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stk

  • Construction Overview
    • Introduction
    • Topology Graph
    • Building Blocks
  • Basic Examples
    • Creating Building Blocks
    • Specifying Multiple Functional Groups
    • Constructing Molecules
    • Using Built-in Optimizers During Construction
    • Using RDKit to Optimize Molecular Structures
    • Writing Molecular Files
    • Placing and Retrieving Molecules From a Database
      • Requirements
      • Molecules and Building Blocks
      • Constructed Molecules
    • Placing and Retrieving Molecular Property Values From a Database
      • Requirements
      • Storing Values
    • Specifying Functional Groups Individually
    • Changing Bonder and Deleter Atoms in Functional Group Factories
    • Handling Molecules with Metal Atoms and Dative Bonds
    • Making Keys for Molecules with Dative Bonds
    • Creating New Topology Graphs with Existing Vertices
    • Extending stk
  • Video Tutorials
    • Basics of stk
    • Functional Groups in stk
    • Cage Building
    • Hierarchical Construction with stk
    • Using stko with stk
    • Databases and stk-vis in stk
    • Host-Guest Conformers with stk

Molecules

  • Building Block
  • Constructed Molecule
  • Functional Groups
    • Alcohol
    • Aldehyde
    • Alkene
    • Alkyne
    • Amide
    • Boronic Acid
    • Bromo
    • Carboxylic Acid
    • Dibromo
    • Difluoro
    • Diol
    • Fluoro
    • Generic Functional Group
    • Iodo
    • Primary Amino
    • Ring Amine
    • Secondary Amino
    • Single Atom
    • Thioacid
    • Thiol
  • Functional Group Factories
    • Alcohol Factory
    • Aldehyde Factory
    • Amide Factory
    • Boronic Acid Factory
    • Bromo Factory
    • Carboxylic Acid Factory
    • Dibromo Factory
    • Difluoro Factory
    • Diol Factory
    • Fluoro Factory
    • Iodo Factory
    • Primary Amino Factory
    • Ring Amine Factory
    • Secondary Amino Factory
    • SMARTS Functional Group Factory
    • Terminal Alkene Factory
    • Terminal Alkyne Factory
    • Thioacid Factory
    • Thiol Factory
  • Key Makers
    • InChI
    • InChIKey
    • SMILES
  • Reactions
    • One One Reaction
    • One Two Reaction
    • Ring Amine Reaction
    • Two Two Reaction
    • Dative Reaction
  • Reaction Factories
    • Generic Reaction Factory
    • Dative Reaction Factory
  • Writers
    • MDL Mol
    • PDB
    • Turbomole
    • XYZ

Topology Graphs

  • Polymers
    • Linear (this is a link, click me)
  • Organic & Metal-Organic Cages
    • Organic
      • One Plus One
      • Two Plus Two
      • Two Plus Three
      • Two Plus Four
      • Three Plus Six
      • Four Plus Four
      • Four Plus Six
      • Four Plus Six 2
      • Four Plus Eight
      • Five Plus Ten
      • Six Plus Eight
      • Six Plus Nine
      • Six Plus Twelve
      • Eight Plus Twelve
      • Eight Plus Sixteen
      • Ten Plus Twenty
      • Twelve Plus Thirty
      • Twenty Plus Thirty
    • Metal-Organic
      • M2L4 Lantern
      • M3L3 Triangle
      • M3L6
      • M4L4 Square
      • M4L4 Tetrahedron
      • M4L6 Tetrahedron Spacer
      • M4L6 Tetrahedron
      • M4L8
      • M6L2L3 Prism
      • M6L12 Cube
      • M8L6 Cube
      • M12L24
      • M24L48
  • Covalent Organic Frameworks
    • Hexagonal
    • Honeycomb
    • Kagome
    • Linkerless Honeycomb
    • Square
    • Periodic Hexagonal
    • Periodic Honeycomb
    • Periodic Kagome
    • Periodic Linkerless Honeycomb
    • Periodic Square
  • Metal Complexes
    • Paddlewheel
    • Porphyrin
    • Octahedral
    • Octahedral Lambda
    • Octahedral Delta
    • Square Planar
    • Bidentate Square Planar
    • Cis Protected Square Planar
  • Host Guest Complex
  • Macrocycle
  • [n]Rotaxane
  • Adding Topology Graphs
  • Optimizers
    • Collapser
    • Periodic Collapser
    • MCHammer
    • Spinner
    • NullOptimizer

Molecular Databases

  • Molecule
    • Molecule MongoDB
  • Constructed Molecule
    • Constructed Molecule MongoDB
  • Value
    • Value MongoDB

Evolutionary Algorithm

  • Overview
  • Basic Example
    • Introduction
    • EA Components
    • Basic EA Loop
      • Adding a Database
    • Plotting the EA Progress
    • Review
    • Defining EA Components
      • Defining a Database
    • Final Version
  • Intermediate Example
    • Introduction
    • Defining a New Fitness Calculator
    • Defining a Fitness Normalizer
    • Caching Fitness Values
    • Plotting Selection
    • Final Version
  • Fitness Calculators
    • Fitness Function
    • Property Vector
  • Fitness Normalizers
    • Add
    • Divide By Mean
    • Multiply
    • Normalizer Sequence
    • Null Fitness Normalizer
    • Power
    • Replace Fitness
    • Shift Up
    • Sum
  • Selection
    • Above Average
    • Best
    • Filter Batches
    • Filter Molecules
    • Remove Batches
    • Remove Molecules
    • Roulette
    • Stochastic Universal Sampling
    • Tournament
    • Worst
  • Mutation
    • Molecule
      • Random Building Block
      • Random Topology Graph
      • Similar Building Block
    • Compound
      • Random Mutator
  • Crossover
    • Molecule
      • Genetic Recombination
    • Compound
      • Random Crosser
  • Plotting
    • Progress
    • Selection

Modules

  • Modules
    • stk package
      • Subpackages
        • stk.databases package
        • stk.ea package
        • stk.molecular package
        • stk.serialization package
        • stk.utilities package
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