Selection class. More...

#include <selection.h>

Classes
class	iterator
	Random-access forward iterator for Selection. More...

Public Member Functions
Modification of existing selection
void	append (const Selection &sel)
	Append another selection to this one.

void	append (int ind)
	Append absolute index to selection.

void	append (const std::vector< Selection > &sel_vec)
	Append several selections to this one.

void	remove (const Selection &sel)
	Remove all atoms of sel from current selection.

void	remove (int ind)
	Remove given absolute index from current selection.

void	invert ()
	Inverts selection in place by selecting those atoms which were not selected.

void	set_system (const System &sys)
	Sets new system for selection. More...

void	modify (std::string str, int fr=0)
	Modifies selection string in existing selection. More...

void	modify (int ind1, int ind2)
	Modifies selection using the range of indexes.

void	modify (const std::vector< int > &ind)
	Modifies selection using vector of indexes Vector may be in any order and may contain duplicates.

void	modify (std::vector< int >::iterator it1, std::vector< int >::iterator it2)
	Modifies selection using pair of iterators to index vector Vector may be in any order and may contain duplicates.

void	modify (const std::function< void(const System &, int, std::vector< int > &)> &callback, int fr=0)
	Modifies selection using user-defined callback. More...

void	modify (const System &sys, std::string str, int fr=0)
	Convenience method, which combines set_system and modify(str)

void	modify (const System &sys, int ind1, int ind2)
	Convenience method, which combines set_system and modify(int,int)

void	modify (const System &sys, const std::vector< int > &ind)
	Convenience method, which combines set_system and modify(vector<int>)

void	modify (const System &sys, std::vector< int >::iterator it1, std::vector< int >::iterator it2)
	Convenience method, which combines set_system and modify(iter,iter)

void	modify (const System &sys, const std::function< void(const System &, int, std::vector< int > &)> &callback, int fr=0)
	Convenience method, which combines set_system and modify(callback)

void	apply ()
	Recomputes selection without re-parsing selection text. More...

void	update ()
	Recomputes selection completely. More...

void	clear ()
	Clears selection and frees memory. More...

Sub-selections
Selection	select (std::string str)
	Sub-selections allow selecting atoms inside existing selection (narrowing or refining existing selection in other terms). More...

Selection	operator() (std::string str)

Selection	select (int ind1, int ind2)
	Local selection indexes are used!

Selection	operator() (int ind1, int ind2)

Selection	select (const std::vector< int > &ind)
	Local selection indexes are used!

Selection	operator() (const std::vector< int > &ind)

Iterator access
std::vector< int >::const_iterator	index_begin () const
	Get const iterator for begin of index.

std::vector< int >::const_iterator	index_end () const
	Get const iterator for the end of index.

std::back_insert_iterator< std::vector< int > >	index_back_inserter ()
	Get back_insert_iterator for index.

iterator	begin ()
	Begin iterator.

iterator	end ()
	End iterator.

Get and set functions
int	get_frame () const
	Get current frame selection is pointing to.

void	set_frame (int fr)
	Set current frame for selection. More...

System *	get_system () const
	Get pointer to the system, which is pointed by this selection.

std::string	get_text () const
	Get selection text If selection is not textual returns generated index-based text "index i j k...".

std::vector< int >	get_index () const
	Get vector of all indexes in selection.

std::vector< char >	get_chain (bool unique=false) const
	Get vector of all chains in selection.

void	set_chain (const std::vector< char > &data)
	Set chains from supplied vector. More...

void	set_chain (char data)
	Sets chain of all selected atoms to the same given value.

std::vector< int >	get_resid (bool unique=false) const
	Get vector of all resid's in selection. More...

void	set_resid (const std::vector< int > &data)
	Set resid's in selection from supplied vector. More...

void	set_resid (int data)
	Sets resid of all selected atoms to the same given value.

std::vector< std::string >	get_name (bool unique=false) const
	Get vector of all atom names in selection.

void	set_name (const std::vector< std::string > &data)
	Set atom names in selection from supplied vector. More...

void	set_name (std::string data)
	Sets atom names of all selected atoms to the same given value.

std::vector< std::string >	get_resname (bool unique=false) const
	Get vector of all resnames in selection.

void	set_resname (const std::vector< std::string > &data)
	Set resnames in selection from supplied vector. More...

void	set_resname (std::string data)
	Sets resnames of all selected atoms to the same given value.

std::vector< int >	get_resindex (bool unique=false) const
	Get vector of all resindexes in selection. More...

