cdxml-toolkit 0.5.0__tar.gz → 0.5.2__tar.gz

{cdxml_toolkit-0.5.0/cdxml_toolkit.egg-info → cdxml_toolkit-0.5.2}/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.4
 Name: cdxml-toolkit
-Version: 0.5.0
-Summary: Python toolkit for ChemDraw CDXML reaction scheme processing, layout, and rendering.
+Version: 0.5.2
+Summary: MCP server and Python toolkit for perception, rendering, and analysis of molecules and reaction schemes in ChemDraw CDXML.
 Author: Hiu Fung Kevin Lee
 License-Expression: MIT
 Project-URL: Homepage, https://github.com/leehiufung911/cdxml-toolkit
@@ -22,40 +22,25 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 License-File: NOTICE.md
 Requires-Dist: lxml>=4.6
-Provides-Extra: rdkit
-Requires-Dist: rdkit>=2023.03; extra == "rdkit"
-Provides-Extra: chemdraw
-Requires-Dist: pywin32>=300; extra == "chemdraw"
-Provides-Extra: image
-Requires-Dist: opencv-python>=4.5; extra == "image"
-Requires-Dist: Pillow>=9.0; extra == "image"
-Provides-Extra: office
-Requires-Dist: python-pptx>=0.6; extra == "office"
-Requires-Dist: python-docx>=0.8; extra == "office"
-Requires-Dist: olefile>=0.46; extra == "office"
-Provides-Extra: yaml
-Requires-Dist: pyyaml>=5.4; extra == "yaml"
-Provides-Extra: mcp
-Requires-Dist: mcp>=1.0; extra == "mcp"
-Requires-Dist: pyyaml>=5.4; extra == "mcp"
-Provides-Extra: analysis
-Requires-Dist: pdfplumber>=0.7; extra == "analysis"
-Provides-Extra: chemscript
-Requires-Dist: pythonnet>=3.0; extra == "chemscript"
-Provides-Extra: decimer
-Requires-Dist: tensorflow>=2.16; extra == "decimer"
-Requires-Dist: decimer>=2.6; extra == "decimer"
-Requires-Dist: pymupdf>=1.20; extra == "decimer"
-Provides-Extra: ocr
-Requires-Dist: pytesseract>=0.3; extra == "ocr"
-Provides-Extra: opsin
-Requires-Dist: py2opsin>=1.0; extra == "opsin"
-Provides-Extra: all
-Requires-Dist: cdxml-toolkit[analysis,chemdraw,chemscript,image,mcp,office,opsin,rdkit,yaml]; extra == "all"
-Provides-Extra: full
-Requires-Dist: cdxml-toolkit[all,decimer,ocr]; extra == "full"
+Requires-Dist: rdkit>=2023.03
+Requires-Dist: pywin32>=300
+Requires-Dist: opencv-python>=4.5
+Requires-Dist: Pillow>=9.0
+Requires-Dist: python-pptx>=0.6
+Requires-Dist: python-docx>=0.8
+Requires-Dist: olefile>=0.46
+Requires-Dist: pyyaml>=5.4
+Requires-Dist: mcp>=1.0
+Requires-Dist: pdfplumber>=0.7
+Requires-Dist: pythonnet>=3.0
+Requires-Dist: tensorflow>=2.16
+Requires-Dist: decimer>=2.6
+Requires-Dist: pymupdf>=1.20
+Requires-Dist: pytesseract>=0.3
+Requires-Dist: py2opsin>=1.0
+Requires-Dist: pytest>=7.0
 Provides-Extra: dev
-Requires-Dist: cdxml-toolkit[all]; extra == "dev"
+Requires-Dist: cdxml-toolkit; extra == "dev"
 Requires-Dist: pytest>=7.0; extra == "dev"
 Dynamic: license-file
 
