Classes
struct	coord_3D
struct	vectormag_3D
struct	coord_nD
struct	nD_index
struct	nD_ptrs
struct	coord_nDi
struct	plane
struct	boxinfo
Defines
#define	PI 3.1415926535897932384626433832795028
#define	get_vector_from_coords(a, b) coord_to_vec(subtract_coord(b,a))
Functions
void	rotate_vector_to_Z_list (coord_3D *, int, vectormag_3D)
coord_3D	get_geometric_center (coord_3D *c, int nc)
coord_3D	get_geometric_center_dp (coord_3D **c, int nc)
plane	get_plane (coord_3D, coord_3D, coord_3D)
plane	get_plane_for_ring (int n, coord_3D **r)
double	get_signed_distance_from_point_to_plane (plane p, coord_3D pt)
vectormag_3D	normalize_vec (vectormag_3D)
vectormag_3D	scalarmult_vec (vectormag_3D, double)
vectormag_3D	add_vec (vectormag_3D, vectormag_3D)
vectormag_3D	subtract_vec (vectormag_3D, vectormag_3D)
coord_3D	scalarmult_coord (coord_3D, double)
coord_3D	add_coord (coord_3D, coord_3D)
coord_3D	subtract_coord (coord_3D, coord_3D)
vectormag_3D	get_crossprod (vectormag_3D, vectormag_3D)
double	get_dotprod (vectormag_3D, vectormag_3D)
double	get_magnitude (vectormag_3D)
vectormag_3D	zero_vec ()
coord_3D	zero_coord ()
coord_3D	vec_to_coord (vectormag_3D)
vectormag_3D	coord_to_vec (coord_3D)
void	initialize_coord_3D (coord_3D *c)
void	initialize_vectormag_3D (vectormag_3D *v)
void	initialize_plane (plane *p)
double	get_angle_between_vectors (vectormag_3D a, vectormag_3D b)
double	get_angle_ABC_points (coord_3D a, coord_3D b, coord_3D c)
double	get_dihedral_ABCD_points (coord_3D a, coord_3D b, coord_3D c, coord_3D d)
double	get_distance_AB_points (coord_3D a, coord_3D b)
void	translate_coords_dp_list (coord_3D **coords, int num_coords, coord_3D shift)
double *	create_rotation_matrix (coord_3D point, vectormag_3D direction, double theta)
void	destroy_rotation_matrix (double *matrix)
void	apply_rotation_matrix_to_coord_p (coord_3D c, double matrix)
void	rotate_coords_about_axis_dp_list (coord_3D **coords, int num_coords, coord_3D point, vectormag_3D direction, double theta)
coord_3D	get_cartesian_point_from_internal_coords (coord_3D a, coord_3D b, coord_3D c, double theta, double phi, double distance)
void	orient_coords2_to_coords1_dp_list (coord_3D *coords, int num_coords, const coord_3D bond_atom_a, coord_3D bond_atom_b, double distance, const coord_3D angle_atom_a, double theta, coord_3D angle_atom_b, double rho, const coord_3D dih_atom_a, coord_3D dih_atom_b, double tau, const coord_3D tor_atom_a, const coord_3D ref_angle_a, double phi, coord_3D tor_atom_b, coord_3D *ref_atom_b, double omega)
void	translate_residue_by_XYZ (residue *r, int xs, int xd, coord_3D)
void	translate_molecule_by_XYZ (molecule *m, int xs, int xd, coord_3D)
void	translate_ensemble_by_XYZ (ensemble *e, int xs, int xd, coord_3D)
void	translate_zero_to_coord_M (molecule *m, int xs, int xd, coord_3D)
coord_3D **	atoms_to_coord_list (atom **atoms, int num_atoms)
void	rotate_vector_to_Z_M (molecule *m, int xs, int xd, int vs, int vd, vectormag_3D vec)
void	normalize_molecule_vectors (molecule *m, int vs, int vd)
void	normalize_ensemble_vectors (ensemble *e, int vs, int vd)
void	shift_molecule_atoms_by_vector_scale (molecule *m, int xs, int xd, int vr, double scale)
vectormag_3D	get_molecule_point_charge_dipole (molecule m, int xs, int chgsrc, atype AT)
void	rollMolecule (molecule *m, double rad)
void	pitchMolecule (molecule *m, double rad)
void	yawMolecule (molecule *m, double rad)
void	rollAssembly (assembly *a, double rad)
void	pitchAssembly (assembly *a, double rad)
void	yawAssembly (assembly *a, double rad)
double	get_distance_from_point_to_plane (plane p, coord_3D pt, int absl)
double	get_angle_between_plane_and_vector (plane p, coord_3D pt1, coord_3D pt2)

