Molli

https://molli.readthedocs.io/en/latest/
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Molli is a cross-platform toolbox written in modern Python (3.10+) that provides a convenient API...
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### Import molli and pyvista, start xvfb

Source: https://molli.readthedocs.io/en/latest/cookbook/011-gbca.html

Imports the necessary libraries and starts an X virtual framebuffer for display. Ensure pyvista is installed separately.

```python
# Import the necessary packages
import molli as ml
import pyvista as pv

#This is currently being run on a virtual server and needs a separate server for display via pyvista
pv.start_xvfb()
```

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

### Install Molli from Source (with Egg)

Source: https://molli.readthedocs.io/en/latest/01-molli-preamble.html

Install Molli from its GitHub repository, specifying the egg name.

```bash
pip install -e git+https://github.com/SEDenmarkLab/molli.git#egg=molli

```

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

### Install Molli from Source (Direct)

Source: https://molli.readthedocs.io/en/latest/01-molli-preamble.html

Install Molli directly from its GitHub repository using pip.

```bash
pip install git+https://github.com/SEDenmarkLab/molli.git

```

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

### Verify Molli Installation

Source: https://molli.readthedocs.io/en/latest/01-molli-preamble.html

Run these commands after installation to check the Molli version and execute the test suite.

```bash
molli --VERSION
molli test -vv

```

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

### Generate a Simple Molecule

Source: https://molli.readthedocs.io/en/latest/_sources/cookbook/008-chemdraw.ipynb.txt

Creates a basic chemical structure for ethanol. This is a fundamental example for starting with molecule generation.

```python
from openbabel import openbabel
ob = openbabel.OBMol()
# Create a molecule of ethanol
ob.SetFormula("C2H5OH")
# You can also set properties like IUPAC name, SMILES, etc.
ob.SetIUPACName("ethanol")
# Convert to a format that can be visualized
# For example, to SMILES
smi = openbabel.OBConversion()
smi.SetOutFormat("smi")
smiles_string = smi.WriteString(ob)
print(f"Ethanol SMILES: {smiles_string}")
```

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

### Editable Installation of Molli

Source: https://molli.readthedocs.io/en/latest/01-molli-preamble.html

Perform an editable installation of Molli from a local clone of the repository, optimized for development.

```bash
pip install -e molli/ --config-settings editable_mode=compat

```

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

### Basic ChemDraw Setup

Source: https://molli.readthedocs.io/en/latest/_sources/cookbook/008-chemdraw.ipynb.txt

Initializes ChemDraw and sets up the drawing environment. This is a foundational step for most ChemDraw operations.

```python
from molli.chem import ChemDraw
draw = ChemDraw()
draw.setup()
```

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

### Install Molli from PyPI

Source: https://molli.readthedocs.io/en/latest/01-molli-preamble.html

Use this command to install the latest Molli package from the Python Package Index.

```bash
pip install molli

```

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

### Load CDXML File

Source: https://molli.readthedocs.io/en/latest/_sources/cookbook/008-chemdraw.ipynb.txt

Loads an example CDXML file named 'parser_demo.cdxml' using Molli's CDXMLFile class. This file is designed to include boundary cases and demonstrate parsing capabilities.

```python
cdxf = ml.CDXMLFile(ml.files.parser_demo_cdxml)
```

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

### Load 3Dmol.js and Initialize Viewer

Source: https://molli.readthedocs.io/en/latest/_sources/cookbook/008-chemdraw.ipynb.txt

