pteros::System Class Reference

The system of atoms. More...

#include <system.h>

Public Member Functions
AtomIterator	atoms_begin ()
	Iterators and indexing {.
AtomIterator	atoms_end ()
std::vector< Frame >::iterator	traj_begin ()
std::vector< Frame >::iterator	traj_end ()
AtomHandler	operator[] (const std::pair< int, int > &ind_fr)
Constructors and operators
	System ()
	Default constructor.
	System (std::string fname)
	Constructor creating system from file.
	System (const System &other)
	Copy constructor.
System &	operator= (const System &other)
	Assignment operator.
	System (const Selection &sel)
	Constructing new System from Selection of other system.
virtual	~System ()
	Destructor.
Adding, deleting and ordering groups of atoms
These methods update resindexes automatically.
Selection	append (const System &sys)
	Append other system to this one Returns selection corresponding to appended atoms.
Selection	append (const Selection &sel, bool current_frame=false)
	Append atoms from selection to this system. More...
Selection	append (const Atom &at, Vector3f_const_ref coord)
	Append single atom to this system Returns selection corresponding to appended atom.
Selection	append (const AtomHandler &at)
	Append Atom_proxy object to this system Returns selection corresponding to appended atom. More...
void	rearrange (const std::vector< std::string > &sel_strings)
	Rearranges the atoms in the order of provided selection strings. More...
void	rearrange (const std::vector< Selection > &sel_vec)
	Rearranges the atoms in the order of provided selections. More...
void	rearrange (const std::vector< std::string > &begin_strings, const std::vector< std::string > &end_strings)
	Rearranges the atoms in the order of provided selection strings. More...
void	rearrange (const std::vector< Selection > &begin_vec, const std::vector< Selection > &end_vec)
	Rearranges the atoms in the order of provided selections. More...
std::vector< std::pair< std::string, int > >	rearrange_by_resname ()
	Rearranges the atoms in the alphabetical order of residue names. More...
void	keep (const std::string &sel_str)
	Keep only atoms given by selection string.
void	keep (const Selection &sel)
	Keep only atoms from given selection.
void	remove (const std::string &sel_str)
	Remove atoms given by selection string.
void	remove (Selection &sel)
	Remove atoms of given selection. More...
void	distribute (const Selection sel, Vector3i_const_ref ncopies, Matrix3f_const_ref shift)
	Creates multiple copies of selection in the system and distributes them in a grid given by 3 translation vectors. More...
General properties
int	num_frames () const
	Returns the number of frames in selection.
int	num_atoms () const
	Returns the number of atoms in selection.
Selecting atoms.
These functions are just convenience adaptors for constructors of Selection class: // Conventional way: sys = System("structure.pdb"); Selection sel(s,"name CA"); // Shorter way: auto sel = sys.select("name CA"); // Even shorter way using operator (): auto sel = sys("name CA"); It also allows writing "one-liners" like this: System("file.pdb").select("name CA").write("ca.pdb");
Selection	select (std::string str, int fr=0)
Selection	operator() (std::string str, int fr=0)
Selection	select (int ind1, int ind2)
Selection	operator() (int ind1, int ind2)
Selection	select (const std::vector< int > &ind)
Selection	operator() (const std::vector< int > &ind)
Selection	select (std::vector< int >::iterator it1, std::vector< int >::iterator it2)
Selection	operator() (std::vector< int >::iterator it1, std::vector< int >::iterator it2)
Selection	select (const std::function< void(const System &, int, std::vector< int > &)> &callback, int fr=0)
Selection	operator() (const std::function< void(const System &, int, std::vector< int > &)> &callback, int fr=0)
Selection	select_all () const
	Convenience functions to select all.
Selection	operator() ()
File IO
void	load (std::string fname, int b=0, int e=-1, int skip=0, std::function< bool(System *, int)> on_frame=0)
	Read structure, trajectory or topology from file. More...
bool	load (const std::unique_ptr< FileHandler > &handler, FileContent what, std::function< bool(System *, int)> on_frame=0)
	Load data into System from the pre-opened file handler. More...
void	write (std::string fname, int b=-1, int e=-1) const
void	write (const std::unique_ptr< FileHandler > &handler, FileContent what, int b=-1, int e=-1) const
std::vector< std::pair< std::string, Selection > >	load_gromacs_ndx (std::string fname)
	Load Gromacs .ndx file and crease selections acording to it from existing system Returns a vector of pairs {name,Selection}.
Input filtering
void	set_filter (std::string str)
	Filters narrow set of atoms and coordinates which are loaded from data files. More...
void	set_filter (int ind1, int ind2)