Eigen::MatrixXf	get_xyz (bool make_row_major_matrix=false) const
	Get coordinates of all atoms in this selection for the current frame By default columnt of the matrix contain atom coordinates. More...

void	set_xyz (MatrixXf_const_ref coord)
	Set coordinates of this selection for current frame.

std::vector< float >	get_mass () const
	Get masses of all atoms in selection.

void	set_mass (const std::vector< float > &m)
	Set atom masses in selection to the values from supplied vector. More...

void	set_mass (float data)
	Sets masses of all selected atoms to the same given value.

std::vector< float >	get_beta () const
	Get beta.

void	set_beta (const std::vector< float > &data)
	Set beta in selection to the values from supplied vector. More...

void	set_beta (float data)
	Sets beta of all selected atoms to the same given value.

std::vector< float >	get_occupancy () const
	Get occupancy.

void	set_occupancy (const std::vector< float > &data)
	Set occupancy in selection to the values from supplied vector. More...

void	set_occupancy (float data)
	Sets occupancy of all selected atoms to the same given value.

std::vector< float >	get_charge () const
	Get charge.

void	set_charge (const std::vector< float > &data)
	Set charge in selection to the values from supplied vector. More...

void	set_charge (float data)
	Sets charge of all selected atoms to the same given value.

float	get_total_charge () const
	Computes total charge of selection.

std::vector< std::string >	get_tag (bool unique=false) const
	Get tags.

void	set_tag (const std::vector< std::string > &data)
	Set tags in selection to the values from supplied vector. More...

void	set_tag (std::string data)
	Set tags of all selected atoms to the same given value.

Eigen::MatrixXf	get_vel (bool make_row_major_matrix=false) const
	Get velocities of all atoms in this selection for the current frame By default columnt of the matrix contain atom coordinates. More...

void	set_vel (MatrixXf_const_ref data)
	Set velocities of this selection for current frame.

Eigen::MatrixXf	get_force (bool make_row_major_matrix=false) const
	Get forces of all atoms in this selection for the current frame By default columnt of the matrix contain atom coordinates. More...

void	set_force (MatrixXf_const_ref coord)
	Set forces of this selection for current frame.

Computing properties of selection
bool	is_large ()
	Checks if selection is larger than 1/2 of the box size in any dimension. More...

Eigen::Vector3f	center (bool mass_weighted=false, Array3i_const_ref pbc=noPBC, int pbc_atom=-1) const
	Get the center of selection. More...

Eigen::Vector3f	center (const std::vector< float > &weights, Array3i_const_ref pbc=noPBC, int pbc_atom=-1) const

void	minmax (Vector3f_ref min, Vector3f_ref max) const
	Get minimal and maximal coordinates in selection.

float	powersasa (float probe_r=0.14, std::vector< float > area_per_atom=nullptr, float total_volume=nullptr, std::vector< float > *volume_per_atom=nullptr) const
	Get the SASA using powersasa algorithm. Returns area and computes volume and per-atom values if asked.

float	sasa (float probe_r=0.14, std::vector< float > *area_per_atom=nullptr, int n_sphere_points=960) const
	Get SASA using Shrake and Rupley algorithm (slower than powersasa and can't compute volumes)

Eigen::MatrixXf	average_structure (int b=0, int e=-1, bool make_row_major_matrix=false) const
	Computes average structure over the range of frames.

Eigen::MatrixXf	atom_traj (int ind, int b=0, int e=-1, bool make_row_major_matrix=false) const
	Extracts X,Y,Z for given atom index for specified range of frames (gets trajectory of given atom). More...

void	inertia (Vector3f_ref moments, Matrix3f_ref axes, Array3i_const_ref pbc=noPBC, int pbc_atom=-1) const
	Computes the central momens of inertia and principal axes of inertia. More...

float	gyration (Array3i_const_ref pbc=noPBC, int pbc_atom=-1) const
	Computes radius of gyration for selection. More...

Eigen::Vector3f	dipole (bool as_charged=false, Array3i_const_ref pbc=fullPBC, int pbc_atom=-1) const

float	distance (int i, int j, Array3i_const_ref pbc=fullPBC) const
	Get distance between two atoms (periodic in given dimensions if needed). More...

float	angle (int i, int j, int k, Array3i_const_ref pbc=fullPBC) const
	Get angle in degrees between three atoms (periodic in given dimensions if needed). More...

float	dihedral (int i, int j, int k, int l, Array3i_const_ref pbc=fullPBC) const
	Get dihedral angle in degrees between three atoms (periodic in given dimensions if needed). More...

