Choose your file (Format: *.sdf): Example    Format converter

Embed properties or not

Select the preferred molecular preprocessing options

Breaking covalent bonds between metals and organic atoms under certain conditions. (1)

Doing a series of normalization transforms to correct functional groups and recombine charges. (2)

Adding hydrogen atoms. (3)

Removing hydrogen atoms. (4)

Reionize a molecule such that the strongest acids ionize first. (5)

Neutralize molecule by adding/removing hydrogens. Attempts to preserve zwitterions. (6)

Remove specified fragments of molecules. Keep the largest covalent unit in a molecule with multiple fragments. (7)

Get a canonical tautomer by enumerating and scoring all possible tautomers. (8)

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Set the order

If you select multiple items above, please provide a order. Every molecule will be processed by this order.

Set initial coordinates for a molecule

"2D coordinates" - Compute 2D coordinates for a molecule.

"3D coordinates" - Use UFF to optimize a molecule's structure.

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Note:

The default choices and orders(7, 6, 2) are suitable for most cases based on the experience of authors. Users should pick different combinations according to their purpose and their datasets. The wrong choice or combination will trigger corresponding errors, and it is normal.

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