Detailed Description

For functions that perform geometric manipulations or calculations on the chemical structures (e.g. assembly, molecule, etc.), it is often necessary to indicate which set of coordinates are to be used for the calculation. In most cases, it is also possible to perform the calculation on coordinates in one location, but leave those untouched and save the results to another location. The same applies to velocities and vectors.

Special variable names and meanings:

xs, vs, xvs: These are the source data on which to base the calculation.

xd, vd, xvd: These are the locations to which changed data should be stored. Note that this location can typically be the same as the source.

xt, vt, xvt: In these cases, two sets of coordinates are being compared to

The variables above can take on the following values:

-1 This tells the function to use the main coordinate set. That is, use atom.x or atom.xv. This value is not relevant to vectors, where there is not a "main" vector.

0, 1, 2, ... A number greater than or equal to zero indicates the location in an array. These values apply to atom.xa[i], atom.xva[i] and atom.v[i].

-2 This is not available in all functions. It indicates that the entire array should be used. This applies to atom.xa[i], atom.xva[i] and atom.v[i].

-3 This is not available in all functions. It indicates that the main coordinates and the entire corresponding array should be used. This applies to { atom.x + atom.xa[i] } and to { atom.xv and atom.xva[i] }. It does not apply to atom.v[i].

Information about vectors:

All of the functions that involve vectors will set the magnitude of the resulting vector without relying on the entry in the input vector. So, for example, there is no need to get_magnitude before normalizing or multiplying by a scalar.

This also means that the vector manipulation functions here are inefficient in that they recalculate the magnitude every time they are called. If you are doing many vector manipulations in which the magnitude is not relevant, you might consider making a similar set that does not recalculate the magnitude.

Define Documentation

#define get_vector_from_coords	(	a,
		b
	)	coord_to_vec(subtract_coord(b,a))

Definition at line 19 of file geometries.h.

Referenced by get_cartesian_point_from_internal_coords(), and orient_coords2_to_coords1_dp_list().

#define PI 3.1415926535897932384626433832795028

Definition at line 16 of file geometries.h.

Referenced by find_vdw_clashes_pairwize_between_Assemblies(), get_plane_for_ring(), and orient_coords2_to_coords1_dp_list().

Function Documentation

coord_3D add_coord	(	coord_3D	,
		coord_3D
	)

Definition at line 7 of file add_coord.c.

References coord_3D::i, coord_3D::j, and coord_3D::k.

Referenced by shift_molecule_atoms_by_vector_scale().

Here is the caller graph for this function:

vectormag_3D add_vec	(	vectormag_3D	,
		vectormag_3D
	)

Definition at line 7 of file add_vec.c.

References vectormag_3D::d, vectormag_3D::i, vectormag_3D::j, and vectormag_3D::k.

void apply_rotation_matrix_to_coord_p	(	coord_3D *	c,
		double *	matrix
	)

Apply the rotation matrix to the given coordinate

Definition at line 66 of file rotations.c.

References coord_3D::i, coord_3D::j, and coord_3D::k.

Referenced by rotate_coords_about_axis_dp_list().

Here is the caller graph for this function:

coord_3D** atoms_to_coord_list	(	atom **	atoms,
		int	num_atoms
	)

Definition at line 5 of file atoms_to_coord_list.c.

vectormag_3D coord_to_vec ( coord_3D )

Definition at line 7 of file coord_to_vec.c.

References vectormag_3D::d, coord_3D::i, vectormag_3D::i, coord_3D::j, vectormag_3D::j, coord_3D::k, and vectormag_3D::k.

Referenced by get_angle_ABC(), get_angle_ABC_points(), get_dihedral_ABCD_points(), and get_dihedral_bonded_ABCD().

