A class for building nucleic acid strands and evaluating their energies. More...

#include <Chain.h>

Public Member Functions
	Chain (PNAB::Bases bases, const PNAB::Backbone &backbone, std::vector< std::string > strand, std::string ff_type, std::array< unsigned, 2 > &range, bool hexad, std::vector< bool > build_strand={true, false, false, false, false, false}, std::vector< bool > strand_orientation={true, true, true, true, true, true}, double glycosidic_bond_distance=0.0)
	Constructor for the chain class. More...

	~Chain ()
	Destructor for the chain class. More...

PNAB::ConformerData	generateConformerData (double *xyz, PNAB::HelicalParameters &hp, std::vector< double > energy_filter)
	Generate structure and energy data for nucleic acid conformers. More...

Private Member Functions
void	fillConformerEnergyData (double *xyz, PNAB::ConformerData &conf_data, std::vector< double > energy_filter)
	Computes the energy terms for the candidate system and determines whether it satisfies the energy thresholds. More...

void	setupChain (std::vector< PNAB::Base > &strand, OpenBabel::OBMol &chain, std::vector< unsigned > &new_bond_ids, std::vector< unsigned > &deleted_atoms_ids, std::vector< unsigned > &num_base_unit_atoms, std::vector< unsigned > &bb_start_index, std::vector< double * > &base_coords_vec, std::vector< std::vector< unsigned >> &fixed_bonds_vec, const Backbone &backbone, unsigned chain_index)
	Creates the molecule for each strand in the system. More...

void	setupFFConstraints (OpenBabel::OBMol &chain, std::vector< unsigned > &new_bond_ids, std::vector< std::vector< unsigned >> &fixed_bonds_vec, unsigned offset=0)
	Determines the terms that should be ignored during the computation of the bond, angle, and torsional energies. More...

void	setCoordsForChain (double xyz, double conf, PNAB::HelicalParameters &hp, std::vector< unsigned > &num_bu_atoms, std::vector< unsigned > &bb_start_index, std::vector< double * > &base_coords_vec, std::vector< unsigned > &deleted_atoms_ids, unsigned chain_index)
	Set the coordinates for each strand in the system. More...

void	orderResidues (OpenBabel::OBMol *molecule)
	Orders the residues in the molecules correctly. More...

Private Attributes
std::vector< OpenBabel::OBMol >	v_chain_ = std::vector<OpenBabel::OBMol>(6)
	A vector of OpenBabel::OBMol containing the molecules for each strand in the system. More...

OpenBabel::OBMol	combined_chain_
	An OpenBabel::OBMol molecule containing the structure of the whole system. More...

std::vector< std::vector< unsigned > >	v_new_bond_ids_ = std::vector<std::vector<unsigned>>(6)
	a vector containing a vector of the IDs of the atoms forming new bonds between the nucleotides in each strand More...

std::vector< std::vector< unsigned > >	v_deleted_atoms_ids_ = std::vector<std::vector<unsigned>>(6)
	A vector containing a vector of the IDs of the atoms deleted in each strand because of the formation of new bonds. More...

std::vector< std::vector< unsigned > >	v_num_bu_A_mol_atoms_ = std::vector<std::vector<unsigned>>(6)
	A vector containing a vector of the number of atoms in each BaseUnit for each strand. More...

std::vector< std::vector< std::vector< unsigned > > >	v_fixed_bonds = std::vector<std::vector<std::vector<unsigned>>>(6)
	A vector containing the indices of fixed rotatable bonds for each strad. More...

std::vector< std::vector< double * > >	v_base_coords_vec_ = std::vector<std::vector<double*>>(6)
	A vector containing a vector the coordinates of each nucleotide in each strand. More...

unsigned	chain_length_
	The number of nucleotides in the strand. More...

unsigned	n_chains_
	The number of strands in the system. More...

bool	isKCAL_
	Whether the energy computed by openbabel is in kcal/mol. More...

bool	hexad_
	Whether we are building a hexad, RuntimeParameters::is_hexad. More...

std::vector< bool >	strand_orientation_
	A vector containing the orientation of each strand in the hexad, RuntimeParameters::strand_orientation. More...

double	glycosidic_bond_distance_
	The distance of the glycosidic bond, RuntimeParameters::glycosidic_bond_distance. More...