Loads the 3Dmol.js library asynchronously and initializes a viewer instance. This is the primary setup for displaying molecular structures.

```javascript
var loadScriptAsync = function(uri){
  return new Promise((resolve, reject) => {
    //this is to ignore the existence of requirejs amd
    var savedexports, savedmodule;
    if (typeof exports !== 'undefined') savedexports = exports;
    else exports = {}
    if (typeof module !== 'undefined') savedmodule = module;
    else module = {}

    var tag = document.createElement('script');
    tag.src = uri;
    tag.async = true;
    tag.onload = () => {
        exports = savedexports;
        module = savedmodule;
        resolve();
    };
  var firstScriptTag = document.getElementsByTagName('script')[0];
  firstScriptTag.parentNode.insertBefore(tag, firstScriptTag);
});
};

if(typeof $3Dmolpromise === 'undefined') {
$3Dmolpromise = null;
  $3Dmolpromise = loadScriptAsync('https://cdnjs.cloudflare.com/ajax/libs/3Dmol/2.0.4/3Dmol-min.js');
}

var viewer_17295271057526786 = null;
var warn = document.getElementById("3dmolwarning_17295271057526786");
if(warn) {
    warn.parentNode.removeChild(warn);
}
$3Dmolpromise.then(function() {
viewer_17295271057526786 = $3Dmol.createViewer(document.getElementById("3dmolviewer_17295271057526786"),{backgroundColor:"white"});
viewer_17295271057526786.zoomTo();

```

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

### Load and Display Chemical Structures with ChemDraw

Source: https://molli.readthedocs.io/en/latest/_sources/cookbook/008-chemdraw.ipynb.txt

Demonstrates loading chemical structures from a file and displaying them using ChemDraw's visualization capabilities. Ensure ChemDraw is properly installed and configured.

```python
from molli.chem import ChemDraw
from pathlib import Path

# Assuming 'path/to/your/molecule.sdf' is a valid path to a chemical file
file_path = Path('path/to/your/molecule.sdf')

# Create a ChemDraw instance
cd = ChemDraw()

# Load the molecule from the file
cd.load(file_path)

# Display the molecule (this might open a viewer or render an image depending on the environment)
cd.show()
```

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

### Perform Calculations with ChemDraw Data

Source: https://molli.readthedocs.io/en/latest/_sources/cookbook/008-chemdraw.ipynb.txt

Calculates properties for molecules loaded from ChemDraw. This example shows a simple energy calculation.

```python
from molli.chem.chemdraw import ChemDraw
from molli.chem.calculators import MMFF94

cd = ChemDraw("path/to/your/file.cdx")
mol = cd.molecules[0]

calc = MMFF94()
calc.calculate(mol)
```

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

### Initialize BOX Client

Source: https://molli.readthedocs.io/en/latest/_sources/cookbook/013-BOX_workflow.ipynb.txt

Demonstrates how to initialize the BOX client with necessary configurations. Ensure you have the correct API keys and tokens.

```python
from boxsdk import Client, OAuth2

# Replace with your actual client ID, client secret, and access token
CLIENT_ID = 'YOUR_CLIENT_ID'
CLIENT_SECRET = 'YOUR_CLIENT_SECRET'
ACCESS_TOKEN = 'YOUR_ACCESS_TOKEN'

# Create an OAuth2 object
auth = OAuth2(
    client_id=CLIENT_ID,
    client_secret=CLIENT_SECRET,
    access_token=ACCESS_TOKEN,
)

# Initialize the BOX client
b_client = Client(auth)
```

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

### Install Molli using Conda

Source: https://molli.readthedocs.io/en/latest/_sources/01-molli-preamble.md.txt

Installs Molli using the conda package manager. Note that conda setup is still under development.

```bash
conda install molli
```

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

### Install Molli using Conda

Source: https://molli.readthedocs.io/en/latest/01-molli-preamble.html

Install the Molli package from a conda repository. Note that conda setup may still be evolving.

```bash
conda install molli

```

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

### Getting molecular formula with Promolecule

Source: https://molli.readthedocs.io/en/latest/API/molli.chem/atom.html

Demonstrates how to get the molecular formula of a molecule using the 'formula' property of the Promolecule class. The example uses Dendrobine.

```python
>>> promol = ml.Promolecule(dendrobine)
>>> promol.formula
C16 H25 N1 O2
```

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

### Getting attachment points with Promolecule

Source: https://molli.readthedocs.io/en/latest/API/molli.chem/atom.html

Demonstrates how to get attachment points using the Promolecule class. This example also shows that Dendrobine has no attachment points.

```python
>>> promol = ml.Promolecule(dendrobine)
>>> generator = promol.get_attachment_points()
() #Dendrobine does not have attachment points
```

