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.
Use pip like:
$ pip install txt2contincdAssume 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 cmThen 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: 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 centimeterYou 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 = NoneI 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.