stk
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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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stk.utilities package
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stk.utilities package
Submodules
Utilities
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