data/frontend/src/components/convert/FormatConversionView.tsx

// Description: This component handles the format conversion between different chemical notations.
import { useState, useRef } from "react";
// Ensure all used icons are imported
// Assuming these components are correctly implemented and styled for dark/light mode
import SMILESInput from "../common/SMILESInput";
import MoleculeDepiction2D from "../depict/MoleculeDepiction2D";
import { ToolSkeleton } from "@/components/feedback/ToolSkeleton";
import { GlassErrorCard } from "@/components/feedback/GlassErrorCard";
import { EmptyState } from "@/components/feedback/EmptyState";
import { getErrorMessage } from "@/lib/error-messages";
// Assuming this service is configured correctly
import convertService from "../../services/convertService";
import XYZGridResult from "./XYZGridResult";
import type { XYZBatchConversionResult } from "@/types/api";
import {
  AlertCircle,
  ArrowLeftRight,
  ArrowRight,
  Check,
  Clipboard,
  FileText,
  Loader2,
  Upload,
} from "lucide-react";
import { Button } from "@/components/ui/button";
import { cn } from "@/lib/utils";
import {
  Select,
  SelectContent,
  SelectItem,
  SelectTrigger,
  SelectValue,
} from "@/components/ui/select";
import { Input } from "@/components/ui/input";
import { Textarea } from "@/components/ui/textarea";

// Input format options configuration
const INPUT_FORMAT_OPTIONS = [
  { id: "smiles", label: "SMILES" },
  { id: "iupac", label: "IUPAC Name" },
  { id: "selfies", label: "SELFIES" },
  { id: "molsdf", label: "MOL/SDF Block" },
  { id: "cdx", label: "ChemDraw CDX/CDXML" },
  { id: "xyz", label: "XYZ Coordinates" },
];

// Output format options configuration
const OUTPUT_FORMAT_OPTIONS = [
  { id: "smiles", label: "SMILES", method: null },
  {
    id: "canonicalsmiles",
    label: "Canonical SMILES",
    method: "generateCanonicalSMILES",
  },
  { id: "inchi", label: "InChI", method: "generateInChI" },
  { id: "inchikey", label: "InChI Key", method: "generateInChIKey" },
  { id: "cxsmiles", label: "CXSMILES", method: "generateCXSMILES" },
  { id: "selfies", label: "SELFIES", method: "generateSELFIES" },
  { id: "smarts", label: "SMARTS", method: "generateSMARTS" },
  { id: "mol", label: "MOL Block", method: null },
  { id: "sdf", label: "SDF", method: null },
];

// Output formats reachable from XYZ input.
const XYZ_OUTPUT_FORMAT_IDS = new Set(["canonicalsmiles", "inchi", "inchikey", "mol", "sdf"]);

// Toolkit options configuration
const TOOLKIT_OPTIONS = [
  { id: "cdk", label: "CDK (Chemistry Development Kit)" },
  { id: "rdkit", label: "RDKit" },
  { id: "openbabel", label: "OpenBabel" },
];

// Converter options for IUPAC
const IUPAC_CONVERTER_OPTIONS = [{ id: "opsin", label: "OPSIN" }];

// Detect whether input text is SMILES, SELFIES, or IUPAC name
const detectInputFormat = (text) => {
  const trimmed = text.trim();
  if (!trimmed) return null;

  // SELFIES: entirely composed of [token] sequences
  if (/^(\[[\w@=#+\-/\\%;.,^*]+\])+$/.test(trimmed)) return "selfies";

  // IUPAC: word-like name — only lowercase letters, digits, spaces, hyphens, commas,
  // parentheses; and no SMILES ring-closure patterns (letter immediately adjacent to digit)
  if (
    /^[a-z0-9][a-z0-9 ,\-().]*$/.test(trimmed) &&
    !/[a-z]\d/.test(trimmed) &&
    !/\d[a-z]/.test(trimmed)
  ) {
    return "iupac";
  }

  // SMILES: no whitespace, only valid SMILES characters
  if (!/\s/.test(trimmed) && /^[A-Za-z0-9[\]()=#@+\-/.\\%:*]+$/.test(trimmed)) return "smiles";

  // Otherwise assume IUPAC name
  return "iupac";
};

const FormatConversionView = () => {
  const [input, setInput] = useState("");
  const [inputFormat, setInputFormat] = useState("smiles");
  const [outputFormat, setOutputFormat] = useState("canonicalsmiles");
  const [toolkit, setToolkit] = useState("cdk");
  const [iupacConverter, setIupacConverter] = useState("opsin");
  const [result, setResult] = useState("");
  const [loading, setLoading] = useState(false);
  const [error, setError] = useState(null);
  const [copied, setCopied] = useState(false);
  const [autoDetected, setAutoDetected] = useState(false);
  // State for molecular structure display
  const [smilesForStructure, setSmilesForStructure] = useState("");
  const [showStructure, setShowStructure] = useState(false);
  // State for file upload (MOL/SDF)
  const [uploadedFilename, setUploadedFilename] = useState("");
  const fileInputRef = useRef(null);
  // State for CDX/CDXML file upload
  const [cdxFile, setCdxFile] = useState(null);
  const [cdxFilename, setCdxFilename] = useState("");
  const cdxFileInputRef = useRef(null);
  // State for XYZ file upload + bond-perception parameters
  const [xyzFilename, setXyzFilename] = useState("");
  const [xyzCharge, setXyzCharge] = useState(0);
  const [xyzUseHueckel, setXyzUseHueckel] = useState(false);
  const xyzFileInputRef = useRef(null);
  const [xyzBatchResult, setXyzBatchResult] = useState<XYZBatchConversionResult | null>(null);

  // Helper function to ensure molblock is in proper format for backend
  const formatMolblockForBackend = (molblock) => {
    // Normalize line endings first
    let formatted = molblock.replace(/\r\n/g, "\n").replace(/\r/g, "\n");

