PNAB Namespace Reference

The PNAB name space contains all the C++ classes and functions for the proto-Nucleic Acid Builder. More...

Classes
class	Backbone
	Class for holding backbone information. More...
class	Base
	Class to fully define bases (i.e. Adenine, Cytosine) More...
class	Bases
	A class that contains a vector of all the defined bases and a funtion to return a base and the complimentary base for all the bases defined. More...
class	BaseUnit
	Class to hold bases with backbones attached (nucleotides), along with associated necessary information. More...
class	Chain
	A class for building nucleic acid strands and evaluating their energies. More...
class	ConformationSearch
	A rotor search function used to find acceptable conformations of arbitrary backbone and helical parameter combinations. The main class of the proto-Nucleic Acid Builder. More...
struct	ConformerData
	Class to contain important information for an individual conformer. More...
class	HelicalParameters
	A class for holding values for all helical parameters. More...
class	RuntimeParameters
	A class for holding necessary and optional runtime parameters for conformational searches. More...

Functions
std::string	run (PNAB::RuntimeParameters runtime_params, PNAB::Backbone &py_backbone, std::vector< PNAB::Base > py_bases, PNAB::HelicalParameters hp, std::string prefix="run", bool verbose=true)
	A wrapper function to run the search algorithm code from python. More...
	PYBIND11_MODULE (bind, m)
	Exports certain classes to python to allow the user to run the code from python. More...

Detailed Description

The PNAB name space contains all the C++ classes and functions for the proto-Nucleic Acid Builder.

Function Documentation

PYBIND11_MODULE()

PNAB::PYBIND11_MODULE	(	bind	,
		m
	)

Exports certain classes to python to allow the user to run the code from python.

This pybind11 scheme exports only the input runtime, helical, base, and backbone parameters. It exports a single run funtion that can be called from python to run the code.

See also

RuntimeParameters

HelicalParameters

Base

Backbone

run

run()

std::string PNAB::run	(	PNAB::RuntimeParameters	runtime_params,
		PNAB::Backbone &	py_backbone,
		std::vector< PNAB::Base >	py_bases,
		PNAB::HelicalParameters	hp,
		std::string	prefix = "run",
		bool	verbose = true
	)

A wrapper function to run the search algorithm code from python.

Parameters

runtime_params	The runtime parameters defined in the python script
py_backbone	The backbone defined in the python script
py_bases	A vector of the bases defined in the python script
hp	The helical parameters defined in the python script
prefix	A string the prepends the names of the output PDB files, default to "run"
verbose	Whether to print progress report to screen, default to true

Returns

A CSV string containing the properties of the accepted candidates