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molli 1.3.0 documentation

Introduction

molli: Molecular Toolbox Library
Hello, World!

Detailed Package Documentation

molli.chem
- Atom
- Classifications for Types of Atoms
- Bond
- Ensemble
- Geometry
- Legacy
- Library
- Molecule
- Structure
molli.data
molli.descriptor
- ASO
- COV_CN
- GridBased
molli.external
molli.ftypes
- CDXML Parser
molli.math
- Rotation
molli.pipeline: External Drivers

Command Line Reference

molli Command Line

Molli Cookbook

Welcome to molli
Basic objects
Molecule and Atom Introduction
Bond Class
Coordinates and Other Geometric Manipulations
Conformer Ensembles
Libraries and Serialization
Visualization Tools
Reading ChemDraw files
OpenBabel Interface
RDKit Interface
Grid Creation and Grid-Based Descriptor Calculation
Parallelized Calculations and Jobmapping
Workflow Example: Copper-BOX Catalyst Library Construction
molli map script
Library manipulation scripts

Benchmarks and Workflows

Example 1: Recompile MolNet
Example 2: Recompile Crude GeomSet
Example 3: Build a Combinatorial Library
Example 4: Reading and Writing Benchmark
Example 5: GBCA Benchmark
Example 6: GBCA Calculation
- Example 6.1: Calculate ASO and AEIF descriptors
- Example 6.2: Visualize ASO Components
molli Case Study 1: KRAS Barrier Calculation
molli Case Study 2: NMR Prediction of Cladosporin
- molli Study case: Cladosporin GIAO-DFT NMR prediction
- Supplementary Script: workflow.py

Miscellaneous

Inheritance Diagram for Molli
Extensions

Extensions¶

Currently there is one extension for Molli. This extension allows Molli to interact with rdkit

ref:: rdkit

Inheritance Diagram for Molli

Copyright © 2022, Alexander Shved

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