Here is the caller graph for this function:

double* create_rotation_matrix	(	coord_3D	point,
		vectormag_3D	direction,
		double	theta
	)

Create a rotation matrix for a rotation of theta degrees about an axis through the given point in the given direction

Definition at line 16 of file rotations.c.

References vectormag_3D::d, coord_3D::i, vectormag_3D::i, coord_3D::j, vectormag_3D::j, coord_3D::k, vectormag_3D::k, and normalize_vec().

Referenced by rotate_coords_about_axis_dp_list().

Here is the call graph for this function:

Here is the caller graph for this function:

void destroy_rotation_matrix ( double * matrix )

Deallocate the rotation matrix

Definition at line 60 of file rotations.c.

Referenced by rotate_coords_about_axis_dp_list().

Here is the caller graph for this function:

double get_angle_ABC_points	(	coord_3D	a,
		coord_3D	b,
		coord_3D	c
	)

Get angle abc

Definition at line 17 of file coordinate_manipulations.c.

References coord_to_vec(), get_angle_between_vectors(), and subtract_coord().

Referenced by orient_coords2_to_coords1_dp_list().

Here is the call graph for this function:

Here is the caller graph for this function:

double get_angle_between_plane_and_vector	(	plane	p,
		coord_3D	pt1,
		coord_3D	pt2
	)

Definition at line 5 of file get_angle_between_plane_and_vector.c.

References plane::A, plane::B, plane::C, get_dotprod(), coord_3D::i, vectormag_3D::i, coord_3D::j, vectormag_3D::j, coord_3D::k, and vectormag_3D::k.

Here is the call graph for this function:

double get_angle_between_vectors	(	vectormag_3D	a,
		vectormag_3D	b
	)

Get angle between two vectors

Definition at line 12 of file coordinate_manipulations.c.

References get_dotprod(), and normalize_vec().

Referenced by get_angle_ABC(), and get_angle_ABC_points().

Here is the call graph for this function:

Here is the caller graph for this function:

coord_3D get_cartesian_point_from_internal_coords	(	coord_3D	a,
		coord_3D	b,
		coord_3D	c,
		double	theta,
		double	phi,
		double	distance
	)

Calculate coordinate d, where (1) d is distance units from c (2) angle bcd is theta (3) dihedral between planes abc and bcd is phi

Link to derivation:

Note: should probably change the name of this

Definition at line 90 of file rotations.c.

References get_crossprod(), get_vector_from_coords, coord_3D::i, vectormag_3D::i, coord_3D::j, vectormag_3D::j, coord_3D::k, vectormag_3D::k, and normalize_vec().

Referenced by orient_coords2_to_coords1_dp_list().

Here is the call graph for this function:

Here is the caller graph for this function:

vectormag_3D get_crossprod	(	vectormag_3D	,
		vectormag_3D
	)

Definition at line 7 of file get_crossprod.c.

References vectormag_3D::d, vectormag_3D::i, vectormag_3D::j, and vectormag_3D::k.

Referenced by get_cartesian_point_from_internal_coords(), get_dihedral_ABCD_points(), get_dihedral_bonded_ABCD(), get_plane_for_ring(), orient_coords2_to_coords1_dp_list(), rotate_vector_to_Z_list(), and rotate_vector_to_Z_M().

Here is the caller graph for this function:

double get_dihedral_ABCD_points	(	coord_3D	a,
		coord_3D	b,
		coord_3D	c,
		coord_3D	d
	)

Get the dihedral angle between planes abc and bcd

This assumes that the bonding goes as: A-B-C-D or that the input vectors follow an equivalent direction convention. When A and D are eclipsed, the angle is zero.

Definition at line 27 of file coordinate_manipulations.c.

References coord_to_vec(), vectormag_3D::d, get_crossprod(), get_dotprod(), scalarmult_vec(), and subtract_coord().

Referenced by orient_coords2_to_coords1_dp_list().

Here is the call graph for this function:

Here is the caller graph for this function:

double get_distance_AB_points	(	coord_3D	a,
		coord_3D	b
	)

Euclidean distance from x to y

Definition at line 8 of file coordinate_manipulations.c.

References coord_3D::i, coord_3D::j, and coord_3D::k.

double get_distance_from_point_to_plane	(	plane	p,
		coord_3D	pt,
		int	absl
	)

This function will return the distance from a point pt to a plane pt. If absl is set to 0, it returns a signed distance ("above" or "below"). If set to 1, it returns the absolute value.

