#include <stdio.h>
#include <stdlib.h>
#include "bcf_s.h"

Include dependency graph for mode.h:

Data Structures
struct	tagOutputString

struct	tagOutputStream

Macros
#define	TARGET_PLATFORM "Linux"

#define	BUILD_WITH_ENG_OPTIONS 0

#define	BUILD_WITH_AMI 1

#define	ADD_CMLPP 0

#define	COMPILE_ANSI_ONLY

#define	INCHI_VERSION "1"

#define	INCHI_NAME "InChI"

#define	INCHI_NAM_VER_DELIM "="

#define	INCHI_OPTION_PREFX '-'

#define	INCHI_PATH_DELIM '/'

#define	INCHI_ALT_OPT_PREFIX '-'

#define	INCHI_ACD_LABS_PREFIX '-'

#define	bRELEASE_VERSION 1 /* 1=> release version; comment out to disable */

#define	RELEASE_IS_FINAL 1 /* final release */

#define	DISPLAY_DEBUG_DATA_C_POINT 0 /* disabled release version for now */

#define	DISPLAY_ORIG_AT_NUMBERS 1 /* 1 => in an uncanonicalized components display orig. atom numbers (default) */

#define	DISPLAY_ZZ_AS_STAR 1

#define	FIX_ChCh_STEREO_CANON_BUG 1 /* 1=> (NEEDED) */

#define	ADD_ChCh_STEREO_CANON_CHK 0 /* 1 is NOT needed; let it always be 0 */

#define	FIX_ChCh_CONSTIT_CANON_BUG 1 /* 1=> (NEEDED) */

#define	FIX_EITHER_STEREO_IN_AUX_INFO 1 /* 1=> fix bug: Either stereobond direction in Aux_Info; 0=> do not fix */

#define	FIX_NORM_BUG_ADD_ION_PAIR 1 /* 1=> (NEEDED) fix bug: Miscount number of charges when creating an ion pair */

#define	FIX_REM_PROTON_COUNT_BUG 1 /* 1=> (NEEDED) check for number of actually removed protons and issue an error if mismatch */

#define	FIX_READ_AUX_MEM_LEAK 1

#define	FIX_READ_LONG_LINE_BUG 1 /* 1=> (NEEDED) prevent failure when reading AuxInfo and InChI is too long */

#define	FIX_N_V_METAL_BONDS_GPF 1 /* 1=> (NEEDED) InChI v1 GPF bug fix */

#define	BNS_RAD_SEARCH 1 /* 1=> prevent normalization failures due to radical centers */

#define	FIX_ODD_THINGS_REM_Plus_BUG 0

#define	FIX_N_MINUS_NORN_BUG 0

#define	FIX_CANCEL_CHARGE_COUNT_BUG 0

#define	FIX_2D_STEREO_BORDER_CASE 0

#define	FIX_REM_ION_PAIRS_Si_BUG 0

#define	FIX_STEREO_SCALING_BUG 0

#define	FIX_EMPTY_LAYER_BUG 0

#define	FIX_EITHER_DB_AS_NONSTEREO 0

#define	FIX_BOND23_IN_TAUT 0

#define	FIX_TACN_POSSIBLE_BUG 0

#define	FIX_KEEP_H_ON_NH_ANION 0

#define	FIX_AVOID_ADP 0

#define	FIX_NUM_TG 0 /* increase number of t-groups for isothiocyanate */

#define	FIX_CPOINT_BOND_CAP2 0

#define	FIX_ISO_FIXEDH_BUG 1 /* (2007-09-24) 1=> Fix bug: missing fixed-H iso segment in case of single removed D(+) */

#define	FIX_ISO_FIXEDH_BUG_READ 0 /* (2007-09-24) 1=> Accommodate this InChI bug in reading InChI */

#define	FIX_DALKE_BUGS 1

#define	FIX_TRANSPOSITION_CHARGE_BUG 1 /* (2008-01-02) fix bug that leads to missed charge in some cases when /o is present */

#define	FIX_I2I_STEREOCONVERSION_BUG 1 /* (2008-03-06) 1=> Fix bug of i2i conversion SAbs-->(SRel\|\|Srac) */

#define	FIX_I2I_STEREOCONVERSION_BUG2 1 /* (2008-04-02) 1=> Fix bug of i2i conversion (missed empty /t) */

#define	FIX_I2I_STEREOCONVERSION_BUG3 1 /* (2008-04-10) 1=> Fix bug of i2i conversion */

#define	FIX_TERM_H_CHRG_BUG 1 /* (2008-06-06) IPl) */

#define	FIX_AROM_RADICAL 1 /* (2011-05-09) 1=> Fix bug which leads for different InChI */

#define	FIX_STEREOCOUNT_ERR 1 /* (2018-01-09) Supplied by DT */

#define	FIX_IMPOSSIBLE_H_ISOTOPE_BUG 1 /* (2018-01-25) Bug reported by Andrew Dalke, inchi-discuss */

#define	FIX_OLEAN_SPIRO_CHIRALITY_DETECTION_BUG 1

#define	FIX_RENUM_BUG_FOR_CASE_OF_ACIDIC_OH_AT_P_PLUS 1

#define	CHECK_STRTOL_ATNUMB 1

#define	DISABLE_READ_COMPRESSED_INCHI 1

#define	FIX_GAF_2019_1 1

#define	FIX_GAF_2019_2 1

#define	FIX_GAF_2020_GENERIC 1

#define	FIX_OSS_FUZZ_25604 1

#define	FIX_GAF_2020_25607 1

#define	FIX_GAF_2020_25726 1

#define	FIX_GAF_2020_25741 1

#define	FIX_OSS_FUZZ_30162_30343 1

#define	FIX_OSS_FUZZ_25734_28139 1

#define	FIX_CURE53_ISSUE_OOB_ALREADY_HAVE_THIS_MESSAGE 1

#define	FIX_CURE53_ISSUE_HEAP_BUFFER_OVERFLOW_INCHITOINPATOM 1

#define	FIX_CURE53_ISSUE_NULL_DEREFERENCE_MAKE_A_COPY_OF_T_GROUP_INFO 1

#define	FIX_GAF_2019_3 1

#define	FIX_ONE_LINE_INCHI_INPUT_CONVERSION_ISSUE 1

#define	ALLOW_EMPTY_INCHI_AS_INPUT 1 /* Allow "InChI=1//" and standard/beta analogues in input */

#define	I2S_MODIFY_OUTPUT 1 /* 1=> Allow various InChI2InChI output types from cInChI */

#define	FIX_NP_MINUS_BUG 1 /* 2010-03-11 DT Fix for bug reported by Timo Boehme */

#define	FIX_ADJ_RAD 0

#define	SDF_OUTPUT_V2000 1 /* 1=>always output V2000 SDfile, 0=>only if needed */

#define	SDF_OUTPUT_DT 1 /* 1=> all option -SdfAtomsDT to output D and T into SDfile */

#define	CHECK_AROMBOND2ALT 1 /* 1=> check whether arom->alt bond conversion succeeded */

