util.c File Reference

#include <string.h>
#include <stdlib.h>
#include <ctype.h>
#include "mode.h"
#include "util.h"
#include "extr_ct.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)
	Finds chemical symbol for element of given number.
int	get_element_or_pseudoelement_symbol (int nAtNum, char *szElement)
	Finds symbol for element of given number. Accounts for (translates)pseudoelements.
int	el_number_in_internal_ref_table (const char *elname)
int	get_periodic_table_number (const char *elname)
	Get the periodic table number object.
int	if_skip_add_H (int nPeriodicNum)
	Check if no H addition allowed.
int	get_el_valence (int nPeriodicNum, int charge, int val_num)
	Get reference value of atom valence at given charge.
int	get_unusual_el_valence (int nPeriodicNum, int charge, int radical, int bonds_valence, int num_H, int num_bonds)
	Output valence needed to unambiguosly reconstruct 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)
	Output valence needed to unambiguosly reconstruct number of H.
int	detect_unusual_el_valence (int nPeriodicNum, int charge, int radical, int bonds_valence, int num_H, int num_bonds)
	Output valence that does not fit any known valences.
int	get_el_type (int nPeriodicNum)
	Get the el type object.
int	is_el_a_metal (int nPeriodicNum)
	Check if an element is a metal.
int	extract_charges_and_radicals (char *elname, int *pnRadical, int *pnCharge)
	Extract charges and radicals from element name.
int	extract_H_atoms (char *elname, S_CHAR num_iso_H[])
	Extract H atoms from element name.
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)
	Get the number of attached hydrogens.
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)
	Checks if an atom is in the list/path.
int *	is_in_the_ilist (int *pathAtom, int nNextAtom, int nPathLen)
	Checks if an integer is in the list/path.
int	is_ilist_inside (int *ilist, int nlist, int *ilist2, int nlist2)
	Checks if one list of integers is inside another list (ilist in ilist2)
int	nBondsValToMetal (inp_ATOM *at, int iat)
	Gets the number of bond valences to a metal atom.
int	num_of_H (inp_ATOM *at, int iat)
	Get the number of hydrogens.
U_CHAR	ion_el_group (int el)
	Get the element group of an element. The base element rather than the periodic group is used to aid readability.
int	has_other_ion_neigh (inp_ATOM *at, int iat, int iat_ion_neigh)
	Check whether an atom has ion neighbors.
int	has_other_ion_in_sphere_2 (inp_ATOM *at, int iat, int iat_ion_neigh)
	Check whether an atom has ion neighbors within sphere (breath first search (BFS) up to r=2)
int	nNoMetalNumBonds (inp_ATOM *at, int at_no)
	Returns the number of non-metal bonds.
int	nNoMetalBondsValence (inp_ATOM *at, int at_no)
	Returns the number of non-metal bond valences.
int	nNoMetalNeighIndex (inp_ATOM *at, int at_no)
	Get the index of the first element that is not a metal.
int	nNoMetalOtherNeighIndex (inp_ATOM *at, int at_no, int cur_neigh)
	Get the index of an element that is not a metal excluding a given index.
int	nNoMetalOtherNeighIndex2 (inp_ATOM *at, int at_no, int cur_neigh, int cur_neigh2)
	Get the index of an element that is not a metal excluding a 2 given indexes.
int	get_endpoint_valence (U_CHAR el_number)
	Get the endpoint valence object.
int	get_endpoint_valence_KET (U_CHAR el_number)
	Get the endpoint valence KET object.
int	normalize_string (char *name)
	Normalize string (remove leading & trailing spaces, replace consecutive spaces with a single space, remove tabs.)
int	dotify_non_printable_chars (char *line)
	Replace non-ASCII characters with '.',.
int	read_upto_delim (char **pstring, char *field, int maxlen, char *delims)
	Read up to any delimiter from the string.
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 a 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)
	Trim leading and trailing spaces from a string.
void	extract_inchi_substring (char **buf, const char *str, size_t slen)
	Extract InChI substring embedded into a longer string.
void	extract_auxinfo_substring (char **buf, const char *str, size_t slen)
	Extract AuxInfo substring embedded into a longer string.
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)
	Case-insensitive string comparison.
char *	inchi__strnset (char *s, int val, size_t length)
	Set a string to a specified value for a given length.
char *	inchi__strdup (const char *string)
	Duplicate a 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
	)

Output valence that does not fit any known valences.

Parameters

nPeriodicNum	Periodic table number
charge	Charge
radical	Radical
bonds_valence	Bonds valence
num_H	Number of hydrogens
num_bonds	Number of bonds

Returns

int Chemical valence if unusual, 0 otherwise

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dotify_non_printable_chars()

int dotify_non_printable_chars

(

char *

line

)

Replace non-ASCII characters with '.',.

