how to convert sdf file to excel

To convert an SDF (Structured Data File) to an Excel file, you can use a data conversion tool or a programming language like Python. Here are two methods you can follow:

Method 1: Using Python (with Pandas):

  1. Install Python: If you don’t already have Python installed, download and install Python from the official website (https:www.python.orgdownloads).
  2. Install Pandas: Open a command prompt or terminal and install the Pandas library, which will help you work with data easily:

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pip install pandas

  1. Convert SDF to Excel:
    • Create a Python script (e.g., and use the following code as an example to convert the SDF file to Excel:

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import pandas as pd from cheminformatics_toolkit import ChemToDataFrame, AllChem # Read the SDF file sdf_file = “input.sdf” supplier = ChemToDataFrame() supplier.SetData(open(sdf_file).read()) sdf_data = supplier.GetFrame() # Convert to Excel excel_file = “output.xlsx” sdf_data.to_excel(excel_file, index=False)

Replace “input.sdf” with the path to your SDF file and “output.xlsx” with the desired Excel file name.

  1. Run the Script:
    • Save the script and run it using the Python interpreter:

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This will convert the SDF file to an Excel file.

Method 2: Using Data Conversion Software:

You can also use data conversion software like Open Babel or ChemDraw to convert SDF files to Excel. Here’s a general outline of the steps using Open Babel:

  1. Download and Install Open Babel:
    • Visit the Open Babel website ( and download the appropriate version for your operating system.
    • Install the software following the installation instructions provided.
  2. Convert SDF to CSV:
    • Open Babel can convert SDF files to CSV (Comma-Separated Values) format, which can be easily opened in Excel.
    • Open a command prompt or terminal and use the following command to convert the SDF file to CSV:

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obabel input.sdf -O output.csv

Replace “input.sdf” with the path to your SDF file and “output.csv” with the desired CSV file name.

  1. Open CSV in Excel:
    • Open Microsoft Excel.
    • Use the “Open” or “Import” feature to open the CSV file created in the previous step.
    • Excel will guide you through the import process, allowing you to specify delimiters and data types.
  2. Save as Excel:
    • Once the CSV file is open in Excel, you can save it as an Excel file (XLSX or XLS) using the “Save As” option.

These methods should allow you to convert an SDF file to Excel format for further analysis or manipulation in Microsoft Excel.

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