Geometry transformation functions
void	translate (Vector3f_const_ref v)
	Translate selection by given vector.

void	translate_to (Vector3f_const_ref p, bool mass_weighted=false, Array3i_const_ref pbc=noPBC, int pbc_atom=-1)
	Translate center of masses of selection to given point.

void	rotate (Vector3f_const_ref pivot, Vector3f_const_ref axis, float angle)
	Rotate selection around given axis relative to given pivot. More...

void	mirror (int dim, float around=0)
	Mirror selection along one of coordinates around given point.

void	mirror (Vector3f_const_ref normal, Vector3f_const_ref point=Eigen::Vector3f::Zero())
	Mirror selection along arbitrary vector relative to given point.

void	wrap (Array3i_const_ref pbc=fullPBC)
	Wraps whole selection to the periodic box.

void	unwrap (Array3i_const_ref pbc=fullPBC, int pbc_atom=-1)
	Unwraps selection to make it whole if possible (without jumps over periodic box boundary). More...

int	unwrap_bonds (float d, Array3i_const_ref pbc=fullPBC, int pbc_atom=-1)
	Unwraps selection to make it whole (without jumps over periodic box boundary). More...

Eigen::Affine3f	principal_transform (Array3i_const_ref pbc=noPBC, int pbc_atom=-1) const
	Get transform for orienting selection by principal axes. More...

void	principal_orient (Array3i_const_ref pbc=noPBC, int pbc_atom=-1)
	Orient molecule by its principal axes. More...

int	num_residues () const
	Returns total number of residues in selection. Partial residues are also included.

Energy functions
Eigen::Vector2f	non_bond_energy (float cutoff=0, bool pbc=true) const
	Self-energy of selection computed within given interaction cut-off. More...

File IO
void	write (std::string fname, int b=-1, int e=-1) const
	Write structure or trajectory for selection. More...

void	write (const std::unique_ptr< FileHandler > &handler, FileContent what, int b=-1, int e=-1) const

Splitting selection into parts
void	split_by_connectivity (float d, std::vector< Selection > &res, bool periodic=true)
	Split current selection into several selections according to the interatomic distances. More...

void	split_by_residue (std::vector< Selection > &res)
	Split selection by residue index.

void	split_by_molecule (std::vector< Selection > &res)
	Split selection by molecule definition from topology.

void	split_by_chain (std::vector< Selection > &chains)
	Split selection by chain.

void	split_by_contiguous_index (std::vector< Selection > &parts)
	Split selection into contiguous ranges of indexes.

void	split_by_contiguous_residue (std::vector< Selection > &parts)
	Split selection into contiguous ranges of resindexes.

template<class F >
void	split (std::vector< Selection > &parts, F callback)
	Split selection by the values returned by custom callback function. More...

void	each_residue (std::vector< Selection > &sel) const
	Selects each residue, which is referenced by selection. More...

Secondary structure methods
These methods take protein residues referenced by selection and compute DSSP on them.
void	dssp (std::string fname) const
	Determines secondary structure with DSSP algorithm and writes detailed report to file.

void	dssp (std::ostream &os) const
	Determines secondary structure with DSSP algorithm and writes detailed report to stream.

std::string	dssp () const
	Determines secondary structure with DSSP algorithm and return it as a code string. More...

Inline accessors
Used to access the properties of particular atom in selection. The ind passed to these functions is is the selection index, not the global system index. I.e. passing 10 will extract the property of atom with global index index[10] All these function except index could be used as lvalue, which means that it is possible to assign value to them. For example x(10) = 3.14
float &	x (int ind)
	Extracts X for current frame.

float	x (int ind) const

float &	x (int ind, int fr)
	Extracts X for given frame frame fr.

float	x (int ind, int fr) const

float &	y (int ind)
	Extracts Y for current frame.

float	y (int ind) const

float &	y (int ind, int fr)
	Extracts Y for given frame frame fr.

float	y (int ind, int fr) const

float &	z (int ind)
	Extracts Z for current frame.

float	z (int ind) const

float &	z (int ind, int fr)
	Extracts Z for given frame frame fr.

float	z (int ind, int fr) const

Eigen::Vector3f &	xyz (int ind)
	Extracts X,Y and Z for current frame.

const Eigen::Vector3f &	xyz (int ind) const

Eigen::Vector3f &	xyz (int ind, int fr)
	Extracts X,Y and Z for given frame fr.

const Eigen::Vector3f &	xyz (int ind, int fr) const

Eigen::Vector3f *	xyz_ptr (int ind) const
	Returns pointer to the coordinates of given atom for current frame. More...

