#include <math.h>
#include <string.h>
#include "mode.h"
#include "ichister.h"
#include "ichiring.h"
#include "ichi.h"
#include "ichitaut.h"
#include "ichicomp.h"
#include "ichicant.h"
#include "util.h"
#include "bcf_s.h"

Include dependency graph for ichister.c:

Macros
#define	ZTYPE_DOWN (-1) /* should be equal to -ZTYPE_UP */

#define	ZTYPE_NONE 0

#define	ZTYPE_UP 1 /* should be equal to -ZTYPE_DOWN */

#define	ZTYPE_3D 3

#define	ZTYPE_EITHER 9999

#define	ARR_DIM 3 /* djb-rwth: default dimension of arrays */

#define	MIN_ANGLE 0.10 /* 5.73 degrees / / treshold for proximity to in-line angle of 180 deg */

#define	MIN_SINE 0.03 /min edge/plane angle in case the tetrahedra has significantly different edge length /

#define	MIN_ANGLE_RELAXED 0.001

#define	MIN_SINE_RELAXED 0.001

#define	MIN_ANGLE_DBOND 0.087156 /* 5 degrees = max angle considered as too small for unambiguous double bond stereo */

#define	MIN_SINE_OUTSIDE 0.06 /* min edge/plane angle to determine whether the central atom is outside of the tetrahedra */

#define	MIN_SINE_SQUARE 0.125 /* min edge/plane angle in case the tetrahedra is somewhat close to a parallelogram */

#define	MIN_SINE_EDGE 0.167 /* min sine/(min.edge) ratio to avoid undefined in case of long edges */

#define	MIN_LEN_STRAIGHT 1.900 /* min length of two normalized to 1 bonds in a straight line */

#define	MAX_SINE 0.70710678118654752440084436210485 /* 1/sqrt(2)=sin(pi/4) */

#define	MIN_BOND_LEN 0.000001

#define	ZERO_LENGTH MIN_BOND_LEN

#define	ZERO_FLOAT 1.0e-12

#define	BOND_PARITY_UNDEFINED 64

#define	MPY_SINE 1.00 /* was 3.0 */

#define	MAX_EDGE_RATIO 2.50 /* max max/min edge ratio for a tetrahedra close to a parallelogram */

#define	T2D_OKAY 1

#define	T2D_WARN 2

#define	T2D_UNDF 4

#define	ZERO_ANGLE 0.000001

#define	SZELEM1 "C\000","Si", "Ge", "Sn", "As", "B\000",

#define	CCHARGE1 0, 0, 0, 0, 1, -1,

#define	CNUMBONDSANDH1 4, 4, 4, 4, 4, 4,

#define	CCHEMVALENCEH1 4, 4, 4, 4, 4, 4,

#define	CHAS3MEMBRING1 0, 0, 0, 0, 0, 0,

#define	CREQUIRDNEIGH1 0, 0, 0, 0, 3, 0,

#define	SZELEM2 "S\000","S\000","S\000","S\000","Se", "Se", "Se", "Se",

#define	CCHARGE2 0, 0, 1, 1, 0, 0, 1, 1,

#define	CNUMBONDSANDH2 3, 4, 3, 4, 3, 4, 3, 4,

#define	CCHEMVALENCEH2 4, 6, 3, 5, 4, 6, 3, 5,

#define	CHAS3MEMBRING2 0, 0, 0, 0, 0, 0, 0, 0,

#define	CREQUIRDNEIGH2 3, 3, 3, 3, 3, 3, 3, 3,

#define	SZELEM3 "N\000","N\000","N\000","P\000","P\000","P\000", "As",

#define	CCHARGE3 0, 1, 0, 1, 0, 0, 0,

#define	CNUMBONDSANDH3 4, 4, 3, 4, 4, 3, 3,

#define	CCHEMVALENCEH3 5, 4, 3, 4, 5, 3, 3,

#define	CHAS3MEMBRING3 0, 0, 1, 0, 0, 0, 0,

#define	CREQUIRDNEIGH3 3, 3, 1, 3, 3, 2, 2,

#define	PHOSPHINE_STEREO 19 /* the number must match Phosphine number in the comments, see above */

#define	ARSINE_STEREO 20 /* the number must match Arsine number in the comments, see above */

