#include <stdio.h>
#include "ichisize.h"
#include "mode.h"

Include dependency graph for mol_fmt.h:

This graph shows which files directly or indirectly include this file:

Data Structures
struct	A_NUM_LISTS
	NUM_LISTS - Dynamically growing array of numeric lists. More...

struct	tagINT_ARRAY
	INT_ARRAY - Dynamically growing array of int. More...

struct	A_MOL_FMT_SGROUP
	Data structure for Sgroup data (substance group data). More...

struct	A_MOL_FMT_SGROUPS
	MOL_FMT_SGROUPS is a dynamically growing array of pointers to MOL_FMT_SGROUP objects. More...

struct	A_MOL_FMT_HEADER_BLOCK
	Data structure for MOL file header block (3 lines). More...

struct	A_MOL_FMT_ATOM
	Data structure for atom representation in the MOL format. More...

struct	A_MOL_FMT_BOND
	Data structure for bond representation in the MOL format. More...

struct	A_MOL_FMT_v3000
	Data structure for V3000 representation in the MOL format. More...

struct	A_MOL_FMT_CTAB
	Connection table data structure. More...

struct	A_MOL_FMT_DATA
	Data structure for a MOL file. More...

Macros
#define	SD_FMT_END_OF_DATA "$$$$"

#define	MOL_FMT_INPLINELEN 204 /* add cr, lf, double zero termination */

#define	MOL_FMT_MAXLINELEN 200

#define	MOL_FMT_PRESENT 1

#define	MOL_FMT_ABSENT 0

#define	MOL_FMT_QUERY MOL_FMT_ABSENT

#define	MOL_FMT_CPSS MOL_FMT_ABSENT

#define	MOL_FMT_REACT MOL_FMT_ABSENT

#define	MOL_FMT_STRING_DATA 'S'

#define	MOL_FMT_CHAR_INT_DATA 'C'

#define	MOL_FMT_SHORT_INT_DATA 'N'

#define	MOL_FMT_LONG_INT_DATA 'L'

#define	MOL_FMT_DOUBLE_DATA 'D'

#define	MOL_FMT_FLOAT_DATA 'F'

#define	MOL_FMT_JUMP_TO_RIGHT 'J'

#define	MOL_FMT_INT_DATA 'I'

#define	MOL_FMT_MAX_VALUE_LEN 32 /* max length of string containing a numerical value */

#define	MOL_FMT_M_STY_NON 0

#define	MOL_FMT_M_STY_SRU 1

#define	MOL_FMT_M_STY_MON 2

#define	MOL_FMT_M_STY_COP 3

#define	MOL_FMT_M_STY_MOD 4

#define	MOL_FMT_M_STY_CRO 5

#define	MOL_FMT_M_STY_MER 6

#define	MOL_FMT_M_SST_NON 0

#define	MOL_FMT_M_SST_ALT 1

#define	MOL_FMT_M_SST_RAN 2

#define	MOL_FMT_M_SST_BLK 3

#define	MOL_FMT_M_CONN_NON 0

#define	MOL_FMT_M_CONN_HT 1

#define	MOL_FMT_M_CONN_HH 2

#define	MOL_FMT_M_CONN_EU 3

#define	MOL_FMT_V3000_STENON -1

#define	MOL_FMT_V3000_STEABS 1

#define	MOL_FMT_V3000_STEREL 2

#define	MOL_FMT_V3000_STERAC 3

#define	MOL_FMT_V3000_INPLINELEN 32004 /* add cr, lf, double zero termination */

#define	MOL_FMT_V3000_MAXLINELEN 32000

#define	MOL_FMT_V3000_MAXFIELDLEN 4096

#define	ISOTOPIC_SHIFT_FLAG 10000 /* add to isotopic mass if isotopic_mass = */

#define	INCHI_US_CHAR_DEF

Typedefs
typedef signed char	S_CHAR

typedef unsigned char	U_CHAR

typedef struct A_NUM_LISTS	NUM_LISTS
	NUM_LISTS - Dynamically growing array of numeric lists.

typedef struct tagINT_ARRAY	INT_ARRAY
	INT_ARRAY - Dynamically growing array of int.

typedef struct A_MOL_FMT_SGROUP	MOL_FMT_SGROUP
	Data structure for Sgroup data (substance group data).

typedef struct A_MOL_FMT_SGROUPS	MOL_FMT_SGROUPS
	MOL_FMT_SGROUPS is a dynamically growing array of pointers to MOL_FMT_SGROUP objects.

typedef struct A_MOL_FMT_HEADER_BLOCK	MOL_FMT_HEADER_BLOCK
	Data structure for MOL file header block (3 lines).

typedef struct A_MOL_FMT_ATOM	MOL_FMT_ATOM
	Data structure for atom representation in the MOL format.

typedef struct A_MOL_FMT_BOND	MOL_FMT_BOND
	Data structure for bond representation in the MOL format.

typedef struct A_MOL_FMT_v3000	MOL_FMT_v3000
	Data structure for V3000 representation in the MOL format.

typedef struct A_MOL_FMT_CTAB	MOL_FMT_CTAB
	Connection table data structure.

typedef struct A_MOL_FMT_DATA	MOL_FMT_DATA
	Data structure for a MOL file.

Functions
int	NumLists_Alloc (NUM_LISTS *num_lists, int nlists)
	Allocates memory for a specified number of numeric lists.

int	NumLists_ReAlloc (NUM_LISTS *num_lists)
	Reallocates memory for the numeric lists.

int	NumLists_Append (NUM_LISTS num_lists, int list)
	Push new item to the end of array.

void	NumLists_Free (NUM_LISTS *num_lists)
	Frees the memory allocated for the numeric list.

int	IntArray_Alloc (INT_ARRAY *items, int nitems)
	Initializes an INT_ARRAY structure.

int	IntArray_ReAlloc (INT_ARRAY *items)
	Reallocates memory for the INT_ARRAY structure.

int	IntArray_Append (INT_ARRAY *items, int new_item)
	Appends a new item to the INT_ARRAY structure.

int	IntArray_AppendIfAbsent (INT_ARRAY *items, int new_item)
	Appends a new item to the INT_ARRAY structure if it is not already present.

void	IntArray_Reset (INT_ARRAY *items)
	Resets the INT_ARRAY structure to its initial state.

void	IntArray_Free (INT_ARRAY *items)
	Frees the memory allocated for the INT_ARRAY structure.

void	IntArray_DebugPrint (INT_ARRAY *items)
	Prints the contents of the INT_ARRAY structure for debugging purposes.

int	MolFmtSgroup_Create (MOL_FMT_SGROUP **sgroup, int id, int type)
	Allocate new array Sgroup.

void	MolFmtSgroup_Free (MOL_FMT_SGROUP *sgroup)
	Frees the memory allocated for the Sgroup.

int	MolFmtSgroups_Alloc (MOL_FMT_SGROUPS *items, int nitems)
	Allocates memory for a specified number of Sgroup objects.

