PLINDER

https://plinder-org.github.io/plinder/
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### Install Documentation Dependencies

Source: https://plinder-org.github.io/plinder/contribution/documentation.html

Install the necessary requirements to build the documentation. This includes the core package with its documentation extras.

```bash
pip install -e ".[docs]"
```

--------------------------------

### Install Plinder Package

Source: https://plinder-org.github.io/plinder/tutorial/api.html

Install the plinder package using pip. This is the first step to using the library.

```bash
pip install plinder

```

--------------------------------

### Ligand Data Table Example

Source: https://plinder-org.github.io/plinder/dataset.html

Shows an example of the 'ligands_per_system.parquet' table structure, linking PLINDER systems to their ligand details.

```python
pdb_id              system_id                      ligand_rdkit_canonical_smiles ligand_ccd_code                   ligand_id                    inchikeys
0   7o00  7o00__1__1.A_1.B__1.D  CC(=O)N[C@H]1CO[C@H](CO)[C@@H](OC2O[C@H](CO)[C...         HSR-HSR  7o00__1__1.A_1.B__1.D__1.D  JHPFQHGUNGJQIZ-BQBDUENHSA-N
1   7o00  7o00__1__1.A_1.B__1.E  CC(=O)N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)O[C@H]1O             HSR  7o00__1__1.A_1.B__1.E__1.E  OVRNDRQMDRJTHS-FMDGEEDCSA-N
2   7o04      7o04__1__1.A__1.G                        CNCc1cc([N+](=O)[O-])ccc1Cl             4AV      7o04__1__1.A__1.G__1.G  YRTNCUPHKWUHMQ-UHFFFAOYSA-N
3   7o08      7o08__1__1.A__1.C  CC1(C)CCN(Cc2ccc(NCC3(O)CCN(c4cc(NCc5ccccc5)nc...             UXE      7o08__1__1.A__1.C__1.C  GTLDMCHZRAFXCB-UHFFFAOYSA-N
4   7o09      7o09__1__1.A__1.C  CC1(C)CCN(Cc2ccc(N3CCOC4(CCN(c5cc(NCc6ccccc6)n...             UXK      7o09__1__1.A__1.C__1.C  RJEWLHZZXYDBNT-UHFFFAOYSA-N
```

--------------------------------

### Example Input Ligand Coordinates

Source: https://plinder-org.github.io/plinder/examples/4_align_mask_crop.html

Shows an example of 3D coordinates for an input ligand conformer after atom order alignment.

```text
array([[[-0.40725066, -1.47748498,  0.185955  ],
        [ 1.0643663 , -1.31706023,  0.33981289],
        [ 1.51382048, -0.06269305,  1.01334722],
        [ 0.43775803,  1.01633012,  1.02753193],
        [-0.32555831,  0.7522505 , -0.26447634],
        [-1.0585462 ,  1.94667957, -0.76103278],
        [ 1.730437  , -1.48907463, -0.8864381 ],
        [ 2.0006517 , -0.2496771 ,  2.29537409],
        [-0.4092932 ,  0.72044372,  2.10546384],
        [-1.13277182, -0.33267599,  0.01577224],
        [-2.16322047, -1.83693988, -2.49576751],
        [-0.84673963, -2.66539344, -1.30355921]]])
```

--------------------------------

### Example Resolved Ligand Coordinates

Source: https://plinder-org.github.io/plinder/examples/4_align_mask_crop.html

Shows an example of 3D coordinates for a resolved ligand molecule after atom order alignment.

```text
array([[[48.954, 28.186, 62.068],
        [48.681, 29.643, 61.777],
        [48.556, 29.933, 60.282],
        [47.499, 28.988, 59.699],
        [47.948, 27.56 , 59.939],
        [46.992, 26.503, 59.374],
        [49.72 , 30.41 , 62.383],
        [48.255, 31.352, 60.148],
        [46.262, 29.193, 60.366],
        [48.031, 27.383, 61.339],
        [50.647, 25.895, 62.426],
        [50.853, 27.716, 61.696]]])
```