Eigen::Vector3f *	xyz_ptr (int ind, int fr) const

Eigen::Vector3f &	vel (int ind)
	Extracts velocity for current frame.

const Eigen::Vector3f &	vel (int ind) const

Eigen::Vector3f &	vel (int ind, int fr)
	Extracts velocity for given frame fr.

const Eigen::Vector3f &	vel (int ind, int fr) const

Eigen::Vector3f &	force (int ind)
	Extracts force for current frame.

const Eigen::Vector3f &	force (int ind) const

Eigen::Vector3f &	force (int ind, int fr)
	Extracts force for given frame fr.

const Eigen::Vector3f &	force (int ind, int fr) const

int	index (int ind) const
	Extracts type. More...

Atom &	atom (int ind)
	Extracts whole atom.

const Atom &	atom (int ind) const

float	vdw (int ind) const
	Extracts resindex. More...

std::string	element_name (int ind) const
	Extracts element name based on element_number. Read only.

PeriodicBox &	box ()
	Returns periodic box of the frame pointed by selection The same as: More...

const PeriodicBox &	box () const

float &	time ()
	Returns time stamp of the frame pointed by selection The same as: More...

const float &	time () const

Constructors and operators
	Selection ()
	Default constructor for empty selection.

	Selection (const System &sys)
	Associates selection with the system. More...

	Selection (const System &sys, std::string str, int fr=0)
	Textual selection constructor. More...

	Selection (const System &sys, int ind1, int ind2)
	Constructor, which creates selection from the interval of indexes. More...

	Selection (const System &sys, const std::vector< int > &ind)
	Constructor from the vector of indexes Vector may be in any order and may contain duplicates.

	Selection (const System &sys, std::vector< int >::iterator it1, std::vector< int >::iterator it2)
	Constructor from the pair of iterators to int sequence Sequence may be in any order and may contain duplicates.

	Selection (const System &sys, const std::function< void(const System &, int, std::vector< int > &)> &callback, int fr=0)
	Constructor which takes user-defined callback function. More...

	Selection (const Selection &other)
	Copy constructor.

virtual	~Selection ()
	Destructor.

Selection &	operator= (const Selection &other)
	Assignment operator.

bool	operator== (const Selection &other) const
	Equality operator Selection are compared by their indexes.

bool	operator!= (const Selection &other) const
	Inequality operator Selection are compared by their indexes.

AtomHandler	operator[] (int ind)
	Indexing operator. More...

AtomHandler	operator[] (const std::pair< int, int > &ind_fr)
	Indexing operator which sets both index and frame. More...

Selection	operator~ () const
	Creates new Selection, which is a logical negation of existing one. More...

Fitting and RMSD functions
float	rmsd (int fr) const
	RMSD between current and another frame.

float	rmsd (int fr1, int fr2) const
	RMSD between two frames.

void	fit_trajectory (int ref_frame=0, int b=0, int e=-1)
	Fit specified frames in the trajectory to reference frame.

Eigen::Affine3f	fit_transform (int fr1, int fr2) const
	Returns fit transformation between frames fr1 and fr2.

void	fit (int fr1, int fr2)
	Fits frame fr1 to fr2.

void	apply_transform (const Eigen::Affine3f &t)
	Apply transformation.

Utility functions
int	size () const
	Get the size of selection.

bool	text_based () const
	Returns true if selection was created from text string and false if it was constructed 'by hand' by appending indexes or other selections.

bool	coord_dependent () const
	Returns true if selection is coordinate-dependent and is able to recompute itself on the change of frame.

void	flatten ()
	"Flattens" selection by removing coordinate dependence and making it not text-based. More...

std::string	to_gromacs_ndx (std::string name) const
	Returns a string formatted as Gromacs ndx file containing the current selection with given name. More...

int	find_index (int global_index) const
	Finds local index in selection of provided global index Returns -1 if not found.

std::vector< std::vector< int > >	get_internal_bonds (float d, bool periodic=true) const
	Get all bonds within this selection returned as local selection indexes in form 1->[2,3,..]. More...

Detailed Description

Selection class.

Selections are key objects in Pteros. Technically speaking the selection is just an array, which contains indexes of selected atoms in particular system. Selection does not hold the copies of the atoms or their coordinates, it just points to them serving like an alias for certain subset of atoms. Thus selections may overlap arbitrarily. Selections are used to perform various operations on the group of selected atoms. The changes become immediately visible to all other selections, which point to some of changed atoms. Each selection is bound to particular System. There are neither 'parentless' selection nor the selections, which combine the atoms from different systems. Selections are created using the syntax, which is very similar to those used in VMD but with many useful extensions.

Constructor & Destructor Documentation

◆ Selection() [1/4]

Selection::Selection ( const System & sys )

explicit

Associates selection with the system.

