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1 | 1 | # Change Log |
2 | 2 | All notable changes to this repository will be documented in this file. |
3 | 3 |
|
4 | | -## [1.2.1] - 2023-08-12 |
5 | | -### Added |
6 | | -+ [basic_molecular_docking](https://github.com/RyanZR/labodock/blob/main/notebooks/basic_molecular_docking.ipynb) MAJOR Added `--cpu` parameter in %vina |
7 | | -+ [virtual_screening](https://github.com/RyanZR/labodock/blob/main/notebooks/virtual_screening.ipynb) MAJOR Added `--cpu` parameter in %vina |
| 4 | +<br/> |
8 | 5 |
|
9 | | -### Changed |
10 | | -+ [basic_molecular_docking](https://github.com/RyanZR/labodock/blob/main/notebooks/basic_molecular_docking.ipynb) MAJOR Upgraded packages: py3Dmol 2.0.3, rdkit-pypi 2022.9.5, biopython 1.80, openbabel 3.1.1, zlib 1.2.13 |
11 | | -+ [basic_molecular_docking](https://github.com/RyanZR/labodock/blob/main/notebooks/basic_molecular_docking.ipynb) MINOR Renamed LABOGRID to [LaBOX](https://github.com/RyanZR/LaBOX) |
12 | | -+ [virtual_screening](https://github.com/RyanZR/labodock/blob/main/notebooks/virtual_screening.ipynb) MAJOR Upgraded packages: py3Dmol 2.0.3, rdkit-pypi 2022.9.5, biopython 1.80, openbabel 3.1.1, zlib 1.2.13 |
13 | | -+ [virtual_screening](https://github.com/RyanZR/labodock/blob/main/notebooks/virtual_screening.ipynb) MINOR Renamed LABOGRID to [LaBOX](https://github.com/RyanZR/LaBOX) |
| 6 | +## [1.2.2] - 2023-08-14 |
| 7 | +This update applies to both [basic_molecular_docking](https://github.com/RyanZR/labodock/blob/main/notebooks/basic_molecular_docking.ipynb) and [virtual_screening](https://github.com/RyanZR/labodock/blob/main/notebooks/virtual_screening.ipynb). |
| 8 | +### Major Changes |
| 9 | ++ 🐛 Corrected `py3Dmol.view()` function call in all `VIEW_****()` functions by providing valid width and height parameters. |
| 10 | ++ 🐛 Changed initial `count` to `0` in all `VIEW_****()` functions as per above correction. |
| 11 | +### Minor Changes |
| 12 | ++ ⚙️ Renamed `labogrid()` function to `labox()` as per version 1.2.1. |
| 13 | ++ ⚙️ Changed merging DataFrame method from `append()` to `concat()` in `interaction_profiler()` and "Rank docking scores" section*. |
| 14 | ++ ⚙️ Rewritten [CHANGELOG.md](https://github.com/RyanZR/labodock/blob/main/CHANGELOG.md) |
14 | 15 |
|
15 | | -### Fixed |
16 | | -+ [basic_molecular_docking](https://github.com/RyanZR/labodock/blob/main/notebooks/basic_molecular_docking.ipynb) MAJOR Fixed incomplete visualisation of protein-ligand interactions in `VIEW_PILE()` |
17 | | -+ [virtual_screening](https://github.com/RyanZR/labodock/blob/main/notebooks/virtual_screening.ipynb) MAJOR Fixed incomplete visualisation of protein-ligand interactions in `VIEW_PILE()` |
| 16 | +*\* For [virtual_screening](https://github.com/RyanZR/labodock/blob/main/notebooks/virtual_screening.ipynb) only.* |
18 | 17 |
|
19 | | -## [1.2.0] - 2023-02-12 |
20 | | -### Added |
21 | | -+ [basic_molecular_docking](https://github.com/RyanZR/labodock/blob/main/notebooks/basic_molecular_docking.ipynb) MAJOR Added 5 methods for defining grid box |