#define	READ_INCHI_STRING 1 /* 1=> input InChI string and process it */

#define	INCLUDE_NORMALIZATION_ENTRY_POINT 0

#define	KETO_ENOL_TAUT 1 /* include keto-enol tautomerism */

#define	TAUT_15_NON_RING 1 /* 1,5 tautomerism with endpoints not in ring */

#define	TAUT_PT_22_00 1 /* tautomerism rule PT_22_00 */

#define	TAUT_PT_16_00 1 /* tautomerism rule PT_16_00 */

#define	TAUT_PT_06_00 1 /* tautomerism rule PT_06_00 */

#define	TAUT_PT_39_00 1 /* tautomerism rule PT_39_00 */

#define	TAUT_PT_13_00 1 /* tautomerism rule PT_13_00 */

#define	TAUT_PT_18_00 1 /* tautomerism rule PT_18_00 */

#define	UNDERIVATIZE 1 /* split to possible underivatized fragments */

#define	RING2CHAIN 1 /* open rings R-C(-OH)-O-R => R-C(=O) OH-R */

#define	UNDERIVATIZE_REPORT 1 /* if SdfValue found, add to SdfValue a list of removed deriv. agents */

#define	FIX_UNDERIV_TO_SDF /* prevent bond normalization if underivatization result goes to SDF 2013-05-10 DCh */

#define	UNDERIV_RN_AcMe /* 2r1c3 R-N(-X)--C(=O)Me => R-N(-X)H: DERIV_BRIDGE_tN, X is not H */

#define	UNDERIV_RNH_AcMe /* 2r1c3 R-NH--C(=O)Me => R-NH2: DERIV_BRIDGE_NH */

#define	UNDERIV_RO_COX_Me /* 3r1c1 RO-C(=O)Me => ROH: create alcohols from acetates DERIV_RO_COX */

#define	UNDERIV_RO_COX_BENZOATES /* 3r1c2 create alcohols from benzoates DERIV_RO_COX */

#define	UNDERIV_RO_COX_PENTAFLOUROBENZOATES /* 3r1c3 create alcohols from pentafluorobenzoates DERIV_RO_COX -C(=O)C6F5*/

#define	UNDERIV_OOB_nButyl /* 4r2c1 DERIV_RING_O_OUTSIDE_PRECURSOR: 5 at, n-Butyl */

#define	UNDERIV_X_OXIME_TBDMS /* 5r2c3 DERIV_X_OXIME: >C=N--O-TBDMS */

#define	UNDERIV_X_OXIME_TMS /* 5r2c2 DERIV_X_OXIME: >C=N--O-TMS */

#define	UNDERIV_PYRROLIDIDES /* 7r1c1 DERIV_RING2_PRRLDD_OUTSIDE_PRECUR */

#define	UNDERIV_ADD_EXPLICIT_H /* Underiv: add removed explict H after underivatization */

#define	HAL_ACID_H_XCHG 1 /* allow iso H exchange to HX (X=halogen) and H2Y (Y=halcogen) */

#define	CANON_FIXH_TRANS 1 /* produce canonical fixed-H transposition */

#define	STEREO_WEDGE_ONLY 1 /* 1=> only pointed ends stereo bonds define stereo; 0=> both ends */

#define	REMOVE_ION_PAIRS_EARLY 1 /* 1=> new preprocessing: step 1 before disconnecting metals in fix_odd_things() */

#define	REMOVE_ION_PAIRS_DISC_STRU 1 /* 1=> new post-preprocessing: remove charhes after metal disconnection */

#define	REMOVE_ION_PAIRS_FIX_BONDS 1 /* 1=> step2: set unchangeable bonds around removed ion pairs */

#define	S_VI_O_PLUS_METAL_FIX_BOND 1 /* 1=> count double bond M-O(+)=S as O=S in S(VI) ans S(VIII) fixing bonds */

#define	N_V_STEREOBONDS 1 /* 1=> detect stereobonds incident to N(V); 0 => don't */

#define	REMOVE_ION_PAIRS_ORIG_STRU

#define	DISCONNECT_SALTS 1 /* 1=>disconnect metal atoms from salts, 0=>dont / / djb-rwth: default 1 */

#define	TEST_REMOVE_S_ATOMS

#define	CHARGED_SALTS_ONLY

#define	BNS_PROTECT_FROM_TAUT 1 /* 1=> do not allow testing of bonds to acetyl or nitro */

#define	BNS_MARK_EDGE_2_DISCONNECT 1 /* 1=> mark edge as temp forbidden instead of disconnection */

#define	REPLACE_ALT_WITH_TAUT 1 /* 1 => replace alt bonds with tautomeric bonds in case of standard t-groups */

#define	MOVE_CHARGES 1 /* 1 => take moveable charges into account */

#define	NEUTRALIZE_ENDPOINTS 1 /* 1 => before checking whether an H is moveable make 2 endpoints neutral */

#define	FIX_H_CHECKING_TAUT 1 /* 1 => Fix moveable H or (-) before checking if taut. exchange is possible */

#define	ALWAYS_ADD_TG_ON_THE_FLY 1 /* 1 => disables radical calcellation by taut-charge movement */

#define	IGNORE_SINGLE_ENDPOINTS 1 /* 1 => see FindAccessibleEndPoints() in INChITaut.c */

#define	INCL_NON_SALT_CANDIDATATES

#define	SALT_WITH_PROTONS 1 /* 1=> (new new) include proton migrarion C-SH, =C-OH, NH+ */

#define	OPPOSITE_CHARGE_IN_CGROUP 1 /* 1=> allow N(-) in (+) c-group, 0=> disallow */

#define	MOVE_PPLUS_TO_REMOVE_PROTONS

#define	ADD_MOVEABLE_O_PLUS 1 /* 1=> allow charges on O(+) to move */

#define	DISCONNECT_METALS 1 /* make main layer disconnected / / djb-rwth: default 1 */

#define	RECONNECT_METALS

#define	CHECK_METAL_VALENCE 0 /* 1=> disconnect only metals that have abnormal valence */

#define	bREUSE_INCHI

#define	OUTPUT_CONNECTED_METAL_ONLY

#define	EMBED_REC_METALS_INCHI

#define	bOUTPUT_ONE_STRUCT_TIME 1 /* 1 => output each structure time (non-release only) */

#define	INCHI_NUM 2 /* = array size; member indexes: */

#define	INCHI_BAS 0 /* 0 => disconnected or normal */

#define	INCHI_REC 1 /* 1 => reconnected */

#define	TAUT_NUM 2 /* = array size; member indexes: */

#define	TAUT_NON 0 /* 0 => normal structure */

#define	TAUT_YES 1 /* 1 => tautomeric */

#define	TAUT_INI 2 /* 2 => intermediate tautomeric structure */

#define	ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */

#define	OUT_N1 0 /* non-tautomeric only */

#define	OUT_T1 1 /* tautomeric if present otherwise non-tautomeric */

#define	OUT_NT 2 /* only non-taut representations of tautomeric */

#define	OUT_TN

#define	OUT_NN 4 /* only non-taut representations: non-taut else tautomeric */

#define	NEW_STEREOCENTER_CHECK 1 /* 1 => add new stereocenter categories (see bCanInpAtomBeAStereoCenter(...)) */

#define	MIN_SB_RING_SIZE 8 /* do not assume stereo bonds in rings containing 3..MIN_SB_RING_SIZE-1 atoms */

#define	REMOVE_KNOWN_NONSTEREO 1 /* 1=> check in advance known stereo to remove parities from non-stereogenic elements */

#define	REMOVE_CALC_NONSTEREO 1 /* 1=> check new stereo numberings to remove parities from non-stereogenic elements */

#define	PROPAGATE_ILL_DEF_STEREO 1 /* 1=> if at least one of the pair of constitutionally identical (far) neighbors */

#define	ONLY_DOUBLE_BOND_STEREO 0 /* 1=> no alt bond stereo, no taut. bond attachment to stereo bond */

#define	ONE_BAD_SB_NEIGHBOR 1 /* 1 => allow 1 "bad" bond type neighbor to a stereobond atom. 2004-06-02 */