Parameters

line	Pointer to the input line

Returns

int Number of replacements

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el_number_in_internal_ref_table()

int el_number_in_internal_ref_table

(

const char *

elname

)

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extract_auxinfo_substring()

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

Extract AuxInfo substring embedded into a longer string.

Parameters

buf	Pointer to output buffer
str	Pointer to input string
slen	Length of the input string

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extract_charges_and_radicals()

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

Extract charges and radicals from element name.

Parameters

elname	Element name
pnRadical	Number of radicals
pnCharge	Number of charges

Returns

int Number of charges or radicals extracted

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extract_H_atoms()

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

Extract H atoms from element name.

Parameters

elname	Element name
num_iso_H	Number of isotopic H

Returns

int Number of H atoms extracted

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extract_inchi_substring()

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

Extract InChI substring embedded into a longer string.

Parameters

buf	Pointer to output buffer
str	Pointer to input string
slen	Length of the input string

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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

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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

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get_el_type()

int get_el_type

(

int

nPeriodicNum

)

Get the el type object.

Parameters

nPeriodicNum

Periodic table number

Returns

int Element type

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get_el_valence()

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

Get reference value of atom valence at given charge.

Parameters

nPeriodicNum	Periodic table number
charge	Charge
val_num	Valence number

Returns

int Reference valence value

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get_element_chemical_symbol()

int get_element_chemical_symbol	(	int	nAtNum,
		char *	szElement
	)

Finds chemical symbol for element of given number.

Parameters

nAtNum	Atom number
szElement	Pointer to chemical symbol

Returns

int Returns 0 if OK and -1 if element was not found.

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get_element_or_pseudoelement_symbol()

int get_element_or_pseudoelement_symbol	(	int	nAtNum,
		char *	szElement
	)

Finds symbol for element of given number. Accounts for (translates)pseudoelements.

Parameters

nAtNum	Atom number
szElement	Pointer to chemical symbol

Returns

int Returns 0 if OK and -1 if element was not found.

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get_endpoint_valence()

int get_endpoint_valence

(

U_CHAR

el_number

)

Get the endpoint valence object.

Parameters

el_number

Element number

Returns

int 3 if No, 2 if O, S, SE, TE or 0 otherwise

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get_endpoint_valence_KET()

int get_endpoint_valence_KET

(

U_CHAR

el_number

)

Get the endpoint valence KET object.

Parameters

el_number

Element number

Returns

int 4 if C, 2 if O or 0 otherwise

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get_num_H()

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

Get the number of attached hydrogens.

Parameters

elname	Element name
inp_num_H	Input number of H
num_iso_H	Number of isotopic H
charge	Charge
radical	Radical
chem_bonds_valence	Number of chemical valence bonds
atom_input_valence	Number of atom valence
bAliased	Flag indicating whether the atom is aliased??
bDoNotAddH	Flag indicating whether to add hydrogens
bHasMetalNeighbor	Flag indicating whether there is a metal neighbor

Returns

int Number of attached hydrogens

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get_periodic_table_number()

int get_periodic_table_number

(

const char *

elname

)

Get the periodic table number object.

Parameters

elname

Pointer to element name

Returns

int Periodic table number

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get_unusual_el_valence()

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

Output valence needed to unambiguosly reconstruct bonds.

Parameters

nPeriodicNum	Periodic table number
charge	Charge
radical	Radical
bonds_valence	Bonds valence
num_H	Number of hydrogens
num_bonds	Number of bonds

Returns

int Valence needed to unambiguously reconstruct bonds

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has_other_ion_in_sphere_2()

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

Check whether an atom has ion neighbors within sphere (breath first search (BFS) up to r=2)

Parameters

at	Pointer to atom array
iat	Atom id
iat_ion_neigh	Atom id of ion neighbor

Returns

int Number of ions in sphere

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has_other_ion_neigh()

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

Check whether an atom has ion neighbors.

Parameters

at	Pointer to atom array
iat	Atom id
iat_ion_neigh	Atom id of ion neighbor

Returns

int Returns 1 for having an ion neighbor, 0 for none

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if_skip_add_H()

int if_skip_add_H

(

int

nPeriodicNum

)

Check if no H addition allowed.

Parameters

nPeriodicNum

Periodic table number

Returns

int Non-zero if no H addition is allowed, zero otherwise

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inchi__strdup()

char * inchi__strdup

(

const char *

string

)

Duplicate a string.

Parameters

string

Pointer to the input string

Returns

char* Pointer to the duplicated string

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inchi__strnset()

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

Set a string to a specified value for a given length.

Parameters

s	Pointer to the string
val	Value to set
length	Length of the string to set

Returns

char* Pointer to the modified string

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

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inchi_stricmp()

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

Case-insensitive string comparison.

