https://github.com/augus1999/mol2chemfigpy3

The python 3 version of mol2chemfig package. 🛠️pip install mol2chemfigPy3
https://github.com/augus1999/mol2chemfigpy3

chemfig chemistry chemistry-molecule mol2chemfig molecule python3 tool

Last synced: 25 days ago
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The python 3 version of mol2chemfig package. 🛠️pip install mol2chemfigPy3

• Host: GitHub
• URL: https://github.com/augus1999/mol2chemfigpy3
• Owner: Augus1999
• License: mit
• Created: 2021-09-27T19:59:11.000Z (about 3 years ago)
• Default Branch: main
• Last Pushed: 2024-08-10T01:20:00.000Z (3 months ago)
• Last Synced: 2024-09-28T20:02:29.453Z (about 1 month ago)
• Topics: chemfig, chemistry, chemistry-molecule, mol2chemfig, molecule, python3, tool
• Language: Python
• Homepage: https://augus1999.github.io/mol2chemfigPy3/
• Size: 246 KB
• Stars: 23
• Watchers: 1
• Forks: 3
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# mol2chemfigPy3

[![PyPI](https://img.shields.io/pypi/v/mol2chemfigPy3?color=ff69b4)](https://pypi.org/project/mol2chemfigPy3/)

[![Downloads](https://static.pepy.tech/personalized-badge/mol2chemfigpy3?period=total&units=international_system&left_color=black&right_color=green&left_text=Downloads)](https://pepy.tech/project/mol2chemfigpy3)

![OS](https://img.shields.io/badge/OS-Win%20|%20Linux%20|%20macOS-blue?color=00B16A)

![python](https://img.shields.io/badge/Python->3.8%20-blue.svg?color=dd9b65)

![black](https://img.shields.io/badge/code%20style-black-black)

![pytest](https://github.com/Augus1999/mol2chemfigPy3/actions/workflows/pytest.yml/badge.svg)

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

mol2chemfigPy3 is a translation from py2 to py3 based on

old [mol2chemfig](http://chimpsky.uwaterloo.ca/mol2chemfig/download) version 1.5.

## Install

### install from PyPi

```bash

$ pip install -U mol2chemfigPy3

```

## Usage

### Use in command line

> `mol2chemfig` and `python -m mol2chemfigPy3` are equivalent.

#### 1. getting version

```bash

$ mol2chemfig --version

```

#### 2. getting help

```bash

$ mol2chemfig -h

```

#### 3. some examples

##### 3.1 converting SMILES

```bash

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

```

it will give you

```latex

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

```

##### 3.2 writing to an output file

```bash

$ 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

```bash

$ mol2chemfig -zw -i pubchem 996

```

##### 3.4 reading from a file

```bash

$ 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.

```python

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)](http://chimpsky.uwaterloo.ca/m2cf_static/mol2chemfig-doc.pdf)~~

The website seems down, so here is a mirror [mol2chemfig Documentation Version 1.5](https://mirror.ox.ac.uk/sites/ctan.org/graphics/mol2chemfig/mol2chemfig-doc.pdf)

## License

MIT license