22 | | -+ [basic_molecular_docking](https://github.com/RyanZR/labodock/blob/main/notebooks/basic_molecular_docking.ipynb) MINOR Added `showHs` argument in `VIEW_LIG()` |
23 | | -+ [virtual_screening](https://github.com/RyanZR/labodock/blob/main/notebooks/virtual_screening.ipynb) MAJOR Added 5 methods for defining grid box |
24 | | -+ [virtual_screening](https://github.com/RyanZR/labodock/blob/main/notebooks/virtual_screening.ipynb) MINOR Added `showHs` argument in `VIEW_LIG()` |
| 18 | +<br/> |
25 | 19 |
|
26 | | -### Changed |
27 | | -+ [basic_molecular_docking](https://github.com/RyanZR/labodock/blob/main/notebooks/basic_molecular_docking.ipynb) MINOR Removed `showBestPose` argument in `VIEW_PILE()` |
28 | | -+ [basic_molecular_docking](https://github.com/RyanZR/labodock/blob/main/notebooks/basic_molecular_docking.ipynb) MINOR Removed `AllChem.MMFFOptimizeMolecule()` in `VIEW_LIG()` |
29 | | -+ [virtual_screening](https://github.com/RyanZR/labodock/blob/main/notebooks/virtual_screening.ipynb) MINOR Removed `AllChem.MMFFOptimizeMolecule()` in `VIEW_LIG()` |
| 20 | +## [1.2.1] - 2023-08-12 |
| 21 | +This update applies to both [basic_molecular_docking](https://github.com/RyanZR/labodock/blob/main/notebooks/basic_molecular_docking.ipynb) and [virtual_screening](https://github.com/RyanZR/labodock/blob/main/notebooks/virtual_screening.ipynb). |
| 22 | +### Major Changes |
| 23 | ++ ⬆️ Upgraded packages to support python 3.10: py3Dmol 2.0.3, rdkit-pypi 2022.9.5, biopython 1.80, openbabel 3.1.1, zlib 1.2.13. |
| 24 | ++ ➕ Added `--cpu` parameter in `%vina` for performance improvement. |
| 25 | ++ ➕ Added `os.cpu_count()` to determine number of cpu cores available for `--cpu` usage. |
| 26 | ++ 🐛 Fixed incomplete visualisation of protein-ligand interactions in `VIEW_PILE()`. |
| 27 | +### Minor Changes |
| 28 | ++ ⚙️ Renamed **`LABOGRID`** to **[`LaBOX`](https://github.com/RyanZR/LaBOX)**. |
30 | 29 |
|
31 | | -### Fixed |
32 | | -+ [basic_molecular_docking](https://github.com/RyanZR/labodock/blob/main/notebooks/basic_molecular_docking.ipynb) MINOR Fixed spelling mistake in "*Display 3D binding mode*" section |
33 | | -+ [virtual_screening](https://github.com/RyanZR/labodock/blob/main/notebooks/virtual_screening.ipynb) MINOR Fixed spelling mistake in "*Display 3D binding mode*" section |
| 30 | +<br/> |
34 | 31 |
|
35 | | -## [1.0.0] - 2023-02-08 |
36 | | -### Added |
37 | | -+ [basic_molecular_docking](https://github.com/RyanZR/labodock/blob/main/notebooks/basic_molecular_docking.ipynb) MAJOR Added into 📁 notebooks. |
38 | | -+ [virtual_screening](https://github.com/RyanZR/labodock/blob/main/notebooks/virtual_screening.ipynb) MAJOR Added into 📁 notebooks. |
39 | | - |
40 | | -### Changed |
41 | | -+ [🍊MOUNTAIN_V2](https://github.com/RyanZR/labodock/blob/main/deprecated/%F0%9F%8D%8AMOUNTAIN_V2.ipynb) MAJOR No longer support and superseded by [basic_molecular_docking.ipynb](https://github.com/RyanZR/labodock/blob/main/notebooks/basic_molecular_docking.ipynb). |