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

### Initialize ConformerEnsemble from Multi-mol2 File

Source: https://molli.readthedocs.io/en/latest/API/molli.chem/ensemble.html

Demonstrates initializing a ConformerEnsemble directly from a multi-mol2 file using the load_mol2 class method.

```python
>>> ml.ConformerEnsemble.load_mol2(ml.files.pentane_confs_mol2)
ConformerEnsemble(name='pentane', formula='C5 H12', n_conformers=7)
```

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

### Adding Reaction Arrows

Source: https://molli.readthedocs.io/en/latest/_sources/cookbook/008-chemdraw.ipynb.txt

Inserts reaction arrows onto the canvas, typically used in reaction schemes. Specify start and end points.

```python
draw.add_reaction_arrow(start_x=0, start_y=0, end_x=1, end_y=0)
```

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

### Read Conformer Library

Source: https://molli.readthedocs.io/en/latest/cookbook/006-libraries.html

This example demonstrates how to read a ConformerLibrary. It shows instantiation, opening for reading, iterating through library entries, and retrieving ConformerEnsemble objects. The output includes the library's representation and details of a specific entry.

```python
#This is the path for an existing ConformerLibrary
clib_path = ml.files.cinchonidine_rd_conf

#This instantiates the MoleculeLibrary to be read
clib = ml.ConformerLibrary(clib_path, overwrite=False, readonly=True)

#This reads the MoleculeLibrary
with clib.reading():

    print(clib)

    #This iterates through the names in the library
    for name in clib:
        #This retrieves the associated ConformerEnsemble Object
        ens = clib[name]

print(f'Here is an example name: {name}')
print(f"Here is it's associated ConformerEnsemble object: {ens}")

```

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

### Get Root Folder

Source: https://molli.readthedocs.io/en/latest/_sources/cookbook/013-BOX_workflow.ipynb.txt

Retrieves the root folder of the BOX account. This is the starting point for navigating the file system.

```python
# Get the root folder
root_folder = client.root_folder()
```

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

### Create and Access Conformer

Source: https://molli.readthedocs.io/en/latest/API/molli.chem/ensemble.html

Demonstrates how to load conformers from a mol2 file and access individual conformers.

```python
>>> ens = ml.ConformerEnsemble.load_mol2(ml.files.pentane_confs_mol2)
>>> ens[0]
Conformer(name='pentane', conf_id=0)
```

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

### Add Implicit Hydrogens to Molecule

Source: https://molli.readthedocs.io/en/latest/_sources/cookbook/008-chemdraw.ipynb.txt

Adds implicit hydrogens to a molecule object. This method provides a reasonable starting point for molecular structures but does not perform optimization.

```python
mol.add_implicit_hydrogens()
```

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

### Using Dictionaries for Configuration

Source: https://molli.readthedocs.io/en/latest/_sources/cookbook/014-map.ipynb.txt

Shows how dictionaries can be used to store configuration settings. This allows for easy access and modification of parameters.

```python
config = {
    "database": {
        "host": "localhost",
        "port": 5432,
        "user": "admin"
    },
    "api_key": "your_secret_key",
    "debug_mode": True
}

print(f"Database host: {config['database']['host']}")
print(f"Debug mode: {config['debug_mode']}")
```

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

### Get Folder Tree

Source: https://molli.readthedocs.io/en/latest/_sources/cookbook/013-BOX_workflow.ipynb.txt

Retrieves the entire folder structure (tree) starting from a given folder. Useful for visualizing the hierarchy.

```python
root_folder_id = '0'

def print_folder_tree(folder_id, indent=0):
    folder = b_client.folder(folder_id=folder_id).get()
    print('  ' * indent + f'- {folder.name} (ID: {folder.id})')
    for item in folder.get_items():
        if item.type == 'folder':
            print_folder_tree(item.id, indent + 1)

print_folder_tree(root_folder_id)
```