--------------------------------

### Example Parquet File Columns

Source: https://plinder-org.github.io/plinder/dataset.html

This example displays the columns typically found in the parquet files within the protein similarity dataset. It includes query and target system identifiers, mapping details, similarity metrics, and the source database.

```text
                    query_system target_system protein_mapping protein_mapper  ...    source                            metric  mapping search_db
1070886    1b5d__1__1.A_1.B__1.D        1b49_A         1.A:0.A       foldseek  ...    mmseqs         protein_qcov_weighted_max  1.A:0.A       apo
1070887    1b5d__1__1.A_1.B__1.D        1b49_A         1.A:0.A       foldseek  ...    mmseqs                  protein_qcov_max  1.A:0.A       apo
1070888    1b5d__1__1.A_1.B__1.D        1b49_A         1.A:0.A       foldseek  ...      both       protein_fident_weighted_max  1.A:0.A       apo
1070889    1b5d__1__1.A_1.B__1.D        1b49_A         1.A:0.A       foldseek  ...      both                protein_fident_max  1.A:0.A       apo
1070890    1b5d__1__1.A_1.B__1.D        1b49_A         1.A:0.A       foldseek  ...    mmseqs  protein_fident_qcov_weighted_max  1.A:0.A       apo
...                          ...           ...             ...            ...  ...       ...                               ...      ...       ...
213471528      7eek__1__1.A__1.I        1uor_A         1.A:0.A       foldseek  ...  foldseek    protein_lddt_qcov_weighted_max  1.A:0.A       apo
213471529      7eek__1__1.A__1.I        1uor_A         1.A:0.A       foldseek  ...  foldseek             protein_lddt_qcov_max  1.A:0.A       apo
213471536      7eek__1__1.A__1.I        1uor_A         1.A:0.A       foldseek  ...  foldseek                       pocket_lddt     None       apo
213471540      7eek__1__1.A__1.I        6zl1_A         1.A:0.A       foldseek  ...  foldseek                       pocket_lddt     None       apo
213471541      7eek__1__1.A__1.I        6zl1_B         1.A:0.B       foldseek  ...  foldseek                       pocket_lddt     None       apo


```

--------------------------------

### Ligand Similarity Scores Table Example

Source: https://plinder-org.github.io/plinder/dataset.html

Presents an example of the 'ligand_scores' table format, showing query and target ligand IDs along with their maximum Tanimoto similarity.

```python
   query_ligand_id  target_ligand_id  tanimoto_similarity_max
0            35300              6943                      100
1            35300             35300                      100
2            35300             13911                       94
3            35300             44243                       90
4            35300             24003                       90
```

--------------------------------

### Install Data Requirements

Source: https://plinder-org.github.io/plinder/contribution/development.html

Install additional dependencies for the plinder.data subpackage using pip. This is necessary for Linux environments.

```bash
$ pip install -r requirements_data.txt

```

--------------------------------

### Enable Pre-commit Hooks

Source: https://plinder-org.github.io/plinder/contribution/development.html

Install pre-commit hooks to automatically run code quality checks, mirroring the CI process.

```bash
$ pre-commit install

```

--------------------------------

### Example Atom Order Stacks

Source: https://plinder-org.github.io/plinder/examples/4_align_mask_crop.html

Illustrates the format of atom order stacks, showing reordering of template and holo atom indices.

```text
(array([[ 2, 10,  8,  6,  4,  5, 11,  9,  7,  3,  0,  1]]),
 array([[ 0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11]]))
```

--------------------------------

### Directory Structure Example

Source: https://plinder-org.github.io/plinder/dataset.html

Illustrates the subdirectory structure within the 'dbs/' directory, containing CSV files with PDB IDs.

```bash
|-- subdbs
|   |-- apo.csv
|   |-- holo.csv
|   |-- pred.csv
```

--------------------------------

### Import SplitPropertiesPlotter

Source: https://plinder-org.github.io/plinder/examples/6_custom_split.html

Import the necessary class for plotting split properties. Ensure plinder is installed.

```python
from plinder.core.split.plot import SplitPropertiesPlotter
```

--------------------------------

### Example output of dataset statistics

Source: https://plinder-org.github.io/plinder/examples/2_query_filter_index.html

Example output showing the counts of ligand chains, systems, biounits, and PDB IDs in the PLINDEX dataset.

```text
Number of ligand chains: 419538
Number of systems: 309972
Number of biounits: 108206
Number of PDB IDs: 77474
```

--------------------------------

### Clone Plinder Repository

Source: https://plinder-org.github.io/plinder/contribution/development.html

Clone the official GitHub repository to start development.

```bash
$ git clone https://github.com/plinder-org/plinder.git

