semvec/pypi-packages huggingface dataset:
qml 0.4.0.27
Quantum Machine Learning
Keywords: Machine Learning

QML: A Python Toolkit for Quantum Machine Learning
==================================================

|Build Status| |doi| |doi|

QML is a Python2/3-compatible toolkit for representation learning of
properties of molecules and solids.

Current list of contributors:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

-  Anders S. Christensen (University of Basel)
-  Felix A. Faber (University of Basel)
-  Bing Huang (University of Basel)
-  Lars A. Bratholm (University of Copenhagen)
-  Alexandre Tkatchenko (University of Luxembourg)
-  Klaus-Robert Muller (Technische Universitat Berlin/Korea University)
-  O. Anatole von Lilienfeld (University of Basel)

1) Citing QML:
--------------

Until the preprint is available from arXiv, please cite this GitHub
repository as:

::

    AS Christensen, LA Bratholm, FA Faber, B Huang, A Tkatchenko, KR Muller, OA von Lilienfeld (2017) "QML: A Python Toolkit for Quantum Machine Learning" https://github.com/qmlcode/qml

2) Get help:
------------

Documentation and installation instruction is found at:
http://www.qmlcode.org/

3) License:
-----------

QML is freely available under the terms of the MIT license.

.. |Build Status| image:: https://travis-ci.org/qmlcode/qml.svg?branch=master
   :target: https://travis-ci.org/qmlcode/qml
.. |doi| image:: https://badge.fury.io/py/qml.svg
   :target: https://badge.fury.io/py/qml
.. |doi| image:: https://zenodo.org/badge/89045103.svg
   :target: https://zenodo.org/badge/latestdoi/89045103
cigar-coordinates 0.0.1
To get the coordinates of a given CIGAR string. By Guanliang MENG, see https://github.com/linzhi2013/cigar_coordinates.
Requires Python: >=3

# cigar_coordinates

## 1 Introduction

`cigar_coordinates` is a tool To get the coordinates of a given CIGAR string. CIGARs are in respect of the reference sequence. By Guanliang MENG, see https://github.com/linzhi2013/cigar_coordinates. 

`cigar_coordinates` understands the following CIGAR characters:

       seq - - - N N N O O O
    refseq - N O N - O O N -
     cigar P n D B u U M N I


## 2 Installation

    pip install cigar_coordinates

There will be a command `cigar_coordinates` created under the same directory as your `pip` command.

## 3 Usage
    
    $ cigar_coordinates
    usage: cigar_coordinates [-h] -c <STR> [-s <INT>] [-q] [-d {+,-}]

    To get the coordinates of a given CIGAR string.
    By Guanliang MENG, see https://github.com/linzhi2013/cigar_coordinates.

    I understand the following CIGAR types:

         seq - - - N N N O O O
      refseq - N O N - O O N -
       cigar P n D B u U M N I

    The output coordinates are closed intervals.

    optional arguments:
      -h, --help  show this help message and exit
      -c <STR>    input CIGAR string
      -s <INT>    the start coordinate on the sequence, whatever the gene
                  direction is, this option is always the smaller one. [1]
      -q          the '-s' option is about query sequence, not refseq [True]
      -d {+,-}    the gene direction [+]

## 4 Example
  
For a gene: ND1;len=945;\[2444:3389\]\(\+\)

    $ cigar_coordinates -c 6D166M268N511M -s 2444
    6D  2444  2444
    166M  2444  2609
    268N  2610  2877
    511M  2878  3388

## 5 Author
Guanliang MENG

## 6 Citation
Currently I have no plan to publish `cigar_coordinates`.
msa-cigars 0.0.1
To return CIGAR strings of a multiple sequences alignment
Requires Python: >=3

# msa_cigars

## 1 Introduction

`msa_cigars` is a tool to get the CIGARs of a multiple sequence alignment. ONE alignment in the input file is assumed! CIGARs are in respect of the reference sequence. By Guanliang MENG, see https://github.com/linzhi2013/msa_cigars. 

## 2 Installation

    pip install msa_cigars

There will be a command `msa_cigars` created under the same directory as your `pip` command.

## 3 Usage
    
    $ msa_cigars
    usage: msa_cigars [-h] -i <FILE> -refseq_id <STR> [-n <STR>] [-g <STR>]
                     [-f <FORMAT>] [-o <FILE>]

        To get the CIGARs of a multiple sequence alignment.
        ONE alignment in the input file is assumed!

        CIGARs are in respect of the reference sequence.

        'O' normal bases, e.g. A, T, G, C
        '-' deletion
        'N' unknown base

            seq - - - N N N O O O
         refseq - N O N - O O N -
          cigar P n D B u U M N I

        By Guanliang MENG,
        see https://github.com/linzhi2013/msa_cigars.

        optional arguments:
          -h, --help        show this help message and exit
          -i <FILE>         input msa file
          -refseq_id <STR>  MsaCigars class uses regular expression to find out the
                            sequence id of refseq. Thus, make sure the value of
                            'refseq_id' option is unique among the input msa file.
          -n <STR>          character of unknown base [N]
          -g <STR>          character of gap base [-]
          -f <FORMAT>       the msa format [fasta]
          -o <FILE>         outfile name [stdout]


## 4 Author
Guanliang MENG

## 5 Citation
Currently I have no plan to publish `msa_cigars`.

However, since `msa_cigars` makes use of `Biopython`, you should also cite it if you use `breakSeqInNs_then_translate` in your work:

    Peter J. A. Cock, Tiago Antao, Jeffrey T. Chang, Brad A. Chapman, Cymon J. Cox, Andrew Dalke, Iddo Friedberg, Thomas Hamelryck, Frank Kauff, Bartek Wilczynski, Michiel J. L. de Hoon: “Biopython: freely available Python tools for computational molecular biology and bioinformatics”. Bioinformatics 25 (11), 1422–1423 (2009). https://doi.org/10.1093/bioinformatics/btp163

Please go to `http://www.biopython.org/` for more details.