    // Clean up - remove trailing spaces from each line and trim
    formatted = formatted
      .split("\n")
      .map((line) => line.trimEnd())
      .join("\n")
      .trim();

    // V2000/V3000 molblocks have a 3-line header: name, program/timestamp, comment.
    // CDK-style molblocks omit the name line (start with program line), so we
    // prepend an empty name line.  Molblocks that already include a name line
    // (e.g. Actelion MolfileCreator) must NOT get an extra blank line.
    const lines = formatted.split("\n");
    const countsIdx = lines.findIndex((l) => /V[23]000/.test(l));
    if (countsIdx >= 0 && countsIdx <= 2) {
      // Counts line found too early → name line is missing → add blank name
      formatted = "\n" + formatted;
    }

    // Ensure it ends with M  END followed by a newline
    if (!formatted.endsWith("M  END\n")) {
      if (formatted.endsWith("M  END")) {
        formatted += "\n";
      }
    }

    return formatted;
  };

  // Handle file upload for MOL/SDF files
  const handleFileUpload = (e) => {
    const file = e.target.files[0];
    if (!file) return;

    // Reset error and filename
    setError(null);
    setUploadedFilename("");

    // Validate file extension
    const fileName = file.name.toLowerCase();
    if (!fileName.endsWith(".mol") && !fileName.endsWith(".sdf")) {
      setError("Please upload a valid .mol or .sdf file.");
      return;
    }

    setUploadedFilename(file.name);

    const reader = new FileReader();

    reader.onload = (event) => {
      try {
        let fileContent = event.target.result;

        // Normalize line endings and trim
        fileContent = fileContent.replace(/\r\n/g, "\n").replace(/\r/g, "\n").trim();

        // Validate molblock format
        if (!fileContent.includes("M  END")) {
          setError(
            'Invalid file format: The uploaded file does not appear to be a valid MOL/SDF file (missing "M  END").'
          );
          setInput("");
          return;
        }

        // Check for multiple molecules
        const molBlockCount = (fileContent.match(/M {2}END/g) || []).length;
        if (molBlockCount > 1) {
          setError(
            "Multiple molecules detected in file. Please upload a file containing only one molecule."
          );
          setInput("");
          return;
        }

        // Set the content to the input
        setInput(fileContent);
        setError(null);
      } catch (err) {
        console.error("File reading error:", err);
        setError("Failed to process the uploaded file. Please ensure it's a valid MOL/SDF file.");
        setInput("");
      }
    };

    reader.onerror = () => {
      setError("Failed to read the uploaded file. Please ensure it's a valid text file.");
      setInput("");
    };

    reader.readAsText(file);
  };

  // Clear uploaded MOL/SDF file
  const handleClearFile = () => {
    setUploadedFilename("");
    setInput("");
    if (fileInputRef.current) {
      fileInputRef.current.value = "";
    }
  };

  // Handle CDX/CDXML file selection
  const handleCdxFileUpload = (e) => {
    const file = e.target.files[0];
    if (!file) return;
    setError(null);
    const name = file.name.toLowerCase();
    if (!name.endsWith(".cdx") && !name.endsWith(".cdxml")) {
      setError("Please upload a valid .cdx or .cdxml file.");
      return;
    }
    setCdxFile(file);
    setCdxFilename(file.name);
  };

  // Clear uploaded CDX file
  const handleClearCdxFile = () => {
    setCdxFile(null);
    setCdxFilename("");
    if (cdxFileInputRef.current) {
      cdxFileInputRef.current.value = "";
    }
  };

  // Handle XYZ file selection — read as text and place in the input textarea.
  const handleXyzFileUpload = (e) => {
    const file = e.target.files[0];
    if (!file) return;
    setError(null);
    if (!file.name.toLowerCase().endsWith(".xyz")) {
      setError("Please upload a valid .xyz file.");
      return;
    }
    setXyzFilename(file.name);
    const reader = new FileReader();
    reader.onload = (event) => {
      const content = event.target.result;
      setInput(typeof content === "string" ? content : "");
    };
    reader.onerror = () => setError("Failed to read the uploaded XYZ file.");
    reader.readAsText(file);
  };

  // Clear uploaded XYZ file
  const handleClearXyzFile = () => {
    setXyzFilename("");
    setInput("");
    setXyzBatchResult(null);
    if (xyzFileInputRef.current) {
      xyzFileInputRef.current.value = "";
    }
  };

  // When input format changes, automatically update output format if needed
  const handleInputFormatChange = (format) => {
    setInputFormat(format);
    setAutoDetected(false);

    // Clear MOL/SDF file when switching away from molsdf
    if (format !== "molsdf") {
      handleClearFile();
    }
    // Clear CDX file when switching away from cdx
    if (format !== "cdx") {
      handleClearCdxFile();
    }
    // Clear XYZ file when switching away from xyz
    if (format !== "xyz") {
      handleClearXyzFile();
    }

    // Lock output format based on input type
    if (format === "iupac" || format === "selfies" || format === "molsdf") {
      setOutputFormat("smiles");
    } else if (format === "cdx") {
      setOutputFormat("mol");
    } else if (format === "xyz") {
      // XYZ: default to canonical SMILES; cap toolkit to rdkit/openbabel.
      setOutputFormat("canonicalsmiles");
      if (toolkit === "cdk") setToolkit("rdkit");
    }
  };

  // Handle text input changes with auto-format detection
  const handleInputChange = (value) => {
    setInput(value);
    if (inputFormat === "molsdf") return;

    const detected = detectInputFormat(value);
    if (!value.trim()) {
      setAutoDetected(false);
      return;
    }
    if (detected && detected !== inputFormat) {
      setInputFormat(detected);
      setAutoDetected(true);
      if (detected === "iupac" || detected === "selfies") {
        setOutputFormat("smiles");
      } else if (detected === "smiles") {
        setOutputFormat("canonicalsmiles");
      }
    }
  };