```

--------------------------------

### Get Ligand SDF and SMILES Paths

Source: https://plinder-org.github.io/plinder/tutorial/api.html

Access the file paths for ligand SDF and SMILES strings associated with the system. Requires the PlinderSystem object.

```python
print(plinder_system.ligand_sdfs)
print(plinder_system.smiles)
```

```text
{'1.W': '/home/runner/.local/share/plinder/2024-06/tutorial/systems/4agi__1__1.C__1.W/ligand_files/1.W.sdf'}
{'1.W': 'C[Se][C@@H]1O[C@@H](C)[C@@H](O)[C@@H](O)[C@@H]1O'}
```

--------------------------------

### Get Configuration

Source: https://plinder-org.github.io/plinder/tutorial/api.html

Retrieves the current Plinder configuration, allowing verification of local and remote data paths.

```APIDOC
## get_config()

### Description
Accesses the PLINDER global configuration to check settings like local and remote data paths.

### Method
`plinder.core.get_config()`

### Parameters
None

### Response
- **cfg** (object) - An object containing configuration details, including `data.plinder_dir` and `data.plinder_remote`.

### Request Example
```python
import plinder.core

cfg = plinder.core.get_config()
print(f"local cache directory: {cfg.data.plinder_dir}")
print(f"remote data directory: {cfg.data.plinder_remote}")
```

### Response Example
```
local cache directory: /home/runner/.local/share/plinder/2024-06/tutorial
remote data directory: gs://plinder/2024-06/tutorial
```
```

--------------------------------

### Configure Environment Variables for Plinder

Source: https://plinder-org.github.io/plinder/tutorial/api.html

Set environment variables to specify the release and iteration of the Plinder dataset. This example uses a tutorial dataset.

```bash
%env PLINDER_LOG_LEVEL=0
%env PLINDER_ITERATION=tutorial

```

```bash
env: PLINDER_LOG_LEVEL=0
env: PLINDER_ITERATION=tutorial

```

--------------------------------

### Get Receptor Structure and Sequence Paths

Source: https://plinder-org.github.io/plinder/tutorial/api.html

Retrieve file paths for the receptor PDB, CIF structures, and sequences. Requires the PlinderSystem object.

```python
print(plinder_system.receptor_pdb)
print(plinder_system.receptor_cif)
print(plinder_system.sequences)
```

```text
/home/runner/.local/share/plinder/2024-06/tutorial/systems/4agi__1__1.C__1.W/receptor.pdb
/home/runner/.local/share/plinder/2024-06/tutorial/systems/4agi__1__1.C__1.W/receptor.cif
{'1.C': 'MSTPGAQQVLFRTGIAAVNSTNHLRVYFQDVYGSIRESLYEGSWANGTEKNVIGNAKLGSPVAATSKELKHIRVYTLTEGNTLQEFAYDSGTGWYNGGLGGAKFQVAPYSXIAAVFLAGTDALQLRIYAQKPDNTIQEYMWNGDGWKEGTNLGGALPGTGIGATSFRYTDYNGPSIRIWFQTDDLKLVQRAYDPHKGWYPDLVTIFDRAPPRTAIAATSFGAGNSSIYMRIYFVNSDNTIWQVCWDHGKGYHDKGTITPVIQGSEVAIISWGSFANNGPDLRLYFQNGTYISAVSEWVWNRAHGSQLGRSALPPA'}
```

--------------------------------

### Access Receptor FASTA and Sequences

Source: https://plinder-org.github.io/plinder/examples/3_access_system_files.html

Get the file path for the receptor's FASTA sequence and the dictionary of canonical sequences for protein chains.

```python
plinder_system.sequences_fasta, plinder_system.sequences
```

```python
('/home/runner/.local/share/plinder/2024-06/v2/systems/4agi__1__1.C__1.W/sequences.fasta',
 {'1.C': 'MSTPGAQQVLFRTGIAAVNSTNHLRVYFQDVYGSIRESLYEGSWANGTEKNVIGNAKLGSPVAATSKELKHIRVYTLTEGNTLQEFAYDSGTGWYNGGLGGAKFQVAPYSXIAAVFLAGTDALQLRIYAQKPDNTIQEYMWNGDGWKEGTNLGGALPGTGIGATSFRYTDYNGPSIRIWFQTDDLKLVQRAYDPHKGWYPDLVTIFDRAPPRTAIAATSFGAGNSSIYMRIYFVNSDNTIWQVCWDHGKGYHDKGTITPVIQGSEVAIISWGSFANNGPDLRLYFQNGTYISAVSEWVWNRAHGSQLGRSALPPA'})
```

