAO,GAAG,EAAE,CAAC,GAAG,CAAC,eAAe,CAAC,GAAG,CAAC,CAAC;IACvC,CAAC,EAAE,CAAC,IAAI,CAAC,CAAC,CAAC;IAEX,OAAO,CACN,YACC,SAAS,EAAE,EAAE,CAAC,WAAW,EAAE,SAAS,CAAC,EACrC,QAAQ,EAAE,IAAI,CAAC,IAAI,EACnB,IAAI,EAAE,GAAG,EACT,IAAI,EAAE,IAAI,CAAC,IAAI,YAEd,QAAQ,GACN,CACJ,CAAC;AACH,CAAC"}

package/dist/cn.d.ts

@@ -0,0 +1,12 @@
+import { type ClassValue } from "clsx";
+/**
+ * Smartly combines multiple tailwind class names into a single string.
+ *
+ * @see https://github.com/lukeed/clsx
+ * @see https://github.com/dcastil/tailwind-merge
+ *
+ * @param inputs - The class names to be combined.
+ * @returns The combined class names as a string.
+ */
+export declare function cn(...inputs: ClassValue[]): string;
+//# sourceMappingURL=cn.d.ts.map

package/dist/cn.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"cn.d.ts","sourceRoot":"","sources":["../src/cn.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,UAAU,EAAQ,MAAM,MAAM,CAAC;AAG7C;;;;;;;;GAQG;AACH,wBAAgB,EAAE,CAAC,GAAG,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,CAElD"}

package/dist/cn.js

@@ -0,0 +1,15 @@
+import { clsx } from "clsx";
+import { twMerge } from "tailwind-merge";
+/**
+ * Smartly combines multiple tailwind class names into a single string.
+ *
+ * @see https://github.com/lukeed/clsx
+ * @see https://github.com/dcastil/tailwind-merge
+ *
+ * @param inputs - The class names to be combined.
+ * @returns The combined class names as a string.
+ */
+export function cn(...inputs) {
+    return twMerge(clsx(inputs));
+}
+//# sourceMappingURL=cn.js.map

package/dist/cn.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"cn.js","sourceRoot":"","sources":["../src/cn.ts"],"names":[],"mappings":"AAAA,OAAO,EAAmB,IAAI,EAAE,MAAM,MAAM,CAAC;AAC7C,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAC;AAEzC;;;;;;;;GAQG;AACH,MAAM,UAAU,EAAE,CAAC,GAAG,MAAoB;IACzC,OAAO,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC;AAC9B,CAAC"}

package/dist/getResName1.d.ts

@@ -0,0 +1,21 @@
+/**
+ * Retrieves the character for a given residue name.
+ *
+ * Besides amino acids, this function also
+ * supports charm forcefield, amber forcefield,
+ * DNA nucleotides and RNA nucleotides.
+ *
+ * @param resname - The residue name to retrieve the abbreviated name for.
+ * @returns The abbreviated name for the given resource name, or "X" if no abbreviation is found.
+ *
+ * @example
+ * ```ts
+ * import { getResName1 } from "@i-vresse/haddock3-ui/getResName1";
+ * getResName1("ALA"); // "A"
+ * getResName1("DA"); // "A"
+ * getResName1("A"); // "A"
+ * getResName1("UNK"); // "X"
+ * ```
+ */
+export declare function getResName1(resname: string): "H" | "R" | "K" | "I" | "F" | "L" | "W" | "A" | "M" | "P" | "C" | "N" | "V" | "G" | "S" | "Q" | "Y" | "D" | "E" | "T" | "U" | "O";
+//# sourceMappingURL=getResName1.d.ts.map

package/dist/getResName1.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"getResName1.d.ts","sourceRoot":"","sources":["../src/getResName1.ts"],"names":[],"mappings":"AA2DA;;;;;;;;;;;;;;;;;;GAkBG;AACH,wBAAgB,WAAW,CAAC,OAAO,EAAE,MAAM,qIAE1C"}

package/dist/getResName1.js

@@ -0,0 +1,78 @@
+/*
+ * NGL does not have single letter for DNA or RNA, but molstar does.
+ * Use molstar implementation from
+ * https://github.com/molstar/molstar/blob/5a2ee03b48e1822c8843d65eb18d578af0579b9f/src/mol-model/sequence/constants.ts#L18-L85
+ */
+const Name2OneLetter = {
+    HIS: "H",
+    ARG: "R",
+    LYS: "K",
+    ILE: "I",
+    PHE: "F",
+    LEU: "L",
+    TRP: "W",
+    ALA: "A",
+    MET: "M",
+    PRO: "P",
+    CYS: "C",
+    ASN: "N",
+    VAL: "V",
+    GLY: "G",
+    SER: "S",
+    GLN: "Q",
+    TYR: "Y",
+    ASP: "D",
+    GLU: "E",
+    THR: "T",
+    SEC: "U", // as per IUPAC definition
+    PYL: "O", // as per IUPAC definition
+    // charmm ff
+    HSD: "H",
+    HSE: "H",
+    HSP: "H",
+    LSN: "K",
+    ASPP: "D",
+    GLUP: "E",
+    // amber ff
+    HID: "H",
+    HIE: "H",
+    HIP: "H",
+    LYN: "K",
+    ASH: "D",
+    GLH: "E",
+    // DNA
+    DA: "A",
+    DC: "C",
+    DG: "G",
+    DT: "T",
+    DU: "U",
+    // RNA
+    A: "A",
+    C: "C",
+    G: "G",
+    T: "T",
+    U: "U",
+};
+/**
+ * Retrieves the character for a given residue name.
+ *
+ * Besides amino acids, this function also
+ * supports charm forcefield, amber forcefield,
+ * DNA nucleotides and RNA nucleotides.
+ *
+ * @param resname - The residue name to retrieve the abbreviated name for.
+ * @returns The abbreviated name for the given resource name, or "X" if no abbreviation is found.
+ *
+ * @example
+ * ```ts
+ * import { getResName1 } from "@i-vresse/haddock3-ui/getResName1";
+ * getResName1("ALA"); // "A"
+ * getResName1("DA"); // "A"
+ * getResName1("A"); // "A"
+ * getResName1("UNK"); // "X"
+ * ```
+ */
+export function getResName1(resname) {
+    return Name2OneLetter[resname] || "X";
+}
+//# sourceMappingURL=getResName1.js.map

package/dist/getResName1.js.map

@@ -0,0 +1 @@
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package/dist/index.d.ts

@@ -0,0 +1,6 @@
+export { NGLComponent, NGLResidues, NGLStage, SimpleViewer, LigandViewer, Viewer, } from "./molviewer.js";
+export { PickIn3D, ResiduesSelect } from "./toggles.js";
+export { CopyToClipBoardIcon } from "./CopyToClipBoardIcon.js";
+export { LinkToFile } from "./LinkToFile.js";
+export { HiddenFileInput } from "./HiddenFileInput.js";
+//# sourceMappingURL=index.d.ts.map

package/dist/index.d.ts.map

@@ -0,0 +1 @@
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