int	MolFmtSgroups_ReAlloc (MOL_FMT_SGROUPS *items)
	Expand array of Sgroups.

int	MolFmtSgroups_Append (MOL_FMT_SGROUPS *items, int id, int type)
	Appends a new Sgroup to the array.

void	MolFmtSgroups_Free (MOL_FMT_SGROUPS *items)
	Frees the memory allocated for the MOL_FMT_SGROUPS list.

int	MolFmtSgroups_GetIndexBySgroupId (int id, MOL_FMT_SGROUPS *items)
	Gets the index of a Sgroup by its ID.

static MOL_FMT_DATA *	MolfileReadDataLines (INCHI_IOSTREAM inp_file, MOL_FMT_HEADER_BLOCK OnlyHeaderBlock, MOL_FMT_CTAB OnlyCTab, int bGetOrigCoord, int treat_polymers, int err, char *pStrErr, int bNoWarnings)
	Reads header lines and connection table block from input SD or MOL file, ignore STEXT block, queries, and 3D features.

static int	MolfileReadHeaderLines (MOL_FMT_HEADER_BLOCK hdr, INCHI_IOSTREAM inp_file, char *pStrErr)
	Reads header lines from input MOL file. A MOL file can have 3 header lines: (1) the name of the molecule, (2) details about the software used and (3) a comment line.

static int	MolfileReadCountsLine (MOL_FMT_CTAB ctab, INCHI_IOSTREAM inp_file, char *pStrErr)
	Reads counts line from input MOL file, includes information about the number of atoms, bonds, and atom lists, the chiral flag setting, and the Ctab version.

static int	MolfileReadAtomsBlock (MOL_FMT_CTAB ctab, INCHI_IOSTREAM inp_file, int err, char *pStrErr)
	Reads an atom block from input MOL file (V2000).

static int	MolfileReadBondsBlock (MOL_FMT_CTAB ctab, INCHI_IOSTREAM inp_file, int err, char *pStrErr)
	Reads a bond block from input MOL file (V2000)

MOL_FMT_DATA *	ReadMolfile (INCHI_IOSTREAM inp_file, MOL_FMT_HEADER_BLOCK OnlyHeaderBlock, MOL_FMT_CTAB OnlyCTab, int bGetOrigCoord, int treat_polymers, int pseudos_allowed, char pname, int lname, unsigned long Id, const char pSdfLabel, char pSdfValue, int err, char *pStrErr, int bNoWarnings)
	Reads a substance text block.

int	MolfileStrnread (char dest, char source, int len, char **first_space)
	Read a string from a source buffer into a destination buffer.

int	MolfileReadField (void data, int field_len, int data_type, char *line_ptr)
	Extract the 'data' in the MOL file field at given text position 'line_ptr'.

long	MolfileExtractStrucNum (MOL_FMT_HEADER_BLOCK *pHdr)
	Extract the MOL file number from the header name line like "Structure #22".

int	MolfileHasNoChemStruc (MOL_FMT_DATA *mfdata)
	Check if the MOL file has no chemical structure.

int	MolfileSaveCopy (INCHI_IOSTREAM inp_file, long fPtrStart, long fPtrEnd, FILE outfile, long num)
	Copy MOL-formatted data of SDF record or Molfile to another file.

int	MolfileGetXYZDimAndNormFactors (MOL_FMT_DATA mfdata, int find_norm_factors, double x0, double y0, double z0, double xmin, double ymin, double zmin, double scaler, int err, char pStrErr)
	Get xyz dimensionality and normalization factors in the MOL file.

MOL_FMT_DATA *	FreeMolfileData (MOL_FMT_DATA *mfdata)
	Free MOL file data structure.

int	MolfileV3000Init (MOL_FMT_CTAB ctab, char pStrErr)
	Initialize V3000 connection table in MOL file data structure.

int	MolfileV3000ReadCTABBeginAndCountsLine (MOL_FMT_CTAB ctab, INCHI_IOSTREAM inp_file, char *pStrErr)
	Read V3000 head (begin and counts line) of in MOL file data structure from input file stream.

int	MolfileV3000ReadAtomsBlock (MOL_FMT_CTAB ctab, INCHI_IOSTREAM inp_file, int err, char *pStrErr)
	Read V3000 atoms block in MOL file data structure from input file stream.

int	MolfileV3000ReadBondsBlock (MOL_FMT_CTAB ctab, INCHI_IOSTREAM inp_file, int err, char *pStrErr)
	Read V3000 bonds block in MOL file data structure from input file stream.

int	MolfileV3000ReadTailOfCTAB (MOL_FMT_CTAB ctab, INCHI_IOSTREAM inp_file, int err, char *pStrErr)
	Read V3000 tail (haptic bonds, stereo collections, Sgroups, 3D constraints, collections, end line) in to the MOL file data structure from input file stream.

int	MolfileV3000ReadHapticBond (MOL_FMT_CTAB ctab, char line_ptr, int num_list, char pStrErr)
	Read V3000 haptic bond information from the input line.

int	MolfileV3000ReadStereoCollection (MOL_FMT_CTAB ctab, char line_ptr, int num_list, char pStrErr)
	Read V3000 stereo collection information from the input line.

int	MolfileV3000ReadSGroup (MOL_FMT_CTAB ctab, INCHI_IOSTREAM inp_file, int err, char *pStrErr)
	Read V3000 Sgroup information from the input file stream into the MOL file data structure.

int	MolfileV3000Read3DBlock (MOL_FMT_CTAB ctab, INCHI_IOSTREAM inp_file, int err, char *pStrErr)
	Read V3000 3D constraints block in MOL file data structure from input file stream.

int	MolfileV3000ReadCollections (MOL_FMT_CTAB ctab, INCHI_IOSTREAM inp_file, int err, char *pStrErr)
	Read V3000 collections block in MOL file data structure from input file stream.

int	DeleteMolfileV3000Info (MOL_FMT_v3000 *v3000)
	Free memory allocated for V3000 specific data in the MOL file data structure.

char *	inchi_fgetsLf_V3000 (char line, INCHI_IOSTREAM inp_stream)
	Read a line from the input file stream, handling V3000 line continuations: Extended version of inchi_fgetsLf which is able of reading concatenated lines (ending with '-') of V3000 Molfile. Also removes "M V30 " prefix" and normalizes the rest of string.

int	get_V3000_input_line_to_strbuf (INCHI_IOS_STRING buf, INCHI_IOSTREAM inp_stream)
	Get a V3000 input line and store it in a string buffer.

int	MolfileV3000ReadField (void data, int data_type, char *line_ptr)
	Extract the 'data' in specified mol file field at given text position 'line_ptr'.

int	MolfileV3000ReadKeyword (char key, char *line_ptr)
	Read keyword from the specified line.

int	SDFileSkipExtraData (INCHI_IOSTREAM inp_file, unsigned long CAS_num, char comment, int lcomment, char name, int lname, int prev_err, const char pSdfLabel, char pSdfValue, char *pStrErr, int bNoWarnings)
	Skip extra data in SDF file after the MOL file data.

int	SDFileIdentifyLabel (char inp_line, const char pSdfLabel)
	Identify if the given line matches the specified SDF label.

unsigned long	SDFileExtractCASNo (char *line)
	Extract CAS number from the given line.

