Index

A

About Acknowledgements API Documentation Atoms 2D Coordinates Calculation 2D Coordinates Property, [1] 3D Coordinates Array Property, [1], [2], [3] 3D Coordinates Calculation 3D Coordinates Property, [1], [2], [3], [4], [5] Allred-Rochow Electronegativity Query Amide-type Carbon Check Amide-type Nitrogen Check Aromaticity Flag Property, [1], [2], [3], [4], [5] Aromaticity Perception, [1], [2], [3], [4] Atom Mapping ID Property, [1], [2] Atomic Weight Query Bridgehead Atom Check Carbonyl-type Carbon Check Chain ID Property, [1] CIP Priority Calculation, [1] CIP Priority Property, [1] Connected Aromatic Atom Count Query Connected Carbon Atom Count Query Connected Chain Atom Count Query Connected Halogen Atom Count Query Connected Heavy Atom Count Query Connected Heteroatom Count Query Connected Hydrogen Atom Count Query Connected Ring Atom Count Query Covalent Radius Query Descriptor Generation Effective Polarizability Calculation Element Name Query Environment Extraction, [1] Exerted Inductive Effect Calculation Formal Charge Property H-Bond Acceptor Check H-Bond Acceptor Type Perception H-Bond Acceptor Type Property H-Bond Donor Check H-Bond Donor Type Perception H-Bond Donor Type Property Halogen Class Check Heavy Atom Check Heavy Neighbor Atom Count Retrieval Hybrid Polarizability Query Hybridization State Perception, [1], [2], [3], [4] Hybridization State Property, [1], [2], [3], [4], [5] Hydrogen Type Inquiry Hydrophobicity Calculation Hydrophobicity Property Implicit Hydrogen Count Calculation, [1], [2], [3], [4] Implicit Hydrogen Count Property, [1], [2], [3], [4], [5], [6] Incident Aromatic Bond Count Query Incident Chain Bond Count Query Incident Double Bond Count Query Incident Heavy Atom Bond Count Query Incident Ring Bond Count Query Incident Rotatable Bond Count Query Incident Single Bond Count Query Incident Triple Bond Count Query Invertible Nitrogen Check IUPAC Group Query Lone-pair Electronegativity Calculation Main Group Element Class Check Metal Class Check MHMO Pi Charge Property MMFF94 Atom Typing, [1] MMFF94 Numeric Type Property, [1] MMFF94 Partial Charge Calculation, [1] MMFF94 Partial Charge Property, [1] MMFF94 Symbolic Type Property, [1] Noble gas Class Check Non-Metal Class Check PEOE Sigma Charge Property PEOE Sigma Electronegativity Property Pi Electronegativity Calculation Planar Nitrogen Check Property Calculation, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26] PTE Period Number Query Residue Sequence Number Property, [1] Residue Three-Letter Code Property, [1] Ring Flag Property, [1], [2], [3], [4] Ring Membership Perception, [1], [2], [3], [4] Semi-Metal Class Check Spiro Center Check Stereo Center Flag Property, [1], [2] Stereo Center Perception, [1], [2] Stereo Descriptor Calculation, [1], [2] Stereo Descriptor Property, [1], [2], [3], [4], [5] Steric Number Query Supported Chemical Element Check Sybyl Type Perception Sybyl Type Property Symbol Property, [1], [2] Total Partial Charge Calculation Transition Metal Class Check Type Property, [1], [2] Unsaturatedness Check Valence Electron Count Calculation Valence Electron Count Query Valence Query VdW Radius Query VSEPR Coordination Geometry Query

Authors

B

Bibliography Biological Macromolecules Binding Site Characterization Input, [1] Ligand Interaction Analysis Primary Structure Analysis, [1] Processing, [1] Residue Processing, [1] Bonds 2D Stereo Flag Calculation 2D Stereo Flag Property, [1] Aromaticity Flag Property, [1], [2], [3], [4], [5] Aromaticity Perception, [1], [2], [3], [4] MMFF94 Bond Type Index Property, [1] MMFF94 Bond Typing, [1] Order Property Property Calculation, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26], [27] Ring Flag Property, [1], [2], [3], [4] Ring Membership Perception, [1], [2], [3], [4] Rotatability Check Stereo Center Flag Property, [1] Stereo Center Perception, [1] Stereo Descriptor Calculation, [1] Stereo Descriptor Property, [1], [2], [3]

Building CDPKit

C

Citing CLI Applications 3D Structure Generation Conformer Generation, [1] Gaussian Shape-based Screening Pharmacophore Screening, [1], [2], [3] Similarity Screening Stereoisomer Enumeration Substructure Searching Tautomer Generation

D

Data Formats CDF, [1], [2], [3] MDL SD-Files, [1], [2], [3], [4] mmCIF, [1] MMTF, [1] MOL2, [1] PDB, [1] PLY PML, [1], [2], [3] R3D SMARTS, [1], [2] SMILES, [1], [2], [3], [4], [5], [6] STL WRL

Descriptors Daylight Fingerprint Generation ECFP Fingerprint Generation FAME Atom Environment Fingerprint Generation MDL MACCS Key Generation Morgan Fingerprint Generation Pharmacophore Fingerprint Generation PubChem Fingerprint Generation Receptor Binding Pocket Descriptor Generation

