util.h File Reference

#include "inpdef.h"

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Macros
#define	EL_NUMBER_H   ((U_CHAR)1)
#define	EL_NUMBER_B   ((U_CHAR)5)
#define	EL_NUMBER_C   ((U_CHAR)6)
#define	EL_NUMBER_N   ((U_CHAR)7)
#define	EL_NUMBER_O   ((U_CHAR)8)
#define	EL_NUMBER_F   ((U_CHAR)9)
#define	EL_NUMBER_SI   ((U_CHAR)14)
#define	EL_NUMBER_P   ((U_CHAR)15)
#define	EL_NUMBER_S   ((U_CHAR)16)
#define	EL_NUMBER_CL   ((U_CHAR)17)
#define	EL_NUMBER_GE   ((U_CHAR)32)
#define	EL_NUMBER_AS   ((U_CHAR)33)
#define	EL_NUMBER_SE   ((U_CHAR)34)
#define	EL_NUMBER_BR   ((U_CHAR)35)
#define	EL_NUMBER_SB   ((U_CHAR)51)
#define	EL_NUMBER_TE   ((U_CHAR)52)
#define	EL_NUMBER_I   ((U_CHAR)53)
#define	EL_NUMBER_PO   ((U_CHAR)84)
#define	EL_NUMBER_AT   ((U_CHAR)85)
#define	EL_NUMBER_ZY   ((U_CHAR)119)
#define	EL_NUMBER_ZZ   ((U_CHAR)120)
#define	ALPHA_BASE   27
#define	INCHI_BUILD_PLATFORM   ""
#define	INCHI_BUILD_DEBUG   ""
#define	INCHI_SRC_REV   ""
#define	INCHI_BUILD_COMPILER   ""

Functions
int	get_atomic_mass (const char *elname)
	Get the atomic mass object.
int	get_atomic_mass_from_elnum (int nAtNum)
	Get the atomic mass from elnum object.
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.
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	normalize_string (char *name)
	Normalize string (remove leading & trailing spaces, replace consecutive spaces with a single space, remove tabs.)
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.
int	dotify_non_printable_chars (char *line)
	Replace non-ASCII characters with '.',.
char *	lrtrim (char *p, int *nLen)
	Trim leading and trailing spaces from a string.
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.
void	mystrrev (char *p)
	Reverse a string in place.
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.
long	inchi_strtol (const char *str, const char **p, int base)
	Convert string to long integer.
double	inchi_strtod (const char *str, const char **p)
	Convert string to double.
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)
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	extract_orig_nums_from_auxinfo_string (char *saux, int *orig)
	Parse AuxInfostring and get a list of original atom numbers orig[cano_num].
int	extract_nonstereo_eq_classes_from_auxinfo_string (char *saux, int nat, int *orig, int *have_eclass_info, int *eclass, int *eclass_by_origs)
	Parse AuxInfostring and get non-stereo equivalence classes.
int	extract_stereo_info_from_inchi_string (char *sinchi, int nat, int *orig, int *at_stereo_mark)
	Extract stereo information from InChI string.
int	extract_all_backbone_bonds_from_inchi_string (char *sinchi, int *n_all_bkb_orig, int *orig, int *all_bkb_orig)
	Extract all backbone bonds from InChI string.
int	get_periodic_table_number (const char *elname)
	Get the periodic table number object.
int	is_el_a_metal (int nPeriodicNum)
	Check if an element is a metal.
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	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	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.
int	get_el_type (int nPeriodicNum)
	Get the el type object.
int	if_skip_add_H (int nPeriodicNum)
	Check if no H addition allowed.
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	MakeRemovedProtonsString (int nNumRemovedProtons, NUM_H *nNumExchgIsotopicH, NUM_H *nNumRemovedProtonsIsotopic, int bIsotopic, char *szRemovedProtons, int *num_removed_iso_H)
	Creates a string from the removed protons (?)
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	nBondsValToMetal (inp_ATOM *at, int iat)
	Gets the number of bond valences to a metal atom.
int	nBondsValenceInpAt (const inp_ATOM *at, int *nNumAltBonds, int *nNumWrongBonds)
	Gets the number of bond valences.
int	bHeteroAtomMayHaveXchgIsoH (inp_ATOM *atom, int iat)
	Checks whether a hetero atom may have exchangeable isotopic hydrogens.
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	SetBitFree (struct tagCANON_GLOBALS *pCG)
	Frees bit string in canonicalisation data structure.
void	WriteCoord (char *str, double x)
	Write coordinate (double) to string.

Variables
const int	ERR_ELEM
const int	nElDataLen

Macro Definition Documentation

ALPHA_BASE

#define ALPHA_BASE   27

EL_NUMBER_AS

#define EL_NUMBER_AS   ((U_CHAR)33)

EL_NUMBER_AT

#define EL_NUMBER_AT   ((U_CHAR)85)

EL_NUMBER_B

#define EL_NUMBER_B   ((U_CHAR)5)

EL_NUMBER_BR

#define EL_NUMBER_BR   ((U_CHAR)35)

EL_NUMBER_C

#define EL_NUMBER_C   ((U_CHAR)6)

EL_NUMBER_CL

#define EL_NUMBER_CL   ((U_CHAR)17)

EL_NUMBER_F

#define EL_NUMBER_F   ((U_CHAR)9)

EL_NUMBER_GE

#define EL_NUMBER_GE   ((U_CHAR)32)

EL_NUMBER_H

#define EL_NUMBER_H   ((U_CHAR)1)

EL_NUMBER_I

#define EL_NUMBER_I   ((U_CHAR)53)

EL_NUMBER_N

#define EL_NUMBER_N   ((U_CHAR)7)

