strutil.c File Reference

#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include <math.h>
#include "mode.h"
#include "strutil.h"
#include "ichister.h"
#include "ichi_io.h"
#include "ichimain.h"
#include "bcf_s.h"

Include dependency graph for strutil.c:

Data Structures
struct	tagTreeAtom

Macros
#define	FIX_P_IV_Plus_O_Minus
#define	FIRST_NEIGHB2   4
#define	FIRST_CENTER2   5
#define	MAX_NEIGH   6
#define	MIN_BOND_LENGTH   (1.0e-6)
#define	MIN_COS   (1.0e-6)
#define	MIN_BOND_LENGTH2   (MIN_BOND_LENGTH*MIN_BOND_LENGTH)
#define	MAX_BOND_LENGTH   (1.0e30)
#define	NUM_SEGM   20

Typedefs
typedef struct tagTreeAtom	tre_ATOM
typedef enum tagIonAtomType	ION_ATOM_TYPE

Enumerations
enum	tagIonAtomType {   IAT_H = 0 , IAT_C , IAT_N , IAT_P ,   IAT_O , IAT_S , IAT_Se , IAT_Te ,   IAT_F , IAT_Cl , IAT_Br , IAT_I ,   IAT_MAX = 12 }

Functions
int	insertions_sort_AT_RANK (AT_RANK *base, int num)
int	cmp_iso_atw_diff_component_no (const void *a1, const void *a2)
int	cmp_components (const void *a1, const void *a2)
INChI_Stereo *	Alloc_INChI_Stereo (int num_at, int num_bonds)
int	RemoveInpAtBond (inp_ATOM *at, int iat, int k)
int	DisconnectInpAtBond (inp_ATOM *at, AT_NUMB *nOldCompNumber, int iat, int neigh_ord)
int	move_explicit_Hcation (inp_ATOM *at, int num_at, int iat, int iat_H, int bInAllComponents)
int	DisconnectOneLigand (inp_ATOM *at, AT_NUMB *nOldCompNumber, S_CHAR *bMetal, char *elnumber_Heteroat, int num_halogens, int num_atoms, int iMetal, int jLigand, INCHI_MODE *bTautFlagsDone)
int	bIsAmmoniumSalt (inp_ATOM *at, int i, int *piO, int *pk, S_CHAR *num_explicit_H)
int	DisconnectAmmoniumSalt (inp_ATOM *at, int i, int iO, int k, S_CHAR *num_explicit_H)
int	DisconnectMetalSalt (inp_ATOM *at, int i)
int	bIsMetalToDisconnect (inp_ATOM *at, int i, int bCheckMetalValence)
int	get_iat_number (int el_number)
int	tot_unsat (int unsat[])
int	max_unsat (int unsat[])
double	dist3D (inp_ATOM *at1, inp_ATOM *at2)
double	dist2D (inp_ATOM *at1, inp_ATOM *at2)
double	dist_from_segm (double x, double y, double x1, double y1, double x2, double y2)
int	segments_intersect (double x11, double y11, double x12, double y12, double x21, double y21, double x22, double y22)
double	GetMinDistDistribution (inp_ATOM *at, int num_at, int iat, int iat_H, int bInAllComponents, double min_dist[], int num_segm)
int	nFindOneOM (inp_ATOM *at, int at_no, int ord_OM[], int num_OM)
int	the_only_doublet_neigh (inp_ATOM *at, int i1, int *ineigh1, int *ineigh2)
int	fix_non_uniform_drawn_oxoanions (int num_atoms, inp_ATOM *at, int *num_changes)
int	fix_non_uniform_drawn_amidiniums (int num_atoms, inp_ATOM *at, int *num_changes)
void	add_bond_if_unseen (subgraf_pathfinder *spf, int node0, int node, int *nbonds, int **bonds)
int	fix_odd_things (int num_atoms, inp_ATOM *at, int bFixBug, int bFixNonUniformDraw)
	Fix odd things in the input atoms.
int	post_fix_odd_things (int num_atoms, inp_ATOM *at)
	Post-fix odd things in the input atoms (does nothing, returns 0)
int	remove_ion_pairs (int num_atoms, inp_ATOM *at)
	Remove ion pairs from the input atoms.