#define	BREAK_ONE_MORE_SC_TIE 1 /* break one more tie when comparing possible stereocenter neighbors */

#define	BREAK_ALSO_NEIGH_TIE 0 /* post 1.12Beta 2004-08-20: if fixed neighbor has equ neighbors, fix the one with smaller canon. rank */

#define	BREAK_ALSO_NEIGH_TIE_ROTATE 1 /* post 1.12Beta 2004-09-02: break the second in 2nd psition; 1 works, 0 does not (example:MFCD01085607) */

#define	STEREO_CENTER_BONDS_NORM 1 /* set length of the bonds around a stereocenter = 1 before getting the parity */

#define	STEREO_CENTER_BOND4_NORM 0 /* set length of the added bond around a stereocenter = 1 before getting the parity */

#define	NORMALIZE_INP_COORD 0 /* 0=>keep unchanged, 1 => make atom coordinates integer by normalizing to avg bond len 20 */

#define	STEREO_WEDGE_ONLY 1 /* 1=> only pointed ends stereo bonds define stereo; 0=> both ends 1.12Beta */

#define	CHECK_C2v_S4_SYMM 0 /* post-1.12Beta 1=> check if a stereocenter has C2v or S4 symmetry; 0=>old mode */

#define	EQL_H_NUM_TOGETHER 1 /* 1=> output 1-3,5H2 intead of 1-3H2,5H2 (CT_MODE_EQL_H_TOGETHER) */

#define	ABC_CT_NUM_CLOSURES 1 /* 1=> in coinnections compressed format output decimal number of closures instead of '-' */

#define	SINGLET_IS_TRIPLET

#define	FIND_CANON_NE_EQUITABLE 0 /* 0=>normal mode */

#define	EXTR_KNOWN_USED_TO_REMOVE_PARITY 0x000001

#define	EXTR_CALC_USED_TO_REMOVE_PARITY 0x000002

#define	EXTR_2EQL2CENTER_TO_REMOVE_PARITY 0x000004

#define	EXTR_HAS_ATOM_WITH_DEFINED_PARITY 0x000008

#define	EXTR_REMOVE_PARITY_WARNING 0x000010

#define	EXTR_SALT_WAS_DISCONNECTED 0x000020

#define	EXTR_SALT_PROTON_MOVED 0x000040

#define	EXTR_SALT_PROTON_MOVE_ERR_WARN 0x000080

#define	EXTR_METAL_WAS_DISCONNECTED 0x000100

#define	EXTR_METAL_WAS_NOT_DISCONNECTED 0x000200

#define	EXTR_NON_TRIVIAL_STEREO 0x000400 /* (Inv != Abs stereo) && (parities can't be obtained by inverting them) */

#define	EXTR_UNUSUAL_VALENCES 0x000800

#define	EXTR_HAS_METAL_ATOM 0x001000

#define	EXTR_TEST_TAUT3_SALTS_DONE 0x002000 /* non-oxygen t-points used to discover tautomerism of merged t-groups */

#define	EXTR_CANON_NE_EQUITABLE 0x004000 /* find structures where canonical partition is different from equitable */

#define	EXTR_HAS_PROTON_PN 0x008000 /* has movable H+ attached to N or P */

#define	EXTR_HAS_FEATURE 0x010000 /* found a feature */

#define	EXTR_TAUT_TREATMENT_CHARGES 0x020000 /* tautomeric treatment of charges */

#define	EXTR_TRANSPOSITION_EXAMPLES 0x040000 /* extract structures that have different mobile-H and fixed-H orders */

#define	EXTR_MASK 0 /EXTR_TAUT_TREATMENT_CHARGES/ /(EXTR_HAS_FEATURE)/ /(EXTR_UNUSUAL_VALENCES \| EXTR_HAS_METAL_ATOM)/ /* 0 to disable */

#define	EXTR_FLAGS 0 /EXTR_TAUT_TREATMENT_CHARGES/ /(EXTR_HAS_FEATURE)/ /(EXTR_HAS_PROTON_PN)/ /(EXTR_UNUSUAL_VALENCES)/ /(EXTR_CANON_NE_EQUITABLE)/ /(EXTR_TEST_TAUT3_SALTS_DONE)/ /(EXTR_HAS_METAL_ATOM)/ /* (EXTR_NON_TRIVIAL_STEREO)/ /(EXTR_METAL_WAS_DISCONNECTED)/ / (EXTR_REMOVE_PARITY_WARNING)/ /(EXTR_HAS_ATOM_WITH_DEFINED_PARITY) */

#define	TAUT_TROPOLONE_7 1 /* 1=> tautomeric 7-member rings ON */

#define	TAUT_TROPOLONE_5 1 /* 1=> taut. similar to tropolone, 5-member ring */

#define	TAUT_4PYRIDINOL_RINGS 1 /* 1=> OH-C5H4N rings tautomerism */

#define	TAUT_PYRAZOLE_RINGS 1 /* 1=> tautomerizm in pyrazole rings */

#define	TAUT_IGNORE_EQL_ENDPOINTS

#define	TAUT_RINGS_ATTACH_CHAIN 1 /* 1=> allow only chain attachments to tautomeric endpoints */

#define	FIND_RING_SYSTEMS 1 /* 1 => find and mark ring systems, blocks, cut-vertices */

#define	FIND_RINS_SYSTEMS_DISTANCES 0 /* 1 => find ring system and atom distance from terminal */

#define	USE_DISTANCES_FOR_RANKING 0 /* 1 => rank ring systems according to distances from terminal */

#define	DISPLAY_RING_SYSTEMS 0 /* 1 => for debug only; displays: */

#define	bOUTPUT_ONE_STRUCT_TIME 0

#define	TAUT_OTHER 1

#define	APPLY_IMPLICIT_H_DOWN_RULE 0 /* 1=> if 3 non-H atoms around stereocenter are in same plane */

#define	ALLOW_TAUT_ATTACHMENTS_TO_STEREO_BONDS 1 /* 1=> consider bond in an alternating circuit stereogenic */

#define	IGNORE_TGROUP_WITHOUT_H 1 /* ignore tautomeric groups containing charges only */

#define	REMOVE_TGROUP_CHARGE 0 /* 0: do not remove charge information from tautomeric groups */

#define	INCHI_T_NUM_MOVABLE 2

#define	USE_AUX_RANKING 1 /* 1=> get auxiliary ranking to accelerate canonicalization of H layers */

#define	USE_AUX_RANKING_ALL 1 /* 1=> include all vertices in CellGetMinNode() selection 0=> only vertices with highest ranks */

#define	USE_ISO_SORT_KEY_HFIXED

#define	REL_RAC_STEREO_IGN_1_SC 0 /* 1=> drop from InChI sp3 stereo in components that have a single stereocenter */

#define	CMODE_CT 0x000001

#define	CMODE_ISO 0x000002

#define	CMODE_ISO_OUT 0x000004 /* obsolete ? */

#define	CMODE_STEREO 0x000008

#define	CMODE_ISO_STEREO 0x000010

#define	CMODE_TAUT 0x000020

#define	CMODE_NOEQ_STEREO 0x000040 /* 5-24-2002: do not use stereo equivalence to accelerate */

#define	CMODE_REDNDNT_STEREO 0x000080 /* 6-11-2002: do not check for redundant stereo elements */

#define	CMODE_NO_ALT_SBONDS 0x000100 /* 6-14-2002: do not assign stereo to alternating bonds */