#define	AB_NEGATIVE 0x10

#define	AB_UNKNOWN 0x20

#define	ADD_EXPLICIT_HYDROGEN_NEIGH 1

#define	ADD_EXPLICIT_LONE_PAIR_NEIGH 2

Functions
static int	save_a_stereo_bond (int z_prod, int result_action, int at1, int ord1, AT_NUMB stereo_bond_neighbor1, S_CHAR stereo_bond_ord1, S_CHAR stereo_bond_z_prod1, S_CHAR stereo_bond_parity1, int at2, int ord2, AT_NUMB stereo_bond_neighbor2, S_CHAR stereo_bond_ord2, S_CHAR stereo_bond_z_prod2, S_CHAR stereo_bond_parity2)

static double	get_z_coord (inp_ATOM at, int cur_atom, int neigh_no, int nType, int bPointedEdgeStereo)

static double	len3 (const double c[])

static double	len2 (const double c[])

static void *	diff3 (const double a[], const double b[], double result[])

static void	add3 (const double a[], const double b[], double result[])

static void	mult3 (const double a[], double b, double result[])

static void	change_sign3 (const double a[], double result[])

double	dot_prod3 (const double a[], const double b[])

static int	dot_prodchar3 (const S_CHAR a[], const S_CHAR b[])

static double	triple_prod (double a[], double b[], double c[], double *sine_value)

static double	triple_prod_and_min_abs_sine (double at_coord[][3], double *min_sine)

static int	are_3_vect_in_one_plane (double at_coord[][3], double min_sine)

static int	triple_prod_char (inp_ATOM at, int at_1, int i_next_at_1, S_CHAR z_dir1, int at_2, int i_next_at_2, S_CHAR *z_dir2)

static int	CompDble (const void a1, const void a2, void *)

static int	Get2DTetrahedralAmbiguity (CANON_GLOBALS *pCG, double at_coord[][3], int bAddExplicitNeighbor, int bFix2DstereoBorderCase, double vMinAngle)

static double	triple_prod_and_min_abs_sine2 (double at_coord[][3], double central_at_coord[], int bAddedExplicitNeighbor, double min_sine, int bAmbiguous, double vMinSine)

static int	are_4at_in_one_plane (double at_coord[][3], double min_sine)

static int	bInpAtomHasRequirdNeigh (inp_ATOM *at, int cur_at, int RequirdNeighType, int NumDbleBonds, int bStereoAtZz)

static int	bIsSuitableHeteroInpAtom (inp_ATOM *at)

static int	bIsOxide (inp_ATOM *at, int cur_at)

static int	half_stereo_bond_parity (inp_ATOM at, int cur_at, inp_ATOM at_removed_H, int num_removed_H, S_CHAR *z_dir, int bPointedEdgeStereo, int vABParityUnknown)

static int	get_allowed_stereo_bond_type (int bond_type)

static int	can_be_a_stereo_bond_with_isotopic_H (inp_ATOM *at, int cur_at, INCHI_MODE nMode)

static int	half_stereo_bond_action (int nParity, int bUnknown, int bIsotopic, int vABParityUnknown)

static int	set_stereo_bonds_parity (sp_ATOM out_at, inp_ATOM at, int at_1, inp_ATOM at_removed_H, int num_removed_H, INCHI_MODE nMode, QUEUE q, AT_RANK nAtomLevel, S_CHAR cSource, AT_RANK min_sb_ring_size, int bPointedEdgeStereo, int vABParityUnknown)

static int	can_be_a_stereo_atom_with_isotopic_H (inp_ATOM *at, int cur_at, int bPointedEdgeStereo, int bStereoAtZz)

static int	set_stereo_atom_parity (CANON_GLOBALS pCG, sp_ATOM out_at, inp_ATOM at, int cur_at, inp_ATOM at_removed_H, int num_removed_H, int bPointedEdgeStereo, int vABParityUnknown, int LooseTSACheck, int bStereoAtZz)

int	ReconcileCmlIncidentBondParities (inp_ATOM at, int cur_atom, int prev_atom, S_CHAR visited, int bDisconnected)

int	comp_AT_NUMB (const void a1, const void a2, void *)