int	bIsMetalSalt (inp_ATOM *at, int i)
	Check if atom is a metal salt.
int	DisconnectSalts (ORIG_ATOM_DATA *orig_inp_data, int bDisconnect)
	Disconnect salts in the original atom data.
int	bMayDisconnectMetals (ORIG_ATOM_DATA *orig_inp_data, int bCheckMetalValence, INCHI_MODE *bTautFlagsDone)
	Check if metals may be disconnected in the original atom data.
int	DisconnectMetals (ORIG_ATOM_DATA *orig_inp_data, int bCheckMetalValence, INCHI_MODE *bTautFlagsDone)
	Disconnect metals in the original atom data.
int	add_DT_to_num_H (int num_atoms, inp_ATOM *at)
int	remove_terminal_HDT (int num_atoms, inp_ATOM *at, int bFixTermHChrg)
int	bHeteroAtomMayHaveXchgIsoH (inp_ATOM *atom, int iat)
	Checks whether a hetero atom may have exchangeable isotopic hydrogens.
int	bNumHeterAtomHasIsotopicH (inp_ATOM *atom, int num_atoms)
	Check if hetero atoms has isotopic hydrogens.
int	MarkDisconnectedComponents (ORIG_ATOM_DATA *orig_at_data, int bProcessOldCompNumbers)
	Mark disconnected components in the original atom data.
int	ExtractConnectedComponent (inp_ATOM *at, int num_at, int component_number, inp_ATOM *component_at)
	Extract one (connected) component.
int	SetConnectedComponentNumber (inp_ATOM *at, int num_at, int component_number)
	Set the Connected Component Number object.
int	Free_INChI_Stereo (INChI_Stereo *pINChI_Stereo)
	Free INChI_Stereo data structure.
int	Free_INChI (INChI **ppINChI)
	Free INChI data structure.
int	Free_INChI_Members (INChI *pINChI)
	Free INChI members.
INChI *	Alloc_INChI (inp_ATOM *at, int num_at, int *found_num_bonds, int *found_num_isotopic, int nAllocMode)
	Allocate INChI data structure.
int	Free_INChI_Aux (INChI_Aux **ppINChI_Aux)
	Free INChI_Aux data structure.
INChI_Aux *	Alloc_INChI_Aux (int num_at, int num_isotopic_atoms, int nAllocMode, int bOrigCoord)
	Allocate AuxInfo data structure.
void	CompAtomData_GetNumMapping (COMP_ATOM_DATA *adata, int *orig_num, int *curr_num)
int	imat_new (int m, int n, int ***a)
	Allocate integer matrix.
void	imat_free (int m, int **a)
	Free integer matrix.
subgraf *	subgraf_new (ORIG_ATOM_DATA *orig_inp_data, int nnodes, int *nodes)
	Create graph from atom data.
void	subgraf_free (subgraf *sg)
	Free graph data structure.
void	subgraf_debug_trace (subgraf *sg)
	Debug graph data structure.
subgraf_pathfinder *	subgraf_pathfinder_new (subgraf *sg, ORIG_ATOM_DATA *orig_inp_data, int start, int end)
	Allocate new graph pathfinder data structure.
void	subgraf_pathfinder_free (subgraf_pathfinder *spf)
	Frees subgraph pathfinder data structure.
void	subgraf_pathfinder_run (subgraf_pathfinder *spf, int nforbidden, int *forbidden, int *nbonds, int **bonds, int *natoms, int *atoms)
	Find path(s) from subgraf node spf->start to spf->end and fill bonds[nbonds] and atoms[natoms]. Does not traverse through supplied forbidden edges (if not zero/NULL)
int	subgraf_pathfinder_collect_all (subgraf_pathfinder *spf, int nforbidden, int *forbidden, int *atnums)
	Collects atom numbers along path.
void	PrintFileName (const char *fmt, FILE *out_file, const char *szFname)
	Print the file name.

