Options:
-h, --help Print help message and exit (Default:
False)
-b, --version Print program version and exit (Default:
False)
-i, --input How to interpret the argument. With 'file',
mol2chemfig expects a filename. With
'direct', the argument is intrepreted
directly; don't forget to put quotes around
it. With 'pubchem', the argument is treated
as an identifier for the PubChem database.
(Default: file)
-z, --terse Remove all whitespace and comments from the
output. If you can still read it
afterwards, Bill Gates wants your resume
(Default: False)
-r, --strict Abide by Indigo's chemical structure
validation. If true, mol2chemfig will fail
if Indigo reports that something is wrong
with the molecule, like a carbon with five
bonds. If false, mol2chemfig will ignore
such errors (Default: True)
-d, --indent Number of spaces to use for indenting
molecule branches in generated code.
Without effect when 'terse' option is
passed. Affects only the generated tex
code, not the rendered molecule (Default:
4)
-u, --recalculate-coordinates Discard existing coordinate and calculate
new ones from covalent structure. For
smiles input, this is performed implicitly
(Default: False)
-a, --angle Rotate molecule counterclockwise by this
angle (Default: 0.0)
-v, --relative-angles Use relative bond angles (Default: False)
-p, --flip Flip the structure horizontally (Default:
False)
-q, --flop Flip the structure vertically (Default:
False)
-c, --show-carbons Show element symbol for carbon atoms
(Default: False)
-m, --show-methyls Show element symbols for methyl groups
(implied if show-carbons is True) (Default:
False)
-y, --hydrogens How to deal with explicit hydrogen atoms.
One of 'keep', 'add' or 'delete'. Note that
'add' will also trigger calculation of new
coordinates for the entire molecule. Option
'keep' does nothing (Default: keep)
-f, --fancy-bonds Draw fancier double and triple bonds
(Default: False)
-g, --markers Give each atom and each bond a unique
marker that can be used for attaching
electron movement arrows. With value 'a',
atom 2 will be labeled @{a2}, and its bond
to atom 5 @{a2-5}. (Default: None)
-n, --atom-numbers Show the molfile number of each atom next
to it. When this option is set, charges and
implicit hydrogens will not be shown
(Default: False)
-s, --bond-scale How to scale the lengths of bonds (one of
'keep', 'scale', or 'normalize') (Default:
normalize)
-t, --bond-stretch Used as scaling factor (with --bond-
scale=scale) or average (with --bond-
scale=normalize) for bond lengths (Default:
1.0)
-w, --wrap-chemfig Wrap generated code into \chemfig{...}
command (Default: False)
-l, --submol-name If a name is given, wrap generated code
into chemfig \definesubmol{name}{...}
command (Default: None)
-e, --entry-atom Number of first atom to be rendered.
Relevant only if generated code is to be
used as sub-molecule (Default: None)
-x, --exit-atom Number of last atom to be rendered.
Relevant only if generated code is to be
used as sub-molecule (Default: None)
-k, --cross-bond Specify bonds that should be drawn on top
of others they cross over. Give the start
and the end atoms. Example for one bond:
--cross-bond=5-6 Example for two bonds:
--crossbond=4-8,12-13 (Default: None)