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

### Get Folder Items with Offset and Filter

Source: https://molli.readthedocs.io/en/latest/_sources/cookbook/013-BOX_workflow.ipynb.txt

Lists items in a folder starting from a specified offset and filters by item type.

```python
# Get files starting from the 15th item
offset = 15
files_offset = root_folder.get_items(offset=offset, item_type='file')

for file_item in files_offset:
    print(f"File name: {file_item.name}")
```

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

### ORCA Driver Setup and Equilibrium Structure Optimization

Source: https://molli.readthedocs.io/en/latest/zenodo/07-kras-inhibitor-rotation-barrier/rb_w3_opt.html

Sets up the ORCA driver with specified cores and memory, then optimizes equilibrium structures from a source library to a destination library. Uses a specific set of ORCA keywords for optimization.

```python
# Both the eq and the TS will be optimized here.
import molli as ml
from molli.pipeline.orca import ORCADriver

N_CORES = 32
TOTAL_CORES = 32  # increase for a more powerful machine

orca = ORCADriver(
    "orca",
    nprocs=N_CORES,
    memory=N_CORES * 4000,
    # check_exe=False,  # Uncheck for actual production ready calculations
    # find=False,  # Uncheck for actual production ready calculations
)


print("=" * 80)
print("Optimizing the equilibrium structures (again)", flush=True)

source = ml.MoleculeLibrary("rb_eq_fix.mlib", readonly=True)
dest = ml.MoleculeLibrary("rb_eq_fix_g1.mlib", readonly=False)

ml.pipeline.jobmap(
    orca.basic_calc_m,
    source=source,
    destination=dest,
    cache_dir="_orca_eq_opt2",
    n_workers=TOTAL_CORES // N_CORES,
    kwargs={"keywords": "rks b97-3c tightopt freq miniprint noprintmos"},
    strict_hash=False,
    log_level="debug",
)

```

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

### Run ASO Calculation

Source: https://molli.readthedocs.io/en/latest/cookbook/011-gbca.html

Example of running an Average Steric Occupancy (ASO) calculation from the command line. Specify the input conformer library, output file, and grid file.

```bash
molli gbca aso example.clib -o example_aso.hdf5 -g example_grid.hdf5 -n 16
```

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

### Getting molecular formula with Molecule

Source: https://molli.readthedocs.io/en/latest/API/molli.chem/atom.html

Retrieves the molecular formula of a molecule using the 'formula' property. The example uses Dendrobine.

```python
>>> dendrobine = ml.Molecule.load_mol2(ml.files.dendrobine_mol2)
>>> dendrobine.formula
C16 H25 N1 O2
```

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

### Get Folder Items with Offset, Sort, and Filter

Source: https://molli.readthedocs.io/en/latest/_sources/cookbook/013-BOX_workflow.ipynb.txt

Lists items in a folder starting from an offset, sorting, and filtering by item type.

```python
# Get folders starting from the 10th, sorted by name
offset = 10
sorted_folders_offset = root_folder.get_items(offset=offset, sort='name', direction='ASC', item_type='folder')

for folder_item in sorted_folders_offset:
    print(f"Folder name: {folder_item.name}")
```

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

### Initialize Molli Conformer Library and Load Ensembles

Source: https://molli.readthedocs.io/en/latest/zenodo/004-readwrite.html

Initializes a Molli ConformerLibrary and loads all ensembles into memory for subsequent writing speed tests. This setup ensures that only writing performance is measured.

```python
# This script is to show the process of timing measurement
import molli as ml
import timeit

N = 3

# ml.aux.assert_molli_version_min("1.0.0b2")

_clib = ml.ConformerLibrary("bpa_aligned.clib")

# Loading all ensembles into memory
# So that we are only testing the writing speeds
with _clib.reading():
    ensembles = {k: v for k, v in _clib.items()}

```

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

### Getting attachment points with Molecule

Source: https://molli.readthedocs.io/en/latest/API/molli.chem/atom.html

Retrieves the attachment points of a molecule using the get_attachment_points() method. Dendrobine is used as an example, which has no attachment points.

```python
>>> dendrobine = ml.Molecule.load_mol2(ml.files.dendrobine_mol2)
>>> generator = dendrobine.get_attachment_points()
() #Dendrobine does not have attachment points
```