  // When output format changes, we may need to adjust toolkit availability
  const handleOutputFormatChange = (format) => {
    setOutputFormat(format);

    // SMARTS only supports RDKit
    if (format === "smarts") {
      setToolkit("rdkit");
    }
  };

  // Handle form submission for conversion
  const handleSubmit = async (e) => {
    e.preventDefault();
    const trimmedInput = input.trim();
    if (inputFormat !== "cdx" && !trimmedInput) {
      setError("Please enter input data.");
      setResult("");
      return;
    }

    if (inputFormat === "cdx" && !cdxFile) {
      setError("Please upload a .cdx or .cdxml file.");
      return;
    }

    setLoading(true);
    setError(null);
    setResult("");
    setSmilesForStructure("");
    setShowStructure(false);

    try {
      let convertedResult;
      let smilesForDisplay = "";

      // XYZ → SMILES / Canonical SMILES / InChI / InChIKey / MOL / SDF
      if (inputFormat === "xyz") {
        const xyzToolkit = toolkit === "cdk" ? "rdkit" : (toolkit as "rdkit" | "openbabel");
        const batch = await convertService.convertXYZ(trimmedInput, {
          charge: xyzCharge,
          useHueckel: xyzUseHueckel,
          toolkit: xyzToolkit,
        });

        setXyzBatchResult(batch);

        // Multi-frame: the grid renders everything; suppress the single-result panel.
        if (batch.summary.total > 1) {
          setResult("");
          setSmilesForStructure("");
          setShowStructure(false);
          return;
        }

        // Single-frame path: pick the chosen output and reuse the existing UX.
        const only = batch.structures[0];
        if (!only.success) {
          throw new Error(only.error || "XYZ conversion failed");
        }
        smilesForDisplay = only.canonicalsmiles;
        switch (outputFormat) {
          case "smiles":
          case "canonicalsmiles":
            convertedResult = only.canonicalsmiles;
            break;
          case "inchi":
            convertedResult = only.inchi;
            break;
          case "inchikey":
            convertedResult = only.inchikey;
            break;
          case "mol":
            convertedResult = only.molblock;
            break;
          case "sdf":
            convertedResult = batch.sdf;
            break;
          default:
            throw new Error(`Unsupported output format for XYZ input: ${outputFormat}.`);
        }
      } else if (inputFormat === "cdx") {
        // CDX/CDXML → MOL Block
        const molblock = await convertService.convertCDXToMol(cdxFile);
        convertedResult = molblock;
        try {
          smilesForDisplay = await convertService.molblockToSMILES(molblock, "rdkit");
        } catch {
          // Structure preview is optional
        }
      } else if (inputFormat !== "smiles") {
        // Handle MOL/SDF to SMILES conversion
        if (inputFormat === "molsdf") {
          // Format the MOL block properly before sending
          const formattedMolblock = formatMolblockForBackend(trimmedInput);
          const smiles = await convertService.molblockToSMILES(formattedMolblock, toolkit);
          smilesForDisplay = smiles;

          // If the output is SMILES, we're done
          if (outputFormat === "smiles") {
            convertedResult = smiles;
          } else if (outputFormat === "mol") {
            // MOL Block output: generate 2D coordinates from SMILES
            convertedResult = await convertService.generate2DCoordinates(smiles, toolkit);
          } else {
            // Otherwise, convert SMILES to the target format
            const formatOption = OUTPUT_FORMAT_OPTIONS.find((option) => option.id === outputFormat);
            if (!formatOption || !formatOption.method) {
              throw new Error(`Unsupported output format: ${outputFormat}`);
            }

            const method = convertService[formatOption.method];
            if (typeof method !== "function") {
              throw new Error(`Conversion function not available for format: ${outputFormat}`);
            }

            // Convert the SMILES to the target format
            convertedResult = await method(smiles, toolkit);
          }
        } else if (inputFormat !== "cdx") {
          // First convert IUPAC or SELFIES to SMILES
          const smiles = await convertService.generateSMILES(
            trimmedInput,
            inputFormat,
            inputFormat === "iupac" ? iupacConverter : undefined
          );

          // Store SMILES for structure display
          smilesForDisplay = smiles;

          // If the output is SMILES, we're done
          if (outputFormat === "smiles") {
            convertedResult = smiles;
          } else if (outputFormat === "mol") {
            // MOL Block output: generate 2D coordinates from SMILES
            convertedResult = await convertService.generate2DCoordinates(smiles, toolkit);
          } else {
            // Otherwise, convert SMILES to the target format
            const formatOption = OUTPUT_FORMAT_OPTIONS.find((option) => option.id === outputFormat);
            if (!formatOption || !formatOption.method) {
              throw new Error(`Unsupported output format: ${outputFormat}`);
            }

            const method = convertService[formatOption.method];
            if (typeof method !== "function") {
              throw new Error(`Conversion function not available for format: ${outputFormat}`);
            }

            // Convert the SMILES to the target format
            convertedResult = await method(smiles, toolkit);
          }
        }
      } else {
        // Direct SMILES conversion to target format
        // Use the input SMILES for structure display
        smilesForDisplay = trimmedInput;

        if (outputFormat === "smiles") {
          // Just return the input if output is also SMILES
          convertedResult = trimmedInput;
        } else if (outputFormat === "mol") {
          // MOL Block output: generate 2D coordinates from SMILES
          convertedResult = await convertService.generate2DCoordinates(trimmedInput, toolkit);
        } else {
          const formatOption = OUTPUT_FORMAT_OPTIONS.find((option) => option.id === outputFormat);
          if (!formatOption || !formatOption.method) {
            throw new Error(`Unsupported output format: ${outputFormat}`);
          }

          const method = convertService[formatOption.method];
          if (typeof method !== "function") {
            throw new Error(`Conversion function not available for format: ${outputFormat}`);
          }

          convertedResult = await method(trimmedInput, toolkit);
        }
      }

      // Handle cases where conversion might return null/undefined/empty
      if (!convertedResult) {
        setError(`Conversion resulted in empty output.`);
        setResult("");
        setSmilesForStructure("");
        setShowStructure(false);
      } else {
        let finalResult = String(convertedResult);

