Table of Contents

Introduction

• molli: Molecular Toolbox Library
  • About molli
  • Installation
  • Testing the installation
  • Configuration
• Hello, World!
  • Overview
  • Input and output

Detailed Package Documentation

• molli.chem
  • Atom
    • Element
    • ElementLike
    • IMPLICIT_VALENCE
    • AtomType
    • AtomStereo
    • AtomGeom
    • Atom
    • AtomLike
    • Promolecule
    • PromoleculeLike
  • Classifications for Types of Atoms
    • AtomType:
    • AtomStereo
    • AtomGeom
  • Bond
    • BondType
    • BondStereo
    • Bond
    • Connectivity
  • Ensemble
    • ConformerEnsemble
    • Conformer
  • Geometry
    • DistanceUnit
    • CartesianGeometry
  • Legacy
    • ensemble_from_molli_old_xml()
  • Library
    • library_type()
    • MoleculeLibrary
    • ConformerLibrary
  • Molecule
    • Molecule
    • StructureLike
  • Structure
    • Structure
    • Substructure
• 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
    • aso2()
  • COV_CN
    • dftd_coordination_number()
  • GridBased
    • prune()
    • nearest_atom_index()
    • atomic_indicator_field()
    • aso()
    • aeif()
• 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
• molli.ftypes
  • CDXML Parser
    • CDXMLSyntaxWarning
    • validate_label()
    • validate_fragment()
• molli.math
  • Rotation
    • rotation_matrix_from_vectors()
    • rotation_matrix_from_axis()
• molli.pipeline: External Drivers
  • Structure of Jobs
  • External Drivers and Available Methods

Command Line Reference

• molli Command Line
  • About this tutorial
  • Basic structure of molli package.
  • Command line
  • Align
  • Combine
  • Compile
  • GBCA
  • Grid
  • List Names
  • Parse
  • Recollect
  • Show
  • Stats
  • Test
  • Map

Molli Cookbook

• Welcome to molli
  • About this tutorial
  • Basic structure of molli package.
  • Command line
• Basic objects
  • Molecule
  • ConformerEnsemble
  • Substructure
• Molecule and Atom Introduction
  • Molecule
  • Atom class
• Bond Class
  • Bond Deletion
  • Other Miscellaneous Properties of Bonds
• Coordinates and Other Geometric Manipulations
• Conformer Ensembles
  • Key Properties of Conformer Ensemble
  • Key Methods in ConformerEnsemble
  • Potential Unexpected Behavior
• Libraries and Serialization
  • Molecule Library
  • Reading and Writing Multiple Libraries
  • ConformerLibrary
• Visualization Tools
  • Molecule Visualization Example
  • ConformerEnsemble Visualization Example
  • MoleculeLibrary and ConformerLibrary Visualization
  • Visualizaing Molecules with Pyvista
  • Visualizing Molecules with Matplotlib
• Reading ChemDraw files
  • Reading Example
  • Point Chirality Example
  • Reading Label Example
  • Axial Chirality Example
  • Planar Chirality Example
  • Charge Example
  • Charge and Multiplicity Example
  • Multiplicity Example
• OpenBabel Interface
  • CDXMLFile to Optimized Structure Example
  • Multi-Attachment Optimization from CDXML File
• RDKit Interface
  • Object creation
  • Canonicalization of 2D and 3D objects
  • The Atom Filter Class
  • Visualization of Molecules
• Grid Creation and Grid-Based Descriptor Calculation
  • Grid Creation
  • Grid-Based Conformer-Average (GBCA) Descriptor Calculation
• Parallelized Calculations and Jobmapping
  • Example 1: Running a Job on a Local Computer
  • Example 2: Running a Job on a Cluster
  • Example 3: Loading Encoded Output Files
• Workflow Example: Copper-BOX Catalyst Library Construction
  • Part 1: Parsing and Combinatorial Expansion
  • Part 2: Adding Hydrogens and Optimization
  • Example 2: XTB Optimization via Job Mapping
• molli map script
• Library manipulation scripts
  • molli merge
  • molli pick

Benchmarks and Workflows

• Example 1: Recompile MolNet
  • Objectives
  • Prerequisites
  • Hardware Specification for Rerun
  • Step 1. Download the molecule_net.tar.gz archive
  • Step 2. Convert the data to molli .clib format
  • Step 3. Enjoy the concise syntax for operating with the molecule objects
• Example 2: Recompile Crude GeomSet
  • Objectives
  • Prerequisites
  • Hardware Specification for Rerun
  • Step 1. Download the data archive
  • Step 2. Convert the data to molli .clib format
  • Step 3. Enjoy the concise syntax for operating with the molecule objects
  • Step 4. Reimport bonds
• Example 3: Build a Combinatorial Library
  • Hardware Specification for Rerun
  • Overview.
  • Import prerequisite molecules as molli collections
  • Achiral phosphine ligands
  • Chiral phosphine ligands
• Example 4: Reading and Writing Benchmark
  • Hardware Specification for Rerun
  • Writing Times
  • Reading Times
• 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 Scripts
• molli Case Study 2: NMR Prediction of Cladosporin
  • molli Study case: Cladosporin GIAO-DFT NMR prediction
  • Supplementary Script

Miscellaneous

• Inheritance Diagram for Molli
• Extensions

Indices and tables

• Index

• Module Index

• Search Page