--------------------------------

### Initialize PlinderDataset with filters

Source: https://plinder-org.github.io/plinder/examples/5_dataset_and_loader.html

Create a PlinderDataset instance for the 'val' split, filtering for systems with exactly one protein chain and containing 'ATP' as a ligand. Alternate structures are disabled for this example.

```python
val_dataset = PlinderDataset(
    split="val",
    filters=[
        ("system_num_protein_chains", "==", 1),
        ("ligand_unique_ccd_code", "in", {"ATP"}),
    ],
    use_alternate_structures=False,
)
```

--------------------------------

### Get and Print Default Split Config

Source: https://plinder-org.github.io/plinder/examples/6_custom_split.html

Retrieves the default split configuration and prints initial values for validation set size, test set size, and minimum cluster size.

```python
cfg = get_default_config() 
print(f'Validation set size: {cfg.split.num_val}')
print(f'Test set size: {cfg.split.num_test}')
print(f'Minimum size of each cluster in the validation set: {cfg.split.min_val_cluster_size}')
```

--------------------------------

### Query All Annotations

Source: https://plinder-org.github.io/plinder/tutorial/api.html

Query the annotations table to get a pandas DataFrame containing system_id, entry_pdb_id, and split for train and val datasets. Requires importing query_index.

```python
from plinder.core.scores import query_index

# Get system_id, entry_pdb_id, and split columns of train and val splits
query_index()

```

--------------------------------

### Get Ligand Atom Order Stacks

Source: https://plinder-org.github.io/plinder/examples/4_align_mask_crop.html

Obtains the atom order stacks for reordering template and holo ligand structures. This is crucial for aligning atom indices between input and resolved structures.

```python
( 
    input_atom_order_stack,
    holo_atom_order_stack,
) = system_structure.ligand_template2resolved_atom_order_stacks[
    system_structure.ligand_chain_ordered[0]
]
input_atom_order_stack, holo_atom_order_stack
```

--------------------------------

### Build Documentation with Sphinx

Source: https://plinder-org.github.io/plinder/contribution/documentation.html

Build the documentation using Sphinx. Specify the source directory ('docs') and the desired output directory.

```bash
sphinx-build docs <output directory>
```

--------------------------------

### Initialize PlinderSystem

Source: https://plinder-org.github.io/plinder/examples/3_access_system_files.html

Instantiate the PlinderSystem object with a system ID to access its files. Files are downloaded and extracted automatically if not already present.

```python
from plinder.core import PlinderSystem

plinder_system = PlinderSystem(system_id="4agi__1__1.C__1.W")
```

--------------------------------

### Install Plinder in Editable Mode

Source: https://plinder-org.github.io/plinder/contribution/development.html

Install the Plinder package into the active Conda environment in editable mode. This allows for changes to be reflected immediately without reinstallation.

```bash
$ pip install -e .

```

--------------------------------

### Download PLINDER data with gsutil

Source: https://plinder-org.github.io/plinder/tutorial/dataset.html

Set environment variables for release and iteration, create a local directory, and use gsutil to copy data recursively. This method is useful for direct command-line access.

```bash
$ export PLINDER_RELEASE=2024-06
$ export PLINDER_ITERATION=tutorial
$ mkdir -p ~/.local/share/plinder/${PLINDER_RELEASE}/${PLINDER_ITERATION}/
$ gsutil -m cp -r "gs://plinder/${PLINDER_RELEASE}/${PLINDER_ITERATION}/*" ~/.local/share/plinder/${PLINDER_RELEASE}/${PLINDER_ITERATION}/

```

--------------------------------

### Download Full Pinder Dataset

Source: https://plinder-org.github.io/plinder/examples/1_download.html

Use the `plinder_download` command-line tool to download the entire dataset. This process can take approximately one hour and requires about 1TB of storage. Set the `PLINDER_OFFLINE` environment variable to `true` after completion to prevent re-downloading.

```bash
plinder_download --help
usage:
    Download the full plinder dataset for the current configuration.
    Note that even though this is wrapped in a progress bar, the estimated
    completion time can vary wildly as it iterates over larger files vs.
    smaller ones.
    

optional arguments:
  -h, --help            show this help message and exit
  --release RELEASE     plinder release
  --iteration ITERATION
                        plinder iteration
  -y, --yes             skip confirmation


```

--------------------------------

### Get protein residues number

Source: https://plinder-org.github.io/plinder/examples/4_align_mask_crop.html

Returns the residue numbers as they appear in the protein structure.

```APIDOC
## Get protein residues number

### Description
Residue number as they appear in structure.

### Method
```python
system_structure.protein_unique_residue_ids
```

### Response Example
```json
[2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315]
```
```