OpenBabel::OBForceField *	pFF_
	The openbabel force field. Used to compute the energy of the system. More...

std::array< unsigned, 2 >	monomer_bb_index_range_
	Backbone index range for the first nucleotide. More...

std::vector< std::vector< unsigned > >	v_bb_start_index_ = std::vector<std::vector<unsigned>>(6)
	A vector containing a vector of the starting indices of the backbone atoms in the BaseUnit for each strand. More...

std::string	ff_type_
	The force field type (e.g. "GAFF"), RuntimeParameters::ff_type. More...

std::vector< std::vector< unsigned int > >	all_angles_
	A vector of the vector of atom indices forming all the angles for which we need to compute the energy. More...

std::vector< std::vector< unsigned int > >	all_torsions_
	A vector of the vector of atom indices forming all the torsions for which we need to compute the energy. More...

std::vector< bool >	is_fixed_bond
	A vector containing whether the torsional energy term is for a fixed rotatable bond or not. More...

std::vector< bool >	build_strand_
	A vector containing whether a given strand should be built. More...

OpenBabel::OBFFConstraints	constraintsBond_
	Setting all atoms not forming the new bond between the first two nucleotides to be ignored during bond energy computation. More...

OpenBabel::OBFFConstraints	constraintsAng_
	An empty constraint object for angles; Energy groups are used for the angle terms. More...

OpenBabel::OBFFConstraints	constraintsTor_
	An empty constraint object for torsions; Energy groups are used for the torsion terms. More...

OpenBabel::OBFFConstraints	constraintsTot_
	An empty constraint object for van der Waals and total energy terms. No ignored atoms in these computations. More...

Detailed Description

A class for building nucleic acid strands and evaluating their energies.

The class creates the strands by connecting the nucleotides created in the BaseUnit class. It forms bonds between the nucleotides for the given sequence of the nucleobases, and creates duplex or hexad systems if requested. The class also contains functions for computing the energy terms for the system and checking whether the candidates are accepted. Several functions in the class identifies the proper energy terms to be computed for the system (e.g. bond and angle energies).

See also: ConformationSearch; HelicalParameters; RuntimeParameters; BaseUnit; Bases

Constructor & Destructor Documentation

◆ Chain()

Chain::Chain	(	PNAB::Bases	bases,
		const PNAB::Backbone &	backbone,
		std::vector< std::string >	strand,
		std::string	ff_type,
		std::array< unsigned, 2 > &	range,
		bool	hexad,
		std::vector< bool >	build_strand = `{true, false, false, false, false, false}`,
		std::vector< bool >	strand_orientation = `{true, true, true, true, true, true}`,
		double	glycosidic_bond_distance = `0.0`
	)

Constructor for the chain class.

The constructor performs several tasks. It creates an OpenBabel::ForceField object and check that it works as expected. It identifies whether we are working with the canonical nucleobases or with the hexad. For double-stranded and hexad systems, it checks whether the user provided correct comlimentary bases. After all these checks, it proceeds to setup the requested molecules. The constructor does not put correct coordinates for the molecules, but creates the topology of each strand in the system. The constructor also identifies the atoms that should be ignored when computing the separate energies (e.g. bond energy) for the backbone candidates.

Parameters

bases	A vector of the all the defined bases,
backbone	The backbone
strand	A vector of the names of all bases in the strand, RuntimeParameters::strand
ff_type	The force field type, RuntimeParameters::ff_type
range	Backbone index range for the first nucleotide
hexad	Defines whether the 60 degrees rotation for hexads is performed, RuntimeParameters::is_hexad
build_strand	Defines whether to build a given strand, RuntimeParameters::build_strand
strand_orientation	The orientation of each strand in the hexad, RuntimeParameters::strand_orientation
glycosidic_bond_distance	The distance of the glycosidic bond, RuntimeParameters::glycosidic_bond_distance

See also: setupChain; setupFFConstraints

◆ ~Chain()

PNAB::Chain::~Chain ( )

inline

Destructor for the chain class.

