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

Project description

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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.

Project details


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This version
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0.1.0

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