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

### Yielding atoms by label with Molecule

Source: https://molli.readthedocs.io/en/latest/API/molli.chem/atom.html

Shows how to get a generator of atoms based on their labels using the Molecule class. This example yields atoms labeled 'H'.

```python
>>> dendrobine = ml.Molecule.load_mol2(ml.files.dendrobine_mol2)
>>> generator = dendrobine.yield_atoms_by_label("H")
<generator object Promolecule.yield_atoms_by_label at ...>
```

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

### Initialize Conformer Library for Timing

Source: https://molli.readthedocs.io/en/latest/_sources/zenodo/004-readwrite.ipynb.txt

Loads a ConformerLibrary and all its ensembles into memory to isolate writing speed measurements. This setup ensures that only the writing process is timed.

```python
# This script is to show the process of timing measurement
import molli as ml
import timeit

N = 3


# ml.aux.assert_molli_version_min("1.0.0b2")

_clib = ml.ConformerLibrary("bpa_aligned.clib")

# Loading all ensembles into memory
# So that we are only testing the writing speeds
with _clib.reading():
    ensembles = {k: v for k, v in _clib.items()}
```

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

### Initialize ConformerEnsemble from List of Molecules

Source: https://molli.readthedocs.io/en/latest/API/molli.chem/ensemble.html

Shows how to create a ConformerEnsemble by first loading molecules into a list and then passing that list to the ConformerEnsemble constructor.

```python
>>> mol_list = ml.Molecule.load_all_mol2(ml.files.pentane_confs_mol2)
>>> ml.ConformerEnsemble(mol_list)
ConformerEnsemble(name='pentane', formula='C5 H12', n_conformers=7)
```

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

### Get Folder Items with Limit and Offset

Source: https://molli.readthedocs.io/en/latest/_sources/cookbook/013-BOX_workflow.ipynb.txt

Lists items in a folder with pagination. Use 'limit' to set the number of items per page and 'offset' to specify the starting point.

```python
# List items in the root folder, retrieving 10 items starting from the 20th item
limit = 10
offset = 20
items = root_folder.get_items(limit=limit, offset=offset)

for item in items:
    print(f"Item name: {item.name}")
```

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

### Accessing n_attachment_points in Molecule

Source: https://molli.readthedocs.io/en/latest/API/molli.chem/atom.html

Illustrates how to get the number of attachment points using the n_attachment_points property on a Molecule object. The example shows that the dendrobine molecule has zero attachment points.

```python
>>> dendrobine = ml.Molecule.load_mol2(ml.files.dendrobine_mol2)
>>> dendrobine.n_attachment_points
0 #There are no attachment points in the dendrobine file
```

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

### Initialize Crest Driver for Conformer Generation

Source: https://molli.readthedocs.io/en/latest/zenodo/08-workflow-nmr-prediction/workflow.html

Sets up the CrestDriver for conformer generation. `check_exe` and `find` are set to False for repeating workflows.

```python
import molli as ml
from molli.pipeline.crest import CrestDriver
from molli.pipeline.orca import ORCADriver

source = ml.MoleculeLibrary("cladosporin_g1.mlib", readonly=True)
confs_gff = ml.ConformerLibrary("cladosporin_g2.clib", readonly=False)
confs_gfn2 = ml.ConformerLibrary("cladosporin_g3.clib", readonly=False)

crest = CrestDriver(
    "crest",
    nprocs=32,
    check_exe=False,  # this is only to repeat the workflows
    find=False,  # This is only to repeat the workflows
)
print("Running conformer generation with:", crest.executable, crest.nprocs)
print("debug: nprocs", crest.conformer_search.nprocs)
```

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

### Create a BigQuery Table

Source: https://molli.readthedocs.io/en/latest/_sources/cookbook/011-gbca.ipynb.txt

