util.c File Reference

#include <ctype.h>
#include <stdlib.h>
#include <string.h>
#include "mode.h"
#include "extr_ct.h"
#include "util.h"
#include "bcf_s.h"

Include dependency graph for util.c:

Data Structures
struct	tagElData

Macros
#define	is_ascii(c)   ((unsigned)(c) < 0x80)
#define	MIN_ATOM_CHARGE   (-2)
#define	MAX_ATOM_CHARGE   2
#define	NEUTRAL_STATE   (-MIN_ATOM_CHARGE)
#define	NUM_ATOM_CHARGES   (MAX_ATOM_CHARGE - MIN_ATOM_CHARGE + 1)
#define	MAX_NUM_VALENCES   5 /* max. number + 1 to provide zero termination */
#define	MAXQ   16
#define	__MYTOLOWER(c)   (((c) >= 'A') && ((c) <= 'Z') ? ((c) - 'A' + 'a') : (c))

Typedefs
typedef struct tagElData	ELDATA

Functions
int	get_element_chemical_symbol (int nAtNum, char *szElement)
int	get_element_or_pseudoelement_symbol (int nAtNum, char *szElement)
int	el_number_in_internal_ref_table (const char *elname)
int	get_periodic_table_number (const char *elname)
int	if_skip_add_H (int nPeriodicNum)
int	get_el_valence (int nPeriodicNum, int charge, int val_num)
int	get_unusual_el_valence (int nPeriodicNum, int charge, int radical, int bonds_valence, int num_H, int num_bonds)
int	needed_unusual_el_valence (int nPeriodicNum, int charge, int radical, int bonds_valence, int actual_bonds_valence, int num_H, int num_bonds)
int	detect_unusual_el_valence (int nPeriodicNum, int charge, int radical, int bonds_valence, int num_H, int num_bonds)
int	get_el_type (int nPeriodicNum)
int	is_el_a_metal (int nPeriodicNum)
int	extract_charges_and_radicals (char *elname, int *pnRadical, int *pnCharge)
int	extract_H_atoms (char *elname, S_CHAR num_iso_H[])
int	get_num_H (const char *elname, int inp_num_H, S_CHAR inp_num_iso_H[], int charge, int radical, int chem_bonds_valence, int atom_input_valence, int bAliased, int bDoNotAddH, int bHasMetalNeighbor)
int	get_atomic_mass_from_elnum (int nAtNum)
	Get the atomic mass from elnum object.
int	get_atomic_mass (const char *elname)
	Get the atomic mass object.
AT_NUMB *	is_in_the_list (AT_NUMB *pathAtom, AT_NUMB nNextAtom, int nPathLen)
int *	is_in_the_ilist (int *pathAtom, int nNextAtom, int nPathLen)
int	is_ilist_inside (int *ilist, int nlist, int *ilist2, int nlist2)
int	nBondsValToMetal (inp_ATOM *at, int iat)
int	num_of_H (inp_ATOM *at, int iat)
U_CHAR	ion_el_group (int el)
int	has_other_ion_neigh (inp_ATOM *at, int iat, int iat_ion_neigh)
int	has_other_ion_in_sphere_2 (inp_ATOM *at, int iat, int iat_ion_neigh)
int	nNoMetalNumBonds (inp_ATOM *at, int at_no)
int	nNoMetalBondsValence (inp_ATOM *at, int at_no)
int	nNoMetalNeighIndex (inp_ATOM *at, int at_no)
int	nNoMetalOtherNeighIndex (inp_ATOM *at, int at_no, int cur_neigh)
int	nNoMetalOtherNeighIndex2 (inp_ATOM *at, int at_no, int cur_neigh, int cur_neigh2)
int	get_endpoint_valence (U_CHAR el_number)
int	get_endpoint_valence_KET (U_CHAR el_number)
int	normalize_string (char *name)
int	dotify_non_printable_chars (char *line)
int	read_upto_delim (char **pstring, char *field, int maxlen, char *delims)
int	is_matching_any_delim (char c, char *delims)
	Check if a character is in the list of possible delimiters.
void	remove_trailing_spaces (char *p)
	Remove trailing spaces from a string.
void	remove_one_lf (char *p)
	Remove one line feed character from the end of the string.
int	mystrncpy (char *target, const char *source, unsigned maxlen)
	Copies up to maxlen characters INCLUDING end null from source to target. Fills out the rest of the target with null bytes. Protected from non-zero-terminated source and overlapped target/source.
char *	lrtrim (char *p, int *nLen)
	Remove leading and trailing white spaces.
void	extract_inchi_substring (char **buf, const char *str, size_t slen)
void	extract_auxinfo_substring (char **buf, const char *str, size_t slen)
int	inchi_memicmp (const void *p1, const void *p2, size_t length)
	Compare two memory blocks in a case-insensitive manner.
int	inchi_stricmp (const char *s1, const char *s2)
char *	inchi__strnset (char *s, int val, size_t length)
char *	inchi__strdup (const char *string)