Definition at line 6 of file get_distance_from_point_to_plane.c.

References plane::A, plane::B, plane::C, coord_3D::i, coord_3D::j, and coord_3D::k.

double get_dotprod	(	vectormag_3D	,
		vectormag_3D
	)

Definition at line 8 of file get_dotprod.c.

References vectormag_3D::i, vectormag_3D::j, and vectormag_3D::k.

Referenced by get_angle_between_plane_and_vector(), get_angle_between_vectors(), get_angle_two_vectors(), get_dihedral_ABCD_points(), and get_dihedral_bonded_ABCD().

Here is the caller graph for this function:

coord_3D get_geometric_center	(	coord_3D *	c,
		int	nc
	)

Definition at line 9 of file get_geometric_center.c.

References coord_3D::i, coord_3D::j, coord_3D::k, and mywhine().

Here is the call graph for this function:

coord_3D get_geometric_center_dp	(	coord_3D **	c,
		int	nc
	)

Definition at line 36 of file get_geometric_center.c.

References coord_3D::i, coord_3D::j, coord_3D::k, and mywhine().

Here is the call graph for this function:

double get_magnitude ( vectormag_3D )

Definition at line 7 of file get_magnitude.c.

References vectormag_3D::i, vectormag_3D::j, and vectormag_3D::k.

Referenced by get_molecule_point_charge_dipole(), and rotate_vector_to_Z_M().

Here is the caller graph for this function:

vectormag_3D get_molecule_point_charge_dipole	(	molecule *	m,
		int	xs,
		int	chgsrc,
		atype *	AT
	)

Definition at line 17 of file get_dipole.c.

References residue::a, atom::ch, vectormag_3D::d, get_magnitude(), get_molecule_COM(), coord_3D::i, vectormag_3D::i, coord_3D::j, vectormag_3D::j, coord_3D::k, vectormag_3D::k, mywhine(), residue::na, molecule::nr, molecule::r, atom::x, atom::xa, and zero_vec().

Here is the call graph for this function:

plane get_plane	(	coord_3D	,
		coord_3D	,
		coord_3D
	)

Definition at line 8 of file get_plane.c.

References plane::A, plane::B, plane::C, plane::D, coord_3D::i, coord_3D::j, and coord_3D::k.

plane get_plane_for_ring	(	int	n,
		coord_3D **	r
	)

Definition at line 6 of file get_ring_pucker_plane.c.

References plane::A, plane::B, plane::C, vectormag_3D::d, plane::D, get_crossprod(), coord_3D::i, vectormag_3D::i, coord_3D::j, vectormag_3D::j, coord_3D::k, vectormag_3D::k, and PI.

Here is the call graph for this function:

double get_signed_distance_from_point_to_plane	(	plane	p,
		coord_3D	pt
	)

Definition at line 6 of file get_signed_distance_from_point_to_plane.c.

References plane::A, plane::B, plane::C, plane::D, coord_3D::i, coord_3D::j, and coord_3D::k.

void initialize_coord_3D ( coord_3D * c )

Definition at line 22 of file initialize_GLYstruct.c.

References coord_3D::i, coord_3D::j, and coord_3D::k.

void initialize_plane ( plane * p )

Definition at line 32 of file initialize_GLYstruct.c.

References plane::A, plane::B, plane::C, and plane::D.

void initialize_vectormag_3D ( vectormag_3D * v )

Definition at line 27 of file initialize_GLYstruct.c.

References vectormag_3D::d, vectormag_3D::i, vectormag_3D::j, and vectormag_3D::k.

void normalize_ensemble_vectors	(	ensemble *	e,
		int	vs,
		int	vd
	)

Definition at line 32 of file normalize_X_vectors.c.

References ensemble::nm, and normalize_molecule_vectors().

Here is the call graph for this function:

void normalize_molecule_vectors	(	molecule *	m,
		int	vs,
		int	vd
	)

Definition at line 11 of file normalize_X_vectors.c.

References residue::a, mywhine(), residue::na, normalize_vec(), molecule::nr, molecule::r, and atom::v.

Referenced by normalize_ensemble_vectors().

