This program is a toolbox for computing spectra of the FMO complex.
If you have poetry installed, just download the source code for this directory, navigate to it in your terminal, and do the following:
$ poetry build
$ python -m pip install --user dist/fmo_analysis-X.Y.Z-py3-none-any.whl
where X.Y.Z is the version number of the package.
You can alternatively install the package straight from GitHub using pip:
$ python -m pip install --user git+git@github.com:savikhin-lab/fmo_analysis.git
You can see which commands are available from the command line:
$ fmo-analysis --help
Usage: fmo-analysis [OPTIONS] COMMAND [ARGS]...
Options:
--version Show the version and exit.
--help Show this message and exit.
Commands:
align Rotate the structures for the best alignment between...
conf2spec Generate spectra from one or more 'conf*.csv' files.
default-config Prints the default configuration for analysis.
pigviz Plot the positions of all pigments to inspect alignment.
You can get further help for a command via fmo-analysis <command> --help, which will display all of the options and flags available to the command:
Usage: fmo-analysis conf2spec [OPTIONS]
Generate spectra from one or more 'conf*.csv' files.
Options:
-c, --config FILENAME A config file used to override default values
in the analysis. See 'default-config' for the
default values.
-i, --input-dir DIRECTORY The directory containing the 'conf*.csv'
files. [required]
-o, --output-dir DIRECTORY The directory in which the analysis results
will be stored. [required]
--overwrite If specified, overwrite the data in the output
directory.
-b, --bandwidth FLOAT The bandwidth for each transition.
-d, --delete-pigment INTEGER The pigment to delete (0 means none).
-f, --save-figs Save intermediate spectra. An average spectrum
is still saved when this flag is not
specified.
-s, --save-intermediate Save intermediate results as CSVs
-e, --empirical The Hamiltonian is empirical, so don't apply
diagonal shifts.
-n, --normalize Normalize the total dipole strength to 1
--help Show this message and exit.
The most useful modules in this package are util and exciton.
This module handles finding, loading, and parsing of conf*.csv files. There are also facilities for saving a Hamiltonian and a set of pigments formatted as a conf file. This is useful for instance if you've shifted elements of a Hamiltonian and want to save the shifted conf for later use.
This module also contains the set of default configuration options for computing spectra in a dictionary called util.DEFAULT_CONFIG. However, all of the functions that compute spectra require a util.Config object. What's the difference? A util.Config object is read-only, which prevents you from accidentally changing the config while you're computing spectra. To change the configuration you can make a copy of util.DEFAULT_CONFIG, set the dictionary entries that you care about, and then create your util.Config object.
Note that util.DEFAULT_CONFIG includes a constant diagonal shift because the data from YB needs a shift in order to be at the correct wavelength. The empirical Hamiltonians don't need this shift, so it's important to set the shift_diag option to 0 when computing spectra from empirical Hamiltonians.
This module handles computing spectra. In order to compute spectra, you first need a configuration (util.Config). This object sets the bandwidth, which pigment to delete (if any), etc.
Licensed under either of
- Apache License, Version 2.0, (LICENSE-APACHE or http://www.apache.org/licenses/LICENSE-2.0)
- MIT license (LICENSE-MIT or http://opensource.org/licenses/MIT)
at your option.
Unless you explicitly state otherwise, any contribution intentionally submitted for inclusion in the work by you, as defined in the Apache-2.0 license, shall be dual licensed as above, without any additional terms or conditions.