        // Remove surrounding double quotes if present
        if (finalResult.length >= 2 && finalResult.startsWith('"') && finalResult.endsWith('"')) {
          finalResult = finalResult.substring(1, finalResult.length - 1);
        }

        setResult(finalResult);

        // Set SMILES for structure display if we have a valid SMILES
        if (smilesForDisplay && smilesForDisplay.trim()) {
          // Clean up SMILES string - remove quotes and trim
          let cleanedSmiles = smilesForDisplay.trim();
          if (cleanedSmiles.startsWith('"') && cleanedSmiles.endsWith('"')) {
            cleanedSmiles = cleanedSmiles.substring(1, cleanedSmiles.length - 1);
          }

          setSmilesForStructure(cleanedSmiles);
          setShowStructure(true);
        }
      }
    } catch (err) {
      console.error("Conversion failed:", err);
      setError(getErrorMessage("convert", err));
      setResult("");
    } finally {
      setLoading(false);
    }
  };

  // Handle copying the result to clipboard
  const handleCopyResult = () => {
    if (!result || !navigator.clipboard) return;

    navigator.clipboard
      .writeText(result)
      .then(() => {
        setCopied(true);
        setTimeout(() => setCopied(false), 2000);
      })
      .catch((err) => {
        console.error("Failed to copy result:", err);
        setError("Failed to copy result to clipboard.");
      });
  };

  // Determine if toolkit selection should be shown based on input/output format
  const showToolkitSelection =
    (inputFormat === "smiles" || inputFormat === "molsdf" || inputFormat === "xyz") &&
    outputFormat !== "selfies" &&
    outputFormat !== "smarts" &&
    inputFormat !== "cdx";

  // Determine if IUPAC converter selection should be shown
  const showIupacConverterSelection = inputFormat === "iupac";

  return (
    <div className="space-y-6 p-4 md:p-6">
      {/* Input and Options Card */}
      <div className="bg-white dark:bg-gray-800 p-6 rounded-lg shadow-md dark:shadow-lg border border-gray-200 dark:border-gray-700">
        <h2 className="text-xl font-semibold text-gray-800 dark:text-blue-400 mb-4">
          Format Conversion
        </h2>

        <form onSubmit={handleSubmit} className="space-y-4">
          {/* Input Format Selection */}
          <div>
            <div className="flex items-center justify-between mb-1">
              <label
                htmlFor="input-format-select"
                className="block text-sm font-medium text-gray-700 dark:text-gray-300"
              >
                Input Format
              </label>
              {autoDetected && (
                <span className="inline-flex items-center px-2 py-0.5 rounded-sm text-xs font-medium bg-blue-100 text-blue-700 dark:bg-blue-900/40 dark:text-blue-300">
                  Auto-detected
                </span>
              )}
            </div>
            <Select value={inputFormat} onValueChange={handleInputFormatChange}>
              <SelectTrigger id="input-format-select" className="w-full">
                <SelectValue placeholder="Select input format" />
              </SelectTrigger>
              <SelectContent>
                {INPUT_FORMAT_OPTIONS.map((option) => (
                  <SelectItem key={option.id} value={option.id}>
                    {option.label}
                  </SelectItem>
                ))}
              </SelectContent>
            </Select>
          </div>

          {/* IUPAC Converter Selection (conditionally shown) */}
          {showIupacConverterSelection && (
            <div>
              <label
                htmlFor="iupac-converter-select"
                className="block text-sm font-medium text-gray-700 dark:text-gray-300 mb-1"
              >
                IUPAC Converter
              </label>
              <Select value={iupacConverter} onValueChange={setIupacConverter}>
                <SelectTrigger id="iupac-converter-select" className="w-full">
                  <SelectValue placeholder="Select converter" />
                </SelectTrigger>
                <SelectContent>
                  {IUPAC_CONVERTER_OPTIONS.map((option) => (
                    <SelectItem key={option.id} value={option.id}>
                      {option.label}
                    </SelectItem>
                  ))}
                </SelectContent>
              </Select>
              <p className="mt-1 text-xs text-gray-500 dark:text-gray-400">
                OPSIN is used to convert IUPAC names to SMILES
              </p>
            </div>
          )}