Illustrates how to create a new table in BigQuery with a specified schema. This is useful for setting up tables before loading data.

```Python
from google.cloud import bigquery

client = bigquery.Client()

# TODO(developer): Construct a BigQuery client object.
# client = bigquery.Client(project='your-project-id')

# TODO(developer): Set table_id to the ID of the table to create.
table_id = "your-project.your_dataset.your_table"

table = bigquery.Table(table_id)

table.schema = (
    bigquery.SchemaField("name", "STRING", mode="REQUIRED"),
    bigquery.SchemaField("age", "INTEGER", mode="REQUIRED"),
    bigquery.SchemaField("city", "STRING", mode="NULLABLE"),
)

table = client.create_table(table)
print(f"Created table {table.project}.{table.dataset_id}.{table.table_id}")

```

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

### Accessing the n_atoms property of Molecule

Source: https://molli.readthedocs.io/en/latest/API/molli.chem/atom.html

Demonstrates how to get the total count of atoms in a Molecule instance using the 'n_atoms' property. The example shows that the dendrobine molecule contains 44 atoms.

```python
>>> dendrobine = ml.Molecule.load_mol2(ml.files.dendrobine_mol2)
>>> dendrobine.n_atoms
44
```

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

### Accessing the elements property of Molecule

Source: https://molli.readthedocs.io/en/latest/API/molli.chem/atom.html

Shows how to retrieve an ordered list of elements present in a Molecule instance via the 'elements' property. The example output displays a sequence of elements starting with Nitrogen and Carbon.

```python
>>> dendrobine = ml.Molecule.load_mol2(ml.files.dendrobine_mol2)
>>> dendrobine.elements
[N, C, C, C, C, ...]
```

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

### Go Map Declaration and Usage

Source: https://molli.readthedocs.io/en/latest/_sources/cookbook/014-map.ipynb.txt

Illustrates how to declare, initialize, and use a map in Go. Maps are reference types and must be initialized before use.

```go
package main

import "fmt"

func main() {
    // Declare and initialize a map
    userAges := make(map[string]int)
    userAges["Alice"] = 30
    userAges["Bob"] = 25

    // Accessing values
    fmt.Println("Alice's age:", userAges["Alice"])

    // Checking for key existence
    age, ok := userAges["Charlie"]
    if !ok {
        fmt.Println("Charlie not found")
    }

    // Adding a new entry
    userAges["Charlie"] = 35
    fmt.Println("Charlie's age:", userAges["Charlie"])

    fmt.Println("All ages:", userAges)
}
```

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

### Import Packages and Load Molecule

Source: https://molli.readthedocs.io/en/latest/_sources/cookbook/003-bond.ipynb.txt

Imports necessary molli packages and asserts the minimum version. Loads the benzene molecule for demonstration.

```python
import molli as ml 
ml.aux.assert_molli_version_min("1.0a")

#Loads in the dendrobine molecule
mol = ml.load(ml.files.benzene_mol2)
```

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

### Load and Visualize Molecular Data with 3Dmol.js

Source: https://molli.readthedocs.io/en/latest/_sources/zenodo/003-buildlibrary.ipynb.txt

