Metadata-Version: 1.1
Name: txt2contincd
Version: 0.1.0
Summary: Convert raw text data files into a CONTIN-CD input file.
Home-page: https://github.com/lambdalisue/txt2contincd
Author: Alisue
Author-email: lambdalisue@hashnote.net
License: MIT
Download-URL: https://github.com/lambdalisue/txt2contincd/tarball/master
Description: txt2contincd
        ==========================
        .. image:: https://secure.travis-ci.org/lambdalisue/txt2contincd.png?branch=master
            :target: http://travis-ci.org/lambdalisue/txt2contincd
            :alt: Build status
        
        .. image:: https://coveralls.io/repos/lambdalisue/txt2contincd/badge.png?branch=master
            :target: https://coveralls.io/r/lambdalisue/txt2contincd/
            :alt: Coverage
        
        .. image:: https://pypip.in/d/txt2contincd/badge.png
            :target: https://pypi.python.org/pypi/txt2contincd/
            :alt: Downloads
        
        .. image:: https://pypip.in/v/txt2contincd/badge.png
            :target: https://pypi.python.org/pypi/txt2contincd/
            :alt: Latest version
        
        .. image:: https://pypip.in/wheel/txt2contincd/badge.png
            :target: https://pypi.python.org/pypi/txt2contincd/
            :alt: Wheel Status
        
        .. image:: https://pypip.in/egg/txt2contincd/badge.png
            :target: https://pypi.python.org/pypi/txt2contincd/
            :alt: Egg Status
        
        .. image:: https://pypip.in/license/txt2contincd/badge.png
            :target: https://pypi.python.org/pypi/txt2contincd/
            :alt: License
        
        txt2contincd convert raw text data files into a
        `CONTIN-CD <http://s-provencher.com/pages/contin-cd.shtml>`_ input file.
        It use `maidenhair <https://github.com/lambdalisue/maidenhair>`_ for reading raw
        text files so any kind of raw text file can be used if there is a maidenhair
        plugins.
        
        Installation
        ------------
        Use pip_ like::
        
            $ pip install txt2contincd
        
        .. _pip:  https://pypi.python.org/pypi/pip
        
        Quick Usage
        -------------
        Assume that you have measured the far-UV CD spectrum with the following condition::
        
            The number of residues (amino acids):   260 aa
            The molecular weight of the protein:    29.07 kDa
            The concentration of the protein:       0.303 mg/mL
            The length of the light pathway:        0.1 cm
        
        Then run *txt2contincd* with
        
            % txt2contincd -n 260 -m 29.07 -c 0.303 -L 0.1 <raw CD spectrum>
        
        It will produce ``contin-cd.in`` file.
        
        Usage
        ------
        
        ::
        
            usage: txt2contincd [-h] [-v] [-p PARSER] [-l LOADER] [-u USING] [-a] [-s]
                                [-o OUTPUT] [-n NUMBER] [-m MOLECULAR_WEIGHT]
                                [-c CONCENTRATION]
                                [--molar-concentration MOLAR_CONCENTRATION] [-L LENGTH]
                                pathname
        
            positional arguments:
            pathname              An unix grob style filename pattern for the data files
        
            optional arguments:
            -h, --help            show this help message and exit
            -v, --version         show program's version number and exit
        
            Reading options:
            -p PARSER, --parser PARSER
                                    A maidenhair parser name which will be used to parse
                                    the raw text data.
            -l LOADER, --loader LOADER
                                    A maidenhair loader name which will be used to load
                                    the raw text data.
            -u USING, --using USING
                                    A colon (:) separated column indexes. It is used for
                                    limiting the reading columns.
            -a, --average         Calculate the average value of the specified data.
            -s, --no-strict       Do not strict the wavelength range into 190-240 .
            -o OUTPUT, --output OUTPUT
                                    A output filename. The default is "contin-cd.in".
        
            Experimental properties:
            -n NUMBER, --number NUMBER
                                    The number of residues (amino acids) in the sample.
            -m MOLECULAR_WEIGHT, --molecular-weight MOLECULAR_WEIGHT
                                    A molecular weight of the sample in kDa (=kg/mol).
            -c CONCENTRATION, --concentration CONCENTRATION
                                    A concentration of the sample in g/L. See --molar-
                                    concentration as an alternative.
            --molar-concentration MOLAR_CONCENTRATION
                                    A molar concentration of the sample in mol/L. It is
                                    used as an alternative option of --concentration.
            -L LENGTH, --length LENGTH
                                    A light pathway length (cuvette length) in centimeter
        
        Preference
        -----------
        You can create configure file as ``~/.config/txt2contincd/txt2contincd.cfg`` (Linux),
        ``~/.txt2contincd.cfg`` (Mac), or ``%APPDATA%\txt2contincd\txt2contincd.cfg`` (Windows).
        
        The default preference is equal to the configure file as below::
        
            [default]
            parser = 'parsers.PlainParser'
            loader = 'loaders.PlainLoader'
            using = None
            average = False
            strict = True
            output = 'contin-cd.in'
        
            [experiment]
            number = None
            molecular_weight = None
            concentration = None
            molar_concentration = None
            length = None
        
        I don't use Microsoft Windows so the location of the configure file in Windows
        might be wrong.
        Let me know if there are any mistakes.
        
Keywords: raw text data convert CONTINT
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2.6
Classifier: Programming Language :: Python :: 2.7