          {/* Input Field */}
          <div>
            {inputFormat === "xyz" ? (
              <>
                <label className="block text-sm font-medium text-gray-700 dark:text-gray-300 mb-1">
                  XYZ File Upload
                </label>
                <label
                  htmlFor="xyz-file-upload"
                  className="group relative flex items-center justify-center px-6 py-4 border-2 border-dashed border-gray-300 dark:border-gray-600 rounded-xl cursor-pointer hover:border-blue-500 dark:hover:border-blue-400 hover:bg-blue-50 dark:hover:bg-blue-900/10 transition-all duration-300 bg-linear-to-br from-gray-50 to-gray-100 dark:from-gray-800/50 dark:to-gray-800/30 hover:shadow-md"
                >
                  <input
                    ref={xyzFileInputRef}
                    id="xyz-file-upload"
                    type="file"
                    accept=".xyz,text/plain"
                    onChange={handleXyzFileUpload}
                    className="hidden"
                  />
                  <div className="flex items-center space-x-3">
                    <div className="p-2 bg-blue-100 dark:bg-blue-900/30 rounded-lg group-hover:bg-blue-200 dark:group-hover:bg-blue-800/40 transition-colors duration-300">
                      <Upload className="h-6 w-6 text-blue-600 dark:text-blue-400 group-hover:scale-110 transition-transform duration-300" />
                    </div>
                    <div className="text-left">
                      <span className="block text-sm font-semibold text-gray-800 dark:text-gray-200 group-hover:text-blue-600 dark:group-hover:text-blue-400 transition-colors duration-300">
                        {xyzFilename || "Choose XYZ File"}
                      </span>
                      <span className="block text-xs text-gray-500 dark:text-gray-400 mt-0.5">
                        Plain-text XYZ coordinates (atom count, comment, then `element x y z`)
                      </span>
                    </div>
                  </div>
                </label>
                {xyzFilename && (
                  <div className="mt-3 flex items-center justify-between p-3 bg-linear-to-r from-blue-50 to-indigo-50 dark:from-blue-900/20 dark:to-indigo-900/20 border border-blue-200 dark:border-blue-800 rounded-lg shadow-xs">
                    <div className="flex items-center space-x-2 flex-1 min-w-0">
                      <div className="p-1.5 bg-blue-100 dark:bg-blue-800/40 rounded-md">
                        <FileText className="h-4 w-4 text-blue-600 dark:text-blue-400" />
                      </div>
                      <span className="text-sm font-medium text-blue-900 dark:text-blue-100 truncate">
                        {xyzFilename}
                      </span>
                      <span className="text-xs text-blue-600 dark:text-blue-400 bg-blue-100 dark:bg-blue-800/40 px-2 py-0.5 rounded-full">
                        Loaded
                      </span>
                    </div>
                    <Button
                      variant="outline"
                      type="button"
                      onClick={handleClearXyzFile}
                      className="ml-3 px-3 py-1 text-sm font-medium text-blue-700 dark:text-blue-300 hover:text-white hover:bg-blue-600 dark:hover:bg-blue-500 border-blue-300 dark:border-blue-700 rounded-md"
                    >
                      Clear
                    </Button>
                  </div>
                )}
                <p className="mt-2 mb-3 text-xs text-center text-gray-500 dark:text-gray-400 font-medium">
                  Or paste XYZ content below
                </p>
                <Textarea
                  id="xyz-input"
                  value={input}
                  onChange={(e) => setInput(e.target.value)}
                  placeholder={
                    "Paste XYZ block here...\n\nExample (water):\n3\nwater\nO    0.0000    0.0000    0.0000\nH    0.7572    0.5860    0.0000\nH   -0.7572    0.5860    0.0000"
                  }
                  rows={10}
                  required
                  className="font-mono text-sm"
                />
                <div className="mt-3 grid grid-cols-1 sm:grid-cols-2 gap-3">
                  <div>
                    <label
                      htmlFor="xyz-charge"
                      className="block text-xs font-medium text-gray-700 dark:text-gray-300 mb-1"
                    >
                      Net Charge
                    </label>
                    <Input
                      id="xyz-charge"
                      type="number"
                      min={-10}
                      max={10}
                      step={1}
                      value={xyzCharge}
                      onChange={(e) => {
                        const v = parseInt(e.target.value, 10);
                        setXyzCharge(Number.isFinite(v) ? v : 0);
                      }}
                      disabled={toolkit === "openbabel"}
                      className="w-full"
                    />
                    <p className="mt-1 text-[11px] text-gray-500 dark:text-gray-400">
                      e.g. -1 for acetate. Used by RDKit (xyz2mol). OpenBabel ignores charge.
                    </p>
                  </div>
                  <div>
                    <label className="block text-xs font-medium text-gray-700 dark:text-gray-300 mb-1">
                      Bond Perception
                    </label>
                    <label className="inline-flex items-center gap-2 mt-1.5">
                      <input
                        type="checkbox"
                        checked={xyzUseHueckel}
                        onChange={(e) => setXyzUseHueckel(e.target.checked)}
                        disabled={toolkit === "openbabel"}
                        className="rounded border-gray-300"
                      />
                      <span className="text-sm text-gray-700 dark:text-gray-300">
                        Use extended Hückel (RDKit only)
                      </span>
                    </label>
                    <p className="mt-1 text-[11px] text-gray-500 dark:text-gray-400">
                      Slower; better for unusual valences.
                    </p>
                  </div>
                </div>
                <p className="mt-2 text-xs text-gray-500 dark:text-gray-400">
                  Bond orders are perceived from 3D coordinates. CDK is not supported (its core
                  distribution lacks XYZ→bond perception).
                </p>
              </>
            ) : inputFormat === "cdx" ? (
              <>
                <label className="block text-sm font-medium text-gray-700 dark:text-gray-300 mb-1">
                  ChemDraw File Upload
                </label>
                <label
                  htmlFor="cdx-file-upload"
                  className="group relative flex items-center justify-center px-6 py-4 border-2 border-dashed border-gray-300 dark:border-gray-600 rounded-xl cursor-pointer hover:border-blue-500 dark:hover:border-blue-400 hover:bg-blue-50 dark:hover:bg-blue-900/10 transition-all duration-300 bg-linear-to-br from-gray-50 to-gray-100 dark:from-gray-800/50 dark:to-gray-800/30 hover:shadow-md"
                >
                  <input
                    ref={cdxFileInputRef}
                    id="cdx-file-upload"
                    type="file"
                    accept=".cdx,.cdxml"
                    onChange={handleCdxFileUpload}
                    className="hidden"
                  />
                  <div className="flex items-center space-x-3">
                    <div className="p-2 bg-blue-100 dark:bg-blue-900/30 rounded-lg group-hover:bg-blue-200 dark:group-hover:bg-blue-800/40 transition-colors duration-300">
                      <Upload className="h-6 w-6 text-blue-600 dark:text-blue-400 group-hover:scale-110 transition-transform duration-300" />
                    </div>
                    <div className="text-left">
                      <span className="block text-sm font-semibold text-gray-800 dark:text-gray-200 group-hover:text-blue-600 dark:group-hover:text-blue-400 transition-colors duration-300">
                        {cdxFilename || "Choose CDX or CDXML File"}
                      </span>
                      <span className="block text-xs text-gray-500 dark:text-gray-400 mt-0.5">
                        .cdx (binary) or .cdxml (XML) formats
                      </span>
                    </div>
                  </div>
                </label>
                {cdxFilename && (
                  <div className="mt-3 flex items-center justify-between p-3 bg-linear-to-r from-blue-50 to-indigo-50 dark:from-blue-900/20 dark:to-indigo-900/20 border border-blue-200 dark:border-blue-800 rounded-lg shadow-xs">
                    <div className="flex items-center space-x-2 flex-1 min-w-0">
                      <div className="p-1.5 bg-blue-100 dark:bg-blue-800/40 rounded-md">
                        <FileText className="h-4 w-4 text-blue-600 dark:text-blue-400" />
                      </div>
                      <span className="text-sm font-medium text-blue-900 dark:text-blue-100 truncate">
                        {cdxFilename}
                      </span>
                      <span className="text-xs text-blue-600 dark:text-blue-400 bg-blue-100 dark:bg-blue-800/40 px-2 py-0.5 rounded-full">
                        Ready
                      </span>
                    </div>
                    <Button
                      variant="outline"
                      type="button"
                      onClick={handleClearCdxFile}
                      className="ml-3 px-3 py-1 text-sm font-medium text-blue-700 dark:text-blue-300 hover:text-white hover:bg-blue-600 dark:hover:bg-blue-500 border-blue-300 dark:border-blue-700 rounded-md"
                    >
                      Clear
                    </Button>
                  </div>
                )}
                <p className="mt-2 text-xs text-gray-500 dark:text-gray-400">
                  Upload a ChemDraw binary (.cdx) or XML (.cdxml) file. The output will be a V2000
                  MOL block.
                </p>
              </>
            ) : inputFormat === "molsdf" ? (
              <>
                <label
                  htmlFor="molsdf-input"
                  className="block text-sm font-medium text-gray-700 dark:text-gray-300 mb-1"
                >
                  MOL/SDF Block Input
                </label>