42 | | -+ [🍊UNION_V2](https://github.com/RyanZR/labodock/blob/main/deprecated/%F0%9F%8D%8AUNION_V2.ipynb) MAJOR No longer support and superseded by [virtual_screening.ipynb](https://github.com/RyanZR/labodock/blob/main/notebooks/virtual_screening.ipynb). |
43 | | -+ [🍊PLIA_V2](https://github.com/RyanZR/labodock/blob/main/deprecated/%F0%9F%8D%8APLIA_V2.ipynb) MAJOR No longer support but integrated into respective notebooks |
| 32 | +## [1.2.0] - 2023-02-12 |
| 33 | +This update primarily focuses on improvements to [virtual_screening](https://github.com/RyanZR/labodock/blob/main/notebooks/virtual_screening.ipynb). |
| 34 | +### Major Changes |
| 35 | ++ ➕ Added 5 new methods for defining grid box. |
| 36 | ++ ➕ Added `showHs` argument in `VIEW_LIG()`. |
| 37 | +### Minor Changes |
| 38 | ++ ⚙️ Corrected a spelling error in the "Display 3D binding mode" section. |
| 39 | ++ ❌ Removed `AllChem.MMFFOptimizeMolecule()` in `VIEW_LIG()`. |
| 40 | + |
| 41 | +<br/> |
| 42 | + |
| 43 | +## [1.1.0] - 2023-02-12 |
| 44 | +This update primarily focuses on improvements to [basic_molecular_docking](https://github.com/RyanZR/labodock/blob/main/notebooks/basic_molecular_docking.ipynb). |
| 45 | +### Major Changes |
| 46 | ++ ➕ Added 5 new methods for defining grid box. |
| 47 | ++ ➕ Added `showHs` argument in `VIEW_LIG()`. |
| 48 | +### Minor Changes |
| 49 | ++ ⚙️ Corrected a spelling error in the "Display 3D binding mode" section. |
| 50 | ++ ❌ Removed `AllChem.MMFFOptimizeMolecule()` in `VIEW_LIG()`. |
| 51 | ++ ❌ Removed `showBestPose` argument in `VIEW_PILE()`. |
| 52 | + |
| 53 | +<br/> |
44 | 54 |
|
45 | | -### Fixed |
46 | | -+ [basic_molecular_docking](https://github.com/RyanZR/labodock/blob/main/notebooks/basic_molecular_docking.ipynb) MINOR Fixed bug in `VIEW_PILE()`. |
| 55 | +## [1.0.0] - 2023-02-08 |
| 56 | +### Major Changes |
| 57 | ++ ➕ Added [basic_molecular_docking](https://github.com/RyanZR/labodock/blob/main/notebooks/basic_molecular_docking.ipynb) to supersede [🍊MOUNTAIN_V2](https://github.com/RyanZR/labodock/blob/main/deprecated/%F0%9F%8D%8AMOUNTAIN_V2.ipynb). |
| 58 | ++ ➕ Added [virtual_screening](https://github.com/RyanZR/labodock/blob/main/notebooks/virtual_screening.ipynb) to supersede [🍊UNION_V2](https://github.com/RyanZR/labodock/blob/main/deprecated/%F0%9F%8D%8AUNION_V2.ipynb). |
| 59 | ++ ➕ Integrated protein-ligand interaction analysis into [basic_molecular_docking](https://github.com/RyanZR/labodock/blob/main/notebooks/basic_molecular_docking.ipynb) and [virtual_screening](https://github.com/RyanZR/labodock/blob/main/notebooks/virtual_screening.ipynb). |
| 60 | ++ 🚫 Deprecated [🍊MOUNTAIN_V2](https://github.com/RyanZR/labodock/blob/main/deprecated/%F0%9F%8D%8AMOUNTAIN_V2.ipynb), [🍊UNION_V2](https://github.com/RyanZR/labodock/blob/main/deprecated/%F0%9F%8D%8AUNION_V2.ipynb) and [🍊UNION_V2](https://github.com/RyanZR/labodock/blob/main/deprecated/%F0%9F%8D%8AUNION_V2.ipynb). |
| 61 | +### Minor Changes |
| 62 | ++ 🐛 Fixed bug in `VIEW_PILE()` for [basic_molecular_docking](https://github.com/RyanZR/labodock/blob/main/notebooks/basic_molecular_docking.ipynb). |
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