Macro Definition Documentation

◆ INCHI_US_CHAR_DEF

#define INCHI_US_CHAR_DEF

◆ ISOTOPIC_SHIFT_FLAG

#define ISOTOPIC_SHIFT_FLAG 10000 /* add to isotopic mass if isotopic_mass = */

◆ MOL_FMT_ABSENT

#define MOL_FMT_ABSENT 0

◆ MOL_FMT_CHAR_INT_DATA

#define MOL_FMT_CHAR_INT_DATA 'C'

◆ MOL_FMT_CPSS

#define MOL_FMT_CPSS MOL_FMT_ABSENT

◆ MOL_FMT_DOUBLE_DATA

#define MOL_FMT_DOUBLE_DATA 'D'

◆ MOL_FMT_FLOAT_DATA

#define MOL_FMT_FLOAT_DATA 'F'

◆ MOL_FMT_INPLINELEN

#define MOL_FMT_INPLINELEN 204 /* add cr, lf, double zero termination */

◆ MOL_FMT_INT_DATA

#define MOL_FMT_INT_DATA 'I'

◆ MOL_FMT_JUMP_TO_RIGHT

#define MOL_FMT_JUMP_TO_RIGHT 'J'

◆ MOL_FMT_LONG_INT_DATA

#define MOL_FMT_LONG_INT_DATA 'L'

◆ MOL_FMT_M_CONN_EU

#define MOL_FMT_M_CONN_EU 3

◆ MOL_FMT_M_CONN_HH

#define MOL_FMT_M_CONN_HH 2

◆ MOL_FMT_M_CONN_HT

#define MOL_FMT_M_CONN_HT 1

◆ MOL_FMT_M_CONN_NON

#define MOL_FMT_M_CONN_NON 0

◆ MOL_FMT_M_SST_ALT

#define MOL_FMT_M_SST_ALT 1

Alternating

◆ MOL_FMT_M_SST_BLK

#define MOL_FMT_M_SST_BLK 3

Block

◆ MOL_FMT_M_SST_NON

#define MOL_FMT_M_SST_NON 0

None

◆ MOL_FMT_M_SST_RAN

#define MOL_FMT_M_SST_RAN 2

Random

◆ MOL_FMT_M_STY_COP

#define MOL_FMT_M_STY_COP 3

Copolymer

◆ MOL_FMT_M_STY_CRO

#define MOL_FMT_M_STY_CRO 5

Crosslink

◆ MOL_FMT_M_STY_MER

#define MOL_FMT_M_STY_MER 6

Mer type

◆ MOL_FMT_M_STY_MOD

#define MOL_FMT_M_STY_MOD 4

Modification

◆ MOL_FMT_M_STY_MON

#define MOL_FMT_M_STY_MON 2

Monomer

◆ MOL_FMT_M_STY_NON

#define MOL_FMT_M_STY_NON 0

None

◆ MOL_FMT_M_STY_SRU

#define MOL_FMT_M_STY_SRU 1

Structure repeating unit

◆ MOL_FMT_MAX_VALUE_LEN

#define MOL_FMT_MAX_VALUE_LEN 32 /* max length of string containing a numerical value */

◆ MOL_FMT_MAXLINELEN

#define MOL_FMT_MAXLINELEN 200

◆ MOL_FMT_PRESENT

#define MOL_FMT_PRESENT 1

◆ MOL_FMT_QUERY

#define MOL_FMT_QUERY MOL_FMT_ABSENT

◆ MOL_FMT_REACT

#define MOL_FMT_REACT MOL_FMT_ABSENT

◆ MOL_FMT_SHORT_INT_DATA

#define MOL_FMT_SHORT_INT_DATA 'N'

◆ MOL_FMT_STRING_DATA

#define MOL_FMT_STRING_DATA 'S'

◆ MOL_FMT_V3000_INPLINELEN

#define MOL_FMT_V3000_INPLINELEN 32004 /* add cr, lf, double zero termination */

◆ MOL_FMT_V3000_MAXFIELDLEN

#define MOL_FMT_V3000_MAXFIELDLEN 4096

◆ MOL_FMT_V3000_MAXLINELEN

#define MOL_FMT_V3000_MAXLINELEN 32000

◆ MOL_FMT_V3000_STEABS

#define MOL_FMT_V3000_STEABS 1

◆ MOL_FMT_V3000_STENON

#define MOL_FMT_V3000_STENON -1

◆ MOL_FMT_V3000_STERAC

#define MOL_FMT_V3000_STERAC 3

◆ MOL_FMT_V3000_STEREL

#define MOL_FMT_V3000_STEREL 2

◆ SD_FMT_END_OF_DATA

#define SD_FMT_END_OF_DATA "$$$$"

Typedef Documentation

◆ INT_ARRAY

typedef struct tagINT_ARRAY INT_ARRAY

INT_ARRAY - Dynamically growing array of int.

Parameters

item	Pointer to the array of integers.
allocated	Amount of memory allocated.
used	Amount of memory used.
increment	Amount to increment when expanding.

◆ MOL_FMT_ATOM

typedef struct A_MOL_FMT_ATOM MOL_FMT_ATOM

Data structure for atom representation in the MOL format.

Parameters

fx	x coordinate: F10.5; Generic
fy	y coordinate: F10.5; Generic
fz	z coordinate: F10.5; Generic
symbol	Element symbol (aaa; up to 6 characters)
mass_difference	Mass difference (dd; (M_ISO); Generic: -3..+4 otherwise 0 or 127=most abund. isotope )
charge	Formal charge (M CHG)
radical	Radical status (M RAD)
stereo_parity	Stereochemical parity (M STY)
H_count_plus_1	Hydrogen count plus one (hhh; Query; Hn means >= n H; H0 means no H)
stereo_care	bbb; Query: 0=ignore; 1=must match
valence	vvv: <vvv: 0=no marking; (1..14)=(1..14); 15=zero valence.Number of bonds includes bonds to impl. H's>
H0_designator	HHH: CPSS
reaction_component_type	rrr: CPSS: 1=reactant, 2=product, 3=intermediate
reaction_component_num	iii: CPSS: 0 to (n-1)
atom_atom_mapping_num	mmm: Reaction: 1..255
cInversionRetentionFlag	nnn: 1=inverted, 2=retained config.; 0=property not applied
exact_change_flag	eee
my_n_impH	number of implicit H calculated for adding H to strings in STDATA
display_tom	Do not hide element's name (applies to C 7-25-98 DCh)
atom_aliased_flag	Do not remove charge/radical/isotope if it is in the alias. 9-3-99 DCh

◆ MOL_FMT_BOND

typedef struct A_MOL_FMT_BOND MOL_FMT_BOND

Data structure for bond representation in the MOL format.

