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obabel: Convert a SMILES string to a 500x500 picture.
$ obabel -:"${SMILES} -O ${path-to-output_file-png} -xp 500
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This command is utilizing the obabel software tool to convert a molecule represented in the Simplified Molecular Input Line Entry System (SMILES) format into an image file in Portable Network Graphics (PNG) format.

Here's a breakdown of the command:

  • obabel: It is the command used to call the obabel tool.
  • -:: This indicates that the input molecule will be passed as an argument directly following the command.
  • "${SMILES}: The SMILES variable represents the SMILES string of the molecule to be converted. It is enclosed within " to avoid potential issues with special characters or spaces.
  • -O: This flag specifies the output file format for the conversion.
  • ${path-to-output_file-png}: This is the path to the desired output file, where the converted image will be saved. You should replace ${path-to-output_file-png} with the actual path on your system, including the desired file name and the .png extension.
  • -xp 500: This option sets the width of the image to be generated. In this case, it sets the image width to 500 pixels. You can modify this value as per your requirements.

In summary, this command takes a molecule represented in SMILES format (specified by ${SMILES}) and uses obabel to convert it into a PNG image file, saving it at the specified output path (${path-to-output_file-png}).

This explanation was created by an AI. In most cases those are correct. But please always be careful and never run a command you are not sure if it is safe.
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