Parameters

sys,Selection content should be set later by calling modify().

◆ Selection() [2/4]

Selection::Selection	(	const System &	sys,
		std::string	str,
		int	fr = `0`
	)

Textual selection constructor.

Parameters

sys	System pointed by this selection
str	Selection string

◆ Selection() [3/4]

Selection::Selection	(	const System &	sys,
		int	ind1,
		int	ind2
	)

Constructor, which creates selection from the interval of indexes.

It is much faster then parsing selection corresponding string, but is limited to contigous interval of indexes.

Parameters

sys	System pointed by this selection
ind1	First index in interval
ind2	Last index in interval (inclusive!)

◆ Selection() [4/4]

pteros::Selection::Selection	(	const System &	sys,
		const std::function< void(const System &, int, std::vector< int > &)> &	callback,
		int	fr = `0`
	)

Constructor which takes user-defined callback function.

Callback takes the system as first argument, target frame number as the second and the vector to be filled by selected atom indexes. Vector may be filled in any order and may contain duplicates.

Warning: Resulting selection is neither coordinate-dependent nor text-based. It won't recompute itself on the frame change even if it involves coordinates.

Member Function Documentation

◆ operator[]() [1/2]

AtomHandler Selection::operator[] ( int ind )

Indexing operator.

Returns an Atom_proxy object, which incapsulates atom and its coordinates for current frame Can only be used as r-value (can not be assigned to) however individual fields of the proxy object are writable

Selection sel(sys,"name CA");
sel[1] = sel[0]; // ERROR! Can't assign to proxy object returned by []!
sel[0].name() = "A"; // OK to write fields of proxy object

Main goal of [] operator is usage in range-based for loops:

Selection sel(sys,"name CA");
for(auto a: sel){
   cout << a.name() << " " << a.x() << endl;
}

Otherwise it is slower than conventional syntax like sel.name(i)

◆ operator[]() [2/2]

AtomHandler Selection::operator[] ( const std::pair< int, int > & ind_fr )

Indexing operator which sets both index and frame.

Takes a pair of values.

Selection sel(sys,"name CA");
int at = 123;
// Assign x coorditate of atom at for frame 0 from frame 1.
sel[{at,0}].x() = sel[{at,1}].x();

◆ operator~()

Selection Selection::operator~ ( ) const

Creates new Selection, which is a logical negation of existing one.

Parent selection is not modified

◆ set_system()

void Selection::set_system ( const System & sys )

Sets new system for selection.

Warning: This clears selection index and leaves it empty!

◆ modify() [1/2]

void Selection::modify	(	std::string	str,
		int	fr = `0`
	)

Modifies selection string in existing selection.

Parameters

str	New value of selection text. Selection is re-parsed immediately with this new value.

◆ modify() [2/2]

void pteros::Selection::modify	(	const std::function< void(const System &, int, std::vector< int > &)> &	callback,
		int	fr = `0`
	)

Modifies selection using user-defined callback.

Callback takes the system as first argument, target frame number as the second and the vector to be filled by selected atom indexes. Vector may be filled in any order and may contain duplicates.

Warning: Resulting selection is neither coordinate-dependent nor text-based. It will not recompute itself on the frame change even if it involves atom coordinates.

◆ apply()

void Selection::apply ( )

Recomputes selection without re-parsing selection text.

Only makes sense for coordinate-dependent selections when the coordinates change. Called authomatically for coordinate-dependent selections by set_frame() If selection is not coordinate-dependent does nothing.

◆ update()

void Selection::update ( )

Recomputes selection completely.

May be used when new file is loaded into the system, or when atoms are created/deleted. Forces re-parsing of selection text. For non-textual selections does nothing.

◆ clear()

void Selection::clear ( )

Clears selection and frees memory.

Selection is still assigned to its system after clearing. Subsequent call of modify() may populate it again.

◆ select()

Selection Selection::select ( std::string str )

Sub-selections allow selecting atoms inside existing selection (narrowing or refining existing selection in other terms).