                {/* File Upload Button */}
                <div className="mb-3">
                  <label
                    htmlFor="mol-file-upload"
                    className="group relative flex items-center justify-center px-6 py-4 border-2 border-dashed border-gray-300 dark:border-gray-600 rounded-xl cursor-pointer hover:border-blue-500 dark:hover:border-blue-400 hover:bg-blue-50 dark:hover:bg-blue-900/10 transition-all duration-300 bg-linear-to-br from-gray-50 to-gray-100 dark:from-gray-800/50 dark:to-gray-800/30 hover:shadow-md"
                  >
                    <input
                      ref={fileInputRef}
                      id="mol-file-upload"
                      type="file"
                      accept=".mol,.sdf"
                      onChange={handleFileUpload}
                      className="hidden"
                    />
                    <div className="flex items-center space-x-3">
                      <div className="p-2 bg-blue-100 dark:bg-blue-900/30 rounded-lg group-hover:bg-blue-200 dark:group-hover:bg-blue-800/40 transition-colors duration-300">
                        <Upload className="h-6 w-6 text-blue-600 dark:text-blue-400 group-hover:scale-110 transition-transform duration-300" />
                      </div>
                      <div className="text-left">
                        <span className="block text-sm font-semibold text-gray-800 dark:text-gray-200 group-hover:text-blue-600 dark:group-hover:text-blue-400 transition-colors duration-300">
                          {uploadedFilename || "Choose MOL/SDF File"}
                        </span>
                        <span className="block text-xs text-gray-500 dark:text-gray-400 mt-0.5">
                          .mol or .sdf formats supported
                        </span>
                      </div>
                    </div>
                  </label>
                  <p className="mt-2 text-xs text-center text-gray-500 dark:text-gray-400 font-medium">
                    Or paste MOL/SDF content below
                  </p>
                </div>

                {/* Display uploaded filename with clear option */}
                {uploadedFilename && (
                  <div className="mb-3 flex items-center justify-between p-3 bg-linear-to-r from-blue-50 to-indigo-50 dark:from-blue-900/20 dark:to-indigo-900/20 border border-blue-200 dark:border-blue-800 rounded-lg shadow-xs animate-fadeIn">
                    <div className="flex items-center space-x-2 flex-1 min-w-0">
                      <div className="p-1.5 bg-blue-100 dark:bg-blue-800/40 rounded-md">
                        <FileText className="h-4 w-4 text-blue-600 dark:text-blue-400" />
                      </div>
                      <span className="text-sm font-medium text-blue-900 dark:text-blue-100 truncate">
                        {uploadedFilename}
                      </span>
                      <span className="text-xs text-blue-600 dark:text-blue-400 bg-blue-100 dark:bg-blue-800/40 px-2 py-0.5 rounded-full">
                        Loaded
                      </span>
                    </div>
                    <Button
                      variant="outline"
                      type="button"
                      onClick={handleClearFile}
                      className="ml-3 px-3 py-1 text-sm font-medium text-blue-700 dark:text-blue-300 hover:text-white hover:bg-blue-600 dark:hover:bg-blue-500 border-blue-300 dark:border-blue-700 rounded-md"
                    >
                      Clear
                    </Button>
                  </div>
                )}