Parameters

atnum1	First atom number.
atnum2	Second atom number.
bond_type	Type of bond (single, double, triple, etc.).
bond_stereo	Stereo information for the bond.
bond_topology	Topology information for the bond.
react_center_status	Reaction center status information.

◆ MOL_FMT_CTAB

typedef struct A_MOL_FMT_CTAB MOL_FMT_CTAB

Connection table data structure.

Parameters

n_atoms	Number of atoms in the molecule.
n_bonds	Number of bonds in the molecule.
n_atom_lists	Number of atom lists.
chiral_flag	Chiral flag indicating the presence of chiral centers.
n_stext_entries	Number of stereo text entries.
n_reaction_components_plus_1	Number of reaction components.
n_reactants	Number of reactants.
n_products	Number of products.
n_intermediates	Number of intermediates.
n_property_lines	Number of property lines.
follow_inchi_1_treating_iso_mass	Flag indicating whether to follow InChI-1 treating isotopic mass.
version_string	Version string indicating the format version.
atoms	Pointer to the array of atom block data structure.
bonds	Pointer to the array of bond block data structure.
coords	Pointer to the array of coordinate data structure.
sgroups	Growable array of pointers to Sgroup objects.
v3000	Pointer to the V3000 specific data structure.

◆ MOL_FMT_DATA

typedef struct A_MOL_FMT_DATA MOL_FMT_DATA

Data structure for a MOL file.

Parameters

hdr	Header block data structure.
ctab	Connection table data structure.

◆ MOL_FMT_HEADER_BLOCK

typedef struct A_MOL_FMT_HEADER_BLOCK MOL_FMT_HEADER_BLOCK

Data structure for MOL file header block (3 lines).

Parameters

molname	Name of molecule (up to 80 characters)
line2	Second line of the header (the whole line2, up to 80 chars)
user_initls	User initials (2 bytes; char)
prog_name	Program name (8 bytes; char)
month	Month (2 bytes; integral)
day	Day (2 bytes; integral)
year	Year (2 bytes; integral)
hour	Hour (2 bytes; integral)
minute	Minute (2 bytes; integral )
dim_code	Dimensional code (2 bytes, dimensional code, char)
scaling_factor1	Scaling factor 1 (2 bytes, I2)
scaling_factor2	Scaling factor 2 (10 bytes, F10.5 )
energy	Energy (10 bytes, F10.5 )
internal_regno	Internal registration number (6 bytes, integral)
comment	Comment (Line #3, up to 80 characters)

◆ MOL_FMT_SGROUP

typedef struct A_MOL_FMT_SGROUP MOL_FMT_SGROUP

Data structure for Sgroup data (substance group data).

Parameters

id	it is what is called 'Sgroup number' in CTFile
type	Sgroup type: SUP = superatom, MUL = multiple group, SRU = SRU type, MON = monomer, MER = Mer type, COP = copolymer, CRO = crosslink, MOD = modification, GRA = graft, COM = component, MIX = mixture, FOR = formulation, DAT = data Sgroup, ANY = any polymer, GEN = generic
subtype	(SST)
conn	(SCN) Connectivity
label	what is called 'unique Sgroup identifier' in CTFile (SLB)
xbr1	bracket ends coordinates (SDI)
xbr2	bracket ends coordinates (SDI)
smt	Sgroup Subscript (SMT)
alist	list of atom indices (AL)
blist	list of bond indices (BL)

◆ MOL_FMT_SGROUPS

typedef struct A_MOL_FMT_SGROUPS MOL_FMT_SGROUPS

MOL_FMT_SGROUPS is a dynamically growing array of pointers to MOL_FMT_SGROUP objects.

Parameters

group	Pointer to the growable array of pointers to MOL_FMT_SGROUPs
allocated	Number of allocated objects
used	Number of used objects
increment	Array expansion increment

◆ MOL_FMT_v3000

typedef struct A_MOL_FMT_v3000 MOL_FMT_v3000

Data structure for V3000 representation in the MOL format.

Parameters

n_non_star_atoms	Number of non-star atoms.
n_star_atoms	Number of star atoms.
atom_index_orig	Original atom indices as supplied.
atom_index_fin	Final atom indices, with -1 for star atoms.
n_sgroups	Number of S-groups.
n_3d_constraints	Number of 3D constraints.
n_collections	Number of collections.
n_non_haptic_bonds	Number of non-haptic bonds.
n_haptic_bonds	Number of haptic bonds.
haptic_bonds	Pointer to the list of haptic bonds (int* contains bond type, non-star atom number, nendpts, then endpts themselves).
n_steabs	Number of absolute stereo groups.
steabs	Pointer to the list of absolute stereo groups (e.g. R and S).
n_sterel	Number of relative stereo groups.
sterel	Pointer to the list of relative stereo groups (OR - describes the orientation of groups relative to each other, such as in cis- and trans-isomers).
n_sterac	Number of racemic stereo groups.
sterac	Pointer to the list of racemic stereo groups (AND - equal 50:50 mixture of two enantiomers of a chiral molecule).

◆ NUM_LISTS

typedef struct A_NUM_LISTS NUM_LISTS

NUM_LISTS - Dynamically growing array of numeric lists.

Parameters

lists	Pointer to the array of integer lists.
allocated	Amount of memory allocated.
used	Amount of memory used.
increment	Amount to increment when expanding.

◆ S_CHAR

typedef signed char S_CHAR

◆ U_CHAR

typedef unsigned char U_CHAR

Function Documentation

◆ DeleteMolfileV3000Info()

int DeleteMolfileV3000Info ( MOL_FMT_v3000 * v3000 )

Free memory allocated for V3000 specific data in the MOL file data structure.

Parameters

v3000 Pointer to the V3000 specific data structure to free.

Returns: 0.

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◆ FreeMolfileData()

MOL_FMT_DATA * FreeMolfileData ( MOL_FMT_DATA * mfdata )

Free MOL file data structure.

Parameters

mfdata Pointer to the MOL file data structure to free.

Returns: NULL pointer.

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◆ get_V3000_input_line_to_strbuf()

int get_V3000_input_line_to_strbuf	(	INCHI_IOS_STRING *	buf,
		INCHI_IOSTREAM *	inp_stream
	)

Get a V3000 input line and store it in a string buffer.

Parameters

buf	Pointer to the string buffer to store the line.
inp_stream	Pointer to the input file stream.

Returns: Length of buffer stored on success, -1 on failure.

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◆ inchi_fgetsLf_V3000()

char * inchi_fgetsLf_V3000	(	char *	line,
		INCHI_IOSTREAM *	inp_stream
	)

Read a line from the input file stream, handling V3000 line continuations: Extended version of inchi_fgetsLf which is able of reading concatenated lines (ending with '-') of V3000 Molfile. Also removes "M V30 " prefix" and normalizes the rest of string.