Macro Definition Documentation

FIRST_CENTER2

#define FIRST_CENTER2   5

FIRST_NEIGHB2

#define FIRST_NEIGHB2   4

FIX_P_IV_Plus_O_Minus

#define FIX_P_IV_Plus_O_Minus

MAX_BOND_LENGTH

#define MAX_BOND_LENGTH   (1.0e30)

MAX_NEIGH

#define MAX_NEIGH   6

MIN_BOND_LENGTH

#define MIN_BOND_LENGTH   (1.0e-6)

MIN_BOND_LENGTH2

#define MIN_BOND_LENGTH2   (MIN_BOND_LENGTH*MIN_BOND_LENGTH)

MIN_COS

#define MIN_COS   (1.0e-6)

NUM_SEGM

#define NUM_SEGM   20

Typedef Documentation

ION_ATOM_TYPE

typedef enum tagIonAtomType ION_ATOM_TYPE

tre_ATOM

typedef struct tagTreeAtom tre_ATOM

Enumeration Type Documentation

tagIonAtomType

enum tagIonAtomType

Enumerator
IAT_H
IAT_C
IAT_N
IAT_P
IAT_O
IAT_S
IAT_Se
IAT_Te
IAT_F
IAT_Cl
IAT_Br
IAT_I
IAT_MAX

Function Documentation

add_bond_if_unseen()

void add_bond_if_unseen	(	subgraf_pathfinder *	spf,
		int	node0,
		int	node,
		int *	nbonds,
		int **	bonds
	)

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add_DT_to_num_H()

int add_DT_to_num_H	(	int	num_atoms,
		inp_ATOM *	at
	)

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Alloc_INChI()

INChI * Alloc_INChI	(	inp_ATOM *	at,
		int	num_at,
		int *	found_num_bonds,
		int *	found_num_isotopic,
		int	nAllocMode
	)

Allocate INChI data structure.

Parameters

at	Pointer to atom array
num_at	Number of atoms
found_num_bonds	Pointer to number of bonds
found_num_isotopic	Pointer to number of isotopic atoms
nAllocMode	Allocation mode

Returns

INChI* Pointer to allocated INChI

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Alloc_INChI_Aux()

INChI_Aux * Alloc_INChI_Aux	(	int	num_at,
		int	num_isotopic_atoms,
		int	nAllocMode,
		int	bOrigData
	)

Allocate AuxInfo data structure.

Parameters

num_at	Number of atoms
num_isotopic_atoms	Number of isotopic atoms
nAllocMode	Allocation mode
bOrigData	Flag indicating if the atom data is original

Returns

INChI_Aux* Pointer to allocated INChI_Aux or NULL if failed

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Alloc_INChI_Stereo()

INChI_Stereo * Alloc_INChI_Stereo	(	int	num_at,
		int	num_bonds
	)

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bHeteroAtomMayHaveXchgIsoH()

int bHeteroAtomMayHaveXchgIsoH	(	inp_ATOM *	atom,
		int	iat
	)

Checks whether a hetero atom may have exchangeable isotopic hydrogens.

Parameters

atom	Pointer to atom list
iat	Atom number

Returns

int 2 if atom is hydrogen (?) ,1 if yes, 0 if no

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bIsAmmoniumSalt()

int bIsAmmoniumSalt	(	inp_ATOM *	at,
		int	i,
		int *	piO,
		int *	pk,
		S_CHAR *	num_explicit_H
	)

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bIsMetalSalt()

int bIsMetalSalt	(	inp_ATOM *	at,
		int	i
	)

Check if atom is a metal salt.