--------------------------------

### Initialize SplitPropertiesPlotter

Source: https://plinder-org.github.io/plinder/examples/6_custom_split.html

Initialize the plotter from data and split files. Specify the data directory and the path to the split file.

```python
plotter = SplitPropertiesPlotter.from_files(
    data_dir = Path(plinder_local_storage),
    split_file = Path(f'{plinder_local_storage}/splits/split_{split_name}.parquet'),
)
```

--------------------------------

### Get canonical protein sequence

Source: https://plinder-org.github.io/plinder/examples/4_align_mask_crop.html

Retrieves the canonical sequence of the protein, typically from SEQRES records.

```APIDOC
## Get canonical protein sequence

### Description
Retrieves the canonical sequence of the protein, typically from SEQRES records.

### Method
```python
system_structure.protein_sequence
```

### Response Example
```json
{"1.C": "MSTPGAQQVLFRTGIAAVNSTNHLRVYFQDVYGSIRESLYEGSWANGTEKNVIGNAKLGSPVAATSKELKHIRVYTLTEGNTLQEFAYDSGTGWYNGGLGGAKFQVAPYSXIAAVFLAGTDALQLRIYAQKPDNTIQEYMWNGDGWKEGTNLGGALPGTGIGATSFRYTDYNGPSIRIWFQTDDLKLVQRAYDPHKGWYPDLVTIFDRAPPRTAIAATSFGAGNSSIYMRIYFVNSDNTIWQVCWDHGKGYHDKGTITPVIQGSEVAIISWGSFANNGPDLRLYFQNGTYISAVSEWVWNRAHGSQLGRSALPPA"}
```
```

--------------------------------

### Get number of atoms of protein molecule

Source: https://plinder-org.github.io/plinder/examples/4_align_mask_crop.html

Retrieves the total number of atoms in the protein molecule.

```APIDOC
## Get number of atoms of protein molecule

### Description
Retrieves the total number of atoms in the protein molecule.

### Method
```python
system_structure.protein_n_atoms
```

### Response Example
```json
2443
```
```

--------------------------------

### Get protein residue names

Source: https://plinder-org.github.io/plinder/examples/4_align_mask_crop.html

Retrieves a list of all unique residue names found in the protein structure.

```APIDOC
## Get protein residue names

### Description
Retrieves a list of all unique residue names found in the protein structure.

### Method
```python
system_structure.protein_unique_residue_names
```

### Response Example
```json
["ALA", "ARG", "ASN", "ASP", "CSD", "CSK", "GLN", "GLU", "GLY", "HIS", "ILE", "LEU", "LYS", "MET", "PHE", "PRO", "SER", "THR", "TRP", "TYR", "VAL"]
```
```

--------------------------------

### Create and Activate Conda Environment

Source: https://plinder-org.github.io/plinder/contribution/development.html

Create a Conda environment from the provided environment.yml file and activate it. This is recommended for managing complex dependencies.

```bash
$ mamba env create -f environment.yml
$ mamba activate plinder

```

--------------------------------

### Get Protein Coordinates

Source: https://plinder-org.github.io/plinder/examples/4_align_mask_crop.html

Accesses the 3D coordinates for all atoms belonging to protein molecules within the structure.

```python
system_structure.protein_coords
```

```text
[array([[48.761, 52.015, 58.719],
        [48.178, 50.968, 57.827],
        [49.186, 50.593, 56.712],
        [...,
        [50.066, 42.485, 54.198],
        [47.368, 43.433, 55.544],
        [50.022, 44.674, 54.248]], dtype=float32)]
```

--------------------------------

### Get Ordered Protein Chains

Source: https://plinder-org.github.io/plinder/examples/4_align_mask_crop.html

Retrieves a list of protein chain identifiers in the order they appear in the structure.

```python
system_structure.protein_chain_ordered
```

```text
['1.C']
```

--------------------------------

### get_config

Source: https://plinder-org.github.io/plinder/api/core/index.html

Retrieves the application configuration.

```APIDOC
## Function: get_config

### Description
Retrieves the application configuration.

### Usage
```python
from plinder.core import get_config

config = get_config()
```
```

--------------------------------

### PlinderSystem

Source: https://plinder-org.github.io/plinder/api/core/index.html

Core class for interacting with a single system and its assets.

```APIDOC
## Class: PlinderSystem

### Description
Core class for interacting with a single system and its assets.

### Usage
```python
from plinder.core import PlinderSystem

system = PlinderSystem()
```
```

--------------------------------

### Access Ligand SMILES Strings

Source: https://plinder-org.github.io/plinder/examples/3_access_system_files.html