                <Textarea
                  id="molsdf-input"
                  value={input}
                  onChange={(e) => setInput(e.target.value)}
                  placeholder="Paste MOL or SDF block here...&#10;&#10;Example:&#10;  CDK     09012308392D&#10;&#10;  2  1  0  0  0  0  0  0  0  0999 V2000&#10;    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0&#10;    1.5000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0&#10;  1  2  1  0  0  0  0&#10;M  END"
                  rows={12}
                  required
                  className="font-mono text-sm"
                />
                <p className="mt-1 text-xs text-gray-500 dark:text-gray-400">
                  Upload a file or paste a MOL or SDF block. If SDF format is detected (contains
                  $$$$), only the first molecule will be processed.
                </p>
              </>
            ) : inputFormat !== "cdx" ? (
              <>
                <SMILESInput
                  value={input}
                  onChange={handleInputChange}
                  label={
                    inputFormat === "smiles"
                      ? "SMILES Input"
                      : inputFormat === "iupac"
                        ? "IUPAC Name"
                        : "SELFIES Input"
                  }
                  placeholder={
                    inputFormat === "smiles"
                      ? "Enter SMILES notation..."
                      : inputFormat === "iupac"
                        ? "Enter IUPAC chemical name..."
                        : "Enter SELFIES notation..."
                  }
                  required
                />

                {inputFormat === "iupac" && (
                  <p className="mt-1 text-xs text-gray-500 dark:text-gray-400">
                    Example: 1,3,7-trimethylpurine-2,6-dione (caffeine)
                  </p>
                )}
                {inputFormat === "selfies" && (
                  <p className="mt-1 text-xs text-gray-500 dark:text-gray-400">
                    Example:
                    [C][N][C][=Branch1][C][=O][N][=Branch2][C][=Branch1][C][=O][N][Ring1][C]
                  </p>
                )}
              </>
            ) : null}
          </div>

          {/* Conversion Direction Indicator */}
          <div className="flex items-center justify-center py-4">
            <div className="grow h-px bg-gray-200 dark:bg-gray-700"></div>
            <div className="mx-4 bg-gray-100 dark:bg-gray-700 p-2 rounded-full ring-1 ring-gray-300 dark:ring-gray-600">
              <ArrowRight className="h-6 w-6 text-blue-600 dark:text-blue-400" />
            </div>
            <div className="grow h-px bg-gray-200 dark:bg-gray-700"></div>
          </div>

          {/* Output Format Selection */}
          <div>
            <label
              htmlFor="output-format-select"
              className="block text-sm font-medium text-gray-700 dark:text-gray-300 mb-1"
            >
              Output Format
            </label>
            <Select
              value={outputFormat}
              onValueChange={handleOutputFormatChange}
              disabled={inputFormat !== "smiles" && inputFormat !== "xyz"}
            >
              <SelectTrigger
                id="output-format-select"
                className={cn(
                  "w-full",
                  inputFormat !== "smiles" &&
                    inputFormat !== "xyz" &&
                    "opacity-50 cursor-not-allowed"
                )}
              >
                <SelectValue placeholder="Select output format" />
              </SelectTrigger>
              <SelectContent>
                {OUTPUT_FORMAT_OPTIONS.filter((option) => {
                  if (inputFormat === "xyz") return XYZ_OUTPUT_FORMAT_IDS.has(option.id);
                  // SDF output is only meaningful for XYZ input today.
                  if (option.id === "sdf") return false;
                  return true;
                }).map((option) => (
                  <SelectItem key={option.id} value={option.id}>
                    {option.label}
                  </SelectItem>
                ))}
              </SelectContent>
            </Select>
            {(inputFormat === "iupac" || inputFormat === "selfies" || inputFormat === "molsdf") && (
              <p className="mt-1 text-xs text-gray-500 dark:text-gray-400">
                {inputFormat === "iupac"
                  ? "IUPAC names"
                  : inputFormat === "selfies"
                    ? "SELFIES"
                    : "MOL/SDF blocks"}{" "}
                can only be converted to SMILES format
              </p>
            )}
            {inputFormat === "cdx" && (
              <p className="mt-1 text-xs text-gray-500 dark:text-gray-400">
                ChemDraw CDX/CDXML files are converted to a V2000 MOL block.
              </p>
            )}
            {outputFormat === "smarts" && (
              <p className="mt-1 text-xs text-gray-500 dark:text-gray-400">
                SMARTS (SMiles ARbitrary Target Specification) is an extension of SMILES for
                describing molecular patterns and properties. It's used for substructure searching
                and matching.
              </p>
            )}
          </div>

          {/* Toolkit Selection (conditionally shown) */}
          {showToolkitSelection && (
            <div>
              <label
                htmlFor="toolkit-select-convert"
                className="block text-sm font-medium text-gray-700 dark:text-gray-300 mb-1"
              >
                Toolkit
              </label>
              <Select value={toolkit} onValueChange={setToolkit}>
                <SelectTrigger id="toolkit-select-convert" className="w-full">
                  <SelectValue placeholder="Select toolkit" />
                </SelectTrigger>
                <SelectContent>
                  {TOOLKIT_OPTIONS.filter((option) => {
                    // MOL/SDF only supports CDK and RDKit
                    if (inputFormat === "molsdf") {
                      return option.id === "cdk" || option.id === "rdkit";
                    }
                    // XYZ supports RDKit (xyz2mol) and OpenBabel; CDK lacks bond perception.
                    if (inputFormat === "xyz") {
                      return option.id === "rdkit" || option.id === "openbabel";
                    }
                    return true;
                  }).map((option) => (
                    <SelectItem key={option.id} value={option.id}>
                      {option.label}
                    </SelectItem>
                  ))}
                </SelectContent>
              </Select>
              <p className="mt-1 text-xs text-gray-500 dark:text-gray-400">
                {inputFormat === "molsdf"
                  ? "MOL/SDF conversion supports CDK and RDKit toolkits."
                  : "Note: Toolkit support may vary for different format conversions."}
              </p>
            </div>
          )}