@@ -172,12 +157,11 @@ Expected: 2 tool calls (resolve_name, draw_molecule), produces an aspirin CDXML
 **Prerequisites:** Windows with ChemDraw (ChemOffice 2015+) and ChemScript installed.
 
 ```bash
-# From GitHub — recommended install (includes RDKit, MCP server, ChemDraw COM,
-# Office support, PDF parsing, image processing, and ChemScript bridge)
-pip install "cdxml-toolkit[all] @ git+https://github.com/leehiufung911/cdxml-toolkit.git@main"
+# From PyPI (recommended)
+pip install cdxml-toolkit
 
-# With DECIMER neural image extraction (extract_structures_from_image)
-pip install "cdxml-toolkit[all,decimer] @ git+https://github.com/leehiufung911/cdxml-toolkit.git@main"
+# From GitHub (latest development version)
+pip install "cdxml-toolkit @ git+https://github.com/leehiufung911/cdxml-toolkit.git@main"
 
 # Development (editable install)
 git clone https://github.com/leehiufung911/cdxml-toolkit.git
@@ -185,18 +169,7 @@ cd cdxml-toolkit
 pip install -e ".[dev]"
 ```
 
-**Required:** `lxml>=4.6`. **Recommended:** `rdkit>=2023.03` (needed for scheme rendering).
-
-### Extras
-
-| Extra | What it includes | Notes |
-|-------|-----------------|-------|
-| `[all]` | RDKit, pywin32, image, Office, YAML, PDF analysis, MCP server, pythonnet, py2opsin | **Use this.** Everything most users need. |
-| `[decimer]` | TensorFlow, DECIMER, PyMuPDF | Neural image-to-SMILES. Adds ~1 GB. |
-| `[full]` | `[all]` + `[decimer]` + `[ocr]` | Everything pip-installable. |
-| `[rdkit]` | RDKit only | Minimal install for scripting. |
-| `[mcp]` | MCP server + PyYAML | MCP server only (no RDKit/Office). |
-| `[dev]` | `[all]` + pytest | For running the test suite. |
+Everything is included by default: RDKit, MCP server, ChemDraw COM, Office support, PDF analysis, image processing, ChemScript bridge, DECIMER neural image extraction, OPSIN, and OCR.
 
 ### Name resolution tiers
 

{cdxml_toolkit-0.5.0 → cdxml_toolkit-0.5.2}/README.md

@@ -111,12 +111,11 @@ Expected: 2 tool calls (resolve_name, draw_molecule), produces an aspirin CDXML
 **Prerequisites:** Windows with ChemDraw (ChemOffice 2015+) and ChemScript installed.
 
 ```bash
-# From GitHub — recommended install (includes RDKit, MCP server, ChemDraw COM,
-# Office support, PDF parsing, image processing, and ChemScript bridge)
-pip install "cdxml-toolkit[all] @ git+https://github.com/leehiufung911/cdxml-toolkit.git@main"
+# From PyPI (recommended)
+pip install cdxml-toolkit
 
-# With DECIMER neural image extraction (extract_structures_from_image)
-pip install "cdxml-toolkit[all,decimer] @ git+https://github.com/leehiufung911/cdxml-toolkit.git@main"
+# From GitHub (latest development version)
+pip install "cdxml-toolkit @ git+https://github.com/leehiufung911/cdxml-toolkit.git@main"
 
 # Development (editable install)
 git clone https://github.com/leehiufung911/cdxml-toolkit.git
@@ -124,18 +123,7 @@ cd cdxml-toolkit
 pip install -e ".[dev]"
 ```
 
-**Required:** `lxml>=4.6`. **Recommended:** `rdkit>=2023.03` (needed for scheme rendering).
-
-### Extras
-
-| Extra | What it includes | Notes |
-|-------|-----------------|-------|
-| `[all]` | RDKit, pywin32, image, Office, YAML, PDF analysis, MCP server, pythonnet, py2opsin | **Use this.** Everything most users need. |
-| `[decimer]` | TensorFlow, DECIMER, PyMuPDF | Neural image-to-SMILES. Adds ~1 GB. |
-| `[full]` | `[all]` + `[decimer]` + `[ocr]` | Everything pip-installable. |
-| `[rdkit]` | RDKit only | Minimal install for scripting. |
-| `[mcp]` | MCP server + PyYAML | MCP server only (no RDKit/Office). |
-| `[dev]` | `[all]` + pytest | For running the test suite. |
+Everything is included by default: RDKit, MCP server, ChemDraw COM, Office support, PDF analysis, image processing, ChemScript bridge, DECIMER neural image extraction, OPSIN, and OCR.
 