Get the SMILES strings for the ligands. The dictionary keys correspond to ligand identifiers.

```python
plinder_system.smiles
```

```python
{'1.W': 'C[Se][C@@H]1O[C@@H](C)[C@@H](O)[C@@H](O)[C@@H]1O'}
```

--------------------------------

### Download PLINDER data with plinder package

Source: https://plinder-org.github.io/plinder/tutorial/dataset.html

Use the plinder_download command to fetch data. The --yes flag bypasses confirmation prompts.

```bash
# adding --yes will skip all confirmation prompts
plinder_download --release 2024-06 --iteration tutorial --yes

```

--------------------------------

### Ligand Symmetry Mapping

Source: https://plinder-org.github.io/plinder/examples/4_align_mask_crop.html

Shows how to access ligand templates, resolved molecules, and atom order mappings when symmetry is present in the ligand.

```python
structure_with_symmetry_in_ligand = PlinderSystem(
    system_id="4v2y__1__1.A__1.E"
).holo_structure
structure_with_symmetry_in_ligand.input_ligand_templates[
    structure_with_symmetry_in_ligand.ligand_chain_ordered[0]
]
```

```python
structure_with_symmetry_in_ligand.resolved_ligand_mols[
    structure_with_symmetry_in_ligand.ligand_chain_ordered[0]
]
```

```python
structure_with_symmetry_in_ligand.ligand_template2resolved_atom_order_stacks[
    structure_with_symmetry_in_ligand.ligand_chain_ordered[0]
]
```

```python
(array([[17, 16, 18,  1,  0,  2,  3,  4,  5, 10,  9,  8, 13,  7, 15, 12,
         11, 14,  6],
        [17, 16, 18,  1,  0,  2,  3,  4,  5, 11, 12, 13,  8, 15,  7,  9,
         10,  6, 14]]),
 array([[ 0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12, 13, 14, 15,
         16, 17, 18],
        [ 0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12, 13, 14, 15,
         16, 17, 18]]))
```

--------------------------------

### Query All System Splits

Source: https://plinder-org.github.io/plinder/tutorial/api.html

Use `query_index` with `splits=['*']` to retrieve all systems, including those in 'train', 'val', 'test', and 'removed' splits, as well as 'unassigned' systems. This provides a comprehensive dataset for analysis.

```python
df = query_index(columns=cols_of_interest, splits=["*"])
df.drop_duplicates("system_id")["split"].value_counts()
```

--------------------------------

### Get protein structure atom names

Source: https://plinder-org.github.io/plinder/examples/4_align_mask_crop.html

Returns all unique atom names present in the protein structure, exactly as they appear.

```APIDOC
## Get protein structure atom names

### Description
Returns all atoms names the same way they appear in the structure.

### Method
```python
system_structure.protein_unique_atom_names
```

### Response Example
```json
["C", "CA", "CB", "CD", "CD1", "CD2", "CE", "CE1", "CE2", "CE3", "CG", "CG1", "CG2", "CH2", "CM", "CZ", "CZ2", "CZ3", "N", "ND1", "ND2", "NE", "NE1", "NE2", "NH1", "NH2", "NZ", "O", "OD1", "OD2", "OE1", "OE2", "OG", "OG1", "OH", "OXT", "SD", "SE", "SG"]
```
```

--------------------------------

### Run Tox Tests, Type Checks, and Linting

Source: https://plinder-org.github.io/plinder/contribution/development.html

Execute tests, type checks, and code linting using tox. Refer to tox.ini for detailed configurations.

```bash
$ tox -e test
$ tox -e type
$ tox -e lint

```

--------------------------------

### Get All Protein Chains

Source: https://plinder-org.github.io/plinder/examples/4_align_mask_crop.html

Lists all unique protein chain identifiers present in the structure, without preserving their original order.

```python
system_structure.protein_chains
```

```text
['1.C']
```

--------------------------------

### get_manifest()

Source: https://plinder-org.github.io/plinder/api/core/plinder.core.get_manifest.html

Fetches the manifest and caches it. It can optionally accept configuration and plindex as arguments.

```APIDOC
## get_manifest()

### Description
Fetches the manifest and caches it.

### Parameters
#### Optional Parameters
- **cfg** (DictConfig) - The plinder-core config.
- **plindex** (pd.DataFrame) - The plindex.

### Returns
- **pd.DataFrame** - The manifest.
```

