igrow is a multithreaded structure-based drug design tool for computational drug discovery. It is inspired by AutoGrow, and is hosted by GitHub at https://github.com/HongjianLi/igrow under Apache License 2.0.
- igrow uses idock as backend docking engine.
- igrow supports halogen replacement and branch replacement in addition to hydrogen replacement.
- igrow digests ligands and fragments in pdbqt format, saving the effort of frequently calling the prepare_ligand4 python script.
- igrow invents its own io service pool in order to reuse threads and maintain a high CPU utilization throughout the entire synthsizing procedure. The io service pool parallelizes the creation of mutants and children in each generation.
- igrow utilizes flyweight pattern to cache fragments and dynamic pointer vector to cache and sort ligands.
- igrow traces the sources of generated ligands and dumps the statistics in csv format so that users can easily get to know how the ligands are synthesized from the initial elite ligands and fragments.
- Arch Linux 3.12.9 x86_64 and CLANG 3.4
- Windows 7 SP1 x64 and Visual Studio 2013 Update 1
igrow depends on Boost C++ Libraries. Boost 1.55.0 is supported. The must-be-built libraries required by igrow are System, Filesystem and Program Options. An unofficial header-only library, Boost.Process, is also required by igrow. The file process.zip must be extracted to the Boost distribution tree in order to pass compilation.
The Makefile uses clang as the default compiler. To compile, simply run
make
One may modify the Makefile to use a different compiler or different compilation options.
The generated objects will be placed in the obj folder, and the generated executable will be placed in the bin folder.
Visual Studio 2013 solution and project files are provided. To compile, simply run
msbuild /t:Build /p:Configuration=Release
Or one may open igrow.sln in Visual Studio 2013 and do a full rebuild.
The generated objects will be placed in the obj folder, and the generated executable will be placed in the bin folder.
First add igrow to your PATH environment variable.
To display a full list of available options, simply run the program without arguments
igrow
The examples folder contains several use cases. For example, to grow TMC278 and dock the generated ligands against HIV-RT of PDB ID 2ZD1,
cd examples/2ZD1
One can supply the options from command line arguments
igrow --initial_generation_csv ../../../idock/examples/2ZD1/ZINC/log.csv --fragment_folder ../../fragments --idock_config idock.cfg
Or one can instruct igrow to load the options from a configuration file
igrow --config igrow.cfg
Documentations in both HTML and LaTeX formats can be esaily created by running doxygen
doxygen igrow.dox
The created documents will be placed in doc folder. To compile LaTeX files into PDF, one must have pdflatex installed.
make -C doc/latex
The generated PDF will be refman.pdf.
- Used idock as backend docking engine.
- Supported direct PDBQT manipulation without file format conversion.
- Used dynamic pointer vector to cache ligands.
- Used flyweight pattern to cache fragments.
- Supported dumping statistics and traceability of created ligands.
- Allowed users to specify the ranges of several chemical properties such as molecular weight.
- Allowed users to specify the number of failures of GA operations as a stopping criterion.
- Used docked atom coordinates to construct child ligands of the next generation.
- Parallelized mutation and crossover operations.
- Provided precompiled executables for 64-bit Linux and Windows.