Parameters

s1	Pointer to first string
s2	Pointer to second string

Returns

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

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ion_el_group()

U_CHAR ion_el_group

(

int

el

)

Get the element group of an element. The base element rather than the periodic group is used to aid readability.

Parameters

el	Element number

Returns

U_CHAR Returns element group (NitrogenGroup = 7 (EL_NUMBER_N), OxygenGroup = 8 (EL_NUMBER_O), Carbon = 6 (EL_NUMBER_C))

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is_el_a_metal()

int is_el_a_metal

(

int

nPeriodicNum

)

Check if an element is a metal.

Parameters

nPeriodicNum

Periodic table number

Returns

int 1 if the element is a metal, 0 otherwise

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is_ilist_inside()

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

Checks if one list of integers is inside another list (ilist in ilist2)

Parameters

ilist	Pointer to the first list of integers
nlist	Length of ilist
ilist2	Pointer to the second list of integers
nlist2	Length of ilist2

Returns

int Returns 1 if ilist is inside ilist2, 0 otherwise

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is_in_the_ilist()

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

Checks if an integer is in the list/path.

Parameters

pathAtom	Pointer to the list/path of integers
nNextAtom	Integer to find
nPathLen	Length of the list/path

Returns

int* Pointer to the found integer in the list/path, NULL if not found

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is_in_the_list()

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

Checks if an atom is in the list/path.

Parameters

pathAtom	Pointer to the list/path of atoms
nNextAtom	Atom to find
nPathLen	List length

Returns

AT_NUMB* Pointer to the found atom in the list/path, NULL if not found

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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

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lrtrim()

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

Trim leading and trailing spaces from a string.

Parameters

p	Pointer to the input string
nLen	Length of the trimmed string

Returns

char* Pointer to the trimmed string

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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

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nBondsValToMetal()

int nBondsValToMetal	(	inp_ATOM *	at,
		int	iat
	)

Gets the number of bond valences to a metal atom.

Parameters

at	Pointer to atom list
iat	Atom number

Returns

int Number of bond valences, -1 if bond to metal order is not well defined

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needed_unusual_el_valence()

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

Output valence needed to unambiguosly reconstruct number of H.

Parameters

nPeriodicNum	Periodic table number
charge	Charge
radical	Radical
bonds_valence	Bonds valence
actual_bonds_val	Actual bonds valence
num_H	Number of hydrogens
num_bonds	Number of bonds

Returns

int Chemical valence needed to unambiguously reconstruct number of H

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nNoMetalBondsValence()

int nNoMetalBondsValence	(	inp_ATOM *	at,
		int	at_no
	)

Returns the number of non-metal bond valences.

Parameters

at	Pointer to atom list
at_no	Atom number

Returns

int Number of non-metal bond valences

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nNoMetalNeighIndex()

int nNoMetalNeighIndex	(	inp_ATOM *	at,
		int	at_no
	)

Get the index of the first element that is not a metal.

Parameters

at	Pointer to atom list
at_no	Atom number

Returns

int Atom index, -1 if nothing found

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nNoMetalNumBonds()

int nNoMetalNumBonds	(	inp_ATOM *	at,
		int	at_no
	)

Returns the number of non-metal bonds.

Parameters

at	Pointer to atom list
at_no	Atom number

Returns

int Number of number of no metal bonds

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nNoMetalOtherNeighIndex()

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

Get the index of an element that is not a metal excluding a given index.

Parameters

at	Pointer to atom list
at_no	Atom number
cur_neigh	Excluding atom number

Returns

int Atom index, -1 if nothing found

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nNoMetalOtherNeighIndex2()

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

Get the index of an element that is not a metal excluding a 2 given indexes.

Parameters

at	Pointer to atom list
at_no	Atom number
cur_neigh	Excluding atom number 1
cur_neigh2	Excluding atom number 2

Returns

int Atom index, -1 if nothing found

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normalize_string()

int normalize_string

(

char *

name

)

Normalize string (remove leading & trailing spaces, replace consecutive spaces with a single space, remove tabs.)

Parameters

name	Input string to normalize

Returns

int Number of characters in normalized string

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num_of_H()

int num_of_H	(	inp_ATOM *	at,
		int	iat
	)

Get the number of hydrogens.

Parameters

at	Pointer to atom list
iat	Input atom id

Returns

int Number of total hydrogens atoms

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read_upto_delim()

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

Read up to any delimiter from the string.

Parameters

pstring	Pointer to input string
field	Pointer to output field
maxlen	Maximum length of the field
delims	Delimiters

Returns

int

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remove_one_lf()

void remove_one_lf

(

char *

p

)

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

Parameters

p	Input string

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remove_trailing_spaces()

void remove_trailing_spaces

(

char *

p

)

Remove trailing spaces from a string.

Parameters

p	Input string

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Variable Documentation

ElData

const ELDATA ElData[]

ERR_ELEM

const int ERR_ELEM = 255

nElDataLen

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