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Welcome to MadFast Similarity search

Command line distribution version 0.3.5

This is a preliminary release of the MadFast Similarity Search tools. Some of the functionalities, documentations and examples are in an incomplete state. For details see the ISSUES document. This version is intended to use only through the provided command line interfaces (found in the bin/ directory) or through the REST API. JAVA API usage needs further considerations; for details see Notes on API usage. If you have any question feel free to contact us at disco-team@chemaxon.com.

Getting started guide
A step-by-step introduction to setting up and
running MadFast Similarity Search with an overview
of its licensing and system requirements.
Browse documentation

Walktrough

REST API/Web UI introduction

Launching an embedded HTTP server to provide a simple REST style API/Web UI for remote clients and for desktop (GUI) users.

REST API security considerations

Security considerations regarding the deployment of the MadFast embedded server into production environments.

Introduction to overlap analysis

Launch and visualize the results of a similarity based overlap analysis of two datasets.

Basic search workflow

Basic similarity search workflow including processing of molecule files, generating descriptors and launching similarity searches from the command line.

Using custom binary descriptors

Basic workflow around using custom binary descriptors. In this example the descriptors (fingerprints) are available in the form of a binary string and not generated by the integrated tools.

Using custom float descriptors

Basic workflow around using custom float vector descriptors.

Store additional data

Work in progress development. Additional data (SDF properties, ChemicalTerms expressions) can be calculated/stored for structures. Storing and visualizing such additional data currently possible only for similarity based overlap analysis

Prepare public molecule sets

Instructions for downloading and preparation of publicly available molecule sets to be used with MadFast tools.

References

Command line interfaces

Brief description of the command line interfaces (CLIs) found in directory bin/.

Self contained examples

Brief description of the self contained example workflows found in directory examples/.

Glossary

With explanation of specific terms used in the documentation/api.

API documentations

REST API

Generated by tool Enunciate.

Java API

For reference only. Contains generated Java API documentation for various parts of the MadFast (Overlap), descriptors, clustering and ChemAxon backend classes. Many of these classes in this documentation do not belong to the ChemAxon public APIs.

Notes on API usage

Details on the limitations of the Java API provided in this distribution.

Other

Getting started guide

A step-by-step introduction of the available functionalities. This guide also contains details on licensing system requirements.

Installing dependencies on Windows version 10

A step-by-step walkthrough with screenshots on downloading and installing prerequisites (Java, CygWin, ChemAxon license) on Windows 10.

Performance overview

Expected performance and resource usage of various tasks, benchmarked on multiple computers.

Changes

List of changes, including incompatible changes.

Issues

List of known issues.

Introduction to REST API

A presentation.

Advanced topics

Details of searchStorage

Details on the command line tool searchStorage internals.

Overlap analysis context

Introduction to the concepts of overlap analysis contexts.

Metric customization

Introduction for using other than default comparison metrics.

Profiling and execution statistics

Introduction to code execution instrumentation and benchmarking. This document details the usage of options -prof and -stat.

Server memory optimization

Introduction and case study of optimizing memory settings for exposing large (>100M) datasets.

Verification and benchmarking of concurrent implementations

Describes a verification workflow to compare generated descriptors with a reference.

Experimental features

Asynchronous server loading

Follow server startup and data loading through the Web UI and REST API.

Asynchronous search tasks

Experimental, work in progress possibility to launch long running asynchronous tasks progress reporting and cancellation.

Raw file handling

Experimental, work in progress possibility of the MadFast REST server to accept, store and retrieve arbitrary (small) raw binary content.

Using MadFast Web UI JS library

Experimental, work in progress approach to allow reusing/modifying MadFast Web UI through a supplied JS client library.
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