int	GetHalfStereobond0DParity (inp_ATOM *at, int cur_at, AT_NUMB nSbNeighOrigAtNumb[], int nNumExplictAttachments, int bond_parity, int nFlag)

int	GetStereocenter0DParity (CANON_GLOBALS pCG, inp_ATOM at, int cur_at, int j1, AT_NUMB nSbNeighOrigAtNumb[], int nFlag)

int	GetSbNeighOrigAtNumb (inp_ATOM at, int cur_at, inp_ATOM at_removed_H, int num_removed_H, AT_NUMB nSbNeighOrigAtNumb[])

int	FixSb0DParities (inp_ATOM at, int chain_length, int at_1, int i_next_at_1, S_CHAR z_dir1[], int at_2, int i_next_at_2, S_CHAR z_dir2[], int pparity1, int *pparity2)

void *	cross_prod3 (const double a[], const double b[], double result[])

int	bCanInpAtomBeAStereoCenter (inp_ATOM *at, int cur_at, int bPointedEdgeStereo, int bStereoAtZz)

int	bAtomHasValence3 (char *elname, S_CHAR charge, S_CHAR radical)

int	bCanAtomHaveAStereoBond (char *elname, S_CHAR charge, S_CHAR radical)

int	bCanAtomBeMiddleAllene (char *elname, S_CHAR charge, S_CHAR radical)

int	bCanAtomBeTerminalAllene (char *elname, S_CHAR charge, S_CHAR radical)

int	FixUnkn0DStereoBonds (inp_ATOM *at, int num_at)
	Fix unknown stereo bonds in the input atoms.

int	set_stereo_parity (CANON_GLOBALS pCG, inp_ATOM at, sp_ATOM at_output, int num_at, int num_removed_H, int nMaxNumStereoAtoms, int *nMaxNumStereoBonds, INCHI_MODE nMode, int bPointedEdgeStereo, int vABParityUnknown, int bLooseTSACheck, int bStereoAtZz)

int	ReconcileAllCmlBondParities (inp_ATOM *at, int num_atoms, int bDisconnected)
	Reconcile all CML bond parities in the input atoms.

int	get_opposite_sb_atom (inp_ATOM at, int cur_atom, int icur2nxt, int pnxt_atom, int pinxt2cur, int pinxt_sb_parity_ord)

Macro Definition Documentation

◆ AB_NEGATIVE

#define AB_NEGATIVE 0x10

◆ AB_UNKNOWN

#define AB_UNKNOWN 0x20

◆ ADD_EXPLICIT_HYDROGEN_NEIGH

#define ADD_EXPLICIT_HYDROGEN_NEIGH 1

◆ ADD_EXPLICIT_LONE_PAIR_NEIGH

#define ADD_EXPLICIT_LONE_PAIR_NEIGH 2

◆ ARR_DIM

#define ARR_DIM 3 /* djb-rwth: default dimension of arrays */

◆ ARSINE_STEREO

#define ARSINE_STEREO 20 /* the number must match Arsine number in the comments, see above */

