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Simmate Documentation
GitHub
Home
Getting Started
Getting Started
Overview
1. Installation
1. Installation
Quick Start
a) Install Anaconda
b) Intro to the command line
c) Create your environment
d) Explore Simmate commands
e) Set up a Local Server
2. Workflows
2. Workflows
Quick Start
a) Configure the database
b) Make a input structure
c) View all workflows
d) Configure QE
e) Run a workflow
(extra) Submit to a cluster
3. Toolkit
3. Toolkit
Quick Start
a) Intro to Python (& Spyder)
b) The Structure class
e) Advanced classes
4. Database
4. Database
Quick Start
a) View data w. DBeaver
b) How tables are built
c) Workflow data
d) Third-party data
5. Custom workflows
5. Custom workflows
Quick Start
a) Basic workflows
b) Chemistry workflows
b) Class-based workflows
6. Custom apps & tables
6. Custom apps & tables
a) Create an app
b) Create a custom table
c) Adding app workflows
7. Use a cloud database
7. Use a cloud database
Quickstart
a) Private vs shared
b) Building a database
8. Computational resources
8. Computational resources
Quickstart
a) Intro to workers
Wrap up
Extra Examples
Extra Examples
Overview
Example-001
Example-002
Full Guides
Full Guides
Overview
Apps
Apps
Basic Use
Creating custom apps
Website
Website
Creating views
Creating components
Creating components
Overview
Frontend Elements
Frontend Elements
text_input
text_area
number_input
button
radio
molecule_input
selectbox
checkbox
search_box
Backend Mix-ins
Setup & Config
REST API
Workflows
Workflows
Naming Conventions
Basic Use
Creating basic workflows
Creating nested workflows
Creating "S3" workflows
Database
Database
Overview
Basic use
Workflow data
Third-party data
Contributing data
Creating custom tables
Toolkit
Toolkit
Molecules
Molecules
Overview
Single Molecule
Single Molecule
Quick Start
Molecule Loading
Molecule Exporting
Cleaning & Prep
Common Properties
Common Analyses
SMARTS sets
Many Molecules
Many Molecules
Featurizers
Clustering
ChemSpace Mapping
Similarity & Diversity
Crystal Structures
Crystal Structures
Overview
PyMatGen Help
PyMatGen Help
Structure
Lattice
Sites
Composition
Extras
Extras
Configuration
Contributing
Contributing
First time setup
Creating & submitting changes
Extra notes & tips
Maintainer notes
Utilities
Parameters
Apps
Apps
Overview
AFLOW
BadELF
BadELF
Background
Quick Start
Running in Python
ElfAnalyzerToolkit
ElfAnalyzerToolkit
Background
Usage
Bader (henkelman)
BCPC
CAS Registry
Chembl
ChemSpace
COD
eMolecules
Enamine
EPPO Global Database
Evolutionary Searches
JARVIS
Materials Project
OQMD
PDB
Quantum Espresso
RDKit
VASP
VASP
Overview
Installation
Workflows
Warren Lab
++ Experimental Apps
++ Experimental Apps
BIOVIA COMSO
CLEASE
DeepMD
OpenEye OMEGA
Schrodinger
Surflex
Updates
RDkit
ΒΆ
(documentation still being written)