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Another supported value is MOL, denoting an MDL mol file [33].
While the purpose of the getMol function could be described as "export as MOL file", the setMol function could be called "import MOL file" and it can be used for structure input in textual form for further structural modification using FlaME (see example 1).
It is also possible to import MOL files for the corresponding substrates and products, or put the MOL file text into the form.
Fig. 1 Example MOL file format for benzene.
Briefly, each MOL file was converted into a Standard InChI with ChemAxon's MolConverter [33], providing a unique textual representation of the MOL file.
To generate three dimensional low-energy structures from the mol file we used CORINA [25].
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Mol files can be opened in the MyChemise screen and can be saved in mol format.
To generate stereoisomers (as individual MOL files), we used a custom-written Python script.
MOL files, SMILES notations, IUPAC names, and InChI strings are ubiquitous file formats and systematic identifiers for chemical structures.
InChI and InChIKey were generated from these MOL files with inchi-1 executable v. 1.04, 64-bit version for Linux [1].
We drew two-dimensional Lewis structures of the molecules with ISIS-Draw and exported them as MDL MOL files [24].
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com