Parameters

line	Pointer to the buffer to store the read line.
inp_stream	Pointer to the input file stream.

Returns: Pointer to the read line, or NULL on end of file or error.

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◆ IntArray_Alloc()

int IntArray_Alloc	(	INT_ARRAY *	items,
		int	nitems
	)

Initializes an INT_ARRAY structure.

Parameters

items	Pointer to the INT_ARRAY structure to initialize.
nitems	Initial number of items to allocate.

Returns: 0 on success, -1 on failure.

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◆ IntArray_Append()

int IntArray_Append	(	INT_ARRAY *	items,
		int	new_item
	)

Appends a new item to the INT_ARRAY structure.

Parameters

items	Pointer to the INT_ARRAY structure to modify.
new_item	The new item to append.

Returns: 0 on success, -1 on failure.

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◆ IntArray_AppendIfAbsent()

int IntArray_AppendIfAbsent	(	INT_ARRAY *	items,
		int	new_item
	)

Appends a new item to the INT_ARRAY structure if it is not already present.

Parameters

items	Pointer to the INT_ARRAY structure to modify.
new_item	The new item to append.

Returns: 0 on success, -1 on failure.

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◆ IntArray_DebugPrint()

void IntArray_DebugPrint ( INT_ARRAY * items )

Prints the contents of the INT_ARRAY structure for debugging purposes.

Parameters

items Pointer to the INT_ARRAY structure to print.

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◆ IntArray_Free()

void IntArray_Free ( INT_ARRAY * items )

Frees the memory allocated for the INT_ARRAY structure.

Parameters

items Pointer to the INT_ARRAY structure to free.

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◆ IntArray_ReAlloc()

int IntArray_ReAlloc ( INT_ARRAY * items )

Reallocates memory for the INT_ARRAY structure.

Parameters

items Pointer to the INT_ARRAY structure to reallocate.

Returns: 0 on success, -1 on failure.

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◆ IntArray_Reset()

void IntArray_Reset ( INT_ARRAY * items )

Resets the INT_ARRAY structure to its initial state.

Parameters

items Pointer to the INT_ARRAY structure to reset.

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◆ MolfileExtractStrucNum()

long MolfileExtractStrucNum ( MOL_FMT_HEADER_BLOCK * pHdr )

Extract the MOL file number from the header name line like "Structure #22".

Parameters

pHdr	Pointer to the header block.

Returns: The structure number.

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◆ MolfileGetXYZDimAndNormFactors()

int MolfileGetXYZDimAndNormFactors	(	MOL_FMT_DATA *	mfdata,
		int	find_norm_factors,
		double *	x0,
		double *	y0,
		double *	z0,
		double *	xmin,
		double *	ymin,
		double *	zmin,
		double *	scaler,
		int *	err,
		char *	pStrErr
	)

Get xyz dimensionality and normalization factors in the MOL file.

Parameters

mfdata	Pointer to the MOL file data structure.
find_norm_factors	Flag indicating whether to find normalization/scaling factors.
x0	Pointer to the minimum x-coordinate of the molecule.
y0	Pointer to the minimum y-coordinate of the molecule.
z0	Pointer to the minimum z-coordinate of the molecule.
xmin	Pointer to the x-coordinate (is set to 0).
ymin	Pointer to the y-coordinate (is set to 0).
zmin	Pointer to the z-coordinate (is set to 0).
scaler	Pointer to the scaling factor.
err	Pointer to the error code.
pStrErr	Pointer to the error string buffer.

Returns: number of dimensions: 0, 2, 3

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◆ MolfileHasNoChemStruc()

int MolfileHasNoChemStruc ( MOL_FMT_DATA * mfdata )

Check if the MOL file has no chemical structure.

Parameters

mfdata Pointer to the MOL file data structure.

Returns: 1 if no chemical structure, 0 otherwise.

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◆ MolfileReadAtomsBlock()

static int MolfileReadAtomsBlock	(	MOL_FMT_CTAB *	ctab,
		INCHI_IOSTREAM *	inp_file,
		int	err,
		char *	pStrErr
	)

static

Reads an atom block from input MOL file (V2000).

Parameters

ctab	Connection table data structure
inp_file	Input file
err	Error code
pStrErr	Error string

Returns: int Error code, returns 0 - no error, 4 - error: can't interpret atom block, 5 - error: can't interpret second half of atom block?

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◆ MolfileReadBondsBlock()

static int MolfileReadBondsBlock	(	MOL_FMT_CTAB *	ctab,
		INCHI_IOSTREAM *	inp_file,
		int	err,
		char *	pStrErr
	)

static

Reads a bond block from input MOL file (V2000)

Parameters

ctab	Connection table data structure
inp_file	Input file
err	Error code
pStrErr	Error string

Returns: int Error code

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◆ MolfileReadCountsLine()

static int MolfileReadCountsLine	(	MOL_FMT_CTAB *	ctab,
		INCHI_IOSTREAM *	inp_file,
		char *	pStrErr
	)

static

Reads counts line from input MOL file, includes information about the number of atoms, bonds, and atom lists, the chiral flag setting, and the Ctab version.

Parameters

ctab	Connection table data structure
inp_file	Input file
pStrErr	Error string

Returns: int Error code, returns 0 - no error, 3 - error: can't read counts line, -1 - error: out of RAM

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◆ MolfileReadDataLines()

static MOL_FMT_DATA * MolfileReadDataLines	(	INCHI_IOSTREAM *	inp_file,
		MOL_FMT_HEADER_BLOCK *	OnlyHeaderBlock,
		MOL_FMT_CTAB *	OnlyCTab,
		int	bGetOrigCoord,
		int	treat_polymers,
		int *	err,
		char *	pStrErr,
		int	bNoWarnings
	)

static

Reads header lines and connection table block from input SD or MOL file, ignore STEXT block, queries, and 3D features.

Parameters

inp_file	Input file
OnlyHeaderBlock	Output header data structure, return MOL_FMT_DATA will point to it
OnlyCTab	Output connection table data structure, return MOL_FMT_DATA will point to it
bGetOrigCoord	Flag to get original coordinates
treat_polymers	Flag to treat polymers
err	Error code
pStrErr	Error string
bNoWarnings	Flag to show warnings

Returns: MOL_FMT_DATA* returns mol file data structure, includes e.g. header block, connection table, ...

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◆ MolfileReadField()

int MolfileReadField	(	void *	data,
		int	field_len,
		int	data_type,
		char **	line_ptr
	)

Extract the 'data' in the MOL file field at given text position 'line_ptr'.

