EPAM Indigo projects
Copyright (c) 2009-2020 EPAM Systems, Inc.
Licensed under the Apache License version 2.0
Introduction
This repository includes:
- Bingo: Chemistry search engine for Oracle, Microsoft SQL Server and PostgreSQL databases
- Bingo-elastic: Set of APIs for efficient chemistry search in Elasticsearch
- Indigo: Universal cheminformatics library with bindings to .NET, Java and Python, and the following tools:
- Legio: GUI application for combinatorial chemistry
- ChemDiff: Visual comparison of two SDF or SMILES files
- indigo-depict: Molecule and reaction rendering utility
- indigo-cano: Canonical SMILES generator
- indigo-deco: R-Group deconvolution utility
Detailed documentation is available at http://lifescience.opensource.epam.com
Changelogs could be found here:
Download
https://lifescience.opensource.epam.com/download/indigo/index.html
Bindings in public repositories:
- .NET: https://www.nuget.org/packages/Indigo.Net
- Java: https://search.maven.org/search?q=g:com.epam.indigo
- Python: https://pypi.org/project/epam.indigo/
Source code organization
Main directory structure layout:
api
: Indigo API sourcesbingo
: Bingo sourcesbuild_scripts
: CMake and python scripts for building all the sourcesthird_party
: sources for third-party librariesutils
: utilities sourcescommon
|graph
|layout
|molecule
|reaction
|render2d
: indigo-core sources
Each project is placed in the corresponding directory with CMakeList.txt configuration file, that does not include other projects. In order to build the whole project with the correct references you need to use CMake configurations from the build_scripts directory.
Preinstalled build tools
To build the project from the sources, the following tools should be installed:
- GIT 1.8.2+
- GIT-LFS, so GIT can handle Large File Storage. Refer to https://github.com/git-lfs/git-lfs/wiki/Installation
- C/C++ compiler with C++11 support
- Linux: GCC version 4.9+ or Clang version 3.5+
- Windows: Visual Studio 2013+ or MinGW with GCC version 4.9+
- macOS: Clang 3.5+
- CMake 3.0+
- Python 2.7+
- JDK 1.8+
- .NET Standard 2.0
- Maven 3.1+
Build instructions
All the CMake projects are placed in build_scripts
directories. You can use them manually,
or execute preconfigured scripts those do all the job.
Bingo build instructions
To generate project configuration, build the source code, and create the archives for
installation, execute build_scripts/bingo-release.py
:
python build_scripts/bingo-release.py --preset=linux32 --dbms=[postgres|oracle|sqlserver]
There are different cmake presets:
linux32
, linux64
, win32
, win64
, mac10.7
(and also all later mac10.x versions)
There are different dbms targets:
postgres
- PostgreSQLoracle
- Oraclesqlserver
- Microsoft SQL Server
Indigo build instructions
To generate project configuration, build the source code, and create the archives for
installation, execute build_scripts/indigo-release-libs.py
and
build_scripts/indigo-release-utils.py
:
Linux (GCC 4.9+ or Clang 3.5+)
APT-based requirements (Debian or Ubuntu):
sudo apt install cmake libfreetype6-dev libfontconfig1-dev
RPM-based requirements (RedHat, CentOS, Fedora): install Developer Toolset if your OS does not have GCC 4.9+ and then install dependencies:
sudo yum install cmake freetype-devel fontconfig-devel
Build libraries and utils:
python build_scripts/indigo-release-libs.py --preset=linux64
python build_scripts/indigo-release-utils.py --preset=linux64
Windows (Microsoft Visual Studio 2013+ or MinGW with GCC version 4.9+)
python build_scripts/indigo-release-libs.py --preset=win64-2013
python build_scripts/indigo-release-utils.py --preset=win64-2013
Mac OS (Clang 3.5+)
python build_scripts/indigo-release-libs.py --preset=mac10.14
python build_scripts/indigo-release-utils.py --preset=mac10.14
Other presets
There are different presets for the build scripts:
win32-2013
,win64-2013
: Visual Studio 2013win32-2015
,win64-2015
: Visual Studio 2015win32-2017
,win64-2017
: Visual Studio 2017win32-2019
,win64-2019
: Visual Studio 2019win32-mingw
: MinGWwin64-mingw
: MinGW-w64linux32
,linux64
: GCC or Clang on Linux with C++11 supportlinux32-universal
,linux64-universal
: GCC on Linux with statically linked libstdc++ for using on older Linux systems without C++11 supportmac10.7
,mac10.8
,mac10.9
,mac10.10
,mac10.11
,mac10.12
,mac10.12
,mac10.13
,mac10.14
,mac10.15
: target Mac OS X or macOSmac-universal
: targeting Mac OS X 10.7 as first version with C++11 support, should work on all Mac OS X 10.7+ systems
Wrappers build instructions
To generate Java, C#, or Python wrappers after building the binaries, execute:
python build_scripts/indigo-make-by-libs.py --type=[java|dotnet|python]
Available wrapper types: java
, dotnet
, python
.