ROCS v3.0

• Front Matter

• Introduction

• Installation and Platform Notes
  • Licenses
  • General Installation
    • Linux/Unix
    • Windows
    • Mac OS X
  • PVM
    • PVM hosts file
    • PVM Scaling
  • Open MPI
    • Using Open MPI
    • Open MPI License

• vROCS Usage
  • Overview
  • Setup a simple and validation ROCS run
  • Results visualization and analysis
  • Statistics metrics
    • ROC Curve
    • AUC
    • Enrichment
    • p-Value
  • Saving ROCS data
  • ROCS shape query sources
  • Editing ROCS queries in vROCS
    • Query building wizard
    • Manual Query Building
  • vROCS menus
    • File
    • Edit
    • Help

• ROCS Usage
  • Input File Preparation
    • The Database File
    • The Query File
    • Shape Queries
    • Grid Queries
  • Command Line Interface
    • Required Parameters
    • Optional Parameters
  • Example Commands
  • Report File
  • Color Force Field
    • Default Color Files
    • Color File Format

• Tutorials
  • Introduction
  • Build/edit a query using the Wizard
    • Background information
    • Build models using the wizard
    • Visualize the results
    • Save the results
    • Conclusions
  • Build/edit a query manually
    • Background information
    • Build and edit a new query
    • Save query
    • Conclusions
  • Perform a ROCS validation run
    • Background information
    • Setup ROCS run
    • Run ROCS in validation mode
    • Visualize results
    • Compare results from multiple runs
    • Save results
    • Conclusions
  • Perform a simple ROCS run
    • Background information
    • Setup ROCS run
    • Run a simple ROCS run
    • Visualize and save results
    • Conclusions
  • Perform a ROCS run from the command line
    • Background information
    • Setup ROCS run
    • Run a simple ROCS run
    • Visualize and save results
    • Conclusions

• Theory
  • Molecular Shape
  • Shape Characteristics and the Use of Gaussians
  • Color Features

• Utilities
  • makerocsdb
  • checkcff
  • chunker
    • Command Line Parameters
    • Examples
  • hlmerge
    • Command Line Parameters
    • Examples

• Release Notes
  • ROCS 3.0.0
    • New Features
    • Bug Fixes
  • ROCS 2.4.2
    • Bug Fixes
  • ROCS 2.4.1
    • New Features
    • Bug Fixes
  • ROCS 2.3.1
    • Bug fixes
  • ROCS 2.3.0
    • Enhancements
  • ROCS 2.2
    • Enhancements
    • Bug fixes

• List of selected ROCS publications

• Bibliography