This is a simple template library for basic operations on proteins.
- Operating system: GNU/Linux
- C++ compiler: gcc4.6 (or newer) or equivalent
- Eigen3 (required)
- boost, cgal (optional)
BioCpp is C++0x standard.
BioCpp uses Eigen3 for atom coordinates, geometrical transformations and this kind of stuffs. So you need to download it from here.
Eigen3 needs no installation: simply download the source code and extract it.
The only thing to keep in mind is that the compiler must be able to find the
Eigen header files. Simply add the path to the extracted folder to your
CPLUS_INCLUDE_PATH. In order to achieve this you can export the path at
login by adding
export CPLUS_INCLUDE_PATH=$CPLUS_INCLUDE_PATH:/path-to-header-files/to your .bashrc and/or .bash_profile file if you are using bash or sh
shell or, alternatively,
if ( $?CPLUS_INCLUDE_PATH ) then
setenv CPLUS_INCLUDE_PATH {$CPLUS_INCLUDE_PATH}:/path-to-header-files/
else
setenv CPLUS_INCLUDE_PATH /path-to-header-files/
endifto your .cshrc file if you are using tcsh or csh.
Some optional functionalities require other external libraries:
-
topology is based on boost graph library. You can download boost from here. Please notice that in the near future boost will be used extensively in BioCpp
-
morphology uses cgal for protein surface reconstruction.
BioCpp now uses cmake as building system. A typical usage is
cd /path-to-biocpp/build/debug/
cmake ../..
make allYou can adapt the compilation to your setup by passing flags to the compiler. For examples
CXX=g++46 cmake ../../ -DCMAKE_CXX_FLAGS="${CMAKE_CXX_FLAGS}
-Wl,-rpath,/usr/local/gcc46/lib64" -DCMAKE_BUILD_TYPE=DebugIn order to use BioCpp in your project simply:
-
add the path containing the source code to your
CPLUS_INCLUDE_PATH. In order to do this you can pass the path/path-to/biocpp/src/to cmake. Alternatively you can export/path-to/biocpp/src/by following the previous instructions. -
import BioCpp header file
#include <BioCpp.h>Including the whole library in your project is usually not necessary. This is why BioCpp.h provides only few basic features. If your project requires more features, add them by using one (or more) of the following directives:
| Directive | Description |
|---|---|
| BIOCPP_INCLUDE_ID | Add standard identifiers for amino acids, atoms, elements, ... |
| BIOCPP_INCLUDE_DPSS | Add definitions of secondary stuctures according to dssp |
| BIOCPP_INCLUDE_MORPHOLOGY | Compute solvent-accessible surface area |
| BIOCPP_INCLUDE_RECONSTRUCTION | Compute position of missing atoms |
| BIOCPP_INCLUDE_PDB | Read and write pdb files |
| BIOCPP_INCLUDE_FASTA_ALIGN | Sequence alignment using NeedlemanWunsch algorithm |
| BIOCPP_INCLUDE_FASTA_SUBST_MATRIX_PAM30 | Use PAM30 substitution matrix |
| BIOCPP_INCLUDE_FASTA_SUBST_MATRIX_PAM70 | Use PAM70 substitution matrix |
| BIOCPP_INCLUDE_FASTA_SUBST_MATRIX_BLOSUM45 | Use BLOSUM45 substitution matrix |
| BIOCPP_INCLUDE_FASTA_SUBST_MATRIX_BLOSUM62 | Use BLOSUM62 substitution matrix |
| BIOCPP_INCLUDE_FASTA_SUBST_MATRIX_BLOSUM80 | Use BLOSUM80 substitution matrix |
| BIOCPP_INCLUDE_FASTA_SUBST_MATRIX_ZIMM1 | Use a strict version of BLOSUM62 |
| BIOCPP_INCLUDE_FASTA_SUBST_MATRIX_MATRIX | Use all the substitution matrices |
| BIOCPP_INCLUDE_STANDARD | Add standard definitions of residue, chain, complex and moiety |
| BIOCPP_INCLUDE_SUBST_MATRIX_ALL | Add all the features provided by BioCpp |
By default, if no directives are defined, only base_container and iterators are included (see Documentation and examples).
In order to add directives you can both
#define DIRECTIVE_NAMEbefore including BioCpp.h, or pass the directive name to your compiler. If you use g++, simply
g++ -D DIRECTIVE_NAME ...(see CMakeLists.txt provided in the examples folder).
This is a developing code. Newer versions of BioCpp may not be compatible with
older ones.
For this reason, if you distribute code based on BioCpp, please also provide
the version of BioCpp on which it is based.
Documentation is available in both html and
pdf format.
Documentation is not updated!!