◆ BOND_PARITY_UNDEFINED

#define BOND_PARITY_UNDEFINED 64

◆ CCHARGE1

#define CCHARGE1 0, 0, 0, 0, 1, -1,

◆ CCHARGE2

#define CCHARGE2 0, 0, 1, 1, 0, 0, 1, 1,

◆ CCHARGE3

#define CCHARGE3 0, 1, 0, 1, 0, 0, 0,

◆ CCHEMVALENCEH1

#define CCHEMVALENCEH1 4, 4, 4, 4, 4, 4,

◆ CCHEMVALENCEH2

#define CCHEMVALENCEH2 4, 6, 3, 5, 4, 6, 3, 5,

◆ CCHEMVALENCEH3

#define CCHEMVALENCEH3 5, 4, 3, 4, 5, 3, 3,

◆ CHAS3MEMBRING1

#define CHAS3MEMBRING1 0, 0, 0, 0, 0, 0,

◆ CHAS3MEMBRING2

#define CHAS3MEMBRING2 0, 0, 0, 0, 0, 0, 0, 0,

◆ CHAS3MEMBRING3

#define CHAS3MEMBRING3 0, 0, 1, 0, 0, 0, 0,

◆ CNUMBONDSANDH1

#define CNUMBONDSANDH1 4, 4, 4, 4, 4, 4,

◆ CNUMBONDSANDH2

#define CNUMBONDSANDH2 3, 4, 3, 4, 3, 4, 3, 4,

◆ CNUMBONDSANDH3

#define CNUMBONDSANDH3 4, 4, 3, 4, 4, 3, 3,

◆ CREQUIRDNEIGH1

#define CREQUIRDNEIGH1 0, 0, 0, 0, 3, 0,

◆ CREQUIRDNEIGH2

#define CREQUIRDNEIGH2 3, 3, 3, 3, 3, 3, 3, 3,

◆ CREQUIRDNEIGH3

#define CREQUIRDNEIGH3 3, 3, 1, 3, 3, 2, 2,

◆ MAX_EDGE_RATIO

#define MAX_EDGE_RATIO 2.50 /* max max/min edge ratio for a tetrahedra close to a parallelogram */

◆ MAX_SINE

#define MAX_SINE 0.70710678118654752440084436210485 /* 1/sqrt(2)=sin(pi/4) */

◆ MIN_ANGLE

#define MIN_ANGLE 0.10 /* 5.73 degrees */ /* treshold for proximity to in-line angle of 180 deg */

◆ MIN_ANGLE_DBOND

#define MIN_ANGLE_DBOND 0.087156 /* 5 degrees = max angle considered as too small for unambiguous double bond stereo */

◆ MIN_ANGLE_RELAXED

#define MIN_ANGLE_RELAXED 0.001

◆ MIN_BOND_LEN

#define MIN_BOND_LEN 0.000001

◆ MIN_LEN_STRAIGHT

#define MIN_LEN_STRAIGHT 1.900 /* min length of two normalized to 1 bonds in a straight line */

◆ MIN_SINE

#define MIN_SINE 0.03 /*min edge/plane angle in case the tetrahedra has significantly different edge length */

◆ MIN_SINE_EDGE

#define MIN_SINE_EDGE 0.167 /* min sine/(min.edge) ratio to avoid undefined in case of long edges */

◆ MIN_SINE_OUTSIDE

#define MIN_SINE_OUTSIDE 0.06 /* min edge/plane angle to determine whether the central atom is outside of the tetrahedra */

◆ MIN_SINE_RELAXED

#define MIN_SINE_RELAXED 0.001

◆ MIN_SINE_SQUARE

#define MIN_SINE_SQUARE 0.125 /* min edge/plane angle in case the tetrahedra is somewhat close to a parallelogram */

◆ MPY_SINE

#define MPY_SINE 1.00 /* was 3.0 */

◆ PHOSPHINE_STEREO

#define PHOSPHINE_STEREO 19 /* the number must match Phosphine number in the comments, see above */

◆ SZELEM1

#define SZELEM1 "C\000","Si", "Ge", "Sn", "As", "B\000",

◆ SZELEM2

#define SZELEM2 "S\000","S\000","S\000","S\000","Se", "Se", "Se", "Se",

◆ SZELEM3

#define SZELEM3 "N\000","N\000","N\000","P\000","P\000","P\000", "As",

◆ T2D_OKAY

#define T2D_OKAY 1

◆ T2D_UNDF

#define T2D_UNDF 4

◆ T2D_WARN

#define T2D_WARN 2

◆ ZERO_ANGLE

#define ZERO_ANGLE 0.000001

◆ ZERO_FLOAT

#define ZERO_FLOAT 1.0e-12

◆ ZERO_LENGTH

#define ZERO_LENGTH MIN_BOND_LEN

◆ ZTYPE_3D

#define ZTYPE_3D 3

◆ ZTYPE_DOWN

#define ZTYPE_DOWN (-1) /* should be equal to -ZTYPE_UP */

◆ ZTYPE_EITHER

#define ZTYPE_EITHER 9999

◆ ZTYPE_NONE

#define ZTYPE_NONE 0

◆ ZTYPE_UP

#define ZTYPE_UP 1 /* should be equal to -ZTYPE_DOWN */

Function Documentation

◆ add3()

void add3	(	const double	a[],
		const double	b[],
		double	result[]
	)

static

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◆ are_3_vect_in_one_plane()

int are_3_vect_in_one_plane	(	double	at_coord[][3],
		double	min_sine
	)

static

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◆ are_4at_in_one_plane()

int are_4at_in_one_plane	(	double	at_coord[][3],
		double	min_sine
	)

static

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◆ bAtomHasValence3()

int bAtomHasValence3	(	char *	elname,
		S_CHAR	charge,
		S_CHAR	radical
	)

