segment Struct Reference

#include <tree.h>

Inheritance diagram for segment:

Collaboration diagram for segment:

Public Member Functions
	segment (const vec &origin_, sz begin_, sz end_, const vec &axis_root, const frame &parent)
void	set_conf (const frame &parent, const atomv &atoms, vecv &coords, flv::const_iterator &c)
void	count_torsions (sz &s) const
void	set_derivative (const vecp &force_torque, fl &c) const
void	set_coords (const atomv &atoms, vecv &coords) const
vecp	sum_force_and_torque (const vecv &coords, const vecv &forces) const
vec	local_to_lab (const vec &local_coords) const
vec	local_to_lab_direction (const vec &local_direction) const
const qt &	orientation () const
const vec &	get_origin () const
template<typename F >
void	transform (const F &f)

Public Attributes
sz	begin
sz	end

Protected Member Functions
void	set_orientation (const qt &q)

Protected Attributes
vec	axis
vec	origin
mat	orientation_m
qt	orientation_q

Private Attributes
vec	relative_axis
vec	relative_origin

Constructor & Destructor Documentation

segment::segment ( const vec &  origin_, sz  begin_, sz  end_, const vec &  axis_root, const frame &  parent  )

inline

References axis_frame::axis, eq(), frame::get_origin(), frame::orientation(), frame::origin, qt_identity(), relative_axis, relative_origin, and VINA_CHECK.

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Member Function Documentation

void segment::set_conf ( const frame &  parent, const atomv &  atoms, vecv &  coords, flv::const_iterator &  c  )

inline

References angle_to_quaternion(), axis_frame::axis, frame::local_to_lab(), frame::local_to_lab_direction(), frame::orientation(), frame::origin, quaternion_normalize_approx(), relative_axis, relative_origin, atom_frame::set_coords(), and frame::set_orientation().

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void segment::count_torsions ( sz &  s ) const

inline

void axis_frame::set_derivative ( const vecp &  force_torque, fl &  c  ) const

inlineinherited

References axis_frame::axis.

void atom_frame::set_coords ( const atomv &  atoms, vecv &  coords  ) const

inlineinherited

References atom_range::begin, atom_range::end, frame::local_to_lab(), and VINA_RANGE.

Referenced by rigid_body::set_conf(), set_conf(), and first_segment::set_conf().

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vecp atom_frame::sum_force_and_torque ( const vecv &  coords, const vecv &  forces  ) const

inlineinherited

References atom_range::begin, cross_product(), atom_range::end, frame::origin, and VINA_RANGE.

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vec frame::local_to_lab ( const vec &  local_coords ) const

inlineinherited

References frame::orientation_m, and frame::origin.

Referenced by set_conf(), and atom_frame::set_coords().

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vec frame::local_to_lab_direction ( const vec &  local_direction ) const

inlineinherited

References frame::orientation_m.

Referenced by set_conf().

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const qt& frame::orientation ( ) const

inlineinherited

References frame::orientation_q.

Referenced by segment(), and set_conf().

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const vec& frame::get_origin ( ) const

inlineinherited

References frame::origin.

Referenced by segment().

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void frame::set_orientation ( const qt &  q )

inlineprotectedinherited

References frame::orientation_m, frame::orientation_q, and quaternion_to_r3().

Referenced by rigid_body::set_conf(), set_conf(), and first_segment::set_conf().

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template<typename F >

void atom_range::transform ( const F &  f )

inlineinherited

References atom_range::begin, and atom_range::end.

Referenced by appender::update().

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Member Data Documentation

vec segment::relative_axis

private

Referenced by segment(), and set_conf().

vec segment::relative_origin

private

Referenced by segment(), and set_conf().

vec axis_frame::axis

protectedinherited

Referenced by axis_frame::axis_frame(), segment(), set_conf(), first_segment::set_conf(), and axis_frame::set_derivative().

vec frame::origin

protectedinherited

Referenced by axis_frame::axis_frame(), frame::get_origin(), frame::local_to_lab(), segment(), rigid_body::set_conf(), set_conf(), and atom_frame::sum_force_and_torque().

mat frame::orientation_m

protectedinherited

Referenced by frame::local_to_lab(), frame::local_to_lab_direction(), and frame::set_orientation().

qt frame::orientation_q

protectedinherited

Referenced by frame::orientation(), and frame::set_orientation().

sz atom_range::begin

inherited

Referenced by add_bonds(), model::check_internal_pairs(), conf_independent_inputs::conf_independent_inputs(), terms::evale_robust(), get_atom_range(), model::get_ligand_coords(), model::get_ligand_internal_coords(), model::rmsd_ligands_upper_bound(), atom_frame::set_coords(), ligand::set_range(), atom_frame::sum_force_and_torque(), and atom_range::transform().

sz atom_range::end

inherited

Referenced by add_bonds(), model::check_internal_pairs(), conf_independent_inputs::conf_independent_inputs(), terms::evale_robust(), get_atom_range(), model::get_ligand_coords(), model::get_ligand_internal_coords(), model::rmsd_ligands_upper_bound(), atom_frame::set_coords(), ligand::set_range(), atom_frame::sum_force_and_torque(), and atom_range::transform().

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The documentation for this struct was generated from the following file:

• tree.h