Variables
const ELDATA	ElData []
const int	ERR_ELEM = 255
const int	nElDataLen = sizeof(ElData) / sizeof(ElData[0]) - 1

Macro Definition Documentation

__MYTOLOWER

#define __MYTOLOWER

(

c

)

(((c) >= 'A') && ((c) <= 'Z') ? ((c) - 'A' + 'a') : (c))

is_ascii

#define is_ascii

(

c

)

((unsigned)(c) < 0x80)

MAX_ATOM_CHARGE

#define MAX_ATOM_CHARGE   2

MAX_NUM_VALENCES

#define MAX_NUM_VALENCES   5 /* max. number + 1 to provide zero termination */

MAXQ

#define MAXQ   16

MIN_ATOM_CHARGE

#define MIN_ATOM_CHARGE   (-2)

NEUTRAL_STATE

#define NEUTRAL_STATE   (-MIN_ATOM_CHARGE)

NUM_ATOM_CHARGES

#define NUM_ATOM_CHARGES   (MAX_ATOM_CHARGE - MIN_ATOM_CHARGE + 1)

Typedef Documentation

ELDATA

typedef struct tagElData ELDATA

Function Documentation

detect_unusual_el_valence()

int detect_unusual_el_valence	(	int	nPeriodicNum,
		int	charge,
		int	radical,
		int	bonds_valence,
		int	num_H,
		int	num_bonds
	)

Here is the call graph for this function:

Here is the caller graph for this function:

dotify_non_printable_chars()

int dotify_non_printable_chars

(

char *

line

)

Here is the caller graph for this function:

el_number_in_internal_ref_table()

int el_number_in_internal_ref_table

(

const char *

elname

)

Here is the caller graph for this function:

extract_auxinfo_substring()

void extract_auxinfo_substring	(	char **	buf,
		const char *	str,
		size_t	slen
	)

Here is the caller graph for this function:

extract_charges_and_radicals()

int extract_charges_and_radicals	(	char *	elname,
		int *	pnRadical,
		int *	pnCharge
	)

Here is the caller graph for this function:

extract_H_atoms()

int extract_H_atoms	(	char *	elname,
		S_CHAR	num_iso_H[]
	)

Here is the caller graph for this function:

extract_inchi_substring()

void extract_inchi_substring	(	char **	buf,
		const char *	str,
		size_t	slen
	)

Here is the caller graph for this function:

get_atomic_mass()

int get_atomic_mass

(

const char *

elname

)

Get the atomic mass object.

Parameters

elname

Element name

Returns

Returns the atomic mass as integer

Here is the call graph for this function:

Here is the caller graph for this function:

get_atomic_mass_from_elnum()

int get_atomic_mass_from_elnum

(

int

nAtNum

)

Get the atomic mass from elnum object.