 ### Name resolution tiers
 

{cdxml_toolkit-0.5.0 → cdxml_toolkit-0.5.2}/cdxml_toolkit/mcp_server/server.py

@@ -12,7 +12,7 @@ Tools:
     convert_cdx_cdxml     — Bidirectional CDX ↔ CDXML file conversion
     parse_analysis_file   — LCMS/NMR PDF → peaks and data
     format_lab_entry      — Entry dicts → formatted lab book text
-    extract_cdxml_from_office — PPTX/DOCX → embedded CDXML files
+    extract_cdxml_from_office — PPTX/DOCX/XLS/XLSX → embedded CDXML files
     embed_cdxml_in_office — CDXML → editable OLE object in PPTX/DOCX
     search_compound       — SMILES → exact/similar matches across experiments
     render_to_png         — CDXML → PNG via ChemDraw COM
@@ -1140,16 +1140,17 @@ def extract_cdxml_from_office(
     file_path: str,
     output_dir: Optional[str] = None,
 ) -> dict:
-    """Extract embedded ChemDraw objects from a PPTX or DOCX file.
+    """Extract embedded ChemDraw objects from a PPTX, DOCX, XLS, or XLSX file.
 
-    Office files (PPTX/DOCX) are ZIP archives that may contain ChemDraw OLE
-    objects as binary blobs. This tool extracts every ChemDraw object, converts
-    it to CDXML, and writes the files to output_dir.
+    Office files (PPTX/DOCX/XLSX) are ZIP archives that may contain ChemDraw OLE
+    objects as binary blobs. XLS files are OLE2 compound documents with embedded
+    ChemDraw objects stored in MBD* sub-storages. This tool extracts every
+    ChemDraw object, converts it to CDXML, and writes the files to output_dir.
 
     Requires: olefile. CDX→CDXML conversion uses available backends.
 
     Args:
-        file_path:  Path to a .pptx or .docx file.
+        file_path:  Path to a .pptx, .docx, .xlsx, or .xls file.
         output_dir: Directory for extracted CDXML files. Default: a folder
                     named "<basename>_chemdraw/" next to the input file.
 
@@ -1161,10 +1162,12 @@ def extract_cdxml_from_office(
     if not file_path or not file_path.strip():
         return (
             "Usage: extract_cdxml_from_office(file_path='document.pptx', output_dir='out/')\n"
-            "Extracts embedded ChemDraw objects from PPTX or DOCX files.\n"
+            "Extracts embedded ChemDraw objects from PPTX, DOCX, XLS, or XLSX files.\n"
             "Examples:\n"
             "  extract_cdxml_from_office(file_path='presentation.pptx')\n"
             "  extract_cdxml_from_office(file_path='report.docx', output_dir='extracted/')\n"
+            "  extract_cdxml_from_office(file_path='labbook.xls')\n"
+            "  extract_cdxml_from_office(file_path='labbook.xlsx')\n"
             "Returns: {ok, count, objects:[{cdxml_output, source_path}]}"
         )
 
@@ -1183,8 +1186,9 @@ def extract_cdxml_from_office(
             "ok": False,
             "error": (
                 f"Extraction failed: {e}. "
-                "Ensure the file is a valid .pptx or .docx and that olefile is installed "
-                "(pip install olefile). The file must contain embedded ChemDraw OLE objects."
+                "Ensure the file is a valid .pptx, .docx, .xlsx, or .xls and that olefile "
+                "is installed (pip install olefile). The file must contain embedded "
+                "ChemDraw OLE objects."
             ),
             "input": str(p),
         }