EL_NUMBER_O

#define EL_NUMBER_O   ((U_CHAR)8)

EL_NUMBER_P

#define EL_NUMBER_P   ((U_CHAR)15)

EL_NUMBER_PO

#define EL_NUMBER_PO   ((U_CHAR)84)

EL_NUMBER_S

#define EL_NUMBER_S   ((U_CHAR)16)

EL_NUMBER_SB

#define EL_NUMBER_SB   ((U_CHAR)51)

EL_NUMBER_SE

#define EL_NUMBER_SE   ((U_CHAR)34)

EL_NUMBER_SI

#define EL_NUMBER_SI   ((U_CHAR)14)

EL_NUMBER_TE

#define EL_NUMBER_TE   ((U_CHAR)52)

EL_NUMBER_ZY

#define EL_NUMBER_ZY   ((U_CHAR)119)

EL_NUMBER_ZZ

#define EL_NUMBER_ZZ   ((U_CHAR)120)

INCHI_BUILD_COMPILER

#define INCHI_BUILD_COMPILER   ""

INCHI_BUILD_DEBUG

#define INCHI_BUILD_DEBUG   ""

INCHI_BUILD_PLATFORM

#define INCHI_BUILD_PLATFORM   ""

INCHI_SRC_REV

#define INCHI_SRC_REV   ""

Function Documentation

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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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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extract_all_backbone_bonds_from_inchi_string()

int extract_all_backbone_bonds_from_inchi_string	(	char *	sinchi,
		int *	n_all_bkb_orig,
		int *	orig,
		int *	all_bkb_orig
	)

Extract all backbone bonds from InChI string.

Parameters

sinchi	Pointer to InChI string
n_all_bkb_orig	Pointer to number of all backbone bonds
orig	Pointer to array of original atom numbers
all_bkb_orig	Pointer to output array of all backbone bonds by original atom numbers

Returns

int Status code

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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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extract_nonstereo_eq_classes_from_auxinfo_string()

int extract_nonstereo_eq_classes_from_auxinfo_string	(	char *	saux,
		int	nat,
		int *	orig,
		int *	have_eclass_info,
		int *	eclass,
		int *	eclass_by_origs
	)

Parse AuxInfostring and get non-stereo equivalence classes.

Parameters

saux	Pointer to AuxInfo string
nat	Number of atoms
orig	Pointer to array of original atom numbers
have_eclass_info	Pointer to output flag indicating if equivalence class info is present
eclass	Pointer to output array of equivalence classes by canonical atom number
eclass_by_origs	Pointer to output array of equivalence classes by original atom number

Returns

int Status code

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extract_orig_nums_from_auxinfo_string()

int extract_orig_nums_from_auxinfo_string	(	char *	saux,
		int *	orig
	)

Parse AuxInfostring and get a list of original atom numbers orig[cano_num].

Parameters

saux	Pointer to AuxInfo string
orig	Pointer to output array of original atom numbers

Returns

int Status code

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extract_stereo_info_from_inchi_string()

int extract_stereo_info_from_inchi_string	(	char *	sinchi,
		int	nat,
		int *	orig,
		int *	at_stereo_mark
	)

Extract stereo information from InChI string.

Parameters

sinchi	Pointer to InChI string
nat	Number of atoms
orig	Pointer to array of original atom numbers
at_stereo_mark	Pointer to output array of stereo marks for atoms

Returns

int Status code

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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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inchi_strtod()

double inchi_strtod	(	const char *	str,
		const char **	p
	)

Convert string to double.

Parameters

str	Pointer to the input string
p	Pointer to the position where conversion stopped

Returns

double Converted value

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inchi_strtol()

long inchi_strtol	(	const char *	str,
		const char **	p,
		int	base
	)

Convert string to long integer.

Parameters

str	Pointer to the input string
p	Pointer to the position where conversion stopped
base	Base for conversion

Returns

long Converted value

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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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MakeRemovedProtonsString()

int MakeRemovedProtonsString	(	int	nNumRemovedProtons,
		NUM_H *	nNumExchgIsotopicH,
		NUM_H *	nNumRemovedProtonsIsotopic,
		int	bIsotopic,
		char *	szRemovedProtons,
		int *	num_removed_iso_H
	)

Creates a string from the removed protons (?)

Parameters

nNumRemovedProtons	Number of removed protons
nNumExchgIsotopicH	Pointer to number of exchangeable isotopic hydrogens
nNumRemovedProtonsIsotopic	Pointer to array of removed protons
bIsotopic	Flag to handle isotopes
szRemovedProtons	Pointer to the removed protons
num_removed_iso_H	Pointer to the number of removed isotopic hydrogens

Returns

int

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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mystrrev()

void mystrrev

(

char *

p

)

Reverse a string in place.

Parameters

p	Pointer to the string to reverse

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nBondsValenceInpAt()

int nBondsValenceInpAt	(	const inp_ATOM *	at,
		int *	nNumAltBonds,
		int *	nNumWrongBonds
	)

Gets the number of bond valences.

Parameters

at	Pointer to atom list
nNumAltBonds	Pointer to the number of alternative bonds (4)
nNumWrongBonds	Pointer to the number of wrong bonds

Returns

int The number of bond valences

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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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SetBitFree()

int SetBitFree

(

struct tagCANON_GLOBALS *

pCG

)

Frees bit string in canonicalisation data structure.

Parameters

pCG	Canonicalisation data structure

Returns

int 1 if success, 0 if failed

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WriteCoord()

void WriteCoord	(	char *	str,
		double	x
	)

Write coordinate (double) to string.

Parameters

str	Pointer to output string
x	Input double

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Variable Documentation

ERR_ELEM

const int ERR_ELEM

extern

nElDataLen

const int nElDataLen

extern