Parameters

nAtNum

Element number

Returns

Returns the atomic mass as integer

Here is the caller graph for this function:

get_el_type()

int get_el_type

(

int

nPeriodicNum

)

Here is the caller graph for this function:

get_el_valence()

int get_el_valence	(	int	nPeriodicNum,
		int	charge,
		int	val_num
	)

Here is the caller graph for this function:

get_element_chemical_symbol()

int get_element_chemical_symbol	(	int	nAtNum,
		char *	szElement
	)

Here is the caller graph for this function:

get_element_or_pseudoelement_symbol()

int get_element_or_pseudoelement_symbol	(	int	nAtNum,
		char *	szElement
	)

Here is the caller graph for this function:

get_endpoint_valence()

int get_endpoint_valence

(

U_CHAR

el_number

)

Here is the caller graph for this function:

get_endpoint_valence_KET()

int get_endpoint_valence_KET

(

U_CHAR

el_number

)

Here is the caller graph for this function:

get_num_H()

int get_num_H	(	const char *	elname,
		int	inp_num_H,
		S_CHAR	inp_num_iso_H[],
		int	charge,
		int	radical,
		int	chem_bonds_valence,
		int	atom_input_valence,
		int	bAliased,
		int	bDoNotAddH,
		int	bHasMetalNeighbor
	)

Here is the call graph for this function:

Here is the caller graph for this function:

get_periodic_table_number()

int get_periodic_table_number

(

const char *

elname

)

Here is the call graph for this function:

Here is the caller graph for this function:

get_unusual_el_valence()

int get_unusual_el_valence	(	int	nPeriodicNum,
		int	charge,
		int	radical,
		int	bonds_valence,
		int	num_H,
		int	num_bonds
	)

Here is the call graph for this function:

Here is the caller graph for this function:

has_other_ion_in_sphere_2()

int has_other_ion_in_sphere_2	(	inp_ATOM *	at,
		int	iat,
		int	iat_ion_neigh
	)

Here is the call graph for this function:

Here is the caller graph for this function:

has_other_ion_neigh()

int has_other_ion_neigh	(	inp_ATOM *	at,
		int	iat,
		int	iat_ion_neigh
	)

Here is the call graph for this function:

Here is the caller graph for this function:

if_skip_add_H()

int if_skip_add_H

(

int

nPeriodicNum

)

Here is the caller graph for this function:

inchi__strdup()

char * inchi__strdup

(

const char *

string

)

Here is the caller graph for this function:

inchi__strnset()

char * inchi__strnset	(	char *	s,
		int	val,
		size_t	length
	)

inchi_memicmp()

int inchi_memicmp	(	const void *	p1,
		const void *	p2,
		size_t	length
	)

Compare two memory blocks in a case-insensitive manner.

Parameters

p1	Pointer to the first memory block.
p2	Pointer to the second memory block.
length	Number of bytes to compare.

Returns

int < 0 if p1 < p2, 0 if p1 == p2, > 0 if p1 > p2

Here is the caller graph for this function:

inchi_stricmp()

int inchi_stricmp	(	const char *	s1,
		const char *	s2
	)

Here is the caller graph for this function:

ion_el_group()

U_CHAR ion_el_group

(

int

el

)

Here is the caller graph for this function:

is_el_a_metal()

int is_el_a_metal

(

int

nPeriodicNum

)

Here is the caller graph for this function:

is_ilist_inside()

int is_ilist_inside	(	int *	ilist,
		int	nlist,
		int *	ilist2,
		int	nlist2
	)

Here is the call graph for this function:

Here is the caller graph for this function:

is_in_the_ilist()

int * is_in_the_ilist	(	int *	pathAtom,
		int	nNextAtom,
		int	nPathLen
	)

Here is the caller graph for this function:

is_in_the_list()

AT_NUMB * is_in_the_list	(	AT_NUMB *	pathAtom,
		AT_NUMB	nNextAtom,
		int	nPathLen
	)

Here is the caller graph for this function:

is_matching_any_delim()

int is_matching_any_delim	(	char	c,
		char *	delims
	)

Check if a character is in the list of possible delimiters.

