CoordgenLibs

This is Schrödinger, Inc's 2D coordinate generation. It was formerly proprietary code, but is now released under the BSD license. The emphasis of these algorithms are on quality of 2D coordinates rather than speed of generation. The algorithm distinguishes itself from many others by doing well with both macrocycles and metal complexes. It also does extremely well on typical drug-like small molecules, and has been validated on millions of compounds.

Schrodinger intends to continue to contribute to this code as it still uses it inside its products, but will also be happy if others contribute pull-requests when there are improvements they would like to make. We'll also be happy to hear bug reports or feature requests from use of this code, though make no guarantee on our ability to process these.

Documentation

Examples and documentation will be added/improved over time

Templates

Coordgen uses templates for some macrocycle systems. The source for the templates is templates.mae. If you're an end user of coordgen, you can add local templates in a file called user_templates.mae in a directory specified by CoordgenTemplates::setTemplateDir(). If you want to update the templates, add new templates to templates.mae and run mol_generator.py to generate the source files.

Usage example

Code for a sample executable is provided in the example_dir directory. Building the example executable is enabled by default, but can be disabled by means of the COORDGEN_BUILD_EXAMPLE option.

Automated Testing

Automated testing is still primarily taking place inside Schrodinger's internal build system, although tests are incrementally being added to the testing directory. Building the tests is enabled by default, but can be disabled by means of the COORDGEN_BUILD_TESTS option.

Memory debugging is, by default, configured to use valgrind. It can be run on the tests by passing -DCMAKE_BUILD_TYPE=Debug to cmake, to enable building the debugging symbols, and then using ctest -T memcheck inside the build directory.

Building from source

Requirements

To build coordgen, you will need to have the following installed in your system:

• CMake version 3.2 or later.
• The development files for the Boost libraries. At least the iostreams and regex components are required. In case of also building the unit tests, the filesystems and unit_test_framework components will also be required.
• A C++ compiler supporting the C++11 standard.
• A compiled instance of the maeparser library or its source code.

In case maeparser is not available on your system, neither as a compiled library or as source code, if a working git executable and an internet connection are available, the builder can automatically download the source and build maeparser for you.

Building

1. Create a build directory inside the the one that contains Coordgen, and move into it:

   mkdir build
   cd build

2. Run cmake to configure the build, passing the path to the directory where the sources are located (just .. if you created build inside the sources directory). At this point, you should add any required flags to the cmake command. Check the 'Options' section in CMakeLists.txt to see which options are available.

   cmake .. -Dmaeparser_DIR=/home/schrodinger/maeparser_install -DCMAKE_INSTALL_PREFIX=/home/schrodinger/coordgen_install`

   A few notes on the maeparser dependency:

   • CMake will, by default, search your system's default library paths for the maeparser library. If a CMAKE_INSTALL_PREFIX was specified to Coordgen, CMake will also search for maeparser there.

   • If you already built and installed maeparser using the CMAKE_INSTALL_PREFIX to set the installation path, you should pass the exact same path to Coordgen with maeparser_DIR.

   • If CMake cannot find a compiled library for maeparser, it will attempt to download the source code from GitHub and build it. The release to be downloaded if the library is not found can be set using the -DMAEPARSER_VERSION flag. The sources will be stored in a directory named like maeparser-{MAEPARSER_VERSION} under the coordgen sources.

   • If maeparser_DIR was passed to CMake, and the library was not found, CMake will NOT download the sources from GitHub (since we expected to find a compiled library).

   • If a copy of maeparser's source is found under the proper path, it be used, instead of being downloaded again.

   • If you want to use Coordgen in a CMake project that also depends on maeparser, set up the maeparser first, as Coordgen will be able to find and use it, without searching for further libraries or compiling it again from the source code.

3. Build and install:

   make -j install