Reads FASTA file and generate one particle per amino acid. More...

#include <io.h>

Inheritance diagram for Faunus::CoarseGrainedFastaFileReader:

Collaboration diagram for Faunus::CoarseGrainedFastaFileReader:

Public Member Functions
	CoarseGrainedFastaFileReader (double bond_length, const Point &initial_particle_position=Point(0, 0, 0))

void	setBondLength (double bond_length)

std::string	loadSequence (std::istream &stream)

Public Member Functions inherited from Faunus::StructureFileReader
ParticleVector &	load (std::istream &stream)
	Load entire stream and populate data.

ParticleVector &	load (std::string_view filename)

Static Public Member Functions
static char	getFastaLetter (std::istream &stream)

Additional Inherited Members
Public Attributes inherited from Faunus::StructureFileReader
ParticleVector	particles

Point	box_length = Point::Zero()

std::vector< std::string >	comments

bool	prefer_charges_from_file
	If applicable, prefer charges from AAM file over `AtomData` More...

bool	box_dimension_support = false

bool	particle_charge_support = false

bool	particle_radius_support = false

Protected Member Functions inherited from Faunus::StructureFileReader
void	getNextLine (std::istream &stream, std::string &destination, const std::string &comment_identifiers)
	Helper function to forward stream. More...

void	handleChargeMismatch (Particle &particle, int atom_index) const
	Policy if charge mismatch.

Static Protected Member Functions inherited from Faunus::StructureFileReader
static size_t	getNumberOfAtoms (const std::string &line)
	Helper function to extract N.

static void	handleRadiusMismatch (const Particle &particle, double radius, int atom_index)
	Policy if radius mismatch.

Protected Attributes inherited from Faunus::StructureFileReader
size_t	expected_number_of_particles = 0

Detailed Description

Reads FASTA file and generate one particle per amino acid.

Positions are generated as a random walk beginning from the given initial_particle_position, advancing in steps of bond_length

The documentation for this class was generated from the following files:

Public Member Functions