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68 changes: 43 additions & 25 deletions README.md
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# WISP

WISP is a trajectory analysis tool that calculates and visualizes allosteric pathways.
It is licensed under the Academic Free License 3.0.
For more information, please see http://opensource.org/licenses/AFL-3.0

WISP is distributed in the hope that it will be useful, but WITHOUT ANY
WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See the GNU General Public License for more details.
## Installation

Copyright 2012 Adam VanWart and Jacob D. Durrant.
If you have any questions, comments, or suggestions, please contact durrantj [at] pitt [dot] edu.
First, you must obtain the WISP code from [GitHub](https://github.com/durrantlab/wisp) either by cloning the repository or downloading and extracting as a ZIP file.
Move into the `wisp` directory and run `pip install .`.
This will install the `wisp` Python package in addition to the `wisp` command-line tool.

The latest version of WISP can be downloaded from [http://git.durrantlab.com/jdurrant/wisp](http://git.durrantlab.com/jdurrant/wisp).

If you use WISP in your work, please cite:

> A.T. Van Wart, J.D. Durrant, L. Votapka, R.E. Amaro. Weighted implementation of suboptimal paths (WISP): An optimized algorithm and tool for dynamical network analysis, J. Chem. Theory Comput. 10 (2014) 511-517
TODO: check that the VMD plugin installation works.

## How to Install the VMD WISP Plugin (Linux/Mac)

1. Unzip the file to a directory of your choice using this command: `tar -xzf wisp.tgz <your directory here>`
2. To use the VMD plugin, add these two lines of code to your `.vmdrc` file
1. To use the VMD plugin, add these two lines of code to your `.vmdrc` file
(usually located in your `~/` directory)
- `set auto_path "$auto_path <your directory here>" ; #(NOTE: this may require the full pathname)`
- `vmd_install_extension wisp wisp_tk_cb "Analysis/Wisp"`
3. Now open VMD: Click Extensions > Analysis > WISP
2. Now open VMD: Click Extensions > Analysis > WISP

## How to Use WISP from the Command Line

To learn how to use wisp from the command line, see the example in the
`./example_commandline/` directory. Here is a simple example:

```python
python wisp.py -pdb_trajectory_filename multi_frame_pdb.pdb -source_residues "X_SER_1 X_LEU_4" -sink_residues X_ARG_37`
wisp -pdb_trajectory_filename multi_frame_pdb.pdb -source_residues "X_SER_1 X_LEU_4" -sink_residues X_ARG_37`
```

## Program Output
Expand Down Expand Up @@ -74,7 +60,7 @@ descriptions of each:
can be loaded into WISP for use in subsequent runs with the
`-load_wisp_saved_matrix` and `-wisp_saved_matrix_filename` parameters.
Thus, the matrix needs only to be calculated once for each trajectory,
rather than every time WISP is executed. Use `python wisp.py -help` for more
rather than every time WISP is executed. Use `wisp -help` for more
information.
- `contact_map_matrix.txt`: A human readable representation of the contact
map. If the user wishes to generate their own contact map rather than
Expand All @@ -94,7 +80,7 @@ descriptions of each:

## Parameter Description

`python wisp.py -help` displays the following text:
`wisp -help` displays the following text:

```text
FILE-SYSTEM PARAMETERS
Expand Down Expand Up @@ -259,7 +245,7 @@ Notes:
uniquely identifiable by the combination of its chain, resname, and resid.
Example:
python wisp.py -pdb_trajectory_filename multi_frame_pdb.pdb
wisp -pdb_trajectory_filename multi_frame_pdb.pdb
-node_definition CA -contact_map_distance_limit 4.5
-load_wisp_saved_matrix false -wisp_saved_matrix_filename
matrix.file -desired_number_of_paths 30 -source_residues
Expand All @@ -270,3 +256,35 @@ Example:
-spline_smoothness 0.05 -vmd_resolution 6 -node_sphere_radius
1.0
```

## Deploying

We use [bump-my-version](https://github.com/callowayproject/bump-my-version) to release a new version.
This will create a git tag that is used by [poetry-dynamic-version](https://github.com/mtkennerly/poetry-dynamic-versioning) to generate version strings and update `CHANGELOG.md`.

For example, to bump the `minor` version you would run the following command.

```bash
poetry run bump-my-version bump minor
```

After releasing a new version, you need to push and include all tags.

```bash
git push --follow-tags
```

## Citation

If you use WISP in your work, please cite:

> A.T. Van Wart, J.D. Durrant, L. Votapka, R.E. Amaro. Weighted implementation of suboptimal paths (WISP): An optimized algorithm and tool for dynamical network analysis, J. Chem. Theory Comput. 10 (2014) 511-517
## License

It is licensed under the [Academic Free License 3.0](http://opensource.org/licenses/AFL-3.0).

WISP is distributed in the hope that it will be useful, but WITHOUT ANY
WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See the GNU General Public License for more details.
2 changes: 1 addition & 1 deletion wisp/cli.py
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Expand Up @@ -473,7 +473,7 @@ def get_help(self):
)
logger.info(
wrapper.fill(
'python wisp.py -pdb_trajectory_filename multi_frame_pdb.pdb -node_definition CA -contact_map_distance_limit 4.5 -load_wisp_saved_matrix false -wisp_saved_matrix_filename matrix.file -desired_number_of_paths 30 -source_residues "X_SER_1 X_LEU_4" -sink_residues X_ARG_37 -number_processors 24 -num_frames_to_load_before_processing 96 -seconds_to_wait_before_parallelizing_path_finding 10.0 -shortest_path_radius 0.2 -longest_path_radius 0.05 -spline_smoothness 0.05 -vmd_resolution 6 -node_sphere_radius 1.0'
'wisp -pdb_trajectory_filename multi_frame_pdb.pdb -node_definition CA -contact_map_distance_limit 4.5 -load_wisp_saved_matrix false -wisp_saved_matrix_filename matrix.file -desired_number_of_paths 30 -source_residues "X_SER_1 X_LEU_4" -sink_residues X_ARG_37 -number_processors 24 -num_frames_to_load_before_processing 96 -seconds_to_wait_before_parallelizing_path_finding 10.0 -shortest_path_radius 0.2 -longest_path_radius 0.05 -spline_smoothness 0.05 -vmd_resolution 6 -node_sphere_radius 1.0'
)
)
logger.info("")
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2 changes: 1 addition & 1 deletion wisp/io.py
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Expand Up @@ -50,7 +50,7 @@ def output_directory_info(params):
+ "\n\n"
)
f.write(
'functionalized_matrix_with_contact_map_applied.pickle: A python pickle file that contains the matrix obtained by multiplying a functionalized correlation matrix and a contact map. This file is not human readable but can be loaded into WISP for use in subsequent runs with the -load_wisp_saved_matrix and -wisp_saved_matrix_filename parameters. Thus, the matrix needs only to be calculated once for each trajectory, rather than every time WISP is executed. Use "python wisp.py -help" for more information.'
'functionalized_matrix_with_contact_map_applied.pickle: A python pickle file that contains the matrix obtained by multiplying a functionalized correlation matrix and a contact map. This file is not human readable but can be loaded into WISP for use in subsequent runs with the -load_wisp_saved_matrix and -wisp_saved_matrix_filename parameters. Thus, the matrix needs only to be calculated once for each trajectory, rather than every time WISP is executed. Use "wisp -help" for more information.'
+ "\n\n"
)
f.write(
Expand Down

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