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molli 1.3.0 documentation
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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
    • Atomic Weights
    • Color CPKs
    • Covalent Radii for Single Bonds
    • Covalent Radii for Grimme’s definition
    • Electron Affinities
    • Electron Groups
    • Van der Waals Radii
  • molli.descriptor
    • ASO
    • COV_CN
    • GridBased
  • molli.external
    • RDKit
    • OpenBabel
    • Morfeus-ML
  • 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 5.1 GBCA Benchmark
    • Example 5.2: Molli XT Benchmark
    • Example 5.3: Sparsity 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
    • Example 7: Rotational barrier prediction in KRAS inhibitors
    • Supplementary Script 1: scan.py
    • Supplementary Script 2: rb_w1_opt.py
    • Supplementary Script 3: rb_w2_opt.py
    • Supplementary Script 4: rb_w3_opt.py
  • 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
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molli.external¶

molli.external

  • RDKit
    • to_rdmol()
    • from_rdmol()
    • rd_visualize()
    • ml_rd_visualize()
    • canonicalize_rdmol()
    • can_mol_order()
    • reorder_molecule()
    • atom_filter
  • OpenBabel
    • to_obmol()
    • from_obmol()
    • load_obmol()
    • loads_obmol()
    • load_all_obmol()
    • loads_all_obmol()
    • from_str_w_ob()
    • to_mol2_w_ob()
    • dumps_obmol()
    • calc_charges()
    • obabel_optimize()
    • optimize_coordination()
  • Morfeus-ML
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