#define	CMODE_RELATIVE_STEREO 0x000200 /* REL All Relative Stereo */

#define	CMODE_RACEMIC_STEREO 0x000400 /* RAC All Racemic Stereo */

#define	CMODE_SC_IGN_ALL_UU 0x000800 /* IAUSC Ignore stereocenters if All Undef/Unknown */

#define	CMODE_SB_IGN_ALL_UU 0x001000 /* IAUSC Ignore stereobonds if All Undef/Unknown */

#define	CANON_MODE_CT (CMODE_CT)

#define	CANON_MODE_TAUT (CMODE_CT\|CMODE_TAUT)

#define	CANON_MODE_ISO (CMODE_CT\|CMODE_ISO\|CMODE_ISO_OUT)

#define	CANON_MODE_STEREO (CMODE_CT\|CMODE_STEREO)

#define	CANON_MODE_ISO_STEREO (CMODE_CT\|CMODE_ISO\|CMODE_ISO_OUT\|CMODE_ISO_STEREO)

#define	CANON_MODE_MASK 0x00FF /* used to determine canonicalization mode */

#define	CT_ATOMID_DONTINCLUDE 1

#define	CT_ATOMID_IS_INITRANK 2

#define	CT_ATOMID_IS_CURRANK 3

#define	CANON_TAUTOMERS 1 /* 1=> process tautomers */

#define	HYDROGENS_IN_INIT_RANKS 1 /* 1=> include num_H in initial ranking */

#define	DOUBLE_BOND_NEIGH_LIST 0 /* 1 => include double bond neighbor in NeighList 2 times */

#define	INCL_NON_6AROM 1 /* 1 => mark all arom. bonds; 0=>mark arom. bonds only in 6-member rings */

#define	CT_SMALLEST /* minimal CT */

#define	CT_NEIGH_SMALLER /* in CT, include neighbors with smaller ranks */

#define	CT_ATOMID CT_ATOMID_IS_CURRANK /CT_ATOMID_DONTINCLUDE /

#define	CT_NEIGH_INCREASE /* in CT, neighbors ranks increase */

#define	USE_SYMMETRY_TO_ACCELERATE 1 /1 => for fast CT canonicalization, to avoid full enumeration /

#define	CT_GREATER_THAN >

#define	CT_INITVALUE ~0

#define	BEST_PARITY 1 /* odd */

#define	WORSE_PARITY 2

#define	CT_NEIGH_SMALLER_THAN <

#define	ALL_ALT_AS_AROMATIC 1 /* 1 => all altrnate bonds (even in cyclooctateraene) treat as aromatic */

#define	ANY_ATOM_IN_ALT_CYCLE 1 /* 1=> accept any atom in alternating bond circuit, 0=>only some */

#define	EXCL_ALL_AROM_BOND_PARITY 0 /* 1 => any arom atom cannot belong to stereo bond. */

#define	ADD_6MEMB_AROM_BOND_PARITY 1 /* 1 => all arom bonds are stereo bonds */

#define	MAX_NUM_STEREO_BONDS 3

#define	MAX_NUM_STEREO_BOND_NEIGH 3

#define	MIN_NUM_STEREO_BOND_NEIGH 2

#define	MAX_NUM_STEREO_ATOM_NEIGH 4

#define	STEREO_AT_MARK 8 /* > MAX_NUM_STEREO_BONDS */

#define	DRAW_AROM_TAUT 1 /* 1=> draw distinct aromatic & tautomer bonds, 0=> don't */

#define	TG_FLAG_TEST_TAUT__ATOMS 0x00000001 /* find regular tautomerism */

#define	TG_FLAG_DISCONNECT_SALTS 0x00000002 /* DISCONNECT_SALTS disconnect */

#define	TG_FLAG_TEST_TAUT__SALTS 0x00000004 /* DISCONNECT_SALTS if possible find long-range H/(-) taut. on =C-OH, >C=O */

#define	TG_FLAG_MOVE_POS_CHARGES 0x00000008 /* MOVE_CHARGES allow long-range movement of N(+), P(+) charges */

#define	TG_FLAG_TEST_TAUT2_SALTS 0x00000010 /* TEST_REMOVE_S_ATOMS multi-attachement long-range H/(-) taut. on =C-OH, >C=O */

#define	TG_FLAG_ALLOW_NO_NEGTV_O 0x00000020 /* CHARGED_SALTS_ONLY=0 (debug) find long-range H-only tautomerism on =C-OH, >C=O */

#define	TG_FLAG_MERGE_TAUT_SALTS 0x00000040 /* DISCONNECT_SALTS merge all "salt"-t-groups and other =C-OH into one t-group */

#define	TG_FLAG_ALL_TAUTOMERIC

#define	TG_FLAG_DISCONNECT_COORD 0x00000080 /* find "coord. centers" and disconnect them */

#define	TG_FLAG_RECONNECT_COORD 0x00000100 /* reconnect disconnected "coord. centers" */

#define	TG_FLAG_CHECK_VALENCE_COORD 0x00000200 /* do not disconnect "coord. centers" with usual valence */

#define	TG_FLAG_MOVE_HPLUS2NEUTR 0x00000400 /* move protons to neutralize */

#define	TG_FLAG_VARIABLE_PROTONS 0x00000800 /* add/remove protons to neutralize */

#define	TG_FLAG_HARD_ADD_REM_PROTONS 0x00001000 /* add/remove protons to neutralize in hard way */

#define	TG_FLAG_POINTED_EDGE_STEREO 0x00002000 /* only pointed edge of stereo bond defines stereo */

#define	TG_FLAG_PHOSPHINE_STEREO 0x00008000 /* add phosphine sp3 stereo */

#define	TG_FLAG_ARSINE_STEREO 0x00010000 /* add arsine sp3 stereo */

#define	TG_FLAG_H_ALREADY_REMOVED 0x00020000 /* processing structure restored from InChI */

#define	TG_FLAG_FIX_SP3_BUG 0x00040000 /* fix sp3 stereo bug: overlapping 2D stereo bond & coordinate scaling */

#define	TG_FLAG_KETO_ENOL_TAUT 0x00080000 /* turn on keto-enol tautomerism detection */

#define	TG_FLAG_1_5_TAUT 0x00100000 /* turn on 1,5 tautomerism detection */

#define	TG_FLAG_FIX_ISO_FIXEDH_BUG 0x00200000 /* fix bug found after v.102b (isotopic H representation) */

#define	TG_FLAG_FIX_TERM_H_CHRG_BUG 0x00400000 /* fix bug found after v.102b (moving H charge in 'remove_terminal_HDT') */

#define	TG_FLAG_PT_22_00 0x00800000

#define	TG_FLAG_PT_16_00 0x01000000

#define	TG_FLAG_PT_06_00 0x02000000

#define	TG_FLAG_PT_39_00 0x04000000

#define	TG_FLAG_PT_13_00 0x08000000

#define	TG_FLAG_PT_18_00 0x10000000

#define	TG_FLAG_MOVE_HPLUS2NEUTR_DONE 0x00000001 /* protons have been moved to neutralize */

#define	TG_FLAG_TEST_TAUT__ATOMS_DONE 0x00000002

#define	TG_FLAG_DISCONNECT_SALTS_DONE 0x00000004

#define	TG_FLAG_TEST_TAUT__SALTS_DONE 0x00000008 /* multiple H tautomerism */

#define	TG_FLAG_MOVE_POS_CHARGES_DONE 0x00000010

#define	TG_FLAG_TEST_TAUT2_SALTS_DONE 0x00000020 /* merged t-groups */

#define	TG_FLAG_ALLOW_NO_NEGTV_O_DONE 0x00000040

#define	TG_FLAG_MERGE_TAUT_SALTS_DONE 0x00000080 /* added non-taut O to taut groups */