cdxml_toolkit-0.5.2/cdxml_toolkit/office/ole_extractor.py

@@ -0,0 +1,374 @@
+#!/usr/bin/env python3
+"""
+OLE Extractor — Extract embedded ChemDraw objects from Office files.
+
+Supports four Office formats:
+  - PPTX / DOCX / XLSX  — ZIP archives containing OLE blobs in known paths.
+  - XLS                  — OLE2 compound documents with MBD* sub-storages.
+
+ChemDraw objects are stored as CDX data inside the OLE "CONTENTS" stream.
+This tool extracts and optionally converts them to CDXML.
+
+Usage:
+    python ole_extractor.py input.pptx [-o output_dir/] [--format cdxml|cdx|both]
+    python ole_extractor.py input.docx [-o output_dir/] [--format cdxml|cdx|both]
+    python ole_extractor.py input.xlsx [-o output_dir/] [--format cdxml|cdx|both]
+    python ole_extractor.py input.xls  [-o output_dir/] [--format cdxml|cdx|both]
+
+Requires: olefile, cdx_converter (for CDXML conversion)
+"""
+
+import argparse
+import io
+import os
+import sys
+import zipfile
+from dataclasses import dataclass, field
+from typing import List, Optional
+
+import olefile
+
+# ChemDraw OLE CLSID (CS ChemDraw Drawing / CS ChemDraw 3D)
+CHEMDRAW_CLSIDS = {
+    "41BA6D21-A02E-11CE-8FD9-0020AFD1F20C",  # ChemDraw Drawing
+}
+
+# CDX binary magic bytes
+CDX_MAGIC = b"VjCD"
+
+# Where Office stores OLE embeddings (ZIP-based formats)
+EMBEDDING_PATTERNS = {
+    ".pptx": "ppt/embeddings/",
+    ".docx": "word/embeddings/",
+    ".xlsx": "xl/embeddings/",
+}
+
+# OLE2-native formats (not ZIP-based) — handled separately
+OLE2_FORMATS = {".xls"}
+
+
+@dataclass
+class ExtractedObject:
+    """A single extracted ChemDraw object."""
+    source_path: str  # path inside ZIP (e.g. ppt/embeddings/oleObject1.bin)
+    cdx_data: bytes
+    cdx_output: Optional[str] = None  # path where CDX was saved
+    cdxml_output: Optional[str] = None  # path where CDXML was saved
+    error: Optional[str] = None
+
+
+def find_ole_entries(zip_path: str) -> List[str]:
+    """List OLE embedding paths inside a PPTX/DOCX/XLSX ZIP."""
+    ext = os.path.splitext(zip_path)[1].lower()
+    prefix = EMBEDDING_PATTERNS.get(ext)
+    if prefix is None:
+        raise ValueError(
+            f"Unsupported ZIP-based file type: {ext}. "
+            f"Use .pptx, .docx, or .xlsx."
+        )
+
+    with zipfile.ZipFile(zip_path, "r") as zf:
+        return [
+            name for name in zf.namelist()
+            if name.startswith(prefix) and name.lower().endswith(".bin")
+        ]
+
+
+def is_chemdraw_ole(ole: olefile.OleFileIO) -> bool:
+    """Check if an OLE container holds a ChemDraw object."""
+    # Check CLSID
+    clsid = ole.root.clsid.upper() if ole.root.clsid else ""
+    if clsid in CHEMDRAW_CLSIDS:
+        return True
+
+    # Check for CONTENTS stream with CDX magic
+    if ole.exists("CONTENTS"):
+        header = ole.openstream("CONTENTS").read(4)
+        if header == CDX_MAGIC:
+            return True
+
+    return False
+
+
+def extract_cdx_from_ole(ole_data: bytes) -> Optional[bytes]:
+    """Extract raw CDX bytes from an OLE compound document."""
+    if not olefile.isOleFile(io.BytesIO(ole_data)):
+        return None
+
+    ole = olefile.OleFileIO(io.BytesIO(ole_data))
+    try:
+        if not is_chemdraw_ole(ole):
+            return None
+
+        if ole.exists("CONTENTS"):
+            cdx = ole.openstream("CONTENTS").read()
+            if cdx[:4] == CDX_MAGIC:
+                return cdx
+
+        # Fallback: check \x01Ole10Native stream
+        if ole.exists("\x01Ole10Native"):
+            data = ole.openstream("\x01Ole10Native").read()
+            # Skip 4-byte length prefix
+            if len(data) > 4 and data[4:8] == CDX_MAGIC:
+                return data[4:]
+
+        return None
+    finally:
+        ole.close()
+
+
+def _get_converter(output_format: str):
+    """Lazy-import cdx_converter if CDXML output is requested."""
+    if output_format not in ("cdxml", "both"):
+        return None
+    try:
+        from ..chemdraw import cdx_converter
+        return cdx_converter
+    except ImportError:
+        print(
+            "Warning: cdx_converter not found. CDX files will be saved "