          {/* Information about toolkit for SMARTS (when relevant) */}
          {outputFormat === "smarts" && (
            <div className="mt-2 p-2 bg-blue-50 dark:bg-blue-900/30 border border-blue-100 dark:border-blue-800 rounded-sm text-xs text-blue-600 dark:text-blue-300">
              <p>SMARTS conversion is only available using RDKit.</p>
            </div>
          )}

          {/* Submit Button */}
          <div className="pt-2">
            <Button
              type="submit"
              disabled={(inputFormat === "cdx" ? !cdxFile : !input.trim()) || loading}
              className={`w-full sm:w-auto px-6 py-2 rounded-lg text-white font-medium flex items-center justify-center transition-colors duration-200 focus:outline-hidden focus:ring-2 focus:ring-offset-2 dark:focus:ring-offset-gray-800 focus:ring-blue-500 ${
                (inputFormat === "cdx" ? !cdxFile : !input.trim()) || loading
                  ? "bg-gray-400 dark:bg-gray-600 cursor-not-allowed"
                  : "bg-blue-600 hover:bg-blue-700 dark:bg-blue-500 dark:hover:bg-blue-600 shadow-xs"
              }`}
            >
              {loading ? (
                <>
                  <Loader2 className="mr-2 h-4 w-4 animate-spin" />
                  Converting...
                </>
              ) : (
                <>
                  <ArrowLeftRight className="mr-2 h-5 w-5" aria-hidden="true" />
                  Convert Format
                </>
              )}
            </Button>
          </div>
        </form>
      </div>

      {/* Loading State */}
      {loading && !result && <ToolSkeleton variant="conversion" />}

      {/* Error Display */}
      {error && !loading && (
        <GlassErrorCard
          message={error}
          onRetry={() => {
            setError(null);
            document.getElementById("smiles-input")?.focus();
          }}
        />
      )}

      {/* XYZ Multi-frame Grid */}
      {xyzBatchResult && xyzBatchResult.summary.total > 1 && !loading && (
        <XYZGridResult result={xyzBatchResult} />
      )}

      {/* Results Display Section */}
      {result && !loading && (
        <div className="bg-white dark:bg-gray-800 p-6 rounded-lg shadow-md dark:shadow-lg border border-gray-200 dark:border-gray-700">
          {/* Results Header */}
          <div className="flex justify-between items-center mb-4 border-b border-gray-200 dark:border-gray-700 pb-2">
            <h3 className="text-lg font-semibold text-gray-900 dark:text-white">Results</h3>
            {/* Copy Button */}
            <Button
              onClick={handleCopyResult}
              className={`p-1.5 rounded-md transition-colors focus:outline-hidden focus:ring-1 focus:ring-blue-500 ${
                copied
                  ? "text-green-500 dark:text-green-500"
                  : "text-gray-500 dark:text-gray-400 hover:text-gray-800 dark:hover:text-white hover:bg-gray-100 dark:hover:bg-gray-700"
              }`}
              title={copied ? "Copied!" : "Copy result to clipboard"}
              aria-label={copied ? "Result Copied" : "Copy Result"}
            >
              {copied ? <Check className="h-5 w-5" /> : <Clipboard className="h-5 w-5" />}
            </Button>
          </div>

          {/* Results Grid Layout */}
          <div className={`grid gap-6 ${showStructure ? "lg:grid-cols-2" : "grid-cols-1"}`}>
            {/* Conversion Result */}
            <div className="space-y-3">
              <h4 className="text-md font-medium text-gray-800 dark:text-gray-200">
                Conversion Result
              </h4>
              {/* Result Display Box */}
              <div className="p-3 bg-gray-100 dark:bg-gray-900 rounded-md font-mono text-sm overflow-x-auto border border-gray-200 dark:border-gray-700 shadow-xs">
                <pre className="whitespace-pre-wrap break-all text-gray-700 dark:text-gray-300">
                  {result}
                </pre>
              </div>
              {/* Conversion Info Text */}
              <div className="text-xs text-gray-500 dark:text-gray-400">
                Converted from{" "}
                {INPUT_FORMAT_OPTIONS.find((o) => o.id === inputFormat)?.label ||
                  inputFormat.toUpperCase()}{" "}
                to{" "}
                {OUTPUT_FORMAT_OPTIONS.find((o) => o.id === outputFormat)?.label ||
                  outputFormat.toUpperCase()}
                {showToolkitSelection &&
                  ` using ${TOOLKIT_OPTIONS.find((o) => o.id === toolkit)?.label || toolkit}`}
                {showIupacConverterSelection &&
                  ` with ${IUPAC_CONVERTER_OPTIONS.find((o) => o.id === iupacConverter)?.label || iupacConverter}`}
                .
              </div>
            </div>

            {/* Molecular Structure */}
            {showStructure && smilesForStructure && (
              <div className="space-y-3">
                <h4 className="text-md font-medium text-gray-800 dark:text-gray-200">
                  Molecular Structure
                </h4>
                <div className="border border-gray-200 dark:border-gray-700 rounded-md overflow-hidden">
                  <MoleculeDepiction2D
                    smiles={smilesForStructure}
                    title="Generated Structure"
                    toolkit="cdk"
                    showCIP={true}
                  />
                </div>
                <div className="text-xs text-gray-500 dark:text-gray-400">
                  Structure generated from SMILES:{" "}
                  <code className="bg-gray-100 dark:bg-gray-800 px-1 rounded-sm text-xs">
                    {smilesForStructure}
                  </code>
                </div>
              </div>
            )}
          </div>
        </div>
      )}

      {/* Initial State Message */}
      {!result && !loading && !error && (
        <div className="bg-blue-50 dark:bg-blue-900/20 border border-blue-200 dark:border-blue-800 rounded-lg p-6 text-center shadow-sm">
          <p className="text-gray-600 dark:text-gray-300">
            Enter input data and select options to perform format conversion.
          </p>
        </div>
      )}
    </div>
  );
};
export default FormatConversionView;