namespace core

Overview

The core classes of the BioShell package. More…

// namespaces

namespace core::algorithms
    namespace core::algorithms::trees
namespace core::alignment
    namespace core::alignment::scoring
    namespace core::alignment::tasks
namespace core::calc
    namespace core::calc::clustering
    namespace core::calc::numeric
    namespace core::calc::statistics
    namespace core::calc::structural
        namespace core::calc::structural::transformations
namespace core::chemical
namespace core::data
    namespace core::data::basic
    namespace core::data::io
    namespace core::data::sequence
    namespace core::data::structural
namespace core::protocols

// typedefs

typedef unsigned char index1
typedef unsigned short int index2
typedef unsigned int index4
typedef double real

// structs

struct BioShellVersion

// classes

class BioShellEnvironment

// global functions

const std::string get_env_var (const std::string& key)

std::ostream& operator<< (
    std::ostream& ostream,
    const BioShellVersion& ver
    )

Detailed Documentation

The core classes of the BioShell package.

Provides methods to read a number of models (aka decoys) from PDB files.

Provides methods to read and write monomer definitions from files in different formats.

A few basic algebraic routines.

Means to calculate a score based on a substitution matrix.

Means to calculates the score of an alignment.

Handles sequences and structures, provides I/O and performs calculations

All models must be composed of the same number of atoms. By default the methods read only C-alpha atoms. This can be changed by passing an appropriate PDB-predicate as an argument

Typedefs

typedef unsigned char index1

one byte unsigned integer-type

typedef unsigned short int index2

two bytes long unsigned integer

typedef unsigned int index4

four bytes long unsigned integer

Global Functions

const std::string get_env_var (const std::string& key)

Returns a shell variable value.

Parameters:

key
  • the variable name, e.g. BIOSHELL_DATA_DIR

Returns:

the variable’s value

std::ostream& operator<< (
    std::ostream& ostream,
    const BioShellVersion& ver
    )

Prints the version onfo nicely.

Parameters:

ostream
  • output stream
ver
  • a version information

Returns:

reference to the output stream