ProLIF-Coloring

Overview

This is an C++ implementation of algorithms capable of generate discrete volume-application-descriptions of protein-ligand interactions.

This implementation is based on ProLIF protein-ligand interaction definitions

This implementation uses RDKit software library in order to handle SMART patterns, geometry calculation and .pdb files import/export

This is part of a project-work for Advanced Computer Architectures course @Polimi

Authors

Project developed by:

• Enrico Tirri

File Structure

• include-base - headers files where:

  • Mesh.hpp - defines the data structure containing the discrete molecule mesh
  • Discretizer.hpp - defines method to transform rdkit molecule into mesh and vice versa
  • Interaction.hpp - defines the basic method interfaces and structure an interaction should have
  • InteractionCollection.hpp - defines the structure the collection of interaction to be applied should have
  • DistanceInteraction.hpp - defines the basic method interface and structure a distance-based interaction should have
  • SingleAngleInteraction.hpp - defines the basic method interface and structure a single-angle-based interaction should have
  • RestrictedBasePIStackingInteraction.hpp - defines the basic method interface and structure a base-pi-stacking-based interaction should have

• include-extended - header files of interaction classes extensions

• src - source file of headers multi-platform implementation

• src-normal - source file of headers cpu based, single threaded implementation

• src-omp - source file of headers cpu based, openmp multithreaded implementation

• src-cuda - source file of headers gpu based, cuda implementation

How to build

In order to build the executable, from the root folder run the following commands:

$ mkdir build
$ cd build
$ cmake .. _FLAGS_
$ make

_FLAGS_ are optional, they can be:

• -D USECUDA=1/0' - specify if to use gpu based, cuda implementation of interactions
• -D CUDA_BLOCK_SIZE=_size_block_ - specify the size of cuda-thread-block to be used
• -D USEOMP=1/0' - specify if to use cpu base, openmp implementation of interactions
• -D OMP_NUM_THREADS=_num_threads_ - specify the number of threads used by omp implementation

How to run

$ ./ProLIF_Coloring input.pdb

where:

• input.pdb - is a path/filename to .pdb input molecule file

Showcase