README.md

mol2chemfigPy3

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

mol2chemfigPy3 is a translation from py2 to py3 based on old mol2chemfig version 1.5.

Install

install from PyPi

$ pip install -U mol2chemfigPy3

Usage

Use in command line

mol2chemfig and python -m mol2chemfigPy3 are equivalent.

1. getting version

$ mol2chemfig --version

2. getting help

$ mol2chemfig -h

3. some examples

3.1 converting SMILES

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

it will give you

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

3.2 writing to an output file

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

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

3.3 searching PubChem database

$ mol2chemfig -zw -i pubchem 996

3.4 reading from a file

$ mol2chemfig -zw peniciling.mol

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

This is not included in the original 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)

The website seems down, so here is a mirror mol2chemfig Documentation Version 1.5

License

MIT license