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"

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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)
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)
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)
int	SetConnectedComponentNumber (inp_ATOM *at, int num_at, int component_number)
int	Free_INChI_Stereo (INChI_Stereo *pINChI_Stereo)
int	Free_INChI (INChI **ppINChI)
int	Free_INChI_Members (INChI *pINChI)
INChI *	Alloc_INChI (inp_ATOM *at, int num_at, int *found_num_bonds, int *found_num_isotopic, int nAllocMode)
int	Free_INChI_Aux (INChI_Aux **ppINChI_Aux)
INChI_Aux *	Alloc_INChI_Aux (int num_at, int num_isotopic_atoms, int nAllocMode, int bOrigCoord)
void	CompAtomData_GetNumMapping (COMP_ATOM_DATA *adata, int *orig_num, int *curr_num)
int	imat_new (int m, int n, int ***a)
void	imat_free (int m, int **a)
subgraf *	subgraf_new (ORIG_ATOM_DATA *orig_inp_data, int nnodes, int *nodes)
void	subgraf_free (subgraf *sg)
void	subgraf_debug_trace (subgraf *sg)
subgraf_pathfinder *	subgraf_pathfinder_new (subgraf *sg, ORIG_ATOM_DATA *orig_inp_data, int start, int end)
void	subgraf_pathfinder_free (subgraf_pathfinder *spf)
void	subgraf_pathfinder_run (subgraf_pathfinder *spf, int nforbidden, int *forbidden, int *nbonds, int **bonds, int *natoms, int *atoms)
int	subgraf_pathfinder_collect_all (subgraf_pathfinder *spf, int nforbidden, int *forbidden, int *atnums)
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
	)

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Alloc_INChI_Aux()

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

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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
	)

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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
	)

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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
	)

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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

)

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Free_INChI_Aux()

int Free_INChI_Aux

(

INChI_Aux **

ppINChI_Aux

)

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Free_INChI_Members()

int Free_INChI_Members

(

INChI *

pINChI

)

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Free_INChI_Stereo()

int Free_INChI_Stereo

(

INChI_Stereo *

pINChI_Stereo

)

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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
	)

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imat_new()

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

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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
	)

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subgraf_debug_trace()

void subgraf_debug_trace

(

subgraf *

sg

)

subgraf_free()

void subgraf_free

(

subgraf *

sg

)

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subgraf_new()

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

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subgraf_pathfinder_collect_all()

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

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subgraf_pathfinder_free()

void subgraf_pathfinder_free

(

subgraf_pathfinder *

spf

)

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subgraf_pathfinder_new()

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

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subgraf_pathfinder_run()

void subgraf_pathfinder_run	(	subgraf_pathfinder *	spf,
		int	nforbidden,
		int *	forbidden,
		int *	nbonds,
		int **	bonds,
		int *	natoms,
		int *	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[]

)