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