Sub-selections could be very useful in the following situation. Suppose that we need to create separate selections for N,C,CA and CB atoms of particular protein residue. With "normal" selections the following code could be used:

Selection sel_N(sys,"protein and resid 1 and name N");
Selection sel_C(sys,"protein and resid 1 and name C");
Selection sel_CA(sys,"protein and resid 1 and name CA");
Selection sel_CB(sys,"protein and resid 1 and name CB");

The problem with this code is that we are looping over all atoms in the system four times, ones in each selection. This is very inefficient since we only need to find our residue with "protein and resid 1" (one loop over all atoms) and then we need to search inside this residue four times (looping over ~10 atoms only). This problem is not apparent for small systems but becomes very painful for the systems with millions of atoms. Subselections solve this problem:

Selection residue1(sys,"protein and resid 1");
auto sel_N = residue1.select("name N");
auto sel_C = residue1.select("name C");
auto sel_CA = residue1.select("name CA");
auto sel_CB = residue1.select("name CB");

Subselections inherit the system and frame from the parent. The search in sub-selections is performed over selected atoms of the parent only (the only exception from this rule are within selections which involve seacrh over all atoms by design).

◆ set_frame()

void Selection::set_frame ( int fr )

Set current frame for selection.

Note: If selection is coordinate-dependent it is re-evaluated by calling apply()

◆ set_chain()

void pteros::Selection::set_chain ( const std::vector< char > & data )

Set chains from supplied vector.

Note: Vector size must be the save as the size of selection.

◆ get_resid()

std::vector<int> pteros::Selection::get_resid ( bool unique = false ) const

Get vector of all resid's in selection.

Warning: Same resid's could be present in different chains!

◆ set_resid()

void pteros::Selection::set_resid ( const std::vector< int > & data )

Set resid's in selection from supplied vector.

Note: Vector size must be the save as the size of selection.

◆ set_name()

void pteros::Selection::set_name ( const std::vector< std::string > & data )

Set atom names in selection from supplied vector.

Note: Vector size must be the save as the size of selection.

◆ set_resname()

void pteros::Selection::set_resname ( const std::vector< std::string > & data )

Set resnames in selection from supplied vector.

Note: Vector size must be the save as the size of selection.

◆ get_resindex()

std::vector<int> pteros::Selection::get_resindex ( bool unique = false ) const

Get vector of all resindexes in selection.

Resindexes are unique regardless the number of the chains.

◆ get_xyz()

MatrixXf Selection::get_xyz ( bool make_row_major_matrix = false ) const

Get coordinates of all atoms in this selection for the current frame By default columnt of the matrix contain atom coordinates.

Optional flag turns this to row-major format (mainly used by python binding)

◆ set_mass()

void pteros::Selection::set_mass ( const std::vector< float > & m )

Set atom masses in selection to the values from supplied vector.

Note: Vector size must be the save as the size of selection.

◆ set_beta()

void pteros::Selection::set_beta ( const std::vector< float > & data )

Set beta in selection to the values from supplied vector.

Note: Vector size must be the save as the size of selection.

◆ set_occupancy()

void pteros::Selection::set_occupancy ( const std::vector< float > & data )

Set occupancy in selection to the values from supplied vector.

Note: Vector size must be the save as the size of selection.

◆ set_charge()

void pteros::Selection::set_charge ( const std::vector< float > & data )

Set charge in selection to the values from supplied vector.

Note: Vector size must be the save as the size of selection.

◆ set_tag()

void pteros::Selection::set_tag ( const std::vector< std::string > & data )

Set tags in selection to the values from supplied vector.

Note: Vector size must be the save as the size of selection.

◆ get_vel()

MatrixXf Selection::get_vel ( bool make_row_major_matrix = false ) const

Get velocities of all atoms in this selection for the current frame By default columnt of the matrix contain atom coordinates.

Optional flag turns this to row-major format (mainly used by python binding)

◆ get_force()

MatrixXf Selection::get_force ( bool make_row_major_matrix = false ) const

Get forces of all atoms in this selection for the current frame By default columnt of the matrix contain atom coordinates.

Optional flag turns this to row-major format (mainly used by python binding)

◆ is_large()

bool Selection::is_large ( )

Checks if selection is larger than 1/2 of the box size in any dimension.

Returns true if so.

◆ center()

Vector3f Selection::center	(	bool	mass_weighted = `false`,
		Array3i_const_ref	pbc = `noPBC`,
		int	pbc_atom = `-1`
	)		const

Get the center of selection.

Parameters

mass_weighted	Use mass-weighting
periodic	Account for periodic boundary conditions.

Warning: If the size of selection is larger than 1/2 of the box size in any dimension you will get incorrect results if periodic is set to true. This is not checked automatically! In this case use one of unwrapping options first.

◆ atom_traj()

MatrixXf Selection::atom_traj	(	int	ind,
		int	b = `0`,
		int	e = `-1`,
		bool	make_row_major_matrix = `false`
	)		const

Extracts X,Y,Z for given atom index for specified range of frames (gets trajectory of given atom).

Result is returned as MatrixXf, where i-th column (or row) is an XYZ vector for frame i.