void	set_filter (const std::vector< int > &ind)
void	set_filter (std::vector< int >::iterator it1, std::vector< int >::iterator it2)
Operations with frames
int	frame_dup (int fr)
	Duplicates given frame and adds it to the end of frame vector.
void	frame_append (const Frame &fr)
	Appends provided frame to trajectory.
void	frame_copy (int fr1, int fr2)
	Copy all frame data from fr1 to fr2. Fr2 is overwritten!
void	frame_delete (int b=0, int e=-1)
	Delete specified range of frames. More...
void	frame_swap (int fr1, int fr2)
	Swaps two specified frames.
Inline accessors
PeriodicBox &	box (int fr=0)
	Read/write access for periodic box for given frame.
const PeriodicBox &	box (int fr=0) const
	Read only access for periodic box for given frame.
float &	time (int fr=0)
	Read/Write access to the time stamp of given frame.
const float &	time (int fr=0) const
	Read only access to the time stamp of given frame.
Eigen::Vector3f &	xyz (int ind, int fr=0)
	Read/Write access for given coordinate of given frame.
const Eigen::Vector3f &	xyz (int ind, int fr=0) const
	Read only access for given coordinate of given frame.
Eigen::Vector3f &	vel (int ind, int fr=0)
	Read/Write access for given velocity of given frame.
const Eigen::Vector3f &	vel (int ind, int fr=0) const
	Read only access for given velocity of given frame.
Eigen::Vector3f &	force (int ind, int fr=0)
	Read/Write access for given force of given frame.
const Eigen::Vector3f &	force (int ind, int fr=0) const
	Read only access for given force of given frame.
Atom &	atom (int ind)
	Read/Write access for given atom.
const Atom &	atom (int ind) const
	Read only access for given atom.
Frame &	frame (int fr)
	Get read/write reference for given frame.
const Frame &	frame (int fr) const
	Get read only reference for given frame.
Manipulating sets of atoms by indexes.
These methods do not update resindexes automatically.
Selection	atoms_dup (const std::vector< int > &ind)
	Adds new atoms, which are duplicates of existing ones by index. Atoms are placed at the end of the system.
Selection	atoms_add (const std::vector< Atom > &atm, const std::vector< Eigen::Vector3f > &crd)
	Adds new atoms from supplied vectors of atoms and coordinates. Atoms are placed at the end of the system.
void	atoms_delete (const std::vector< int > &ind)
	Delete the set of atoms by indexes.
void	atom_move (int i, int j)
	Move atom i to other position. Atom is inserted instead of atom j, shift is performed towards previous position of i.
Selection	atom_clone (int source)
	Duplicate single target atom and puts it immediately after the source. More...
void	atom_swap (int i, int j)
	Swap two atoms.
Selection	atom_add_1h (int target, int at1, int at2, int at3, float dist=0.109, bool pbc=true)
	Add single hydrogen to target atom according to positions of 3 adjacent atoms assuming tetrahedral symmetry.
Selection	atom_add_2h (int target, int at1, int at2, float dist=0.109, bool pbc=true)
	Add two hydrogens to target atom according to positions of 2 adjacent atoms assuming tetrahedral symmetry.
Selection	atom_add_3h (int target, int at1, float dist=0.109, bool pbc=true)
	Add 3 hydrogens to target atom according to positions of single adjacent atom assuming tetrahedral symmetry.
Periodicity-related functions
void	wrap (int fr, Array3i_const_ref pbc=fullPBC)
	Wrap all system to the periodic box for given frame.
Measuring functions
float	distance (int i, int j, int fr, Array3i_const_ref pbc=fullPBC) const
	Get distance between two atoms for given frame (periodic in given dimensions if needed).
float	angle (int i, int j, int k, int fr, Array3i_const_ref pbc=fullPBC) const
	Get angle in degrees between three atoms for given frame (periodic in given dimensions if needed).
float	dihedral (int i, int j, int k, int l, int fr, Array3i_const_ref pbc=fullPBC) const
	Get dihedral angle in degrees between three atoms for given frame (periodic in given dimensions if needed).
Utility functions
void	clear ()
	Clears the system and prepares for loading completely new structure.
bool	force_field_ready ()
ForceField &	get_force_field ()
	Returns internal Force_field object.
void	assign_resindex (int start=0)
	Assign unique resindexes This is usually done automatically upon loading a structure from file.
void	sort_by_resindex ()
	Sorts atoms by resindex arranging atoms with the same resindexes into contigous pieces. More...
void	clear_vel ()
	Delete velocities from all frames. More...
void	clear_force ()
	Delete forces from all frames. More...
Eigen::Vector2f	get_energy_for_list (const std::vector< Eigen::Vector2i > &pairs, const std::vector< float > &dist, std::vector< Eigen::Vector2f > *pair_en=nullptr)
	Low level energy evaluation function Returns total energy Individual pair energies could be returned to pair_en if provided.