#define	TG_FLAG_ALL_SALT_DONE

#define	TG_FLAG_DISCONNECT_COORD_DONE 0x00000100 /* found and disconnected "coord. centers" */

#define	TG_FLAG_CHECK_VALENCE_COORD_DONE 0x00000200 /* did not disconnect "coord. centers" with usual valence */

#define	TG_FLAG_MOVE_CHARGE_COORD_DONE 0x00000400 /* changed charge of a disconnected ligand to fit its valence */

#define	TG_FLAG_FIX_ODD_THINGS_DONE 0x00000800 /* fixed drawing ambiguities in fix_odd_things */

#define	TG_FLAG_TEST_TAUT3_SALTS_DONE 0x00001000 /* merged t-groups + non-O taut atoms */

#define	TG_FLAG_FOUND_SALT_CHARGES_DONE 0x00002000 /* not assigned: preprocessing detected possibility of salt-type tautomerism */

#define	TG_FLAG_FOUND_ISOTOPIC_H_DONE 0x00004000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */

#define	TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE 0x00008000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */

#define	READ_INCHI_OUTPUT_INCHI 0x00000001

#define	READ_INCHI_SPLIT_OUTPUT 0x00000002

#define	READ_INCHI_KEEP_BALANCE_P 0x00000004

#define	READ_INCHI_TO_STRUCTURE 0x00000008

#define	INCHI_IOS_TYPE_NONE 0

#define	INCHI_IOS_TYPE_STRING 1

#define	INCHI_IOS_TYPE_FILE 2

#define	TRACE_MEMORY_LEAKS 0 /* 0: do not change */

#define	INCHI_HEAPCHK /* default: no explicit heap checking during the execution */

#define	inchi_malloc malloc

#define	inchi_calloc calloc

#define	inchi_realloc realloc

#define	inchi_free(X) do{ if(X) free(X); }while(0)

#define	USE_ALLOCA 0

#define	qmalloc(X) inchi_malloc(X)

#define	qfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0)

#define	fast_alloc(X) inchi_malloc(X)

#define	fast_free(X) inchi_free(X)

#define	qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0)

#define	MYREALLOC2(PTRTYPE1, PTRTYPE2, PTR1, PTR2, LEN1, LEN2, ERR)

#define	DEBUG_POLYMERS 0

#define	POLYMERS_NO 0 /* ignore polymers */

#define	POLYMERS_MODERN 1 /* v. 1.06+ way to treat polymers with Zz */

#define	POLYMERS_LEGACY 2 /* v. 1.05 mode, no explicit Zz (internally they are here) */

#define	POLYMERS_LEGACY_PLUS

#define	STEREO_AT_ZZ 0

#define	ALLOW_SUBSTRUCTURE_FILTERING 1

Typedefs
typedef struct tagOutputString	INCHI_IOS_STRING

typedef struct tagOutputStream	INCHI_IOSTREAM

Macro Definition Documentation

◆ ABC_CT_NUM_CLOSURES

#define ABC_CT_NUM_CLOSURES 1 /* 1=> in coinnections compressed format output decimal number of closures instead of '-' */

◆ ADD_6MEMB_AROM_BOND_PARITY

#define ADD_6MEMB_AROM_BOND_PARITY 1 /* 1 => all arom bonds are stereo bonds */

◆ ADD_ChCh_STEREO_CANON_CHK

#define ADD_ChCh_STEREO_CANON_CHK 0 /* 1 is NOT needed; let it always be 0 */

◆ ADD_CMLPP

#define ADD_CMLPP 0

◆ ADD_MOVEABLE_O_PLUS

#define ADD_MOVEABLE_O_PLUS 1 /* 1=> allow charges on O(+) to move */

◆ ALL_ALT_AS_AROMATIC

#define ALL_ALT_AS_AROMATIC 1 /* 1 => all altrnate bonds (even in cyclooctateraene) treat as aromatic */

◆ ALLOW_EMPTY_INCHI_AS_INPUT

#define ALLOW_EMPTY_INCHI_AS_INPUT 1 /* Allow "InChI=1//" and standard/beta analogues in input */

◆ ALLOW_SUBSTRUCTURE_FILTERING

#define ALLOW_SUBSTRUCTURE_FILTERING 1

◆ ALLOW_TAUT_ATTACHMENTS_TO_STEREO_BONDS

#define ALLOW_TAUT_ATTACHMENTS_TO_STEREO_BONDS 1 /* 1=> consider bond in an alternating circuit stereogenic */

◆ ALT_TAUT

#define ALT_TAUT ( X ) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */

◆ ALWAYS_ADD_TG_ON_THE_FLY

#define ALWAYS_ADD_TG_ON_THE_FLY 1 /* 1 => disables radical calcellation by taut-charge movement */

◆ ANY_ATOM_IN_ALT_CYCLE

#define ANY_ATOM_IN_ALT_CYCLE 1 /* 1=> accept any atom in alternating bond circuit, 0=>only some */

◆ APPLY_IMPLICIT_H_DOWN_RULE

#define APPLY_IMPLICIT_H_DOWN_RULE 0 /* 1=> if 3 non-H atoms around stereocenter are in same plane */

◆ BEST_PARITY

#define BEST_PARITY 1 /* odd */

◆ BNS_MARK_EDGE_2_DISCONNECT

#define BNS_MARK_EDGE_2_DISCONNECT 1 /* 1=> mark edge as temp forbidden instead of disconnection */

◆ BNS_PROTECT_FROM_TAUT

#define BNS_PROTECT_FROM_TAUT 1 /* 1=> do not allow testing of bonds to acetyl or nitro */

◆ BNS_RAD_SEARCH

#define BNS_RAD_SEARCH 1 /* 1=> prevent normalization failures due to radical centers */

◆ bOUTPUT_ONE_STRUCT_TIME [1/2]

#define bOUTPUT_ONE_STRUCT_TIME 1 /* 1 => output each structure time (non-release only) */

◆ bOUTPUT_ONE_STRUCT_TIME [2/2]

#define bOUTPUT_ONE_STRUCT_TIME 0

◆ BREAK_ALSO_NEIGH_TIE

#define BREAK_ALSO_NEIGH_TIE 0 /* post 1.12Beta 2004-08-20: if fixed neighbor has equ neighbors, fix the one with smaller canon. rank */

◆ BREAK_ALSO_NEIGH_TIE_ROTATE

#define BREAK_ALSO_NEIGH_TIE_ROTATE 1 /* post 1.12Beta 2004-09-02: break the second in 2nd psition; 1 works, 0 does not (example:MFCD01085607) */

◆ BREAK_ONE_MORE_SC_TIE

#define BREAK_ONE_MORE_SC_TIE 1 /* break one more tie when comparing possible stereocenter neighbors */

◆ bRELEASE_VERSION

#define bRELEASE_VERSION 1 /* 1=> release version; comment out to disable */

◆ bREUSE_INCHI

#define bREUSE_INCHI

Value:

1 /* 1=> do not recalulate INChI for components in reconnected

* structure that are same as in the connected one */

◆ BUILD_WITH_AMI

#define BUILD_WITH_AMI 1

◆ BUILD_WITH_ENG_OPTIONS

#define BUILD_WITH_ENG_OPTIONS 0

◆ CANON_FIXH_TRANS

#define CANON_FIXH_TRANS 1 /* produce canonical fixed-H transposition */

◆ CANON_MODE_CT

#define CANON_MODE_CT (CMODE_CT)