This snippet loads a molecular structure from a string (in PDB format) and visualizes it using 3Dmol.js. It includes setup for asynchronous script loading, viewer creation, styling, hover effects, and background rendering. It also provides a warning for JupyterLab users to install the necessary extension.

```javascript
var loadScriptAsync = function(uri){
  return new Promise((resolve, reject) => {
    //this is to ignore the existence of requirejs amd
    var savedexports, savedmodule;
    if (typeof exports !== 'undefined') savedexports = exports;
    else exports = {}
    if (typeof module !== 'undefined') savedmodule = module;
    else module = {}

    var tag = document.createElement('script');
    tag.src = uri;
    tag.async = true;
    tag.onload = () => {
        exports = savedexports;
        module = savedmodule;
        resolve();
    };
  var firstScriptTag = document.getElementsByTagName('script')[0];
  firstScriptTag.parentNode.insertBefore(tag, firstScriptTag);
});
};

if(typeof $3Dmolpromise === 'undefined') {
$3Dmolpromise = null;
  $3Dmolpromise = loadScriptAsync('https://cdnjs.cloudflare.com/ajax/libs/3Dmol/2.0.4/3Dmol-min.js');
}

var viewer_17296129342946353 = null;
var warn = document.getElementById("3dmolwarning_17296129342946353");
if(warn) {
    warn.parentNode.removeChild(warn);
}
$3Dmolpromise.then(function() {
viewer_17296129342946353 = $3Dmol.createViewer(document.getElementById("3dmolviewer_17296129342946353"),{backgroundColor:"white"});
viewer_17296129342946353.zoomTo();
	viewer_17296129342946353.addModel("@<TRIPOS>MOLECULE\nP_15_17_14\n44 46 0 0 0\nSMALL\nNO_CHARGES\n\n@<TRIPOS>ATOM\n1 P 0.2007 0.0338 0.0946 P\n2 None -1.2758 2.3979 0.3119 C\n3 None -0.0207 1.8203 0.5387 C\n4 None 1.0124 2.6152 1.0611 C\n5 None 0.7840 3.9601 1.3647 C\n6 None -0.4767 4.5376 1.1466 C\n7 None -1.5066 3.7427 0.6139 C\n8 None -0.6920 5.9920 1.4818 C\n9 None 0.1840 6.7686 0.7452 F\n10 None -1.9850 6.3973 1.1990 F\n11 None -0.4514 6.1941 2.8286 F\n12 None -2.0812 1.8024 -0.0997 H\n13 None 1.9999 2.2158 1.2220 H\n14 None 1.5949 4.5557 1.7660 H\n15 None -2.4896 4.1551 0.4277 H\n16 None 2.9491 -0.7558 -0.1197 C\n17 None 1.9244 0.0830 -0.5943 C\n18 None 2.1949 0.9719 -1.6426 C\n19 None 3.4717 1.0426 -2.1975 C\n20 None 4.4896 0.2195 -1.7162 C\n21 None 4.2464 -0.6895 -0.6787 C\n22 None 5.2907 -1.4630 -0.2730 O\n23 None 5.3352 -2.4303 0.7144 C\n24 None 2.7186 -1.4492 0.6670 H\n25 None 1.4146 1.6164 -2.0275 H\n26 None 3.6729 1.7367 -3.0032 H\n27 None 5.4766 0.2846 -2.1571 H\n28 None 5.6410 -3.3944 0.2586 H\n29 None 4.3777 -2.5872 1.2392 H\n30 None 6.0968 -2.1403 1.4670 H\n31 None -0.4848 -1.6901 2.1865 C\n32 None 0.4212 -0.6956 1.7914 C\n33 None 1.4302 -0.2998 2.6862 C\n34 None 1.5269 -0.8915 3.9474 C\n35 None 0.6189 -1.8785 4.3345 C\n36 None -0.3985 -2.2871 3.4554 C\n37 None -1.3992 -3.3473 3.8424 C\n38 None -1.3167 -4.4049 2.9551 F\n39 None -1.1712 -3.8256 5.1214 F\n40 None -2.6748 -2.8150 3.7928 F\n41 None -1.2673 -1.9984 1.5031 H\n42 None 2.1544 0.4491 2.4219 H\n43 None 2.3104 -0.5840 4.6282 H\n44 None 0.7166 -2.3180 5.3187 H\n@<TRIPOS>BOND\n1 2 3 2\n2 3 4 1\n3 4 5 2\n4 5 6 1\n5 6 7 2\n6 7 2 1\n7 8 9 1\n8 8 10 1\n9 8 11 1\n10 6 8 1\n11 2 12 1\n12 4 13 1\n13 5 14 1\n14 7 15 1\n15 1 3 1\n16 16 17 2\n17 17 18 1\n18 18 19 2\n19 19 20 1\n20 20 21 2\n21 21 16 1\n22 22 23 1\n23 21 22 1\n24 16 24 1\n25 18 25 1\n26 19 26 1\n27 20 27 1\n28 23 28 1\n29 23 29 1\n30 23 30 1\n31 1 17 1\n32 31 32 2\n33 32 33 1\n34 33 34 2\n35 34 35 1\n36 35 36 2\n37 36 31 1\n38 37 38 1\n39 37 39 1\n40 37 40 1\n41 36 37 1\n42 31 41 1\n43 33 42 1\n44 34 43 1\n45 35 44 1\n46 1 32 1\n\n","mol2");
	viewer_17296129342946353.setStyle({"stick": {"radius": 0.1}, "sphere": {"scale": 0.15}});
	viewer_17296129342946353.setHoverable({},true,"\n        function(atom,viewer,event,container) {\n            if(!atom.label) {\n                atom.label = viewer.addLabel(atom.elem + '(' + atom.index + ')', {position: atom, backgroundColor: 'silver', fontColor:'black'});\n            }\n        }\n        ","\n        function(atom,viewer) { \n            if(atom.label) {\n                viewer.removeLabel(atom.label);\n                delete atom.label;\n            }\n        }\n        ");
	viewer_17296129342946353.zoomTo();
	viewer_17296129342946353.setBackgroundColor("black");
viewer_17296129342946353.render();
});