Here is the call graph for this function:

Here is the caller graph for this function:

vectormag_3D normalize_vec ( vectormag_3D )

Definition at line 7 of file normalize_vec.c.

References vectormag_3D::d, vectormag_3D::i, vectormag_3D::j, and vectormag_3D::k.

Referenced by create_rotation_matrix(), get_angle_between_vectors(), get_angle_two_vectors(), get_cartesian_point_from_internal_coords(), normalize_molecule_vectors(), rotate_vector_to_Z_list(), and rotate_vector_to_Z_M().

Here is the caller graph for this function:

void orient_coords2_to_coords1_dp_list	(	coord_3D **	coords,
		int	num_coords,
		const coord_3D *	bond_atom_a,
		coord_3D *	bond_atom_b,
		double	distance,
		const coord_3D *	angle_atom_a,
		double	theta,
		coord_3D *	angle_atom_b,
		double	rho,
		const coord_3D *	dih_atom_a,
		coord_3D *	dih_atom_b,
		double	tau,
		const coord_3D *	tor_atom_a,
		const coord_3D *	ref_angle_a,
		double	phi,
		coord_3D *	tor_atom_b,
		coord_3D *	ref_atom_b,
		double	omega
	)

Note: change name/parameter names

Definition at line 149 of file geometry.c.

References cross(), find_attachment_point(), get_angle(), get_angle_ABC_points(), get_cartesian_point_from_internal_coords(), get_crossprod(), get_dihedral(), get_dihedral_ABCD_points(), get_vector, get_vector_from_coords, PI, rotate_coords(), rotate_coords_about_axis_dp_list(), subtract(), subtract_coord(), translate_coords(), and translate_coords_dp_list().

Here is the call graph for this function:

void pitchAssembly	(	assembly *	a,
		double	rad
	)

Definition at line 100 of file rotation.c.

References coord_3D::i, coord_3D::j, and coord_3D::k.

void pitchMolecule	(	molecule *	m,
		double	rad
	)

Definition at line 27 of file rotation.c.

References coord_3D::i, coord_3D::j, and coord_3D::k.

void rollAssembly	(	assembly *	a,
		double	rad
	)

Definition at line 73 of file rotation.c.

References coord_3D::i, coord_3D::j, coord_3D::k, and atom::x.

void rollMolecule	(	molecule *	m,
		double	rad
	)

Definition at line 4 of file rotation.c.

References coord_3D::i, coord_3D::j, coord_3D::k, and atom::x.

void rotate_coords_about_axis_dp_list	(	coord_3D **	coords,
		int	num_coords,
		coord_3D	point,
		vectormag_3D	direction,
		double	theta
	)

Rotate a list of coordinates theta degrees about an axis through the given coordinate in the given direction

Definition at line 76 of file rotations.c.

References apply_rotation_matrix_to_coord_p(), create_rotation_matrix(), and destroy_rotation_matrix().

Referenced by orient_coords2_to_coords1_dp_list().

Here is the call graph for this function:

Here is the caller graph for this function:

void rotate_vector_to_Z_list	(	coord_3D *	,
		int	,
		vectormag_3D
	)

Functions

Definition at line 47 of file rotate_vector_to_Z.c.

References vectormag_3D::d, get_crossprod(), coord_3D::i, vectormag_3D::i, coord_3D::j, vectormag_3D::j, coord_3D::k, vectormag_3D::k, mywhine(), and normalize_vec().

Here is the call graph for this function:

void rotate_vector_to_Z_M	(	molecule *	m,
		int	xs,
		int	xd,
		int	vs,
		int	vd,
		vectormag_3D	vec
	)

This function rotates the coordinate list such that the vector given by vectormag_3D points along the Z (Y, X, other) axis. The orientation of the orthogonal axes is arbitrary.

Definition at line 94 of file rotate_vector_to_Z.c.

References residue::a, vectormag_3D::d, dprint_coord_3D(), dprint_vectormag_3D(), get_crossprod(), get_magnitude(), coord_3D::i, vectormag_3D::i, coord_3D::j, vectormag_3D::j, coord_3D::k, vectormag_3D::k, mywhine(), residue::na, normalize_vec(), molecule::nr, molecule::r, atom::v, atom::x, and atom::xa.