◆ CANON_MODE_ISO

#define CANON_MODE_ISO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT)

◆ CANON_MODE_ISO_STEREO

#define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO)

◆ CANON_MODE_MASK

#define CANON_MODE_MASK 0x00FF /* used to determine canonicalization mode */

◆ CANON_MODE_STEREO

#define CANON_MODE_STEREO (CMODE_CT|CMODE_STEREO)

◆ CANON_MODE_TAUT

#define CANON_MODE_TAUT (CMODE_CT|CMODE_TAUT)

◆ CANON_TAUTOMERS

#define CANON_TAUTOMERS 1 /* 1=> process tautomers */

◆ CHARGED_SALTS_ONLY

#define CHARGED_SALTS_ONLY

Value:

1 /* 1=>(default)do not test far salts tautomerism if

* no negative charge(s) present */

◆ CHECK_AROMBOND2ALT

#define CHECK_AROMBOND2ALT 1 /* 1=> check whether arom->alt bond conversion succeeded */

◆ CHECK_C2v_S4_SYMM

#define CHECK_C2v_S4_SYMM 0 /* post-1.12Beta 1=> check if a stereocenter has C2v or S4 symmetry; 0=>old mode */

◆ CHECK_METAL_VALENCE

#define CHECK_METAL_VALENCE 0 /* 1=> disconnect only metals that have abnormal valence */

◆ CHECK_STRTOL_ATNUMB

#define CHECK_STRTOL_ATNUMB 1

◆ CMODE_CT

#define CMODE_CT 0x000001

◆ CMODE_ISO

#define CMODE_ISO 0x000002

◆ CMODE_ISO_OUT

#define CMODE_ISO_OUT 0x000004 /* obsolete ? */

◆ CMODE_ISO_STEREO

#define CMODE_ISO_STEREO 0x000010

◆ CMODE_NO_ALT_SBONDS

#define CMODE_NO_ALT_SBONDS 0x000100 /* 6-14-2002: do not assign stereo to alternating bonds */

◆ CMODE_NOEQ_STEREO

#define CMODE_NOEQ_STEREO 0x000040 /* 5-24-2002: do not use stereo equivalence to accelerate */

◆ CMODE_RACEMIC_STEREO

#define CMODE_RACEMIC_STEREO 0x000400 /* RAC All Racemic Stereo */

◆ CMODE_REDNDNT_STEREO

#define CMODE_REDNDNT_STEREO 0x000080 /* 6-11-2002: do not check for redundant stereo elements */

◆ CMODE_RELATIVE_STEREO

#define CMODE_RELATIVE_STEREO 0x000200 /* REL All Relative Stereo */

◆ CMODE_SB_IGN_ALL_UU

#define CMODE_SB_IGN_ALL_UU 0x001000 /* IAUSC Ignore stereobonds if All Undef/Unknown */

◆ CMODE_SC_IGN_ALL_UU

#define CMODE_SC_IGN_ALL_UU 0x000800 /* IAUSC Ignore stereocenters if All Undef/Unknown */

◆ CMODE_STEREO

#define CMODE_STEREO 0x000008

◆ CMODE_TAUT

#define CMODE_TAUT 0x000020

◆ COMPILE_ANSI_ONLY

#define COMPILE_ANSI_ONLY

◆ CT_ATOMID

#define CT_ATOMID CT_ATOMID_IS_CURRANK /*CT_ATOMID_DONTINCLUDE */

◆ CT_ATOMID_DONTINCLUDE

#define CT_ATOMID_DONTINCLUDE 1

◆ CT_ATOMID_IS_CURRANK

#define CT_ATOMID_IS_CURRANK 3

◆ CT_ATOMID_IS_INITRANK

#define CT_ATOMID_IS_INITRANK 2

◆ CT_GREATER_THAN

#define CT_GREATER_THAN >

◆ CT_INITVALUE

#define CT_INITVALUE ~0

◆ CT_NEIGH_INCREASE

#define CT_NEIGH_INCREASE /* in CT, neighbors ranks increase */

◆ CT_NEIGH_SMALLER

#define CT_NEIGH_SMALLER /* in CT, include neighbors with smaller ranks */

◆ CT_NEIGH_SMALLER_THAN

#define CT_NEIGH_SMALLER_THAN <

◆ CT_SMALLEST

#define CT_SMALLEST /* minimal CT */

◆ DEBUG_POLYMERS

#define DEBUG_POLYMERS 0

◆ DISABLE_READ_COMPRESSED_INCHI

#define DISABLE_READ_COMPRESSED_INCHI 1

◆ DISCONNECT_METALS

#define DISCONNECT_METALS 1 /* make main layer disconnected */ /* djb-rwth: default 1 */

◆ DISCONNECT_SALTS

#define DISCONNECT_SALTS 1 /* 1=>disconnect metal atoms from salts, 0=>dont */ /* djb-rwth: default 1 */

◆ DISPLAY_DEBUG_DATA_C_POINT

#define DISPLAY_DEBUG_DATA_C_POINT 0 /* disabled release version for now */

◆ DISPLAY_ORIG_AT_NUMBERS

#define DISPLAY_ORIG_AT_NUMBERS 1 /* 1 => in an uncanonicalized components display orig. atom numbers (default) */

◆ DISPLAY_RING_SYSTEMS

#define DISPLAY_RING_SYSTEMS 0 /* 1 => for debug only; displays: */

◆ DISPLAY_ZZ_AS_STAR

#define DISPLAY_ZZ_AS_STAR 1

◆ DOUBLE_BOND_NEIGH_LIST

#define DOUBLE_BOND_NEIGH_LIST 0 /* 1 => include double bond neighbor in NeighList 2 times */

◆ DRAW_AROM_TAUT

#define DRAW_AROM_TAUT 1 /* 1=> draw distinct aromatic & tautomer bonds, 0=> don't */

◆ EMBED_REC_METALS_INCHI

#define EMBED_REC_METALS_INCHI

Value:

1 /* 1=> (default) output Reconnected embedded in Disconnected INChI;

* 0=> separate output */

◆ EQL_H_NUM_TOGETHER

#define EQL_H_NUM_TOGETHER 1 /* 1=> output 1-3,5H2 intead of 1-3H2,5H2 (CT_MODE_EQL_H_TOGETHER) */

◆ EXCL_ALL_AROM_BOND_PARITY

#define EXCL_ALL_AROM_BOND_PARITY 0 /* 1 => any arom atom cannot belong to stereo bond. */

◆ EXTR_2EQL2CENTER_TO_REMOVE_PARITY

#define EXTR_2EQL2CENTER_TO_REMOVE_PARITY 0x000004

◆ EXTR_CALC_USED_TO_REMOVE_PARITY

#define EXTR_CALC_USED_TO_REMOVE_PARITY 0x000002

◆ EXTR_CANON_NE_EQUITABLE

#define EXTR_CANON_NE_EQUITABLE 0x004000 /* find structures where canonical partition is different from equitable */

◆ EXTR_FLAGS

#define EXTR_FLAGS 0 /*EXTR_TAUT_TREATMENT_CHARGES*/ /*(EXTR_HAS_FEATURE)*/ /*(EXTR_HAS_PROTON_PN)*/ /*(EXTR_UNUSUAL_VALENCES)*/ /*(EXTR_CANON_NE_EQUITABLE)*/ /*(EXTR_TEST_TAUT3_SALTS_DONE)*/ /*(EXTR_HAS_METAL_ATOM)*/ /* (EXTR_NON_TRIVIAL_STEREO)*/ /*(EXTR_METAL_WAS_DISCONNECTED)*/ /* (EXTR_REMOVE_PARITY_WARNING)*/ /*(EXTR_HAS_ATOM_WITH_DEFINED_PARITY) */