Parameters

at	Pointer to atom array
i	atom index

Returns

int 1 if metal salt, 0 if not

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bIsMetalToDisconnect()

int bIsMetalToDisconnect	(	inp_ATOM *	at,
		int	i,
		int	bCheckMetalValence
	)

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bMayDisconnectMetals()

int bMayDisconnectMetals	(	ORIG_ATOM_DATA *	orig_inp_data,
		int	bCheckMetalValence,
		INCHI_MODE *	bTautFlagsDone
	)

Check if metals may be disconnected in the original atom data.

Parameters

orig_inp_data	Pointer to original atom data structure
bCheckMetalValence	Flag indicating whether to check metal valence
bTautFlagsDone	Pointer to tautomeric flags done

Returns

int Status code

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bNumHeterAtomHasIsotopicH()

int bNumHeterAtomHasIsotopicH	(	inp_ATOM *	atom,
		int	num_atoms
	)

Check if hetero atoms has isotopic hydrogens.

Parameters

atom	Pointer to atom array
num_atoms	Number of atoms

Returns

int 2 if isotopic atoms, 1 if isotopic hydrogens, 0 if not

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cmp_components()

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

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cmp_iso_atw_diff_component_no()

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

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CompAtomData_GetNumMapping()

void CompAtomData_GetNumMapping	(	COMP_ATOM_DATA *	adata,
		int *	orig_num,
		int *	curr_num
	)

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DisconnectAmmoniumSalt()

int DisconnectAmmoniumSalt	(	inp_ATOM *	at,
		int	i,
		int	iO,
		int	k,
		S_CHAR *	num_explicit_H
	)

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DisconnectInpAtBond()

int DisconnectInpAtBond	(	inp_ATOM *	at,
		AT_NUMB *	nOldCompNumber,
		int	iat,
		int	neigh_ord
	)

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DisconnectMetals()

int DisconnectMetals	(	ORIG_ATOM_DATA *	orig_inp_data,
		int	bCheckMetalValence,
		INCHI_MODE *	bTautFlagsDone
	)

Disconnect metals in the original atom data.

Parameters

orig_inp_data	Pointer to original atom data structure
bCheckMetalValence	Flag indicating whether to check metal valence
bTautFlagsDone	Pointer to tautomeric flags done

Returns

int Status code

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DisconnectMetalSalt()

int DisconnectMetalSalt	(	inp_ATOM *	at,
		int	i
	)

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DisconnectOneLigand()

int DisconnectOneLigand	(	inp_ATOM *	at,
		AT_NUMB *	nOldCompNumber,
		S_CHAR *	bMetal,
		char *	elnumber_Heteroat,
		int	num_halogens,
		int	num_atoms,
		int	iMetal,
		int	jLigand,
		INCHI_MODE *	bTautFlagsDone
	)

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DisconnectSalts()

int DisconnectSalts	(	ORIG_ATOM_DATA *	orig_inp_data,
		int	bDisconnect
	)

Disconnect salts in the original atom data.

Parameters

orig_inp_data	Pointer to original atom data structure
bDisconnect	Flag indicating whether to disconnect salts

Returns

int Status code

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dist2D()

double dist2D	(	inp_ATOM *	at1,
		inp_ATOM *	at2
	)

dist3D()

double dist3D	(	inp_ATOM *	at1,
		inp_ATOM *	at2
	)

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dist_from_segm()

double dist_from_segm	(	double	x,
		double	y,
		double	x1,
		double	y1,
		double	x2,
		double	y2
	)

ExtractConnectedComponent()

int ExtractConnectedComponent	(	inp_ATOM *	at,
		int	num_at,
		int	component_number,
		inp_ATOM *	component_at
	)

Extract one (connected) component.