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◆ bCanAtomBeMiddleAllene()

int bCanAtomBeMiddleAllene	(	char *	elname,
		S_CHAR	charge,
		S_CHAR	radical
	)

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◆ bCanAtomBeTerminalAllene()

int bCanAtomBeTerminalAllene	(	char *	elname,
		S_CHAR	charge,
		S_CHAR	radical
	)

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◆ bCanAtomHaveAStereoBond()

int bCanAtomHaveAStereoBond	(	char *	elname,
		S_CHAR	charge,
		S_CHAR	radical
	)

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◆ bCanInpAtomBeAStereoCenter()

int bCanInpAtomBeAStereoCenter	(	inp_ATOM *	at,
		int	cur_at,
		int	bPointedEdgeStereo,
		int	bStereoAtZz
	)

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◆ bInpAtomHasRequirdNeigh()

int bInpAtomHasRequirdNeigh	(	inp_ATOM *	at,
		int	cur_at,
		int	RequirdNeighType,
		int	NumDbleBonds,
		int	bStereoAtZz
	)

static

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◆ bIsOxide()

int bIsOxide	(	inp_ATOM *	at,
		int	cur_at
	)

static

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◆ bIsSuitableHeteroInpAtom()

int bIsSuitableHeteroInpAtom ( inp_ATOM * at )

static

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◆ can_be_a_stereo_atom_with_isotopic_H()

int can_be_a_stereo_atom_with_isotopic_H	(	inp_ATOM *	at,
		int	cur_at,
		int	bPointedEdgeStereo,
		int	bStereoAtZz
	)

static

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◆ can_be_a_stereo_bond_with_isotopic_H()

int can_be_a_stereo_bond_with_isotopic_H	(	inp_ATOM *	at,
		int	cur_at,
		INCHI_MODE	nMode
	)

static

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◆ change_sign3()

void change_sign3	(	const double	a[],
		double	result[]
	)

static

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◆ comp_AT_NUMB()

int comp_AT_NUMB	(	const void *	a1,
		const void *	a2,
		void *	p
	)

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◆ CompDble()

int CompDble	(	const void *	a1,
		const void *	a2,
		void *	p
	)

static

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◆ cross_prod3()

void * cross_prod3	(	const double	a[],
		const double	b[],
		double	result[]
	)

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◆ diff3()

void * diff3	(	const double	a[],
		const double	b[],
		double	result[]
	)

static

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◆ dot_prod3()

double dot_prod3	(	const double	a[],
		const double	b[]
	)

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◆ dot_prodchar3()

int dot_prodchar3	(	const S_CHAR	a[],
		const S_CHAR	b[]
	)

static

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◆ FixSb0DParities()

int FixSb0DParities	(	inp_ATOM *	at,
		int	chain_length,
		int	at_1,
		int	i_next_at_1,
		S_CHAR	z_dir1[],
		int	at_2,
		int	i_next_at_2,
		S_CHAR	z_dir2[],
		int *	pparity1,
		int *	pparity2
	)

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◆ FixUnkn0DStereoBonds()

int FixUnkn0DStereoBonds	(	inp_ATOM *	at,
		int	num_at
	)

Fix unknown stereo bonds in the input atoms.

Parameters

at	Pointer to the atom data
num_at	Pointer to the number of atoms

Returns: int Number of fixed stereo bonds

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◆ Get2DTetrahedralAmbiguity()

int Get2DTetrahedralAmbiguity	(	CANON_GLOBALS *	pCG,
		double	at_coord[][3],
		int	bAddExplicitNeighbor,
		int	bFix2DstereoBorderCase,
		double	vMinAngle
	)

static

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◆ get_allowed_stereo_bond_type()

int get_allowed_stereo_bond_type ( int bond_type )

static

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◆ get_opposite_sb_atom()

int get_opposite_sb_atom	(	inp_ATOM *	at,
		int	cur_atom,
		int	icur2nxt,
		int *	pnxt_atom,
		int *	pinxt2cur,
		int *	pinxt_sb_parity_ord
	)