Parameters

data	Pointer to the destination buffer.
field_len	Length of the field to read. For MOL_FMT_STRING_DATA does not include trailing zero, that is actual length of the string pointed by 'data' should be at least field_len+1 bytes. For numerical data 'field_len' is length of input data field For numerical integral data field_len <= 0 means read up to first non-numeric character as strtod() does ("free format")
data_type	Type of the data to read. E.g. MOL_FMT_STRING_DATA, MOL_FMT_CHAR_INT_DATA, etc.
line_ptr	Pointer to a variable that will receive the address of the next line.

Returns: for MOL_FMT_STRING_DATA: number of bytes excluding trailing zero for all others: 1=success; 0 = empty; -1 = error

on exit *line_ptr points to the next byte after the last entered

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◆ MolfileReadHeaderLines()

static int MolfileReadHeaderLines	(	MOL_FMT_HEADER_BLOCK *	hdr,
		INCHI_IOSTREAM *	inp_file,
		char *	pStrErr
	)

static

Reads header lines from input MOL file. A MOL file can have 3 header lines: (1) the name of the molecule, (2) details about the software used and (3) a comment line.

Parameters

hdr	Output header data structure
inp_file	Input file
pStrErr	Error string

Returns: * int Error code, retuns 0 - no error, 1 - error: can't read header block name, 3 - error: can't read header block 2 line, 7 - error: cant' read header block comment line

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◆ MolfileSaveCopy()

int MolfileSaveCopy	(	INCHI_IOSTREAM *	inp_file,
		long	fPtrStart,
		long	fPtrEnd,
		FILE *	outfile,
		long	num
	)

Copy MOL-formatted data of SDF record or Molfile to another file.

Parameters

inp_file	Pointer to the input file stream.
fPtrStart	File pointer position to start copying from.
fPtrEnd	File pointer position to stop copying at.
outfile	Pointer to the output file stream.
num	Structure number to write in the header line.

Returns: last position of the output file stream.

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◆ MolfileStrnread()

int MolfileStrnread	(	char *	dest,
		char *	source,
		int	len,
		char **	first_space
	)

Read a string from a source buffer into a destination buffer.

Parameters

dest	Pointer to the destination buffer.
source	Pointer to the source buffer.
len	Length of the string to read.
first_space	Pointer to a variable that will receive the address of the first space character in the source buffer.

Returns: number of actually processed bytes excluding zero terminator.

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◆ MolfileV3000Init()

int MolfileV3000Init	(	MOL_FMT_CTAB *	ctab,
		char *	pStrErr
	)

Initialize V3000 connection table in MOL file data structure.

Parameters

ctab	Pointer to the connection table data structure.
pStrErr	Pointer to the error string buffer.

Returns: 0 on success, -1 on failure.

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◆ MolfileV3000Read3DBlock()

int MolfileV3000Read3DBlock	(	MOL_FMT_CTAB *	ctab,
		INCHI_IOSTREAM *	inp_file,
		int	err,
		char *	pStrErr
	)

Read V3000 3D constraints block in MOL file data structure from input file stream.

Parameters

ctab	Pointer to the connection table data structure.
inp_file	Pointer to the input file stream.
err	Error code.
pStrErr	Pointer to the error string buffer.

Returns: 0: Success (no error encountered, 3D block read correctly) 1: Error (e.g., missing "END 3D" marker, or other parsing errors)

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◆ MolfileV3000ReadAtomsBlock()

int MolfileV3000ReadAtomsBlock	(	MOL_FMT_CTAB *	ctab,
		INCHI_IOSTREAM *	inp_file,
		int	err,
		char *	pStrErr
	)

Read V3000 atoms block in MOL file data structure from input file stream.

Parameters

ctab	Pointer to the connection table data structure.
inp_file	Pointer to the input file stream.
err	Error code.
pStrErr	Pointer to the error string buffer.

Returns: 0 on success, -1 on failure.

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◆ MolfileV3000ReadBondsBlock()

int MolfileV3000ReadBondsBlock	(	MOL_FMT_CTAB *	ctab,
		INCHI_IOSTREAM *	inp_file,
		int	err,
		char *	pStrErr
	)

Read V3000 bonds block in MOL file data structure from input file stream.

Parameters

ctab	Pointer to the connection table data structure.
inp_file	Pointer to the input file stream.
err	Error code.
pStrErr	Pointer to the error string buffer.

Returns: 0: Success (no error, bonds block read correctly), 1: Error: No V3000 Bond block start marker ("BEGIN BOND" missing), 2: Error: Cannot read V3000 bond block line (input line missing or unreadable), 4: Error: Cannot interpret V3000 bond block line (parsing failure) Negative values: If the end-of-data marker ($$$$) is encountered, err is set to -abs(err) (e.g., -1, -2, -4) Other values: If the end marker ("END BOND") is missing, err is set to 1

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◆ MolfileV3000ReadCollections()

int MolfileV3000ReadCollections	(	MOL_FMT_CTAB *	ctab,
		INCHI_IOSTREAM *	inp_file,
		int	err,
		char *	pStrErr
	)

Read V3000 collections block in MOL file data structure from input file stream.

Parameters

ctab	Pointer to the connection table data structure.
inp_file	Pointer to the input file stream.
err	Error code.
pStrErr	Pointer to the error string buffer.

Returns: 0: Success (collections block read and parsed correctly) 7: Error in reading or interpreting V3000 collection lines (parsing failure, unexpected format, missing required fields, etc.)

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◆ MolfileV3000ReadCTABBeginAndCountsLine()

int MolfileV3000ReadCTABBeginAndCountsLine	(	MOL_FMT_CTAB *	ctab,
		INCHI_IOSTREAM *	inp_file,
		char *	pStrErr
	)

Read V3000 head (begin and counts line) of in MOL file data structure from input file stream.

Parameters

ctab	Pointer to the connection table data structure.
inp_file	Pointer to the input file stream.
pStrErr	Pointer to the error string buffer.

Returns: 0 on success, -1 on failure.

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◆ MolfileV3000ReadField()

int MolfileV3000ReadField	(	void *	data,
		int	data_type,
		char **	line_ptr
	)

Extract the 'data' in specified mol file field at given text position 'line_ptr'.

Parameters

data	Pointer to the destination buffer.
data_type	Type of the data to read. E.g. MOL_FMT_STRING_DATA, MOL_FMT_CHAR_INT_DATA, etc.
line_ptr	Pointer to the line buffer.

Returns: for MOL_FMT_STRING_DATA: number of bytes excluding trailing zero for all others: 1=success; 0 = empty

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◆ MolfileV3000ReadHapticBond()

int MolfileV3000ReadHapticBond	(	MOL_FMT_CTAB *	ctab,
		char **	line_ptr,
		int **	num_list,
		char *	pStrErr
	)

Read V3000 haptic bond information from the input line.

Parameters

ctab	Pointer to the connection table data structure.
line_ptr	Pointer to the line buffer.
num_list	Pointer to the list of numbers.
pStrErr	Pointer to the error string buffer.