Parameters

at	Pointer to atom array
num_at	Number of atoms
component_number	Component number
component_at	Pointer to component atom array

Returns

int Number of extracted atoms

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fix_non_uniform_drawn_amidiniums()

int fix_non_uniform_drawn_amidiniums	(	int	num_atoms,
		inp_ATOM *	at,
		int *	num_changes
	)

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fix_non_uniform_drawn_oxoanions()

int fix_non_uniform_drawn_oxoanions	(	int	num_atoms,
		inp_ATOM *	at,
		int *	num_changes
	)

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fix_odd_things()

int fix_odd_things	(	int	num_atoms,
		inp_ATOM *	at,
		int	bFixBug,
		int	bFixNonUniformDraw
	)

Fix odd things in the input atoms.

Parameters

num_atoms	Number of input atoms
at	Array of input atoms
bFixBug	Flag indicating whether to fix bugs
bFixNonUniformDraw	Flag indicating whether to fix non-uniform drawing

Returns

int Status code

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Free_INChI()

int Free_INChI

(

INChI **

ppINChI

)

Free INChI data structure.

Parameters

ppINChI

Pointer to INChI data structure

Returns

int Returns 0

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Free_INChI_Aux()

int Free_INChI_Aux

(

INChI_Aux **

ppINChI_Aux

)

Free INChI_Aux data structure.

Parameters

ppINChI_Aux

Pointer to INChI_Aux data structure

Returns

int Returns 0

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Free_INChI_Members()

int Free_INChI_Members

(

INChI *

pINChI

)

Free INChI members.

Parameters

pINChI

Pointer to INChI data structure

Returns

int Returns 0

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Free_INChI_Stereo()

int Free_INChI_Stereo

(

INChI_Stereo *

pINChI_Stereo

)

Free INChI_Stereo data structure.

Parameters

pINChI_Stereo

Pointer to INChI_Stereo

Returns

int Returns 0

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get_iat_number()

int get_iat_number

(

int

el_number

)

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GetMinDistDistribution()

double GetMinDistDistribution	(	inp_ATOM *	at,
		int	num_at,
		int	iat,
		int	iat_H,
		int	bInAllComponents,
		double	min_dist[],
		int	num_segm
	)

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imat_free()

void imat_free	(	int	m,
		int **	a
	)

Free integer matrix.

Parameters

m	Size of matrix
a	Pointer to matrix

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imat_new()

int imat_new	(	int	m,
		int	n,
		int ***	a
	)

Allocate integer matrix.

Parameters

m	Size of matrix
n	Size of matrix
a	Pointer to matrix

Returns

int 1 if success, 0 if failure

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insertions_sort_AT_RANK()

int insertions_sort_AT_RANK	(	AT_RANK *	base,
		int	num
	)

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MarkDisconnectedComponents()

int MarkDisconnectedComponents	(	ORIG_ATOM_DATA *	orig_at_data,
		int	bProcessOldCompNumbers
	)

Mark disconnected components in the original atom data.

Parameters

orig_at_data	Pointer to original atom data structure
bProcessOldCompNumbers	Flag indicating whether to process old component numbers

Returns

int Status code

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max_unsat()

int max_unsat

(

int

unsat[]

)

move_explicit_Hcation()

int move_explicit_Hcation	(	inp_ATOM *	at,
		int	num_at,
		int	iat,
		int	iat_H,
		int	bInAllComponents
	)

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nFindOneOM()

int nFindOneOM	(	inp_ATOM *	at,
		int	at_no,
		int	ord_OM[],
		int	num_OM
	)

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post_fix_odd_things()

int post_fix_odd_things	(	int	num_atoms,
		inp_ATOM *	at
	)

Post-fix odd things in the input atoms (does nothing, returns 0)

Parameters

num_atoms	Number of input atoms
at	Array of input atoms

Returns

int Status code

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PrintFileName()

void PrintFileName	(	const char *	fmt,
		FILE *	out_file,
		const char *	szFname
	)

Print the file name.

