Name to Structure Format options

Codename

Explanation

ocr

converts names containing OCR (optical character recognition) error.
Example: convert the defective name "3-rnethyl-l-methoxynaphthalene" to SMILES

molconvert 'smiles:T*' -s '3-rnethyl-l-methoxynaphthalene' -f name:ocr

-systematic

disable conversion of systematic names

-common

disable conversion of common names (such as aspirin)

-elements

disable conversion of the name of chemical elements, for instance carbon, sodium, .... Even though "carbon" is not converted, "methane" still is, since it is a molecule name for CH4, not an element.

-ions

disable conversion of atomic ion syntax, for instance "Ca2+".

-groups

disable conversion of groups and fragments, such as "oxo" or "methyl".

-cas

disable the conversion of CAS registry numbers

-casNames

disable the conversion of CAS names

nameField=FIELD

sets the field/property that stores the original name. By default, the molecule title is used.

dict=PATH

specify the location of the custom dictionary. Example: name:dict=C:\Users\Me\MyDictionary.smi .

webservice=URL

enable the usage of a custom webservice at the given URL

Some of these options are mainly useful when configuring which names Document to Structure recognizes.

To enable an option, a + sign can be used before the option name. For instance, both forms ocr and +ocr are accepted to enable this option.