README.md

ProStruct

ProStruct is a protein structure analysis tool with the end goal of becoming a fast and user friendly library.

To achieve fast speeds and maximise performance given the available linear algebra libraries ProStruct uses Armadillo. Armadillo can currently use BLAS/LAPACK, OpenBLAS, MKL and NVBLAS. In addition, the code is parallelised where possible using OpenMP (with intra and intercore optimisations).

In addition, ProStruct is available in Python, Perl and R using SWIG. The list of interfaces will (potentially) continue to grow.

I also try to write C++ code using the latest standards, so you might need a relatively recent compiler to build Prostruct.

Contributions are welcome!

Examples:

C++:

#include <prostruct/prostruct.h>

using namespace prostruct;

auto pdb = PDB<float>("mypdb.pdb");
auto radii = pdb.get_radii(); // arma::Col<float>
auto ks = pdb.compute_kabsch_sander() // arma::Mat<float>

Python:

import prostruct

pdb = prostruct.PDB_float("mypdb.pdb")
radii = pdb.get_radii() # numpy array
ks = pdb.compute_kabsch_sander() # numpy array

The python behaviour can be further extended using SWIG directors, as shown here.

R:

dyn.load(paste("prostruct", .Platform$dynlib.ext, sep=""))
source("prostruct.R")
cacheMetaData(1)

pdb <- PDB_float("mypdb.pdb")
radii = pdb$get_radii() # R vector
ks = pdb$compute_kabsch_sander() # R matrix

Perl:

use prostruct;

my $pdb = new prostruct::PDB_float("mypdb.pdb");
my $radii = $pdb->get_radii(); # Perl array of scalars
my $ks = $pdb->compute_kabsch_sander(); # Perl array of references to arrays of scalars

Build with CMake

Currently ProStruct is only available from source.

mkdir build
cd build
cmake ..
make

To build code with full compiler optimisations run cmake in Release mode:

cmake -DCMAKE_BUILD_TYPE=Release ..

With Python interface:

cmake -DPYTHON_EXECUTABLE=/my/path/to/python -DPYTHON_LIBRARY=/my/path/python/to/lib/libpython3.6m.so -DPYTHON_INCLUDE_DIR=/my/path/to/include/python3.6m/ ..

Known issues:

• On some platforms you might have to compile with -fPIC due to the fmt static library. The compiler will throw an error like this:

  /usr/bin/ld: extern/fmt/libfmt.a(format.cc.o): relocation R_X86_64_PC32 against symbol `_ZN3fmt2v58internal12basic_bufferIcE6resizeEm' can not be used when making a shared object; recompile with -fPIC

  To do this just re-run cmake with this:

  cmake -DCMAKE_POSITION_INDEPENDENT_CODE=ON ...