Member Function Documentation

◆ fillConformerEnergyData()

void Chain::fillConformerEnergyData	(	double *	xyz,
		PNAB::ConformerData &	conf_data,
		std::vector< double >	energy_filter
	)

private

Computes the energy terms for the candidate system and determines whether it satisfies the energy thresholds.

This function uses openbabel to compute the energy for the candidate systems. See the description in setupFFConstraints for the bond, angle, and torsional energies terms. The van der Waals and total energy terms of the systems are computed without any constraints. The energy terms are computed sequentially as follows: bond, angle, torsion, van der Waals, and total energies. If any one of the energy terms does not satisfy the energy thresholds defined in RuntimeParameters::energy_filter, then the candidate is rejected, and we do not proceed to compute the additional energy terms.

Parameters

xyz	The coordinates of the whole system
conf_data	An object that will hold the values of the energy terms, the coordinates, and whether it is accepted.
energy_filter	The energy thresholds for the system, RuntimeParameters::energy_filter

See also: generateConformerData

◆ generateConformerData()

ConformerData Chain::generateConformerData	(	double *	xyz,
		PNAB::HelicalParameters &	hp,
		std::vector< double >	energy_filter
	)

Generate structure and energy data for nucleic acid conformers.

After the conformation search finds a candidate that satisfies the distance threshold, this function is called with the coordinates of the backbone candidate to build the full system and computes its energy properties.

This function calls Chain::setCoordsForChain and Chain::fillConformerEnergyData to setup the coordinates and compute the energies, respectively.

Parameters

xyz	The coordinates of the backbone candidate that satisfied the distance threshold
hp	An instance of HelicalParameters that contains the helical structure data and functions
energy_filter	The energy thresholds for the system, RuntimeParameters::energy_filter

Returns: The conformer energy data, ConformerData, containing whether the candidate is accepted

See also: setCoordsForChain; fillConformerEnergyData; ConformationSearch::RandomSearch; ConformationSearch::MonteCarloSearch; ConformationSearch::SystematicSearch; ConformationSearch::GeneticAlgorithmSearch

◆ orderResidues()

void Chain::orderResidues ( OpenBabel::OBMol * molecule )

private

Orders the residues in the molecules correctly.

This function reverses the order of residues in inverted strands.

Parameters

molecule The OBMol object of the system which will get the correct order

See also: generateConformerData; PNAB::ConformerData

◆ setCoordsForChain()

void Chain::setCoordsForChain	(	double *	xyz,
		double *	conf,
		PNAB::HelicalParameters &	hp,
		std::vector< unsigned > &	num_bu_atoms,
		std::vector< unsigned > &	bb_start_index,
		std::vector< double * > &	base_coords_vec,
		std::vector< unsigned > &	deleted_atoms_ids,
		unsigned	chain_index
	)

private

Set the coordinates for each strand in the system.

This function set the coordinates for each nucleotide in the strand. For DNA- and RNA- like systems, this function can generate anti-parallel strands. For hexad systems, it can generate any combination of the parallel and anti-parallel strands.

Parameters

xyz	An array that will get the coordinates of the strands
conf	An array containing the coordinates of one backbone determined by the search algorithms
hp	An instance of HelicalParameters which has the helical parameters and functions to generate the coordinates
num_bu_atoms	The number of atoms in each BaseUnit
bb_start_index	A vector containing the starting indices of the backbone atoms in the BaseUnit
base_coords_vec	A vector containing the coordinates of each one of the nucleotides
deleted_atoms_ids	A vector containing the indices of the atoms deleted because of the bonding between the nucleotides
chain_index	The index of the strand in the system

See also: setupChain; generateConformerData; HelicalParameters; ConformationSearch

◆ setupChain()

void Chain::setupChain	(	std::vector< PNAB::Base > &	strand,
		OpenBabel::OBMol &	chain,
		std::vector< unsigned > &	new_bond_ids,
		std::vector< unsigned > &	deleted_atoms_ids,
		std::vector< unsigned > &	num_base_unit_atoms,
		std::vector< unsigned > &	bb_start_index,
		std::vector< double * > &	base_coords_vec,
		std::vector< std::vector< unsigned >> &	fixed_bonds_vec,
		const Backbone &	backbone,
		unsigned	chain_index
	)

private

Creates the molecule for each strand in the system.