F

Force Fields MMFF94 Aromaticity Perception, [1] MMFF94 Atom Typing, [1] MMFF94 Bond Typing, [1] MMFF94 Partial Charge Calculation, [1]

G

GUI Applications Molecule/Reaction Data File Inspection

I

Installation from Source using Installer Packages using pip

Introduction

K

Kabsch Alignment

Key Features

L

License

M

Molecules 2D Structure Layout Generation 3D Coordinates-based Alignment, [1] 3D Structure Generation, [1] Aromaticity Perception, [1], [2], [3], [4] Atom 2D Coordinates Calculation Atom 2D Coordinates Manipulation Atom 3D Coordinates Calculation Atom 3D Coordinates Manipulation, [1], [2] Atom 3D Coordinates Processing, [1], [2], [3] Atom 3D Coordinates Transformation, [1] Atom CIP Priority Calculation, [1] Atom Environment Extraction, [1] Atom Hybridization State Perception, [1], [2], [3], [4] Atom Hydrophobicity Calculation Atom Implicit Hydrogen Count Calculation, [1], [2], [3], [4] Atom Order Canonicalization Atom Processing, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] Atom Property Calculation, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26] Atom Ring Membership Perception, [1], [2], [3], [4] Atom Stereo Center Perception, [1], [2] Atom Stereo Descriptor Calculation, [1], [2], [3] Bemis-Murcko Scaffold Analysis Bond 2D Stereo Flag Calculation Bond Processing, [1], [2] Bond Property Calculation, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26], [27] Bond Ring Membership Perception, [1], [2], [3], [4] Bond Stereo Center Perception, [1] Bond Stereo Descriptor Calculation, [1], [2] BRICS Fragmentation Canonical Atom Numbering Calculation ChEMBL Structure Curation Components Perception, [1], [2], [3], [4], [5], [6], [7] Components Processing Components Property, [1], [2], [3], [4], [5], [6], [7], [8] Conformer Alignment, [1] Conformer Ensemble Handling, [1], [2], [3], [4], [5] Conformer Generation, [1], [2] Daylight Fingerprint Generation Descriptor Generation, [1], [2], [3], [4], [5] ECFP Fingerprint Generation Element Histogram Generation Element Histogram Processing FAME Atom Environment Fingerprint Generation Fingerprint Generation, [1], [2], [3], [4] Fragments, [1], [2], [3], [4], [5], [6] Functional Group Analysis Functional Group Perception Gaussian Shape Generation Gaussian Shape-based Alignment, [1] Gaussian Shape-based Alignment Scoring H-Bond Acceptor Atom Type Perceptions H-Bond Donor Atom Type Perceptions Hueckel Molecular Orbital Calculations Hydrogen 3D Coordinates Calculation, [1] Hydrogen Completion, [1], [2], [3], [4], [5] Hydrogen Depletion Input, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26], [27], [28], [29], [30], [31] MDL MACCS Key Generation MMFF94 Aromatic Ring Set Property, [1] MMFF94 Aromaticity Perception, [1] MMFF94 Atom Typing, [1] MMFF94 Bond Typing, [1] MMFF94 Partial Charge Calculation, [1] Morgan Fingerprint Generation Name Property, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] Output, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] PEOE Charges Calculation Pharmacophore Fingerprint Generation Pharmacophore Generation Pharmacophore-based Alignment, [1] Pi Electron System List Property Pi Electron System Perception Preparation for Pharmacophore Generation, [1], [2], [3] Property Calculation, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25] Protonation State Standardization, [1] PubChem Fingerprint Generation RECAP Fragmentation Rule-based Fragmentation SMARTS Parsing, [1], [2], [3] SMILES Generation SMILES Parsing SSSR Perception, [1], [2], [3], [4], [5], [6] SSSR Property, [1], [2], [3], [4], [5], [6] Stereo Center Perception Stereoisomer Enumeration, [1] Structure Structure Data Manipulation, [1] Structure Data Processing, [1], [2] Structure Data Property, [1], [2], [3] Structure Manipulation, [1], [2], [3], [4], [5] Structure Standardization Substructure Editing Substructure Match Processing, [1], [2] Substructure Matching, [1], [2], [3], [4] Sybyl Atom Type Perception Tautomer Generation Topological Distance Matrix Generation, [1], [2] Topological Distance Matrix Property, [1], [2] Torsion Driving

P

People Pharmacophore Features 3D Coordinates Property Disabled Flag Property Geometry Property, [1] Hydrophobicity Property Optional Flag Property Orientation Property, [1], [2] Orientation Vector Length Property Tolerance Property Type Property Weight Property Pharmacophores 3D Visualization Alignment, [1] Alignment Scoring Feature Processing, [1], [2] Fingerprint Generation Generation, [1], [2] Input, [1], [2], [3] Name Property, [1], [2] Output, [1] Preparation for Generation, [1], [2] Processing, [1], [2] Screening

Publications Python CDPL Bindings Code Snippets, [1] Cookbook Examples Getting Started Jupyter Notebook pip PyPI Tutorial

R

Related Software

Release Notes