+            "but CDXML conversion is unavailable.",
+            file=sys.stderr,
+        )
+        return None
+
+
+def _save_extracted_object(
+    cdx_data: bytes,
+    source_path: str,
+    entry_name: str,
+    output_dir: str,
+    output_format: str,
+    convert_method: str,
+    _converter,
+) -> ExtractedObject:
+    """Save a single extracted CDX blob to disk (CDX and/or CDXML)."""
+    obj = ExtractedObject(source_path=source_path, cdx_data=cdx_data)
+
+    # Save CDX
+    if output_format in ("cdx", "both"):
+        cdx_path = os.path.join(output_dir, f"{entry_name}.cdx")
+        with open(cdx_path, "wb") as f:
+            f.write(cdx_data)
+        obj.cdx_output = cdx_path
+
+    # Convert to CDXML
+    if output_format in ("cdxml", "both"):
+        cdxml_path = os.path.join(output_dir, f"{entry_name}.cdxml")
+        if _converter is not None:
+            try:
+                cdxml_str = _converter.convert_cdx_to_cdxml(
+                    cdx_data, method=convert_method
+                )
+                with open(cdxml_path, "w", encoding="utf-8") as f:
+                    f.write(cdxml_str)
+                obj.cdxml_output = cdxml_path
+            except Exception as e:
+                obj.error = f"CDXML conversion failed: {e}"
+                # Still save CDX as fallback
+                if obj.cdx_output is None:
+                    fallback = os.path.join(output_dir, f"{entry_name}.cdx")
+                    with open(fallback, "wb") as f:
+                        f.write(cdx_data)
+                    obj.cdx_output = fallback
+        else:
+            # No converter — save CDX instead
+            if obj.cdx_output is None:
+                fallback = os.path.join(output_dir, f"{entry_name}.cdx")
+                with open(fallback, "wb") as f:
+                    f.write(cdx_data)
+                obj.cdx_output = fallback
+            obj.error = "cdx_converter unavailable; saved CDX only"
+
+    return obj
+
+
+def _extract_from_zip(
+    input_path: str,
+    output_dir: str,
+    output_format: str,
+    convert_method: str,
+    _converter,
+) -> List[ExtractedObject]:
+    """Extract ChemDraw objects from a ZIP-based Office file (PPTX/DOCX/XLSX)."""
+    ole_entries = find_ole_entries(input_path)
+    results = []
+
+    with zipfile.ZipFile(input_path, "r") as zf:
+        for entry in ole_entries:
+            ole_data = zf.read(entry)
+            cdx_data = extract_cdx_from_ole(ole_data)
+
+            if cdx_data is None:
+                # Not a ChemDraw object — skip silently
+                continue
+
+            entry_name = os.path.splitext(os.path.basename(entry))[0]
+            obj = _save_extracted_object(
+                cdx_data, entry, entry_name,
+                output_dir, output_format, convert_method, _converter,
+            )
+            results.append(obj)
+
+    return results
+
+
+def _extract_from_xls(
+    input_path: str,
+    output_dir: str,
+    output_format: str,
+    convert_method: str,
+    _converter,
+) -> List[ExtractedObject]:
+    """Extract ChemDraw objects from an OLE2-native XLS file.
+
+    XLS files are OLE2 compound documents. Embedded objects are stored as
+    sub-storages with names starting with 'MBD' (e.g. MBD078DC381).
+    ChemDraw objects contain a CONTENTS stream with CDX binary data.
+    """
+    results = []
+    ole = olefile.OleFileIO(input_path)
+    try:
+        # Find top-level MBD* storages (embedded OLE objects)
+        seen_storages = set()
+        for entry in ole.listdir(storages=True, streams=False):
+            if len(entry) >= 1 and entry[0].startswith("MBD"):
+                seen_storages.add(entry[0])
+
+        obj_index = 0
+        for storage_name in sorted(seen_storages):
+            contents_path = f"{storage_name}/CONTENTS"
+            if not ole.exists(contents_path):
+                continue
+
+            cdx = ole.openstream(contents_path).read()
+            if len(cdx) < 4 or cdx[:4] != CDX_MAGIC:
+                continue
+
+            obj_index += 1
+            source_path = f"{storage_name}/CONTENTS"
