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txt2contincd 0.1.0

Convert raw text data files into a CONTIN-CD input file.

txt2contincd convert raw text data files into a CONTIN-CD input file. It use 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

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.

 
File Type Py Version Uploaded on Size
txt2contincd-0.1.0.tar.gz (md5) Source 2014-05-10 15KB
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