◆ EXTR_HAS_ATOM_WITH_DEFINED_PARITY

#define EXTR_HAS_ATOM_WITH_DEFINED_PARITY 0x000008

◆ EXTR_HAS_FEATURE

#define EXTR_HAS_FEATURE 0x010000 /* found a feature */

◆ EXTR_HAS_METAL_ATOM

#define EXTR_HAS_METAL_ATOM 0x001000

◆ EXTR_HAS_PROTON_PN

#define EXTR_HAS_PROTON_PN 0x008000 /* has movable H+ attached to N or P */

◆ EXTR_KNOWN_USED_TO_REMOVE_PARITY

#define EXTR_KNOWN_USED_TO_REMOVE_PARITY 0x000001

◆ EXTR_MASK

#define EXTR_MASK 0 /*EXTR_TAUT_TREATMENT_CHARGES*/ /*(EXTR_HAS_FEATURE)*/ /*(EXTR_UNUSUAL_VALENCES | EXTR_HAS_METAL_ATOM)*/ /* 0 to disable */

◆ EXTR_METAL_WAS_DISCONNECTED

#define EXTR_METAL_WAS_DISCONNECTED 0x000100

◆ EXTR_METAL_WAS_NOT_DISCONNECTED

#define EXTR_METAL_WAS_NOT_DISCONNECTED 0x000200

◆ EXTR_NON_TRIVIAL_STEREO

#define EXTR_NON_TRIVIAL_STEREO 0x000400 /* (Inv != Abs stereo) && (parities can't be obtained by inverting them) */

◆ EXTR_REMOVE_PARITY_WARNING

#define EXTR_REMOVE_PARITY_WARNING 0x000010

◆ EXTR_SALT_PROTON_MOVE_ERR_WARN

#define EXTR_SALT_PROTON_MOVE_ERR_WARN 0x000080

◆ EXTR_SALT_PROTON_MOVED

#define EXTR_SALT_PROTON_MOVED 0x000040

◆ EXTR_SALT_WAS_DISCONNECTED

#define EXTR_SALT_WAS_DISCONNECTED 0x000020

◆ EXTR_TAUT_TREATMENT_CHARGES

#define EXTR_TAUT_TREATMENT_CHARGES 0x020000 /* tautomeric treatment of charges */

◆ EXTR_TEST_TAUT3_SALTS_DONE

#define EXTR_TEST_TAUT3_SALTS_DONE 0x002000 /* non-oxygen t-points used to discover tautomerism of merged t-groups */

◆ EXTR_TRANSPOSITION_EXAMPLES

#define EXTR_TRANSPOSITION_EXAMPLES 0x040000 /* extract structures that have different mobile-H and fixed-H orders */

◆ EXTR_UNUSUAL_VALENCES

#define EXTR_UNUSUAL_VALENCES 0x000800

◆ fast_alloc

#define fast_alloc ( X ) inchi_malloc(X)

◆ fast_free

#define fast_free ( X ) inchi_free(X)

◆ FIND_CANON_NE_EQUITABLE

#define FIND_CANON_NE_EQUITABLE 0 /* 0=>normal mode */

◆ FIND_RING_SYSTEMS

#define FIND_RING_SYSTEMS 1 /* 1 => find and mark ring systems, blocks, cut-vertices */

◆ FIND_RINS_SYSTEMS_DISTANCES

#define FIND_RINS_SYSTEMS_DISTANCES 0 /* 1 => find ring system and atom distance from terminal */

◆ FIX_2D_STEREO_BORDER_CASE

#define FIX_2D_STEREO_BORDER_CASE 0

◆ FIX_ADJ_RAD

#define FIX_ADJ_RAD 0

◆ FIX_AROM_RADICAL

#define FIX_AROM_RADICAL 1 /* (2011-05-09) 1=> Fix bug which leads for different InChI */

◆ FIX_AVOID_ADP

#define FIX_AVOID_ADP 0

◆ FIX_BOND23_IN_TAUT

#define FIX_BOND23_IN_TAUT 0

◆ FIX_CANCEL_CHARGE_COUNT_BUG

#define FIX_CANCEL_CHARGE_COUNT_BUG 0

◆ FIX_ChCh_CONSTIT_CANON_BUG

#define FIX_ChCh_CONSTIT_CANON_BUG 1 /* 1=> (NEEDED) */

◆ FIX_ChCh_STEREO_CANON_BUG

#define FIX_ChCh_STEREO_CANON_BUG 1 /* 1=> (NEEDED) */

◆ FIX_CPOINT_BOND_CAP2

#define FIX_CPOINT_BOND_CAP2 0

◆ FIX_CURE53_ISSUE_HEAP_BUFFER_OVERFLOW_INCHITOINPATOM

#define FIX_CURE53_ISSUE_HEAP_BUFFER_OVERFLOW_INCHITOINPATOM 1

◆ FIX_CURE53_ISSUE_NULL_DEREFERENCE_MAKE_A_COPY_OF_T_GROUP_INFO

#define FIX_CURE53_ISSUE_NULL_DEREFERENCE_MAKE_A_COPY_OF_T_GROUP_INFO 1

◆ FIX_CURE53_ISSUE_OOB_ALREADY_HAVE_THIS_MESSAGE

#define FIX_CURE53_ISSUE_OOB_ALREADY_HAVE_THIS_MESSAGE 1

◆ FIX_DALKE_BUGS

#define FIX_DALKE_BUGS 1

◆ FIX_EITHER_DB_AS_NONSTEREO

#define FIX_EITHER_DB_AS_NONSTEREO 0

◆ FIX_EITHER_STEREO_IN_AUX_INFO

#define FIX_EITHER_STEREO_IN_AUX_INFO 1 /* 1=> fix bug: Either stereobond direction in Aux_Info; 0=> do not fix */

◆ FIX_EMPTY_LAYER_BUG

#define FIX_EMPTY_LAYER_BUG 0

◆ FIX_GAF_2019_1

#define FIX_GAF_2019_1 1

◆ FIX_GAF_2019_2

#define FIX_GAF_2019_2 1

◆ FIX_GAF_2019_3

#define FIX_GAF_2019_3 1

◆ FIX_GAF_2020_25607

#define FIX_GAF_2020_25607 1

◆ FIX_GAF_2020_25726

#define FIX_GAF_2020_25726 1

◆ FIX_GAF_2020_25741

#define FIX_GAF_2020_25741 1

◆ FIX_GAF_2020_GENERIC

#define FIX_GAF_2020_GENERIC 1

◆ FIX_H_CHECKING_TAUT

#define FIX_H_CHECKING_TAUT 1 /* 1 => Fix moveable H or (-) before checking if taut. exchange is possible */

◆ FIX_I2I_STEREOCONVERSION_BUG

#define FIX_I2I_STEREOCONVERSION_BUG 1 /* (2008-03-06) 1=> Fix bug of i2i conversion SAbs-->(SRel||Srac) */

◆ FIX_I2I_STEREOCONVERSION_BUG2

#define FIX_I2I_STEREOCONVERSION_BUG2 1 /* (2008-04-02) 1=> Fix bug of i2i conversion (missed empty /t) */

◆ FIX_I2I_STEREOCONVERSION_BUG3

#define FIX_I2I_STEREOCONVERSION_BUG3 1 /* (2008-04-10) 1=> Fix bug of i2i conversion */

