mol2chemfigPy3 1.5.1

python3 version of mol2chemfig

mol2chemfigPy3

Current version 1.5.1 (transferred from mol2chemfig v1.5).

This is NOT an official version of mol2chemfig for python 3.

There are always too few free tools for chemistry, while mol2chemfig is a good one of them. But it was written in python2. Nowadays, who are still using py2? LOL

Simply applying 2to3 to it doesn't work, alas.

mol2chemfigPy3 is a simple translation from py2 to py3 based on old mol2chemfig version 1.5 (the python codes are the same as 1.4🤔 mol2chemfig (uwaterloo.ca)).

Install

build from source

this requires setuptools and wheel installed

• first cd to where setup.py locates

  $ cd <path>
  

• then run

  $ pip install ./
  

If you prefer installing from wheel, you can download here.

install from PyPi

$ pip install -U mol2chemfigPy3

Usage

Use in command line

Attention: to render the colours on Windows platform, run it in modern terminals, e.g. Windows Terminal.

Run, for example:

$ mol2chemfig -zw -i direct "C1=CC=C(C=C1)O"

it will give you \chemfig{OH-[:180,,1]=_[:240]-[:180]=_[:120]-[:60]=_(-[:300])}

Run, for another example:

$ mol2chemfig -zw -i direct "C1=CC=C(C=C1)O" > phenol-smi-terse.tex

it will write result to file phenol-smi-terse.tex

Run, for again another example:

$ mol2chemfig -zw -i pubchem 99

it will give you

\chemfig{O=[:137.9]P(-[:47.9]O-[:107.9,0.62]H)(-[:137.9]O-[:197.9,0.62]H)%
-[:227.9]O-[:287.9](-[:44.9,0.62]H)-[:233.9](-[:179.9]O-[:119.9,0.62]H)(%
-[:116.9,0.62]H)-[:305.9](-[:251.9]N-[:197.8,0.994]=^[:150]N-[:210](%
-[:150,0.62]H)=^[:270]N-[:330](=^[:30](-[:90])-[:342.1,0.994]N%
=^[:54.1,0.994](-[,0.62]H)-[:126,0.994]\phantom{N})-[:270]N(-[:330,0.62]H)%
-[:210,0.62]H)(-[:314.9,0.62]H)-[:17.9]O-[:89.9](-[:161.9])(-[:332.9,0.62]H%
)-[:35.9](-[:55.9,0.62]H)(-[:135.9,0.62]H)-[:335.9]O-[:35.9]P(-[:305.9]O%
-[:245.9,0.62]H)(=[:125.9]O)-[:35.9]O-[:335.9]P(-[:65.9]O-[:125.9,0.62]H)(%
=[:245.9]O)-[:335.9]O-[:35.9](-[:55.9,0.62]H)(-[:135.9,0.62]H)-[:335.9](%
-[:65.9](-[:65.9,0.62]H)(-[:155.9,0.62]H)-[:335.9,0.62]H)(-[:245.9](%
-[:245.9,0.62]H)(-[:335.9,0.62]H)-[:155.9,0.62]H)-[:335.9](-[:275.9]O%
-[:335.9,0.62]H)(-[:215.9,0.62]H)-[:35.9](=[:95.9]O)-[:335.9]N(%
-[:275.9,0.62]H)-[:35.9](-[:55.9,0.62]H)(-[:135.9,0.62]H)-[:335.9](%
-[:235.9,0.62]H)(-[:315.9,0.62]H)-[:35.9](=[:95.9]O)-[:335.9]N(%
-[:275.9,0.62]H)-[:35.9](-[:55.9,0.62]H)(-[:135.9,0.62]H)-[:335.9](%
-[:235.9,0.62]H)(-[:315.9,0.62]H)-[:35.9]S-[:335.9](=[:275.9]O)-[:35.9](%
-[:95.9,0.62]H)=[:335.9](-[:35.9](-[:35.9,0.62]H)(-[:125.9,0.62]H)%
-[:305.9,0.62]H)-[:275.9](-[:185.9,0.62]H)(-[:275.9,0.62]H)-[:5.9,0.62]H}

(it's Coenzyme A, S-(3-methyl-2-butenoate) by the way 😜)

Use as a python package (new add in to this python 3 version)

This is not included in the old Py2 version of mol2chemfig.

mol2chemfigPy3.mol2chemfig(content: str, *args: str, rotate: float = 0.0, aromatic: bool = True, marker: Optional[str] = None, name: Optional[str] = None, relative_angle: bool = False, show_carbon: bool = False, show_methyl: bool = False, inline: bool = False)

e. g.

from mol2chemfigPy3 import mol2chemfig

mol2chemfig('996')  # search the PubChem database

mol2chemfig('C1=CC=C(C=C1)O')  # transfer InChI/SMILES to chemfig

mol2chemfig('.\methanol.smi')  # from a file

Document

See official document mol2chemfig-doc.pdf (uwaterloo.ca)

License

MIT license