This function creates the topology (makes and removes bonds) for each strand in the system. It also determines the indices for all the fixed rotatable bonds in the system.

Parameters

strand	The list of bases in the strand
chain	An empty openbabel molecule to be populated with the topology of the strand
new_bond_ids	An empty vector to be populated with the indices of the atoms forming bonds between the nucleotides
deleted_atoms_ids	An empty vector to be populated with the indices of the atoms deleted because of the bonding between the nucleotides
num_base_unit_atoms	An empty vector to be populated with the number of atoms in each BaseUnit
bb_start_index	An empty vector to be populated with the starting index of the backbone atoms in the BaseUnit
base_coords_vec	An empty vector to be populated with the coordinates of each one of the nucleotides
fixed_bonds_vec	An empty vector to be populated with the indices of fixed bonds in each one of the nucleotides
backbone	An instance of the Backbone class
chain_index	The index of the chain

See also: Chain::Chain

◆ setupFFConstraints()

void Chain::setupFFConstraints	(	OpenBabel::OBMol &	chain,
		std::vector< unsigned > &	new_bond_ids,
		std::vector< std::vector< unsigned >> &	fixed_bonds_vec,
		unsigned	offset = `0`
	)

private

Determines the terms that should be ignored during the computation of the bond, angle, and torsional energies.

For the bond energy, we consider only the one new bond that is formed between the first and second nucleobases in the system. This bond energy is the same for all new bonds, so we do not need to compute it for all of them.

For the angle energy, we consider all the new angles that are formed between the first and second nucleobases in the system. This angle energy is the same for all new bonds, so we do not need to compute it for all of them.

For the torsional energy, we consider all the rotatable bonds in all the nucleobases. There will be some redundant calculations, as some torsional angles will be the same. This code also identifies whether a rotatable torsional angle is fixed or not. For the identified torsional angles, we do not include any torsional angle that runs between the residues, as these are not rotated in the search procedure.

Parameters

chain	The openbabel molecule that contain the topology of the strand
new_bond_ids	A vector containing the indices of the atoms forming bonds between the nucleotides
fixed_bonds_vec	A vector containing the indices of fixed bonds in each one of the nucleotides
offset	The number of atoms that have been processed previously. Used to set correct indices for all the strands.

See also: Chain::Chain; setupChain; fillConformerEnergyData

Member Data Documentation

◆ all_angles_

std::vector<std::vector<unsigned int> > PNAB::Chain::all_angles_

private

A vector of the vector of atom indices forming all the angles for which we need to compute the energy.

◆ all_torsions_

std::vector<std::vector<unsigned int> > PNAB::Chain::all_torsions_

private

A vector of the vector of atom indices forming all the torsions for which we need to compute the energy.

◆ build_strand_

std::vector<bool> PNAB::Chain::build_strand_

private

A vector containing whether a given strand should be built.

◆ chain_length_

unsigned PNAB::Chain::chain_length_

private

The number of nucleotides in the strand.

◆ combined_chain_

OpenBabel::OBMol PNAB::Chain::combined_chain_

private

An OpenBabel::OBMol molecule containing the structure of the whole system.

◆ constraintsAng_

OpenBabel::OBFFConstraints PNAB::Chain::constraintsAng_

private

An empty constraint object for angles; Energy groups are used for the angle terms.

◆ constraintsBond_

OpenBabel::OBFFConstraints PNAB::Chain::constraintsBond_

private

Setting all atoms not forming the new bond between the first two nucleotides to be ignored during bond energy computation.

◆ constraintsTor_

OpenBabel::OBFFConstraints PNAB::Chain::constraintsTor_

private

An empty constraint object for torsions; Energy groups are used for the torsion terms.

◆ constraintsTot_

OpenBabel::OBFFConstraints PNAB::Chain::constraintsTot_

private

An empty constraint object for van der Waals and total energy terms. No ignored atoms in these computations.

◆ ff_type_

std::string PNAB::Chain::ff_type_

private

The force field type (e.g. "GAFF"), RuntimeParameters::ff_type.