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◆ get_z_coord()

double get_z_coord	(	inp_ATOM *	at,
		int	cur_atom,
		int	neigh_no,
		int *	nType,
		int	bPointedEdgeStereo
	)

static

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◆ GetHalfStereobond0DParity()

int GetHalfStereobond0DParity	(	inp_ATOM *	at,
		int	cur_at,
		AT_NUMB	nSbNeighOrigAtNumb[],
		int	nNumExplictAttachments,
		int	bond_parity,
		int	nFlag
	)

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◆ GetSbNeighOrigAtNumb()

int GetSbNeighOrigAtNumb	(	inp_ATOM *	at,
		int	cur_at,
		inp_ATOM *	at_removed_H,
		int	num_removed_H,
		AT_NUMB	nSbNeighOrigAtNumb[]
	)

◆ GetStereocenter0DParity()

int GetStereocenter0DParity	(	CANON_GLOBALS *	pCG,
		inp_ATOM *	at,
		int	cur_at,
		int	j1,
		AT_NUMB	nSbNeighOrigAtNumb[],
		int	nFlag
	)

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◆ half_stereo_bond_action()

int half_stereo_bond_action	(	int	nParity,
		int	bUnknown,
		int	bIsotopic,
		int	vABParityUnknown
	)

static

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◆ half_stereo_bond_parity()

int half_stereo_bond_parity	(	inp_ATOM *	at,
		int	cur_at,
		inp_ATOM *	at_removed_H,
		int	num_removed_H,
		S_CHAR *	z_dir,
		int	bPointedEdgeStereo,
		int	vABParityUnknown
	)

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◆ len2()

double len2 ( const double c[] )

static

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◆ len3()

double len3 ( const double c[] )

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◆ mult3()

void mult3	(	const double	a[],
		double	b,
		double	result[]
	)

static

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◆ ReconcileAllCmlBondParities()

int ReconcileAllCmlBondParities	(	inp_ATOM *	at,
		int	num_atoms,
		int	bDisconnected
	)

Reconcile all CML bond parities in the input atoms.

Parameters

at	Pointer to the atom data
num_atoms	Number of atoms
bDisconnected	Flag for disconnected atoms

Returns: int Status code

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◆ ReconcileCmlIncidentBondParities()

int ReconcileCmlIncidentBondParities	(	inp_ATOM *	at,
		int	cur_atom,
		int	prev_atom,
		S_CHAR *	visited,
		int	bDisconnected
	)

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◆ save_a_stereo_bond()

int save_a_stereo_bond	(	int	z_prod,
		int	result_action,
		int	at1,
		int	ord1,
		AT_NUMB *	stereo_bond_neighbor1,
		S_CHAR *	stereo_bond_ord1,
		S_CHAR *	stereo_bond_z_prod1,
		S_CHAR *	stereo_bond_parity1,
		int	at2,
		int	ord2,
		AT_NUMB *	stereo_bond_neighbor2,
		S_CHAR *	stereo_bond_ord2,
		S_CHAR *	stereo_bond_z_prod2,
		S_CHAR *	stereo_bond_parity2
	)

static

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◆ set_stereo_atom_parity()

int set_stereo_atom_parity	(	CANON_GLOBALS *	pCG,
		sp_ATOM *	out_at,
		inp_ATOM *	at,
		int	cur_at,
		inp_ATOM *	at_removed_H,
		int	num_removed_H,
		int	bPointedEdgeStereo,
		int	vABParityUnknown,
		int	LooseTSACheck,
		int	bStereoAtZz
	)

static

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◆ set_stereo_bonds_parity()

int set_stereo_bonds_parity	(	sp_ATOM *	out_at,
		inp_ATOM *	at,
		int	at_1,
		inp_ATOM *	at_removed_H,
		int	num_removed_H,
		INCHI_MODE	nMode,
		QUEUE *	q,
		AT_RANK *	nAtomLevel,
		S_CHAR *	cSource,
		AT_RANK	min_sb_ring_size,
		int	bPointedEdgeStereo,
		int	vABParityUnknown
	)

static

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◆ set_stereo_parity()

int set_stereo_parity	(	CANON_GLOBALS *	pCG,
		inp_ATOM *	at,
		sp_ATOM *	at_output,
		int	num_at,
		int	num_removed_H,
		int *	nMaxNumStereoAtoms,
		int *	nMaxNumStereoBonds,
		INCHI_MODE	nMode,
		int	bPointedEdgeStereo,
		int	vABParityUnknown,
		int	bLooseTSACheck,
		int	bStereoAtZz
	)

