#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.

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)
	Read MOL file data in to data structures.

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)

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

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)

MOL_FMT_DATA *	FreeMolfileData (MOL_FMT_DATA *mfdata)

int	MolfileV3000Init (MOL_FMT_CTAB ctab, char pStrErr)

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

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

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

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

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

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

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

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

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

int	DeleteMolfileV3000Info (MOL_FMT_v3000 *v3000)

char *	inchi_fgetsLf_V3000 (char line, INCHI_IOSTREAM inp_stream)

int	get_V3000_input_line_to_strbuf (INCHI_IOS_STRING buf, INCHI_IOSTREAM inp_stream)

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

int	MolfileV3000ReadKeyword (char key, char *line_ptr)

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)

int	SDFileIdentifyLabel (char inp_line, const char pSdfLabel)

unsigned long	SDFileExtractCASNo (char *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.
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 )

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◆ FreeMolfileData()

MOL_FMT_DATA * FreeMolfileData ( MOL_FMT_DATA * mfdata )

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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
	)

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◆ inchi_fgetsLf_V3000()

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

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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
	)

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◆ MolfileHasNoChemStruc()

int MolfileHasNoChemStruc ( MOL_FMT_DATA * mfdata )

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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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◆ MolfileSaveCopy()

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

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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
	)

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◆ MolfileV3000Read3DBlock()

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

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◆ MolfileV3000ReadAtomsBlock()

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

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◆ MolfileV3000ReadBondsBlock()

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

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◆ MolfileV3000ReadCollections()

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

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◆ MolfileV3000ReadCTABBeginAndCountsLine()

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

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◆ MolfileV3000ReadField()

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

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◆ MolfileV3000ReadHapticBond()

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

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◆ MolfileV3000ReadKeyword()

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

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◆ MolfileV3000ReadSGroup()

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

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◆ MolfileV3000ReadStereoCollection()

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

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◆ MolfileV3000ReadTailOfCTAB()

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

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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
	)

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 )

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◆ SDFileIdentifyLabel()

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

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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
	)

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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()

◆ MolfileReadField()

◆ MolfileSaveCopy()

◆ MolfileStrnread()

◆ MolfileV3000Init()

◆ MolfileV3000Read3DBlock()

◆ MolfileV3000ReadAtomsBlock()