--------------------------------

### Get Protein Residue IDs

Source: https://plinder-org.github.io/plinder/examples/4_align_mask_crop.html

Retrieves a list of residue numbers as they appear in the structure. This can be useful for mapping sequence positions to structural elements.

```python
system_structure.protein_unique_residue_ids
```

```text
[2,
 3,
 4,
 5,
 6,
 7,
 8,
 9,
 10,
 11,
 12,
 13,
 14,
 15,
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 17,
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 23,
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 107,
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 113,
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 116,
 117,
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 119,
 120,
 121,
 122,
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 124,
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 127,
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 129,
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 271,
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 294,
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 301,
 302,
 303,
 304,
 305,
 306,
 307,
 308,
 309,
 310,
 311,
 312,
 313,
 314,
 315]
```

--------------------------------

### Access Ligand SDF Files

Source: https://plinder-org.github.io/plinder/examples/3_access_system_files.html

Retrieve the file path for the ligand SDF file. The dictionary keys correspond to ligand identifiers.

```python
plinder_system.ligand_sdfs
```

```python
{'1.W': '/home/runner/.local/share/plinder/2024-06/v2/systems/4agi__1__1.C__1.W/ligand_files/1.W.sdf'}
```

--------------------------------

### get_manifest

Source: https://plinder-org.github.io/plinder/api/core/index.html

Fetches and caches the manifest.

```APIDOC
## Function: get_manifest

### Description
Fetches the manifest and caches it locally.

### Usage
```python
from plinder.core import get_manifest

manifest_data = get_manifest()
```
```

--------------------------------

### Get Number of Atoms in Protein Molecule

Source: https://plinder-org.github.io/plinder/examples/4_align_mask_crop.html

Retrieves the total count of atoms within a protein molecule. This is useful for understanding the scale of the protein structure.

```python
system_structure.protein_n_atoms
```

```text
2443
```

--------------------------------

### Create a PyTorch DataLoader

Source: https://plinder-org.github.io/plinder/examples/5_dataset_and_loader.html

Generate a PyTorch DataLoader from the PlinderDataset for batch processing. The loop demonstrates how to fetch and break after the first batch.

```python
val_loader = get_torch_loader(val_dataset)
for data in val_loader:
    test_torch = data
    break
```

--------------------------------

### Display Query Results

Source: https://plinder-org.github.io/plinder/examples/2_query_filter_index.html

Prints the total number of ligands, systems, and PDB entries obtained from the query.

```python
No. ligands: 1357906
```

```python
No. systems: 990260
No. PDB entries: 143800
```

--------------------------------

### Get Plinder Configuration

Source: https://plinder-org.github.io/plinder/tutorial/api.html

Retrieve the Plinder configuration to verify that local and remote data paths are set correctly. This requires importing the config utility.

```python
import plinder.core.utils.config

cfg = plinder.core.get_config()
print(f"local cache directory: {cfg.data.plinder_dir}")
print(f"remote data directory: {cfg.data.plinder_remote}")

```

```text
local cache directory: /home/runner/.local/share/plinder/2024-06/tutorial
remote data directory: gs://plinder/2024-06/tutorial

```

--------------------------------

### Visualize Ligand Properties by Split

Source: https://plinder-org.github.io/plinder/examples/2_query_filter_index.html

Generates bar charts to visualize the mean percentage and counts of different ligand types for train, validation, and test splits. Requires matplotlib and numpy.

```python
labels = [c.replace("ligand_is_", "").capitalize() for c in ligand_types]
bar_colors = plt.cm.Pastel2.colors
split_names = ["train", "val", "test"]
fig, axes = plt.subplots(1, 3, figsize=(10, 3))
for i, split in enumerate(split_names):
    ax = axes[i]
    split_data = plindex[plindex["split"] == split]
    bars = ax.bar(
        labels,
        split_data[ligand_types].mean().mul(100).to_list(),
        width=1,
        color=bar_colors,
        edgecolor="black",
        label=split,
        linewidth=1,
    )
    ax.set_xticks(np.arange(len(labels)), labels, rotation=70)
    ax.set_ylim(0, 100)
    ax.set_title(split.upper())
    counts = split_data[ligand_types].sum().to_list()
    for bar, count in zip(bars, counts):
        ax.text(
            bar.get_x() + bar.get_width() / 2.0,
            bar.get_height() + 2,
            f"{count}",
            ha="center",
            va="bottom",
            rotation=70,
            fontsize=10,
        )
```