Returns: Positive integer (nread > 0): Success; number of bytes/fields read from the haptic bond block. 0: No data read (rare, usually means nothing was parsed). -1: Error; parsing failed at any step (missing '(', invalid count, allocation failure, field read error, missing "ATTACH=ALL", etc.).

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◆ MolfileV3000ReadKeyword()

int MolfileV3000ReadKeyword	(	char *	key,
		char **	line_ptr
	)

Read keyword from the specified line.

Parameters

key	Pointer to the buffer to store the keyword.
line_ptr	Pointer to the line buffer.

Returns: Length of the keyword on success, -1 on failure.

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◆ MolfileV3000ReadSGroup()

int MolfileV3000ReadSGroup	(	MOL_FMT_CTAB *	ctab,
		INCHI_IOSTREAM *	inp_file,
		int	err,
		char *	pStrErr
	)

Read V3000 Sgroup information from the input file stream into the MOL file data structure.

Parameters

ctab	Pointer to the connection table data structure.
inp_file	Pointer to the input file stream.
err	Error code.
pStrErr	Pointer to the error string buffer.

Returns: 0: Success (no error encountered, SGroup read correctly) 1: Error (e.g., missing "END SGROUP" marker, or other parsing errors)

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◆ MolfileV3000ReadStereoCollection()

int MolfileV3000ReadStereoCollection	(	MOL_FMT_CTAB *	ctab,
		char **	line_ptr,
		int **	num_list,
		char *	pStrErr
	)

Read V3000 stereo collection information from the input line.

Parameters

ctab	Pointer to the connection table data structure.
line_ptr	Pointer to the line buffer.
num_list	Pointer to the list of numbers.
pStrErr	Pointer to the error string buffer.

Returns: Positive integer (nread > 0): Success; number of bytes/fields read from the stereo collection block. 0: No data read (rare, usually means nothing was parsed). -1: Error; parsing failed at any step (missing '(', invalid count, allocation failure, field read error, missing "ATTACH=ALL", etc.).

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◆ MolfileV3000ReadTailOfCTAB()

int MolfileV3000ReadTailOfCTAB	(	MOL_FMT_CTAB *	ctab,
		INCHI_IOSTREAM *	inp_file,
		int	err,
		char *	pStrErr
	)

Read V3000 tail (haptic bonds, stereo collections, Sgroups, 3D constraints, collections, end line) in to the MOL file data structure from input file stream.

Parameters

ctab	Pointer to the connection table data structure.
inp_file	Pointer to the input file stream.
err	Error code.
pStrErr	Pointer to the error string buffer.

Returns: 0: Success (no error encountered, tail of CTAB read correctly) 1: Error (e.g., missing "END CTAB" marker, or other parsing errors) 7: Error in reading or interpreting V3000 collection lines 71, 77, etc.: Error codes from sub-blocks (e.g., SGroup, 3DBlock, Collection) plus 70, indicating which sub-block failed Other positive values: Error codes from called functions (e.g., MolfileV3000ReadSGroup, MolfileV3000Read3DBlock, MolfileV3000ReadCollections) plus 70 Negative values: If an end-of-data marker ($$$$) is encountered during an error, the error code may be returned as a negative value (e.g., -1, -7, -71, etc.)

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◆ MolFmtSgroup_Create()

int MolFmtSgroup_Create	(	MOL_FMT_SGROUP **	sgroup,
		int	id,
		int	type
	)

Allocate new array Sgroup.

Parameters

sgroup	Pointer to the Sgroup structure to allocate.
id	Sgroup ID.
type	Sgroup type.

Returns: 0 on success, -1 on failure.

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◆ MolFmtSgroup_Free()

void MolFmtSgroup_Free ( MOL_FMT_SGROUP * sgroup )

Frees the memory allocated for the Sgroup.

Parameters

sgroup Pointer to the Sgroup structure to free.

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◆ MolFmtSgroups_Alloc()

int MolFmtSgroups_Alloc	(	MOL_FMT_SGROUPS *	items,
		int	nitems
	)

Allocates memory for a specified number of Sgroup objects.

Parameters

items	Pointer to the MOL_FMT_SGROUPS structure.
nitems	Number of Sgroup objects to allocate.

Returns: 0 on success, -1 on failure.

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◆ MolFmtSgroups_Append()

int MolFmtSgroups_Append	(	MOL_FMT_SGROUPS *	items,
		int	id,
		int	type
	)

Appends a new Sgroup to the array.

Parameters

items	Pointer to the MOL_FMT_SGROUPS structure.
id	Sgroup ID.
type	Sgroup type.

Returns: 0 on success, -1 on failure.

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◆ MolFmtSgroups_Free()

void MolFmtSgroups_Free ( MOL_FMT_SGROUPS * items )

Frees the memory allocated for the MOL_FMT_SGROUPS list.

Parameters

items Pointer to the MOL_FMT_SGROUPS structure.

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◆ MolFmtSgroups_GetIndexBySgroupId()

int MolFmtSgroups_GetIndexBySgroupId	(	int	id,
		MOL_FMT_SGROUPS *	items
	)

Gets the index of a Sgroup by its ID.

Parameters

id	Sgroup ID.
items	Pointer to the MOL_FMT_SGROUPS structure.

Returns: Index of the Sgroup on success, -1 on failure.

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◆ MolFmtSgroups_ReAlloc()

int MolFmtSgroups_ReAlloc ( MOL_FMT_SGROUPS * items )

Expand array of Sgroups.

Parameters

items Pointer to the MOL_FMT_SGROUPS structure.

Returns: 0 on success, -1 on failure.

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◆ NumLists_Alloc()

int NumLists_Alloc	(	NUM_LISTS *	num_lists,
		int	nlists
	)

Allocates memory for a specified number of numeric lists.

Parameters

num_lists	Pointer to the NUM_LISTS structure.
nlists	Number of lists to allocate.

Returns: 0 on success, -1 on failure.

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◆ NumLists_Append()

int NumLists_Append	(	NUM_LISTS *	num_lists,
		int *	list
	)

Push new item to the end of array.

Parameters

num_lists	Pointer to the NUM_LISTS structure.
list	Pointer to the list of integers to append.

Returns: 0 on success, -1 on failure.

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◆ NumLists_Free()

void NumLists_Free ( NUM_LISTS * num_lists )

Frees the memory allocated for the numeric list.

Parameters

num_lists Pointer to the NUM_LISTS structure.

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◆ NumLists_ReAlloc()

int NumLists_ReAlloc ( NUM_LISTS * num_lists )

Reallocates memory for the numeric lists.

Parameters

num_lists Pointer to the NUM_LISTS structure.

Returns: 0 on success, -1 on failure.