◆ inertia()

void Selection::inertia	(	Vector3f_ref	moments,
		Matrix3f_ref	axes,
		Array3i_const_ref	pbc = `noPBC`,
		int	pbc_atom = `-1`
	)		const

Computes the central momens of inertia and principal axes of inertia.

Warning: If the size of selection is larger than 1/2 of the box size in any dimension you will get incorrect results if periodic is set to true. This is not checked automatically! In this case use one of unwrapping options first.

◆ gyration()

float Selection::gyration	(	Array3i_const_ref	pbc = `noPBC`,
		int	pbc_atom = `-1`
	)		const

Computes radius of gyration for selection.

Warning: If the size of selection is larger than 1/2 of the box size in any dimension you will get incorrect results if periodic is set to true. This is not checked automatically! In this case use one of unwrapping options first.

◆ distance()

float Selection::distance	(	int	i,
		int	j,
		Array3i_const_ref	pbc = `fullPBC`
	)		const

Get distance between two atoms (periodic in given dimensions if needed).

Note: This function takes selection indexes, not absolute indexes.

◆ angle()

float Selection::angle	(	int	i,
		int	j,
		int	k,
		Array3i_const_ref	pbc = `fullPBC`
	)		const

Get angle in degrees between three atoms (periodic in given dimensions if needed).

Note: This function takes selection indexes, not absolute indexes.

◆ dihedral()

float Selection::dihedral	(	int	i,
		int	j,
		int	k,
		int	l,
		Array3i_const_ref	pbc = `fullPBC`
	)		const

Get dihedral angle in degrees between three atoms (periodic in given dimensions if needed).

Note: This function takes selection indexes, not absolute indexes.

◆ rotate()

void Selection::rotate	(	Vector3f_const_ref	pivot,
		Vector3f_const_ref	axis,
		float	angle
	)

Rotate selection around given axis relative to given pivot.

Parameters

pivot	Rotation around this pivot
axis	Rotate around this vector
angle	Rotation angle in radians

◆ unwrap()

void Selection::unwrap	(	Array3i_const_ref	pbc = `fullPBC`,
		int	pbc_atom = `-1`
	)

Unwraps selection to make it whole if possible (without jumps over periodic box boundary).

The periodic center of mass is used as an anchor point if pbc_atom<0.

Warning: If the size of selection is larger than 1/2 of the box size in any dimension unwrap() will not work as expected and will not make selection "compact"! This is not checked automatically.

◆ unwrap_bonds()

int Selection::unwrap_bonds	(	float	d,
		Array3i_const_ref	pbc = `fullPBC`,
		int	pbc_atom = `-1`
	)

Unwraps selection to make it whole (without jumps over periodic box boundary).

based on preserving all bonds. This method works reliably in any case, but is much slower than unwrap()

Parameters

d	Maximal bond length. If 0 bonds from topology are used (if present).
pbc_atom	Local index of the reference atom, which doesn't move.

Returns: Number of disconnected pieces after unwrapping. 1 means solid selection.

◆ principal_transform()

Eigen::Affine3f Selection::principal_transform	(	Array3i_const_ref	pbc = `noPBC`,
		int	pbc_atom = `-1`
	)		const

Get transform for orienting selection by principal axes.

Warning: If the size of selection is larger than 1/2 of the box size in any dimension you will get funny results if

Parameters

is_periodic is set to true.

◆ principal_orient()

void Selection::principal_orient	(	Array3i_const_ref	pbc = `noPBC`,
		int	pbc_atom = `-1`
	)

Orient molecule by its principal axes.

The same as

Eigen::Affine3f tr = sel.principal_transform();

sel.apply_transform(tr);

◆ non_bond_energy()

Vector2f Selection::non_bond_energy	(	float	cutoff = `0`,
		bool	pbc = `true`
	)		const

Self-energy of selection computed within given interaction cut-off.

If cutoff is 0 the cutoff from topology is used.

◆ write()

void Selection::write	(	std::string	fname,
		int	b = `-1`,
		int	e = `-1`
	)		const

Write structure or trajectory for selection.

File type is determined by extension. Frames from b to e are written. If

Parameters

b	is not set or -1 it means current frame If
e	is not set or -1 it means the last frame

◆ flatten()

void Selection::flatten ( )

"Flattens" selection by removing coordinate dependence and making it not text-based.

Resulting selection is equivalent to plain set of indexes "index i1 i2 i3..." Useful to avoid recomputing selection on frame change when tracking given set of atoms

◆ to_gromacs_ndx()

string Selection::to_gromacs_ndx ( std::string name ) const

Returns a string formatted as Gromacs ndx file containing the current selection with given name.

