semvec/pypi-packages huggingface dataset:
pywfn 1.0.7
A python package for wave function analysis
Requires Python: >=3.10
Keywords: chemistry, wave function

# `pywfn` -- 基于python的波函数分析工具

文档： https://www.xiaofei911.top/mkdocs/pywfn/


## 依赖
```
numpy>=2.1.1
rich>=13.8.0
matplotlib>=3.9.2
```
## 运行(CLI)
``` shell
python main.py
```

## 示例(API)
```python
from pywfn.base import Mole
from pywfn.reader import LogReader
from pywfn.atomprop import charge

path="D:\BaiduSyncdisk\gfile\CnHn\C6H6.log" # 高斯输出文件的路径
reader=LogReader(path) # 实例化log文件读取器
mol=Mole(reader) # 实例化分子对象

caler=charge.Calculator(mol) # 实例化原子电荷计算器，传入分子对象
result=caler.mulliken() # 计算mulliken电荷
print(result) # 打印结果
```

## 功能
![](./docs/pywfn_xmind.png)
dnachisel 3.2.16
Optimize DNA sequences under constraints.
Keywords: DNA, gene, design, codon, optimization, constraints, synthetic biology

DNA Chisel
==========

DNA Chisel (complete documentation `here <https://edinburgh-genome-foundry.github.io/DnaChisel/>`_)
is a Python library for optimizing DNA sequences with respect to a set of
constraints and optimization objectives. It comes with over 15 classes of
sequence specifications which can be composed to, for instance, codon-optimize
genes, meet the  constraints of a commercial DNA provider, avoid homologies
between sequences, tune GC content, or all of this at once!

DNA Chisel also allows users to define their own specifications in Python,
making the library suitable for a large range of automated sequence design
applications, and complex custom design projects. It can be used as a Python
library, a command-line interface, or a `web application <https://cuba.genomefoundry.org/sculpt_a_sequence>`_.


Example of use
---------------

.. code:: python

    from dnachisel import *

    # DEFINE THE OPTIMIZATION PROBLEM

    some_sequence = random_dna_sequence(10000)
    problem = DnaOptimizationProblem(
        sequence=some_sequence,
        constraints=[
            AvoidPattern("BsaI_site"),
            EnforceGCContent(mini=0.3, maxi=0.7, window=50),
            EnforceTranslation(location=(500, 1400))
        ],
        objectives=[CodonOptimize(species='e_coli', location=(500, 1400))]
    )

    # SOLVE THE CONSTRAINTS, OPTIMIZE WITH RESPECT TO THE OBJECTIVE

    problem.resolve_constraints()
    problem.optimize()

    # PRINT SUMMARIES TO CHECK THAT CONSTRAINTS PASS

    print(problem.constraints_text_summary())
    print(problem.objectives_text_summary())

Alternatively, DNA Chisel lets you define problems by annotating a Genbank file.
You can also define a problem by annotating directly a Genbank as follows:

.. image:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/DnaChisel/master/docs/_static/images/example_sequence.png
   :alt: [logo]
   :align: center
   :width: 450px

See `this page <https://edinburgh-genome-foundry.github.io/DnaChisel/ref/builtin_specifications.html>`_
for an overview of available specifications.

Infos
-----

**PIP installation:**

.. code:: bash

  pip install dnachisel[reports]

(you can omit the ``[reports]`` suffix if you intend to use dnachisel only
for sequence optimization, without generating figures or PDF reports)

**Web documentation:** `<https://edinburgh-genome-foundry.github.io/DnaChisel/>`_

**Github Page:** `<https://github.com/Edinburgh-Genome-Foundry/DnaChisel>`_

**Live demo:** `<http://cuba.genomefoundry.org/sculpt_a_sequence>`_

**License:** MIT

Copyright 2017 Edinburgh Genome Foundry, University of Edinburgh


More biology software
-----------------------

.. image:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/Edinburgh-Genome-Foundry.github.io/master/static/imgs/logos/egf-codon-horizontal.png
  :target: https://edinburgh-genome-foundry.github.io/

DNA Chisel is part of the `EGF Codons <https://edinburgh-genome-foundry.github.io/>`_ synthetic biology software suite for DNA design, manufacturing and validation.