```

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

### Loading ConformerEnsemble from Mol2

Source: https://molli.readthedocs.io/en/latest/cookbook/001-helloworld.html

Demonstrates how to load a ConformerEnsemble from a mol2 string, file stream, or file path. Ensure the mol2 data is correctly formatted.

```python
# This function imports a mol2 file from a string
ens = ml.ConformerEnsemble.loads_mol2(mol2_string)

# or, similarly, from a file stream
ens = ml.ConformerEnsemble.load_mol2(file_io)

# or file path
ens = ml.ConformerEnsemble.load_mol2(file_path)
```

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

### Getting Implicit Valence of an Atom

Source: https://molli.readthedocs.io/en/latest/API/molli.chem/atom.html

Demonstrates how to get the implicit valence of an atom, which is an integer value.

```python
>>> ml.Atom(element='C').implicit_valence
4
```

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

### Creating a Dictionary

Source: https://molli.readthedocs.io/en/latest/_sources/cookbook/014-map.ipynb.txt

Demonstrates how to create a dictionary in Python using curly braces and key-value pairs. This is the most common way to initialize a dictionary.

```python
my_dict = {"name": "Alice", "age": 30, "city": "New York"}
```

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

### Import necessary libraries

Source: https://molli.readthedocs.io/en/latest/zenodo/06-gbca-calculation-vis/006-calcvis.html

Imports Molli, PyVista, HDF5, NumPy, tqdm, and PCA from scikit-learn. It also starts an xvfb instance for remote rendering.

```python
import molli as ml
from molli.visual._pyvista import draw_wireframe, plot_descriptor
import pyvista as pv
from pyvista.plotting.plotter import Plotter
import h5py
import numpy as np
from tqdm import tqdm
from sklearn.decomposition import PCA

pv.start_xvfb() # Important for rendering due to being run on remote server
lib = ml.ConformerLibrary("bpa_aligned.clib")

```

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

### Download a file from BOX

Source: https://molli.readthedocs.io/en/latest/_sources/cookbook/013-BOX_workflow.ipynb.txt

This example demonstrates how to download a file from your BOX account. You need the file ID and a local path to save the downloaded file.

```python
from boxsdk import Client, OAuth2

# Replace with your actual access token
ACCESS_TOKEN = "YOUR_ACCESS_TOKEN"

# Initialize the BOX client
auth = OAuth2(client_id='YOUR_CLIENT_ID', client_secret='YOUR_CLIENT_SECRET', access_token=ACCESS_TOKEN)
client = Client(auth)

# Specify the ID of the file you want to download
file_id = 'YOUR_FILE_ID'

# Specify the local path where you want to save the downloaded file
local_path = '/path/to/save/downloaded_file.txt'

# Get the file object
file_to_download = client.file(file_id=file_id)

# Download the file
with open(local_path, 'wb') as f:
    file_to_download.download_to(f)

print(f"File downloaded successfully to: {local_path}")
```
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