◆ glycosidic_bond_distance_

double PNAB::Chain::glycosidic_bond_distance_

private

The distance of the glycosidic bond, RuntimeParameters::glycosidic_bond_distance.

◆ hexad_

bool PNAB::Chain::hexad_

private

Whether we are building a hexad, RuntimeParameters::is_hexad.

◆ is_fixed_bond

std::vector<bool> PNAB::Chain::is_fixed_bond

private

A vector containing whether the torsional energy term is for a fixed rotatable bond or not.

◆ isKCAL_

bool PNAB::Chain::isKCAL_

private

Whether the energy computed by openbabel is in kcal/mol.

◆ monomer_bb_index_range_

std::array<unsigned, 2> PNAB::Chain::monomer_bb_index_range_

private

Backbone index range for the first nucleotide.

◆ n_chains_

unsigned PNAB::Chain::n_chains_

private

The number of strands in the system.

◆ pFF_

OpenBabel::OBForceField* PNAB::Chain::pFF_

private

The openbabel force field. Used to compute the energy of the system.

◆ strand_orientation_

std::vector<bool> PNAB::Chain::strand_orientation_

private

A vector containing the orientation of each strand in the hexad, RuntimeParameters::strand_orientation.

◆ v_base_coords_vec_

std::vector<std::vector<double*> > PNAB::Chain::v_base_coords_vec_ = std::vector<std::vector<double*>>(6)

private

A vector containing a vector the coordinates of each nucleotide in each strand.

◆ v_bb_start_index_

std::vector<std::vector<unsigned> > PNAB::Chain::v_bb_start_index_ = std::vector<std::vector<unsigned>>(6)

private

A vector containing a vector of the starting indices of the backbone atoms in the BaseUnit for each strand.

◆ v_chain_

std::vector<OpenBabel::OBMol> PNAB::Chain::v_chain_ = std::vector<OpenBabel::OBMol>(6)

private

A vector of OpenBabel::OBMol containing the molecules for each strand in the system.

◆ v_deleted_atoms_ids_

std::vector<std::vector<unsigned> > PNAB::Chain::v_deleted_atoms_ids_ = std::vector<std::vector<unsigned>>(6)

private

A vector containing a vector of the IDs of the atoms deleted in each strand because of the formation of new bonds.

◆ v_fixed_bonds

std::vector<std::vector<std::vector<unsigned> > > PNAB::Chain::v_fixed_bonds = std::vector<std::vector<std::vector<unsigned>>>(6)

private

A vector containing the indices of fixed rotatable bonds for each strad.

◆ v_new_bond_ids_

std::vector<std::vector<unsigned> > PNAB::Chain::v_new_bond_ids_ = std::vector<std::vector<unsigned>>(6)

private

a vector containing a vector of the IDs of the atoms forming new bonds between the nucleotides in each strand

◆ v_num_bu_A_mol_atoms_

std::vector<std::vector<unsigned> > PNAB::Chain::v_num_bu_A_mol_atoms_ = std::vector<std::vector<unsigned>>(6)

private

A vector containing a vector of the number of atoms in each BaseUnit for each strand.

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

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ Chain()

◆ ~Chain()

Member Function Documentation

◆ fillConformerEnergyData()

◆ generateConformerData()

◆ orderResidues()

◆ setCoordsForChain()

◆ setupChain()

◆ setupFFConstraints()

Member Data Documentation

◆ all_angles_

◆ all_torsions_

◆ build_strand_

◆ chain_length_

◆ combined_chain_

◆ constraintsAng_

◆ constraintsBond_

◆ constraintsTor_

◆ constraintsTot_

◆ ff_type_

◆ glycosidic_bond_distance_

◆ hexad_

◆ is_fixed_bond

◆ isKCAL_

◆ monomer_bb_index_range_

◆ n_chains_

◆ pFF_

◆ strand_orientation_

◆ v_base_coords_vec_

◆ v_bb_start_index_

◆ v_chain_

◆ v_deleted_atoms_ids_

◆ v_fixed_bonds

◆ v_new_bond_ids_

◆ v_num_bu_A_mol_atoms_