--------------------------------

### Read Annotation Table with Pandas

Source: https://plinder-org.github.io/plinder/tutorial/dataset.html

Load the main annotation table from a Parquet file into a pandas DataFrame to inspect its columns. Ensure the 'pandas' library is installed.

```python
>>> df = pd.read_parquet("index/annotation_table.parquet")
>>> df.columns
Index(['entry_pdb_id', 'entry_release_date', 'entry_oligomeric_state',
       'entry_determination_method', 'entry_keywords', 'entry_pH',
       'entry_resolution', 'entry_rfree', 'entry_r', 'entry_clashscore',
       ...
       'ligand_interacting_ligand_chains_UniProt',
       'system_ligand_chains_PANTHER', 'ligand_interacting_ligand_chains_Pfam',
       'ligand_neighboring_ligand_chains_Pfam',
       'ligand_interacting_ligand_chains_PANTHER',
       'ligand_neighboring_ligand_chains_PANTHER',
       'system_ligand_chains_SCOP2', 'system_ligand_chains_SCOP2B',
       'pli_qcov__100__strong__component',
       'protein_lddt_qcov_weighted_sum__100__strong__component'],
      dtype='object', length=500)


```

--------------------------------

### Download specific directories with gsutil

Source: https://plinder-org.github.io/plinder/tutorial/dataset.html

To download only specific directories like 'splits', use gsutil with the -r flag, targeting the desired path within the PLINDER bucket.

```bash
$ gsutil -m cp -r gs://plinder/${PLINDER_RELEASE}/${PLINDER_ITERATION}/splits ~/.local/share/plinder/${PLINDER_RELEASE}/${PLINDER_ITERATION}/

```

--------------------------------

### Get Unique Protein Residue Names

Source: https://plinder-org.github.io/plinder/examples/4_align_mask_crop.html

Retrieves a list of all unique residue names found in the protein structure. This provides a summary of the amino acid types present.

```python
system_structure.protein_unique_residue_names
```

```text
['ALA',
 'ARG',
 'ASN',
 'ASP',
 'CSD',
 'CSK',
 'GLN',
 'GLU',
 'GLY',
 'HIS',
 'ILE',
 'LEU',
 'LYS',
 'MET',
 'PHE',
 'PRO',
 'SER',
 'THR',
 'TRP',
 'TYR',
 'VAL']
```

--------------------------------

### Get Unique Protein Atom Names

Source: https://plinder-org.github.io/plinder/examples/4_align_mask_crop.html

Retrieves a list of all unique atom names present in the protein structure. The names are returned exactly as they appear in the structure data.

```python
system_structure.protein_unique_atom_names
```

```text
['C',
 'CA',
 'CB',
 'CD',
 'CD1',
 'CD2',
 'CE',
 'CE1',
 'CE2',
 'CE3',
 'CG',
 'CG1',
 'CG2',
 'CH2',
 'CM',
 'CZ',
 'CZ2',
 'CZ3',
 'N',
 'ND1',
 'ND2',
 'NE',
 'NE1',
 'NE2',
 'NH1',
 'NH2',
 'NZ',
 'O',
 'OD1',
 'OD2',
 'OE1',
 'OE2',
 'OG',
 'OG1',
 'OH',
 'OXT',
 'SD',
 'SE',
 'SG']
```

--------------------------------

### Access Receptor PDB and CIF Files

Source: https://plinder-org.github.io/plinder/examples/3_access_system_files.html

Retrieve the file paths for the receptor's PDB and CIF formats. The CIF format is recommended.

```python
plinder_system.receptor_pdb, plinder_system.receptor_cif
```

```python
('/home/runner/.local/share/plinder/2024-06/v2/systems/4agi__1__1.C__1.W/receptor.pdb',
 '/home/runner/.local/share/plinder/2024-06/v2/systems/4agi__1__1.C__1.W/receptor.cif')
```

--------------------------------

### Access System Annotations

Source: https://plinder-org.github.io/plinder/tutorial/api.html

Retrieve and print system-level annotations, including the SMILES string of the first ligand. Requires the PlinderSystem object.

```python
system_annotations = plinder_system.system
print(list(system_annotations.keys()))
# Show ligand smiles of the first ligand of a given system
print(system_annotations["ligands"][0]["rdkit_canonical_smiles"])
```

```text
['pdb_id', 'biounit_id', 'ligands', 'ligand_validation', 'pocket_validation', 'pass_criteria']
C[Se][C@@H]1O[C@@H](C)[C@@H](O)[C@@H](O)[C@@H]1O
```
Tokens:
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