Metadata-Version: 2.2
Name: fpocketr
Version: 1.2.1
Summary: Find, characterize, and visualize drug-like pockets in RNA structures.
Author-email: "Seth D. Veenbaas" <sdveenbaas@gmail.com>
License: MIT License
        
        Copyright (c) 2023 Seth D. Veenbaas and the Weeks Lab at the University of North Carolina at Chapel Hill
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
        copies of the Software, and to permit persons to whom the Software is
        furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all
        copies or substantial portions of the Software.
        
        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
        SOFTWARE.
        
Project-URL: Homepage, https://github.com/Weeks-UNC/fpocketR
Project-URL: Issues, https://github.com/Weeks-UNC/fpocketR/issues
Classifier: Programming Language :: Python :: 3
Classifier: Operating System :: OS Independent
Requires-Python: >=3.11
Description-Content-Type: text/markdown
License-File: LICENSE.txt
Requires-Dist: fpocket==4.0.3
Requires-Dist: pymol-open-source==2.5.0
Requires-Dist: prody==2.4.0
Requires-Dist: pandas==2.2.1
Requires-Dist: rdkit==2023.09.6
Requires-Dist: seaborn==0.13.2
Requires-Dist: trimesh==4.2.0

# fpocketR
fpocketR is a modified version of [fpocket 4.0](https://github.com/Discngine/fpocket) and is optimized for finding, characterizing, and visulizing drug-like RNA-ligand binding pockets.

## Installation with Conda

### Windows Users: guide to install WSL and Ubuntu

1. fpocketR requires a Unix/Linux to run properly, this means that Windows users need to activate the Windows Subsystem for Linux (WSL). 

   * [Guide to installing WSL and Ubuntu](https://www.freecodecamp.org/news/how-to-install-wsl2-windows-subsystem-for-linux-2-on-windows-10/)

### Guide to install conda

2. Follow [guide](https://conda.io/projects/conda/en/latest/user-guide/install/index.html) to install conda.

   * **Windows WSL users:** Use [Linux installation guide](https://conda.io/projects/conda/en/latest/user-guide/install/linux.html).

### Install fpocketR

**NOTE for MacOS users**: fpocketR is not compatible with arm-based M1 or M2 processors (only intel (x86) processors).

3. Open your terminal and navigate to the directory where you would like to install the fpocketR package (optional).

        cd <path-to-GitHub-reposities>

    * **Tip for new Windows WSL users:** You can navigate to your Windows file system in the WSL command line by using the following command:

          cd /mnt/c/Users/<your-user-name>


4. Clone the RNAvigate and fpocketR GitHub repositories.

        git clone https://github.com/Weeks-UNC/fpocketR.git

5. Create fpocketR conda environment and install fpocketR and RNAvigate.

        cd fpocketR
        conda env create --file environment.yml
        conda activate fpocketR
        conda develop .

## Demo / Tutorial

[Demonstration of fpocketR usage](https://github.com/Weeks-UNC/fpocketR/blob/main/Demo/fpocketR_demo.md)

## Usage

| Input options                 | Description                                                                                      |
| :---------------------------- | :----------------------------------------------------------------------------------------------- |
| -pdb, --pdb STRING (Required) | Specify a path to a .pdb/.cif file, or a 4 charater PDB indentification code.                    |
| -ss, --ss STRING              | Specify an .nsd file or other secondary structure file to generate a secondary structure figure. |



| fpocket parameter options | Description                                                                                             |
| :------------------------ | :------------------------------------------------------------------------------------------------------ |
| -m, --m FLOAT             | Sets fpocket -m flag. Minimum radius for an a-sphere. (Default: 3.0)                                    |
| -M, --M FLOAT             | Sets fpocket -M flag. Maximium radius for an a-sphere. (Default: 5.7)                                   |
| -i, --i INT               | Sets fpocket -i flag. Minimum number of a-spheres per pocket. (Default: 42)                             |
| -D, --D FLOAT             | Sets fpocket -D flag. alpha sphere clustering distance for forming pockets. (Default: 1.65)             |
| -A, --A INT               | Sets fpocket -A flag. Number of electronegative atoms required to define a polar a-sphere (Deafult: 3). |
| -p, --p FLOAT             | Sets fpocket -p flag. Maximum ratio of apolar a-spheres. (Default: 0)                                   |

| Output options    | Description                                                                   |
| :---------------- | :---------------------------------------------------------------------------- |
| -o, --out STRING  | Path to output parent directory. (Default: fpocketR_out_<fpocket parameters>) |
| -n, --name STRING | Output filename prefix and output subdirectory name. (Default: None)          |
| -y, --yes BOOLEAN | Overwrites output files and directories with same name. (Default: False)      |

| Analysis options           | Description                                                                                                              |
| :------------------------- | :----------------------------------------------------------------------------------------------------------------------- |
| -s, --state INT            | PDB states/model for analysis. Set to 0 for all. (Default: None)                                                         |
| -c, --chain STING          | Chain(s) IDs conatining RNA (case sensitive). List upto 2 chains seperated by a comma (eg. A,B). (Default: A)            |
| -l, --ligand STRING        | PDB ligand identification code (≤ 3 characters).                                                                         |
| -lc, --ligandchain STRING  | Chain containing the ligand of interest. (Default: <first RNA chain>)                                                    |
| -nt, --knownnt PARSE_INT   | List residue indexes of nts in known pocket (e.g. 1,2,3). Known pockets must contact ≥ 3 of the residues. (None).         |
| -off, -offset INT          | Offset between the RNA sequence and PDB structure. offset  = starting index of the PDB sequence - 1 (Default: automatic) |
| -qf, --qualityfilter FLOAT | Minimum fpocket score for a pocket to pass the quality filter. (Default: 0.0)                                            |

| Figure settings               | Description                                                                                 |
| :---------------------------- | :------------------------------------------------------------------------------------------ |
| -dpi, --dpi INT               | Specify 3D figure resolution (dots per linear inch). (Default: 300)                         |
| -zoom, --zoom INT             | Specify zoom buffer distance (Å) to set the feild of view for 3D figures. (Default: 10)     |
| -cp, --connectpocket BOOLEAN  | Visually connects pockets in 2D figures. (Default: False)                                   |
| -al, --alignligand BOOLEAN    | Align output structures to input structure. Useful for multistate analysis. (Default: True) |


