Getting started guide
- JAVA: This version needs Oracle Java SE 8 to run.
- MEMORY: Due to the memory intensive nature of these tools 64 bit operation system and 64 bit java is recommended. Memory requirements are dependent on the number of structures and descriptors exposed. Using 1024 bit fingerprints and ususal small molecules the expected memory requirement is one GB per 3-4 million structures.
- LICENSE: License
MADFASTis required for the core functionality. License
ECFPneeded for using
ECFPfingerprint family, license
MACCSis required for
MACCS-166fingerprints. License for
Name to structureand for
Marvin JSmight needed for certain functionalities. For further questions or to obtain an evaluation or production license feel free to contact us at
The current version is supplied with
bash launcher scripts requiring linux or windows + cygwin to run. An illustrated guide for installing the prerequisites (including CygWin) on Windows is available in Installing dependencies on Windows version 10.
On Max OS X
download-molecules.sh and some documentation examples use
wget; it can be installed using
brew install wget.
Install license file
Make sure that supplied
license.cxl file is installed: the license file should be copyed to its default location. The default location is
.chemaxon/license.cxl (on Unix) or
chemaxon\license.cxl (on Windows + Cygwin). For details see ChemAxon Installing Licenses documentation.
Note that Marvin JS license stored in a separate file, see REST API / Web UI for similarity searches section Advanced server configuration: Additional static content and Self contained examples for details.
Unpack the contents of the downloaded archive. No further compilation or setup needed before invoking the command line interfaces or examples. Note that the launcher scripts in this version need to be invoked directly without using links pointing to them. Further examples will use paths relative to the distributions root directory.
tar xvf madfast-cli-0.3.1.tar cd madfast-cli-0.3.1/
By default the self contained example scripts (detailed below) use the
examples-tmp/ directory to write workfiles and results. Make sure that this directory is writable by the user. Please note that this is usually not required for in production usage.
To verify launch an executable:
A help message similar to the following is expected to appear:
Usage: <main class> [options] Options: -h, -help, --help Print help on usage then exit Default: false -count Max number of structures to input Default: 2147483647 ....
Launch self contained example
Simple search workflow
examples/search-workflow.sh. After the preparation steps this script launches similarity searches against the
drugbank dataset. For more details on the executed workflow see document Basic search workflow. The execution log file and the search results can be found in the work directory which default is
examples-tmp/search-workflow/ in the distribution directory.
# launch self contained example ./examples/search-workflow.sh # Print search results cat examples-tmp/search-workflow/drugbank-all-q1-results.txt cat examples-tmp/search-workflow/drugbank-all-q30-mostsimilars-results.txt
Final search results for searching cyclohexane (SMILES:
C1CCCCC1) against the
drugbank-all dataset (from file
Query Target Dissimilarity 0 Adamantane 0.3333333333333333
First few lines of the final search results for searching the 5 most similars for members of the
vitamins dataset against the
drugbank-all dataset (from file
Query Target Dissimilarity 0 Vitamin A 0.0 0 Alitretinoin 0.14814814814814814 0 Tretinoin 0.14814814814814814 0 Isotretinoin 0.14814814814814814 0 1,3,3-trimethyl-2-[(1E,3E)-3-methylpenta-1,3-dien-1-yl]cyclohexene 0.1956521739130435 1 Alitretinoin 0.14814814814814814 1 Tretinoin 0.14814814814814814 1 Isotretinoin 0.14814814814814814 1 1,3,3-trimethyl-2-[(1E,3E)-3-methylpenta-1,3-dien-1-yl]cyclohexene 0.1956521739130435 1 4-Oxoretinol 0.23333333333333334 2 1,3,3-trimethyl-2-[(1E,3E)-3-methylpenta-1,3-dien-1-yl]cyclohexene 0.02631578947368421 2 Vitamin A 0.17391304347826086 2 (6e)-6-[(2e,4e,6e)-3,7-Dimethylnona-2,4,6,8-Tetraenylidene]-1,5,5-Trimethylcyclohexene 0.2 2 Alitretinoin 0.2962962962962963 2 Tretinoin 0.2962962962962963 3 Thiamine 0.0 3 Thiamin Phosphate 0.15757575757575756 ....
Launch Web UI
examples/rest-api-small.sh. This script calculates
CFP-7 fingerprints for the
nci-250k dataset and launches a web based user interface where real time similarity search of the dataset is available. Profiling and execution statistics data is also collected and exposed. For details on launching the web ui and on other self contained examples see document REST API example.
Preprocessing time is expected to be under a minute on an average machine. After the preprocessing the scripts starts the web ui server which listens http://localhost:8085. When option
-b passed to the example script the Web UI will try to launch the default web browser.
.... Try to launch browser on http://localhost:8085/index.html
A browser window is opened and an index page is displayed:
On the displayed index page select
nci-250k-cfp7 from Molecular descriptors to launch the real time similarity search example.
nci-250k from Molecule set to see the structures in the set.
Scripts exposing multiple, larger datasets, multiple descriptors are also available (rest-api-XXXX.sh). For an overview see document Self contained examples.