Note

same as isspace if delims is " \t\n\v\f\r" (0x20 and 0x09-0x0D)

Parameters

c	Character to check
delims	String of delimiter characters

Returns

int 1 if c is a delimiter, 0 otherwise

Here is the caller graph for this function:

lrtrim()

char * lrtrim	(	char *	p,
		int *	nLen
	)

Remove leading and trailing white spaces.

Parameters

p	Input string
nLen	Output length of the trimmed string

Returns

char* Pointer to the trimmed string

Here is the caller graph for this function:

mystrncpy()

int mystrncpy	(	char *	target,
		const char *	source,
		unsigned	maxlen
	)

Copies up to maxlen characters INCLUDING end null from source to target. Fills out the rest of the target with null bytes. Protected from non-zero-terminated source and overlapped target/source.

Note

If source is NULL or maxlen is 0, nothing is copied and 0 is returned.

Parameters

target	Target string
source	Source string
maxlen	Maximum length to copy

Returns

1 on success, 0 if target is NULL or maxlen is 0 or source is NULL

Here is the caller graph for this function:

nBondsValToMetal()

int nBondsValToMetal	(	inp_ATOM *	at,
		int	iat
	)

Here is the call graph for this function:

Here is the caller graph for this function:

needed_unusual_el_valence()

int needed_unusual_el_valence	(	int	nPeriodicNum,
		int	charge,
		int	radical,
		int	bonds_valence,
		int	actual_bonds_valence,
		int	num_H,
		int	num_bonds
	)

Here is the call graph for this function:

Here is the caller graph for this function:

nNoMetalBondsValence()

int nNoMetalBondsValence	(	inp_ATOM *	at,
		int	at_no
	)

Here is the call graph for this function:

Here is the caller graph for this function:

nNoMetalNeighIndex()

int nNoMetalNeighIndex	(	inp_ATOM *	at,
		int	at_no
	)

Here is the call graph for this function:

Here is the caller graph for this function:

nNoMetalNumBonds()

int nNoMetalNumBonds	(	inp_ATOM *	at,
		int	at_no
	)

Here is the call graph for this function:

Here is the caller graph for this function:

nNoMetalOtherNeighIndex()

int nNoMetalOtherNeighIndex	(	inp_ATOM *	at,
		int	at_no,
		int	cur_neigh
	)

Here is the call graph for this function:

Here is the caller graph for this function:

nNoMetalOtherNeighIndex2()

int nNoMetalOtherNeighIndex2	(	inp_ATOM *	at,
		int	at_no,
		int	cur_neigh,
		int	cur_neigh2
	)

Here is the call graph for this function:

Here is the caller graph for this function:

normalize_string()

int normalize_string

(

char *

name

)

Here is the caller graph for this function:

num_of_H()

int num_of_H	(	inp_ATOM *	at,
		int	iat
	)

Here is the caller graph for this function:

read_upto_delim()

int read_upto_delim	(	char **	pstring,
		char *	field,
		int	maxlen,
		char *	delims
	)

Here is the call graph for this function:

Here is the caller graph for this function:

remove_one_lf()

void remove_one_lf

(

char *

p

)

Remove one line feed character from the end of the string.

Parameters

p	Input string

Here is the caller graph for this function:

remove_trailing_spaces()

void remove_trailing_spaces

(

char *

p

)

Remove trailing spaces from a string.

Parameters

p	Input string

Here is the caller graph for this function:

Variable Documentation

ElData

const ELDATA ElData[]

ERR_ELEM

const int ERR_ELEM = 255

nElDataLen

const int nElDataLen = sizeof(ElData) / sizeof(ElData[0]) - 1