Parameters

fmt	Format string
out_file	Output file pointer
szFname	File name string

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remove_ion_pairs()

int remove_ion_pairs	(	int	num_atoms,
		inp_ATOM *	at
	)

Remove ion pairs from the input atoms.

Parameters

num_atoms	Number of input atoms
at	Array of input atoms

Returns

int Status code

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remove_terminal_HDT()

int remove_terminal_HDT	(	int	num_atoms,
		inp_ATOM *	at,
		int	bFixTermHChrg
	)

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RemoveInpAtBond()

int RemoveInpAtBond	(	inp_ATOM *	at,
		int	iat,
		int	k
	)

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segments_intersect()

int segments_intersect	(	double	x11,
		double	y11,
		double	x12,
		double	y12,
		double	x21,
		double	y21,
		double	x22,
		double	y22
	)

SetConnectedComponentNumber()

int SetConnectedComponentNumber	(	inp_ATOM *	at,
		int	num_at,
		int	component_number
	)

Set the Connected Component Number object.

Parameters

at	Pointer to atom array
num_at	Number of atoms
component_number	Component number

Returns

int Returns 0

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subgraf_debug_trace()

void subgraf_debug_trace

(

subgraf *

sg

)

Debug graph data structure.

Parameters

sg	Pointer to graph

subgraf_free()

void subgraf_free

(

subgraf *

sg

)

Free graph data structure.

Parameters

sg	Pointer to graph

Returns

void Returns NULL (?)

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subgraf_new()

subgraf * subgraf_new	(	ORIG_ATOM_DATA *	orig_inp_data,
		int	nnodes,
		int *	nodes
	)

Create graph from atom data.

Parameters

orig_inp_data	Pointer to original atom data
nnodes	Number of nodes
nodes	Pointer to nodes

Returns

subgraf* NULL if error, a new graph otherwise

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subgraf_pathfinder_collect_all()

int subgraf_pathfinder_collect_all	(	subgraf_pathfinder *	spf,
		int	nforbidden,
		int *	forbidden,
		int *	atnums
	)

Collects atom numbers along path.

Parameters

spf	Pointer to graph pathfinder data structure
nforbidden	Number of edges forbidden for traversal
forbidden	Pointer to forbidden edges
atnums	Pointer to atom numbers

Returns

* int

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subgraf_pathfinder_free()

void subgraf_pathfinder_free

(

subgraf_pathfinder *

spf

)

Frees subgraph pathfinder data structure.

Parameters

spf	Pointer to graph pathfinder data structure

Returns

* void

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subgraf_pathfinder_new()

subgraf_pathfinder * subgraf_pathfinder_new	(	subgraf *	sg,
		ORIG_ATOM_DATA *	orig_inp_data,
		int	start,
		int	end
	)

Allocate new graph pathfinder data structure.

Parameters

sg	Pointer to graph
orig_inp_data	Pointer to original atom data
start	Starting node
end	End node

Returns

subgraf_pathfinder* Returns pointer to graph pathfinder data structure

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subgraf_pathfinder_run()

void subgraf_pathfinder_run	(	subgraf_pathfinder *	spf,
		int	nforbidden,
		int *	forbidden_orig,
		int *	nbonds,
		int **	bonds,
		int *	natoms,
		int *	atoms
	)

Find path(s) from subgraf node spf->start to spf->end and fill bonds[nbonds] and atoms[natoms]. Does not traverse through supplied forbidden edges (if not zero/NULL)

Parameters

spf	Pointer to graph pathfinder data structure
nforbidden	Number of forbidden edges
forbidden_orig	Pointer forbidden edges
nbonds	Number of bonds
bonds	Pointer to bonds
natoms	Number of atoms
atoms	Pointer to atoms

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the_only_doublet_neigh()

int the_only_doublet_neigh	(	inp_ATOM *	at,
		int	i1,
		int *	ineigh1,
		int *	ineigh2
	)

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tot_unsat()

int tot_unsat

(

int

unsat[]

)