Wiki
Version 5 (Carles Marti, 10/02/2021 15:37)
| 1 | 5 | Carles Marti | DockOnSurf |
|---|---|---|---|
| 2 | 5 | Carles Marti | ========== |
| 3 | 1 | Carles Marti | |
| 4 | 5 | Carles Marti | DockOnSurf is a program to automatically find the most stable geometry for molecules |
| 5 | 5 | Carles Marti | on surfaces. |
| 6 | 5 | Carles Marti | |
| 7 | 5 | Carles Marti | webpage: https://forge.cbp.ens-lyon.fr/redmine/projects/dockonsurf |
| 8 | 5 | Carles Marti | |
| 9 | 5 | Carles Marti | |
| 10 | 5 | Carles Marti | Requirements: |
| 11 | 5 | Carles Marti | ------------- |
| 12 | 5 | Carles Marti | |
| 13 | 5 | Carles Marti | * [Python](http://www.python.org/) >= 3.6 |
| 14 | 5 | Carles Marti | * [Matplotlib](https://matplotlib.org) ~= 3.2.1 |
| 15 | 5 | Carles Marti | * [NumPy](http://docs.scipy.org/doc/numpy/reference/) >= 1.16.6 |
| 16 | 5 | Carles Marti | * [RDKit](https://rdkit.org/) ~= 2019.9.3 |
| 17 | 5 | Carles Marti | * [scikit-learn](https://scikit-learn.org/) ~= 0.23.1 |
| 18 | 5 | Carles Marti | * [HDBSCAN](https://hdbscan.readthedocs.io/en/latest/basic_hdbscan.html) ~= 0.8.26 |
| 19 | 5 | Carles Marti | * [ASE](https://wiki.fysik.dtu.dk/ase/) ~= 3.19.1 |
| 20 | 5 | Carles Marti | * [NetworkX](https://networkx.org/) >= 2.4 |
| 21 | 5 | Carles Marti | * [python-daemon](https://pypi.org/project/python-daemon/) ~= 2.2.4 |
| 22 | 5 | Carles Marti | * [pymatgen](https://pymatgen.org/) ~= 2020.11.11 |
| 23 | 5 | Carles Marti | * [pycp2k](https://github.com/SINGROUP/pycp2k) ~= 0.2.2 |
| 24 | 5 | Carles Marti | |
| 25 | 5 | Carles Marti | |
| 26 | 5 | Carles Marti | Installation: |
| 27 | 5 | Carles Marti | ------------- |
| 28 | 5 | Carles Marti | Download the ``dockonsurf`` directory and place it somwhere in your computer: |
| 29 | 5 | Carles Marti | ``` |
| 30 | 5 | Carles Marti | git clone http://forge.cbp.ens-lyon.fr/git/dockonsurf |
| 31 | 5 | Carles Marti | ``` |
| 32 | 5 | Carles Marti | |
| 33 | 5 | Carles Marti | Assuming you download it in your ``HOME``directory, add ``$HOME/dockonsurf`` to your ``PATH`` variable (assuming ``~/dockonsurf`` |
| 34 | 5 | Carles Marti | is where your DockOnSurf folder is) and ensure all python libraries listed |
| 35 | 5 | Carles Marti | in Requirements are installed and available. |
| 36 | 5 | Carles Marti | |
| 37 | 5 | Carles Marti | |
| 38 | 5 | Carles Marti | Testing |
| 39 | 5 | Carles Marti | ------- |
| 40 | 5 | Carles Marti | |
| 41 | 5 | Carles Marti | (To be done) |
| 42 | 5 | Carles Marti | |
| 43 | 5 | Carles Marti | |
| 44 | 5 | Carles Marti | Contact |
| 45 | 5 | Carles Marti | ------- |
| 46 | 5 | Carles Marti | |
| 47 | 5 | Carles Marti | Submit an issue in: |
| 48 | 5 | Carles Marti | https://forge.cbp.ens-lyon.fr/redmine/projects/dockonsurf/issues |
| 49 | 5 | Carles Marti | |
| 50 | 5 | Carles Marti | Please send us bug-reports, patches, code, ideas and questions. |
| 51 | 5 | Carles Marti | |
| 52 | 5 | Carles Marti | |
| 53 | 5 | Carles Marti | Example |
| 54 | 5 | Carles Marti | ------- |
| 55 | 5 | Carles Marti | |
| 56 | 5 | Carles Marti | (To be done) |