PROFASI  Version 1.5
Public Member Functions | Static Public Member Functions | List of all members
prf::AtomCoordinates Class Reference

A class to store the coordinates of an atom. More...

#include <AtomCoordinates.hh>

Public Member Functions

 AtomCoordinates (int i)
 create coordinates for atom with unique_id i
 
Accessing coordinate data

access or modify properties of an individual AtomCoordinates object

double x () const
 
double y () const
 
double z () const
 
void x (double val)
 
void y (double val)
 
void z (double val)
 
int Id () const
 return the unique_id corresponding to the AtomCoordinates object
 
void Id (int i)
 

Static Public Member Functions

static void Initialize (int tot_atoms)
 An important initialization function.
 
static void update (int strt, int iend)
 Update backup coordinates.
 
static void revert (int strt, int iend)
 Revert to backup coordinates.
 
static Vector3 CenterOfMass (int strt, int iend)
 Center of mass of a block of coordinates, expensive!
 
static void center ()
 Move center of mass to origin.
 
static double rgyr (int istrt, int iend)
 Radius of gyration of a block, again, use carefully!
 
static void BlockRotate (double tht, int strt, int iend, AtomCoordinates ax1, AtomCoordinates ax2)
 Rotate a block of atoms.
 
static void BlockRotate (double tht, int strt, int iend, Vector3 org, Vector3 axs)
 Rotate block about given axis and origin.
 
static void BlockTranslate (const Vector3 &amnt, int strt, int iend)
 translate a block of coordinates by given amounts.
 
static void BoundingBox (int i1, int i2, double &xmn, double &xmx, double &ymn, double &ymx, double &zmn, double &zmx)
 find bounding box for atoms between i1 and i2
 
static void EnforceBC (int i1, int i2)
 enforce periodic boundary conditions on atoms between i1 and i2
 
static void write_pdb_box_info (FILE *fp)
 Periodic box information to a pdb file.
 
static void CheckDiff ()
 
static void switch_to_backups ()
 
static void switch_to_regular ()
 Switch back to current coordinates.
 
static void SetBox (double bx)
 Set size of periodic box.
 
static double boxL ()
 access box size
 
static double total_error ()
 difference between present coordinates and backups
 
Static coordinate access without AtomCoordinates object

Access coordinates without an AtomCoordinate object

It is also possible to access the x,y, z coordinates of the i'th atom without ever referring to the atom or an AtomCoordinates object. This is done using static functions using the unique_id of that atom as the argument.

static double xval (int i)
 
static double yval (int i)
 
static double zval (int i)
 
static Vector3 diff_from_backup (int i)
 difference between current and backup coordinates for atom i
 

Three-vector like operations

One can manipulate AtomCoordinates just like three vectors. Algebraic operations are supported among them which yield answers which would be expected had they really been three vectors. Even algebraic operations between an ordinary three vector and an AtomCoordinates object should work seamlessly.

Vector3 value () const
 extract three vector out of the AtomCoordinates object
 
void value (double gx, double gy, double gz)
 assign x,y and z coordinates
 
AtomCoordinatesoperator= (const AtomCoordinates &)
 Copy x,y and z coordinates from another AtomCoordinates object.
 
AtomCoordinatesoperator= (const Vector3 &)
 Assign a Vector3 to an AtomCoordinates.
 
Vector3 operator+ (const AtomCoordinates &) const
 
Vector3 operator+ (const Vector3 &) const
 
AtomCoordinatesoperator+= (const AtomCoordinates &)
 
AtomCoordinatesoperator+= (const Vector3 &)
 
Vector3 operator- (const AtomCoordinates &) const
 
Vector3 operator- (const Vector3 &) const
 
AtomCoordinatesoperator-= (const AtomCoordinates &)
 
AtomCoordinatesoperator-= (const Vector3 &)
 
double dot (const AtomCoordinates &) const
 Scalar product of two AtomCoordinates.
 
double dot (const Vector3 &) const
 Scalar product of an AtomCoordinates object with a Vector3.
 
Vector3 operator* (const AtomCoordinates &) const
 Vector (cross) product of two AtomCoordinates.
 