Warning: Indexes in Gromacs ndx are starting from 1! Thus one is added to all pteros indexes!

◆ get_internal_bonds()

std::vector< std::vector< int > > Selection::get_internal_bonds	(	float	d,
		bool	periodic = `true`
	)		const

Get all bonds within this selection returned as local selection indexes in form 1->[2,3,..].

If d>0 it is used as cutoff if d==0 the bonds from topology are used and periodicity is ignored

◆ split_by_connectivity()

void Selection::split_by_connectivity	(	float	d,
		std::vector< Selection > &	res,
		bool	periodic = `true`
	)

Split current selection into several selections according to the interatomic distances.

Each resulting selection is a group of atoms connected by distances less than d. if d==0 the bonds from topology are used instead and periodic argument is ignored

◆ split()

template<class F >

void pteros::Selection::split	(	std::vector< Selection > &	parts,
		F	callback
	)

inline

Split selection by the values returned by custom callback function.

Signature of callback is: T cb(const Selection&,int) Callback is called for each atom in selection (local index is passed as its second argument)
Callback can return any type usable as a key of std::map. Selection is split into parts according to returned values - all identical values go to the same part.

◆ each_residue()

void Selection::each_residue ( std::vector< Selection > & sel ) const

Selects each residue, which is referenced by selection.

All selections for residues are placed into supplied vector. Handles multiple chains correctly.

◆ dssp()

string Selection::dssp ( ) const

Determines secondary structure with DSSP algorithm and return it as a code string.

Returns: Code string The code is the same as in DSSP: alphahelix: 'H' betabridge: 'B' strand: 'E' helix_3: 'G' helix_5: 'I' turn: 'T' bend: 'S' loop: ' '

◆ xyz_ptr()

Eigen::Vector3f* pteros::Selection::xyz_ptr ( int ind ) const

inline

Returns pointer to the coordinates of given atom for current frame.

Used internally in Grid_searcher.

◆ index()

int pteros::Selection::index ( int ind ) const

inline

Extracts type.

Extracts typename Extracts residue name Extracts chain Extracts atom name Extracts atom mass Extracts atom charge Extracts B-factor Extracts occupancy field Extracts residue number Extracts tag Extracts atom index in the system, which is pointed by selection

◆ vdw()

float Selection::vdw ( int ind ) const

Extracts resindex.

Extracts atomic number Computes VDW radius. Read only. If atomic number is set uses whole periodic table from VMD If no atomic number uses rough guess from Gromacs vdwradii.dat

◆ box()

PeriodicBox& pteros::Selection::box ( )

inline

Returns periodic box of the frame pointed by selection The same as:

sel.get_system()->box(sel.get_frame());

This is a convenience method. The same box is returned by all selection which point to the same frame.

◆ time()

float& pteros::Selection::time ( )

inline

Returns time stamp of the frame pointed by selection The same as:

sel.get_system()->Time(sel.get_frame());

This is a convenience method. The same time is returned by all selection which point to the same frame.

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

include/pteros/core/selection.h
src/core/selection.cpp

Classes

Public Member Functions

Constructors and operators

Fitting and RMSD functions

Utility functions

Detailed Description

Constructor & Destructor Documentation

◆ Selection() [1/4]

◆ Selection() [2/4]

◆ Selection() [3/4]

◆ Selection() [4/4]

Member Function Documentation

◆ operator[]() [1/2]

◆ operator[]() [2/2]

◆ operator~()

◆ set_system()

◆ modify() [1/2]

◆ modify() [2/2]

◆ apply()

◆ update()

◆ clear()

◆ select()

◆ set_frame()

◆ set_chain()

◆ get_resid()

◆ set_resid()

◆ set_name()

◆ set_resname()

◆ get_resindex()

◆ get_xyz()

◆ set_mass()

◆ set_beta()

◆ set_occupancy()

◆ set_charge()

◆ set_tag()

◆ get_vel()

◆ get_force()

◆ is_large()

◆ center()

◆ atom_traj()

◆ inertia()

◆ gyration()

◆ distance()

◆ angle()

◆ dihedral()

◆ rotate()

◆ unwrap()

◆ unwrap_bonds()

◆ principal_transform()

◆ principal_orient()

◆ non_bond_energy()

◆ write()

◆ flatten()

◆ to_gromacs_ndx()

◆ get_internal_bonds()

◆ split_by_connectivity()

◆ split()

◆ each_residue()

◆ dssp()

◆ xyz_ptr()

◆ index()

◆ vdw()

◆ box()

◆ time()