Detailed Description

The system of atoms.

The System is a container for atoms and their coordinates, which are typically loaded from file. All properties of atoms, except the coordinates, are stored in atoms vector. Coordinates are stored as a resizable vector of trajectory frames. The system knows about selections associated with it and sends them signals if selections should adapt to the changes of coordinates of atom properties. Copying and assignment of systems is allowed, but associated selections are not copied.

Member Function Documentation

append() [1/2]

Selection System::append	(	const Selection &	sel,
		bool	current_frame = false
	)

Append atoms from selection to this system.

Selection may belong to any system, not necessary current. Returns selection corresponding to appended atoms.

Parameters

current_frame

if true only the coordinates of current frame in sel are added to all frames of the system.

append() [2/2]

Selection System::append

(

const AtomHandler &

at

)

Append Atom_proxy object to this system Returns selection corresponding to appended atom.

Usage:

Selection sel(s,"name CA");
System new_s;
for(auto& at: sel){
   new_s.append(at);
}

rearrange() [1/4]

void System::rearrange

(

const std::vector< std::string > &

sel_strings

)

Rearranges the atoms in the order of provided selection strings.

Atom, which are not selected are appended at the end in their previous order.

Note

Selections should not overlap (exception is thrown if they are).

rearrange() [2/4]

void System::rearrange

(

const std::vector< Selection > &

sel_vec

)

Rearranges the atoms in the order of provided selections.

Atoms, which are not selected are appended as is at the end.

Note

Selections should not overlap (exception is thrown if they are).

rearrange() [3/4]

void System::rearrange	(	const std::vector< std::string > &	begin_strings,
		const std::vector< std::string > &	end_strings
	)

Rearranges the atoms in the order of provided selection strings.

Parameters

begin_strings	selection strings to begin with.
end_strings	selection strings to end with. Atoms, which are not selected are placed as is between begin and end.

Note

Selections should not overlap (exception is thrown if they are).

rearrange() [4/4]

void System::rearrange	(	const std::vector< Selection > &	begin_vec,
		const std::vector< Selection > &	end_vec
	)

Rearranges the atoms in the order of provided selections.

Parameters

begin_vec	selections to begin with.
end_vec	selections to end with. Atoms, which are not selected are placed as is between begin and end.

Note

Selections should not overlap (exception is thrown if they are).

rearrange_by_resname()

std::vector< std::pair< string, int > > System::rearrange_by_resname

(

)

Rearranges the atoms in the alphabetical order of residue names.

Useful for liquid systems and membranes where each residue is a whole molecule.

Warning

If the molecules contain more than one resiude they will be broken!

Returns

vector of (residue name,number) pairs.

remove()

void System::remove

(

Selection &

sel

)

Remove atoms of given selection.

Warning

Selection becomes invalid after that and is cleared!

distribute()

void System::distribute	(	const Selection	sel,
		Vector3i_const_ref	ncopies,
		Matrix3f_const_ref	shift
	)

Creates multiple copies of selection in the system and distributes them in a grid given by 3 translation vectors.

Vectors are stored column-wise as shift.col(i)

load() [1/2]

void System::load	(	std::string	fname,
		int	b = 0,
		int	e = -1,
		int	skip = 0,
		std::function< bool(System *, int)>	on_frame = 0
	)

Read structure, trajectory or topology from file.

Parameters

b	First frame to read
e	Last frame to read (-1 means up to the end of trajectory)
skip	Read only each skip frames
on_frame	Callback function, which takes pointer to the System as a first argument and the index of current stored frame as the second. If callback returns false loading stops.

load() [2/2]

bool System::load	(	const std::unique_ptr< FileHandler > &	handler,
		FileContent	what,
		std::function< bool(System *, int)>	on_frame = 0
	)

Load data into System from the pre-opened file handler.

This is rather low-level method which provides fine control over what should be read. It can be called several times to read trajectory frames one by one from the same pre-opened file.

set_filter()

void System::set_filter

(

std::string

str

)

Filters narrow set of atoms and coordinates which are loaded from data files.

Only atoms specified by filter are kept in the system. They follow the same rules as ordinary selections but can't be coordinate-dependent and can't be set by callbacs.

Note

Filters do not make loading faster. In fact it becomes slower (up to 2 times for very large frames) and consumes twise as much memory during loading. However when loading finishes the system will contain only selected atoms. If many frames are stored in the system overall memory consumption will be much smaller.

Filter could only be set to empty system (it throws an error otherwise), thus the way of using them is the following:

// Create empty system
System sys;
// Set filter
sys.set_filter("name CA");
// All calls to load will use filter now
sys.load("some_protein.pdb");
sys.load("trajectory.xtc");

Warning

Filters could not be used when loading topologies! load() throws an error if attempting to load topology with filter.

frame_delete()

void System::frame_delete	(	int	b = 0,
		int	e = -1
	)

Delete specified range of frames.

If only

Parameters

b	is supplied deletes all frames from b to the end. If only
e	is supplied deletes all frames from 0 to e

atom_clone()

Selection System::atom_clone

(

int

source

)

Duplicate single target atom and puts it immediately after the source.

If using many times this procedure is slower than doing atoms_dup() and than assign_resindex().

sort_by_resindex()

void System::sort_by_resindex

(

)

Sorts atoms by resindex arranging atoms with the same resindexes into contigous pieces.

Could be called after atom additions or duplications.

clear_vel()

void System::clear_vel

(

)

Delete velocities from all frames.

Does nothing if no velocities.

clear_force()

void System::clear_force

(

)

Delete forces from all frames.

Does nothing if no forces.

---

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

• include/pteros/core/system.h
• src/core/system.cpp
• src/core/utils.cpp