Vector3 operator* (const Vector3 &) const
 Vector product of an AtomCoordinates object with a Vector3.
 
static Vector3 vec (int i)
 statically get the Vector3 representing the coordinates of atom i
 
static void vec (int i, double gx, double gy, double gz)
 statically assign x,y and z values to atom i
 
Vector3 operator+ (const Vector3 &, const AtomCoordinates &)
 
Vector3 operator- (const Vector3 &, const AtomCoordinates &)
 

Distance measure related functions

static double per_sep (double x1, double x2)
 Periodic separation between values x1 and x2.
 
static double pos_per_sep (double x1, double x2)
 Positive definite periodic separation.
 
static double xdist (int i1, int i2)
 components of the periodic dist. between atoms indexed i1 and i2
 
static double ydist (int i1, int i2)
 
static double zdist (int i1, int i2)
 
static double npxdist (int i1, int i2)
 non-periodic versions of the separations along x,y and z axes
 
static double npydist (int i1, int i2)
 
static double npzdist (int i1, int i2)
 
static double sepx (int i, double xpt)
 periodic separation between atom i and a given point along an axis
 
static double sepy (int i, double ypt)
 
static double sepz (int i, double zpt)
 
static Vector3 sepv (int i, Vector3 v)
 
static double psepx (int i, double xpt)
 positive definite periodic separation between atom i and a point
 
static double psepy (int i, double ypt)
 
static double psepz (int i, double zpt)
 
static double s2 (int i1, int i2)
 bare cartessian distance measure between atoms i1 and i2
 
static double s (int i1, int i2)
 
static double dist2 (int i1, int i2)
 distance measure respecting periodic box
 
static double dist (int i1, int i2)
 
static double seps2 (int i, double xpt, double ypt, double zpt)
 Periodic distance measure from a given point.
 
static double pseps2 (int i, double xpt, double ypt, double zpt)
 Distance^2 from a point using positive definite periodic measures.
 
static double seps (int i, double xpt, double ypt, double zpt)
 
static double pseps (int i, double xpt, double ypt, double zpt)
 
static Vector3 diff (int i1, int i2)
 Non-periodic vector difference between i1 and i2.
 
static Vector3 sep (int i1, int i2)
 Periodic vector difference between i1 and i2.
 
static Vector3 psep (int i1, int i2)
 Positive-definite periodic Vector difference between i1 and i2.
 

Detailed Description

AtomCoordinates class is meant to work in two ways. On the one hand it is the x,y and z coordinates of an atom. So, if you subtract two AtomCoordinate objects you get a Vector3. But there are some advantages in not using the Vector3 directly for the coordinates of an atom. In order to impose the periodic boundary condition, one has to check the extent of each molecule of the system along all three axes separately. This is cumbersome if each component of the position vectors is only accessible through the three vector. As far as periodicity is concerned, the different spatial directions have nothing to do with eachother.

Besides, in this implementation, the AtomCoordinates class will actually store coordinates of all atoms in static valarrays. The unique_id of each atom marks the element in the static arrays reserved for that atom. While this is by no means crucial, it has been done for two reasons...

AtomCoordinates also saves a backup set of coordinates for each atom. This helps quickly restore the system when an update is rejected.

Member Function Documentation

void AtomCoordinates::BlockRotate ( double  tht,
int  strt,
int  iend,
AtomCoordinates  ax1,
AtomCoordinates  ax2 
)
static

Rotate a block of atoms between strt and iend by angle tht about the axis passing through the atomCoordinates ax2 and ax1.

void AtomCoordinates::CheckDiff ( )
static

check that the differences between current and backup coordinates are not too big. Mostly a sanity check function Switch to make the back up coordinates the active ones

void AtomCoordinates::Initialize ( int  tot_atoms)
static

The function Initialize(tot_atoms) allocates space for the coordinates of tot_atoms Atoms. It should be called once, at the beginning when the total number of atoms has been determined.

void AtomCoordinates::revert ( int  strt,
int  iend 
)
static

Copy a block of coordinates "backward", so that current values are abandoned and replaced with backup values

static void prf::AtomCoordinates::switch_to_backups ( )
inlinestatic

This does not dump the current coordinates, but causes energy calculations or for that matter any external object to access the backup values as the coordinates of different atoms.

static void prf::AtomCoordinates::switch_to_regular ( )
inlinestatic

This reverses what is done in switch_to_backups

void AtomCoordinates::update ( int  strt,
int  iend 
)
static

Copy a block of coordinates "forward", so that backups are synchronized with the current values


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

PROFASI: Protein Folding and Aggregation Simulator, Version 1.5
© (2005-2016) Anders Irbäck and Sandipan Mohanty
Documentation generated on Mon Jul 18 2016 using Doxygen version 1.8.2