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◆ triple_prod()

double triple_prod	(	double	a[],
		double	b[],
		double	c[],
		double *	sine_value
	)

static

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◆ triple_prod_and_min_abs_sine()

double triple_prod_and_min_abs_sine	(	double	at_coord[][3],
		double *	min_sine
	)

static

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◆ triple_prod_and_min_abs_sine2()

double triple_prod_and_min_abs_sine2	(	double	at_coord[][3],
		double	central_at_coord[],
		int	bAddedExplicitNeighbor,
		double *	min_sine,
		int *	bAmbiguous,
		double	vMinSine
	)

static

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◆ triple_prod_char()

int triple_prod_char	(	inp_ATOM *	at,
		int	at_1,
		int	i_next_at_1,
		S_CHAR *	z_dir1,
		int	at_2,
		int	i_next_at_2,
		S_CHAR *	z_dir2
	)

static

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Macros

Functions

Macro Definition Documentation

◆ AB_NEGATIVE

◆ AB_UNKNOWN

◆ ADD_EXPLICIT_HYDROGEN_NEIGH

◆ ADD_EXPLICIT_LONE_PAIR_NEIGH

◆ ARR_DIM

◆ ARSINE_STEREO

◆ BOND_PARITY_UNDEFINED

◆ CCHARGE1

◆ CCHARGE2

◆ CCHARGE3

◆ CCHEMVALENCEH1

◆ CCHEMVALENCEH2

◆ CCHEMVALENCEH3

◆ CHAS3MEMBRING1

◆ CHAS3MEMBRING2

◆ CHAS3MEMBRING3

◆ CNUMBONDSANDH1

◆ CNUMBONDSANDH2

◆ CNUMBONDSANDH3

◆ CREQUIRDNEIGH1

◆ CREQUIRDNEIGH2

◆ CREQUIRDNEIGH3

◆ MAX_EDGE_RATIO

◆ MAX_SINE

◆ MIN_ANGLE

◆ MIN_ANGLE_DBOND

◆ MIN_ANGLE_RELAXED

◆ MIN_BOND_LEN

◆ MIN_LEN_STRAIGHT

◆ MIN_SINE

◆ MIN_SINE_EDGE

◆ MIN_SINE_OUTSIDE

◆ MIN_SINE_RELAXED

◆ MIN_SINE_SQUARE

◆ MPY_SINE

◆ PHOSPHINE_STEREO

◆ SZELEM1

◆ SZELEM2

◆ SZELEM3

◆ T2D_OKAY

◆ T2D_UNDF

◆ T2D_WARN

◆ ZERO_ANGLE

◆ ZERO_FLOAT

◆ ZERO_LENGTH

◆ ZTYPE_3D

◆ ZTYPE_DOWN

◆ ZTYPE_EITHER

◆ ZTYPE_NONE

◆ ZTYPE_UP

Function Documentation

◆ add3()

◆ are_3_vect_in_one_plane()

◆ are_4at_in_one_plane()

◆ bAtomHasValence3()

◆ bCanAtomBeMiddleAllene()

◆ bCanAtomBeTerminalAllene()

◆ bCanAtomHaveAStereoBond()

◆ bCanInpAtomBeAStereoCenter()

◆ bInpAtomHasRequirdNeigh()

◆ bIsOxide()

◆ bIsSuitableHeteroInpAtom()

◆ can_be_a_stereo_atom_with_isotopic_H()

◆ can_be_a_stereo_bond_with_isotopic_H()

◆ change_sign3()

◆ comp_AT_NUMB()

◆ CompDble()

◆ cross_prod3()

◆ diff3()

◆ dot_prod3()

◆ dot_prodchar3()

◆ FixSb0DParities()

◆ FixUnkn0DStereoBonds()

◆ Get2DTetrahedralAmbiguity()

◆ get_allowed_stereo_bond_type()

◆ get_opposite_sb_atom()

◆ get_z_coord()