+            entry_name = f"oleObject{obj_index}"
+            obj = _save_extracted_object(
+                cdx, source_path, entry_name,
+                output_dir, output_format, convert_method, _converter,
+            )
+            results.append(obj)
+    finally:
+        ole.close()
+
+    return results
+
+
+def extract_from_office(
+    input_path: str,
+    output_dir: Optional[str] = None,
+    output_format: str = "cdxml",
+    convert_method: str = "auto",
+) -> List[ExtractedObject]:
+    """Extract all ChemDraw objects from an Office file.
+
+    Args:
+        input_path: Path to .pptx, .docx, .xlsx, or .xls file.
+        output_dir: Directory for extracted files. Default: <basename>_chemdraw/
+        output_format: "cdx", "cdxml", or "both".
+        convert_method: Backend for CDX→CDXML conversion (passed to cdx_converter).
+
+    Returns:
+        List of ExtractedObject with extraction results.
+    """
+    ext = os.path.splitext(input_path)[1].lower()
+
+    if ext not in EMBEDDING_PATTERNS and ext not in OLE2_FORMATS:
+        raise ValueError(
+            f"Unsupported file type: {ext}. "
+            f"Use .pptx, .docx, .xlsx, or .xls."
+        )
+
+    if output_dir is None:
+        basename = os.path.splitext(os.path.basename(input_path))[0]
+        output_dir = os.path.join(os.path.dirname(input_path) or ".", f"{basename}_chemdraw")
+
+    os.makedirs(output_dir, exist_ok=True)
+    _converter = _get_converter(output_format)
+
+    if ext in OLE2_FORMATS:
+        return _extract_from_xls(
+            input_path, output_dir, output_format, convert_method, _converter,
+        )
+    else:
+        return _extract_from_zip(
+            input_path, output_dir, output_format, convert_method, _converter,
+        )
+
+
+def print_summary(results: List[ExtractedObject], input_path: str) -> None:
+    """Print extraction summary to stdout."""
+    print(f"{'=' * 60}")
+    print(f"OLE Extractor - {os.path.basename(input_path)}")
+    print(f"{'=' * 60}")
+
+    if not results:
+        print("No ChemDraw objects found.")
+        return
+
+    print(f"Found {len(results)} ChemDraw object(s):\n")
+    for i, obj in enumerate(results, 1):
+        print(f"  [{i}] {obj.source_path}")
+        print(f"      CDX size: {len(obj.cdx_data):,} bytes")
+        if obj.cdx_output:
+            print(f"      CDX:   {obj.cdx_output}")
+        if obj.cdxml_output:
+            size = os.path.getsize(obj.cdxml_output)
+            print(f"      CDXML: {obj.cdxml_output} ({size:,} bytes)")
+        if obj.error:
+            print(f"      Note:  {obj.error}")
+        print()
+
+
+# ---------------------------------------------------------------------------
+# CLI
+# ---------------------------------------------------------------------------
+
+def main(argv=None) -> int:
+    parser = argparse.ArgumentParser(
+        description="Extract embedded ChemDraw objects from Office files."
+    )
+    parser.add_argument("input", help="Input file (.pptx, .docx, .xlsx, or .xls)")
+    parser.add_argument(
+        "-o", "--output-dir",
+        help="Output directory (default: <input_basename>_chemdraw/)"
+    )
+    parser.add_argument(
+        "--format",
+        choices=["cdxml", "cdx", "both"],
+        default="cdxml",
+        help="Output format (default: cdxml)"
+    )
+    parser.add_argument(
+        "--method",
+        choices=["auto", "com", "pycdxml", "obabel"],
+        default="auto",
+        help="CDX→CDXML conversion backend (default: auto)"
+    )
+    args = parser.parse_args(argv)
+
+    if not os.path.isfile(args.input):
+        print(f"Error: file not found: {args.input}", file=sys.stderr)
+        return 1
+
+    try:
+        results = extract_from_office(
+            args.input,
+            output_dir=args.output_dir,
+            output_format=args.format,
+            convert_method=args.method,
+        )
+        print_summary(results, args.input)
+        return 0
+    except Exception as e:
+        print(f"Error: {e}", file=sys.stderr)
+        return 1
+
+
+if __name__ == "__main__":
+    sys.exit(main())