https://github.com/gf712/prostruct
Protein structure library for C++ and Python
https://github.com/gf712/prostruct
bioinformatics cpp protein-structure-analysis python swig
Last synced: 7 months ago
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Protein structure library for C++ and Python
- Host: GitHub
- URL: https://github.com/gf712/prostruct
- Owner: gf712
- License: gpl-3.0
- Created: 2018-03-29T15:33:13.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2019-05-31T06:59:52.000Z (over 6 years ago)
- Last Synced: 2025-01-29T21:54:56.412Z (8 months ago)
- Topics: bioinformatics, cpp, protein-structure-analysis, python, swig
- Language: C++
- Homepage:
- Size: 809 KB
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
[](https://travis-ci.org/gf712/ProStruct)
# 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++:
```cpp
#include
using namespace prostruct;
auto pdb = PDB("mypdb.pdb");
auto radii = pdb.get_radii(); // arma::Col
auto ks = pdb.compute_kabsch_sander() // arma::Mat
```
Python:
```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](src/interface/README.md).
R:
```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:
```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.
```bash
mkdir build
cd build
cmake ..
make
```
To build code with full compiler optimisations run cmake in Release mode:
```bash
cmake -DCMAKE_BUILD_TYPE=Release ..
```
With Python interface:
```bash
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:
```bash
/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:
```bash
cmake -DCMAKE_POSITION_INDEPENDENT_CODE=ON ...
```