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obabel: Convert a file of SMILES string to separate 3D .mol files.
$ obabel ${filename-smi} -O ${path-to-output_file-mol} --gen3D -m
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This command uses the obabel utility to convert a chemical structure file from SMILES format to a 3D molecular structure and save it to a specified output file.

Here is a breakdown of the command:

  • ${filename-smi}: This is a placeholder that should be replaced with the actual filename of the input structure file in SMILES format. SMILES (Simplified Molecular Input Line Entry System) is a textual representation of a molecular structure.

  • -O: This option specifies the output file to which the converted 3D structure should be saved. ${path-to-output_file-mol} is a placeholder that should be replaced with the desired path and name for the output file. The output file will be saved in a format compatible with the provided file extension, which in this case is ".mol".

  • --gen3D: This option instructs obabel to generate a 3D structure from the input molecule. It uses algorithms to predict the positions of atoms in 3D space based on the given input.

  • -m: This option enables molecular mechanics, which means that obabel will optimize the generated 3D structure by adjusting the positions of atoms to minimize the potential energy of the molecule. This can result in a more realistic and energetically favorable representation of the molecule.

In summary, this command takes an input structure file in SMILES format, converts it to a 3D molecular structure, optimizes it through molecular mechanics, and saves the resulting structure to an output file in ".mol" format.

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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