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◆ ReadMolfile()

MOL_FMT_DATA * ReadMolfile	(	INCHI_IOSTREAM *	inp_file,
		MOL_FMT_HEADER_BLOCK *	OnlyHeaderBlock,
		MOL_FMT_CTAB *	OnlyCTab,
		int	bGetOrigCoord,
		int	treat_polymers,
		int	pseudos_allowed,
		char *	pname,
		int	lname,
		unsigned long *	Id,
		const char *	pSdfLabel,
		char *	pSdfValue,
		int *	err,
		char *	pStrErr,
		int	bNoWarnings
	)

Reads a substance text block.

Parameters

ctab	Connection table data structure
inp_file	Input file
err	Error code
pStrErr	Error string

Returns: int Error code

Read MOL file data in to data structures.

Parameters

inp_file	Pointer to the input file stream.
OnlyHeaderBlock	Pointer to the header block to read.
OnlyCTab	Pointer to the connection table to read.
bGetOrigCoord	Flag indicating whether to get original coordinates.
treat_polymers	Flag indicating whether to treat polymers.
pseudos_allowed	Flag indicating whether pseudo atoms are allowed.
pname	Pointer to the name buffer.
lname	Length of the name buffer.
Id	Pointer to the ID buffer.
pSdfLabel	Pointer to the SDF label buffer.
pSdfValue	Pointer to the SDF value buffer.
err	Pointer to the error code.
pStrErr	Pointer to the error string buffer.
bNoWarnings	Flag indicating whether to suppress warnings.

Returns: MOL_FMT_DATA*

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◆ SDFileExtractCASNo()

unsigned long SDFileExtractCASNo ( char * line )

Extract CAS number from the given line.

Parameters

line	Pointer to the line containing the CAS number.

Returns: The extracted CAS number, or 0 if not found or invalid.

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◆ SDFileIdentifyLabel()

int SDFileIdentifyLabel	(	char *	inp_line,
		const char *	pSdfLabel
	)

Identify if the given line matches the specified SDF label.

Parameters

inp_line	Pointer to the input line.
pSdfLabel	Pointer to the SDF label to match.

Returns: SDF_DATA_HEADER_USER: The label matches the user-specified label (pSdfLabel). SDF_DATA_HEADER_NAME: The label is "NAME". SDF_DATA_HEADER_COMMENT: The label is "COMMENT". SDF_DATA_HEADER_CAS: The label is "CAS". SDF_DATA_HEADER: The label does not match any of the above (default case).

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◆ SDFileSkipExtraData()

int SDFileSkipExtraData	(	INCHI_IOSTREAM *	inp_file,
		unsigned long *	CAS_num,
		char *	comment,
		int	lcomment,
		char *	name,
		int	lname,
		int	prev_err,
		const char *	pSdfLabel,
		char *	pSdfValue,
		char *	pStrErr,
		int	bNoWarnings
	)

Skip extra data in SDF file after the MOL file data.

Parameters

inp_file	Pointer to the input file stream.
CAS_num	Pointer to the variable to store the CAS number.
comment	Pointer to the buffer to store the comment.
lcomment	Length of the comment buffer.
name	Pointer to the buffer to store the name.
lname	Length of the name buffer.
prev_err	Previous error code.
pSdfLabel	Pointer to the SDF label buffer.
pSdfValue	Pointer to the SDF value buffer.
pStrErr	Pointer to the error string buffer.
bNoWarnings	Flag indicating whether to suppress warnings.

Returns: 0: Success; extra SDF data was skipped without errors. 3: Unexpected SData header line (unexpected contents or format). 5: Only blank lines encountered (all lines empty). 9: Error occurred, but successfully bypassed to the next structure ($$$$ marker found); non-fatal, warning issued. Other values: The function may propagate the value of prev_err if set before entering the loop.

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Data Structures

Macros

Typedefs

Functions

Macro Definition Documentation

◆ INCHI_US_CHAR_DEF

◆ ISOTOPIC_SHIFT_FLAG

◆ MOL_FMT_ABSENT

◆ MOL_FMT_CHAR_INT_DATA

◆ MOL_FMT_CPSS

◆ MOL_FMT_DOUBLE_DATA

◆ MOL_FMT_FLOAT_DATA

◆ MOL_FMT_INPLINELEN

◆ MOL_FMT_INT_DATA

◆ MOL_FMT_JUMP_TO_RIGHT

◆ MOL_FMT_LONG_INT_DATA

◆ MOL_FMT_M_CONN_EU

◆ MOL_FMT_M_CONN_HH

◆ MOL_FMT_M_CONN_HT

◆ MOL_FMT_M_CONN_NON

◆ MOL_FMT_M_SST_ALT

◆ MOL_FMT_M_SST_BLK

◆ MOL_FMT_M_SST_NON

◆ MOL_FMT_M_SST_RAN

◆ MOL_FMT_M_STY_COP

◆ MOL_FMT_M_STY_CRO

◆ MOL_FMT_M_STY_MER

◆ MOL_FMT_M_STY_MOD

◆ MOL_FMT_M_STY_MON

◆ MOL_FMT_M_STY_NON

◆ MOL_FMT_M_STY_SRU

◆ MOL_FMT_MAX_VALUE_LEN

◆ MOL_FMT_MAXLINELEN

◆ MOL_FMT_PRESENT

◆ MOL_FMT_QUERY

◆ MOL_FMT_REACT

◆ MOL_FMT_SHORT_INT_DATA

◆ MOL_FMT_STRING_DATA

◆ MOL_FMT_V3000_INPLINELEN

◆ MOL_FMT_V3000_MAXFIELDLEN

◆ MOL_FMT_V3000_MAXLINELEN

◆ MOL_FMT_V3000_STEABS

◆ MOL_FMT_V3000_STENON

◆ MOL_FMT_V3000_STERAC

◆ MOL_FMT_V3000_STEREL

◆ SD_FMT_END_OF_DATA

Typedef Documentation

◆ INT_ARRAY

◆ MOL_FMT_ATOM

◆ MOL_FMT_BOND

◆ MOL_FMT_CTAB

◆ MOL_FMT_DATA

◆ MOL_FMT_HEADER_BLOCK

◆ MOL_FMT_SGROUP

◆ MOL_FMT_SGROUPS

◆ MOL_FMT_v3000

◆ NUM_LISTS

◆ S_CHAR

◆ U_CHAR

Function Documentation

◆ DeleteMolfileV3000Info()

◆ FreeMolfileData()

◆ get_V3000_input_line_to_strbuf()

◆ inchi_fgetsLf_V3000()

◆ IntArray_Alloc()

◆ IntArray_Append()

◆ IntArray_AppendIfAbsent()

◆ IntArray_DebugPrint()

◆ IntArray_Free()

◆ IntArray_ReAlloc()

◆ IntArray_Reset()

◆ MolfileExtractStrucNum()

◆ MolfileGetXYZDimAndNormFactors()

◆ MolfileHasNoChemStruc()

◆ MolfileReadAtomsBlock()

◆ MolfileReadBondsBlock()

◆ MolfileReadCountsLine()

◆ MolfileReadDataLines()

◆ MolfileReadField()

◆ MolfileReadHeaderLines()