◆ FIX_IMPOSSIBLE_H_ISOTOPE_BUG

#define FIX_IMPOSSIBLE_H_ISOTOPE_BUG 1 /* (2018-01-25) Bug reported by Andrew Dalke, inchi-discuss */

◆ FIX_ISO_FIXEDH_BUG

#define FIX_ISO_FIXEDH_BUG 1 /* (2007-09-24) 1=> Fix bug: missing fixed-H iso segment in case of single removed D(+) */

◆ FIX_ISO_FIXEDH_BUG_READ

#define FIX_ISO_FIXEDH_BUG_READ 0 /* (2007-09-24) 1=> Accommodate this InChI bug in reading InChI */

◆ FIX_KEEP_H_ON_NH_ANION

#define FIX_KEEP_H_ON_NH_ANION 0

◆ FIX_N_MINUS_NORN_BUG

#define FIX_N_MINUS_NORN_BUG 0

◆ FIX_N_V_METAL_BONDS_GPF

#define FIX_N_V_METAL_BONDS_GPF 1 /* 1=> (NEEDED) InChI v1 GPF bug fix */

◆ FIX_NORM_BUG_ADD_ION_PAIR

#define FIX_NORM_BUG_ADD_ION_PAIR 1 /* 1=> (NEEDED) fix bug: Miscount number of charges when creating an ion pair */

◆ FIX_NP_MINUS_BUG

#define FIX_NP_MINUS_BUG 1 /* 2010-03-11 DT Fix for bug reported by Timo Boehme */

◆ FIX_NUM_TG

#define FIX_NUM_TG 0 /* increase number of t-groups for isothiocyanate */

◆ FIX_ODD_THINGS_REM_Plus_BUG

#define FIX_ODD_THINGS_REM_Plus_BUG 0

◆ FIX_OLEAN_SPIRO_CHIRALITY_DETECTION_BUG

#define FIX_OLEAN_SPIRO_CHIRALITY_DETECTION_BUG 1

◆ FIX_ONE_LINE_INCHI_INPUT_CONVERSION_ISSUE

#define FIX_ONE_LINE_INCHI_INPUT_CONVERSION_ISSUE 1

◆ FIX_OSS_FUZZ_25604

#define FIX_OSS_FUZZ_25604 1

◆ FIX_OSS_FUZZ_25734_28139

#define FIX_OSS_FUZZ_25734_28139 1

◆ FIX_OSS_FUZZ_30162_30343

#define FIX_OSS_FUZZ_30162_30343 1

◆ FIX_READ_AUX_MEM_LEAK

#define FIX_READ_AUX_MEM_LEAK 1

◆ FIX_READ_LONG_LINE_BUG

#define FIX_READ_LONG_LINE_BUG 1 /* 1=> (NEEDED) prevent failure when reading AuxInfo and InChI is too long */

◆ FIX_REM_ION_PAIRS_Si_BUG

#define FIX_REM_ION_PAIRS_Si_BUG 0

◆ FIX_REM_PROTON_COUNT_BUG

#define FIX_REM_PROTON_COUNT_BUG 1 /* 1=> (NEEDED) check for number of actually removed protons and issue an error if mismatch */

◆ FIX_RENUM_BUG_FOR_CASE_OF_ACIDIC_OH_AT_P_PLUS

#define FIX_RENUM_BUG_FOR_CASE_OF_ACIDIC_OH_AT_P_PLUS 1

◆ FIX_STEREO_SCALING_BUG

#define FIX_STEREO_SCALING_BUG 0

◆ FIX_STEREOCOUNT_ERR

#define FIX_STEREOCOUNT_ERR 1 /* (2018-01-09) Supplied by DT */

◆ FIX_TACN_POSSIBLE_BUG

#define FIX_TACN_POSSIBLE_BUG 0

◆ FIX_TERM_H_CHRG_BUG

#define FIX_TERM_H_CHRG_BUG 1 /* (2008-06-06) IPl) */

◆ FIX_TRANSPOSITION_CHARGE_BUG

#define FIX_TRANSPOSITION_CHARGE_BUG 1 /* (2008-01-02) fix bug that leads to missed charge in some cases when /o is present */

◆ FIX_UNDERIV_TO_SDF

#define FIX_UNDERIV_TO_SDF /* prevent bond normalization if underivatization result goes to SDF 2013-05-10 DCh */

◆ HAL_ACID_H_XCHG

#define HAL_ACID_H_XCHG 1 /* allow iso H exchange to HX (X=halogen) and H2Y (Y=halcogen) */

◆ HYDROGENS_IN_INIT_RANKS

#define HYDROGENS_IN_INIT_RANKS 1 /* 1=> include num_H in initial ranking */

◆ I2S_MODIFY_OUTPUT

#define I2S_MODIFY_OUTPUT 1 /* 1=> Allow various InChI2InChI output types from cInChI */

◆ IGNORE_SINGLE_ENDPOINTS

#define IGNORE_SINGLE_ENDPOINTS 1 /* 1 => see FindAccessibleEndPoints() in INChITaut.c */

◆ IGNORE_TGROUP_WITHOUT_H

#define IGNORE_TGROUP_WITHOUT_H 1 /* ignore tautomeric groups containing charges only */

◆ INCHI_ACD_LABS_PREFIX

#define INCHI_ACD_LABS_PREFIX '-'

◆ INCHI_ALT_OPT_PREFIX

#define INCHI_ALT_OPT_PREFIX '-'

◆ INCHI_BAS

#define INCHI_BAS 0 /* 0 => disconnected or normal */

◆ inchi_calloc

#define inchi_calloc calloc

◆ inchi_free

#define inchi_free ( X ) do{ if(X) free(X); }while(0)

◆ INCHI_HEAPCHK

#define INCHI_HEAPCHK /* default: no explicit heap checking during the execution */

◆ INCHI_IOS_TYPE_FILE

#define INCHI_IOS_TYPE_FILE 2

◆ INCHI_IOS_TYPE_NONE

#define INCHI_IOS_TYPE_NONE 0

◆ INCHI_IOS_TYPE_STRING

#define INCHI_IOS_TYPE_STRING 1

◆ inchi_malloc

#define inchi_malloc malloc

◆ INCHI_NAM_VER_DELIM

#define INCHI_NAM_VER_DELIM "="

◆ INCHI_NAME

#define INCHI_NAME "InChI"

◆ INCHI_NUM

#define INCHI_NUM 2 /* = array size; member indexes: */

◆ INCHI_OPTION_PREFX

#define INCHI_OPTION_PREFX '-'

◆ INCHI_PATH_DELIM

#define INCHI_PATH_DELIM '/'

◆ inchi_realloc

#define inchi_realloc realloc

◆ INCHI_REC

#define INCHI_REC 1 /* 1 => reconnected */

◆ INCHI_T_NUM_MOVABLE

#define INCHI_T_NUM_MOVABLE 2

◆ INCHI_VERSION

#define INCHI_VERSION "1"

◆ INCL_NON_6AROM

#define INCL_NON_6AROM 1 /* 1 => mark all arom. bonds; 0=>mark arom. bonds only in 6-member rings */

◆ INCL_NON_SALT_CANDIDATATES

#define INCL_NON_SALT_CANDIDATATES

Value:

1 /* 1=> allow H and (-) migrate between "acidic" O and

* other possible endpoints */

◆ INCLUDE_NORMALIZATION_ENTRY_POINT

#define INCLUDE_NORMALIZATION_ENTRY_POINT 0

◆ KETO_ENOL_TAUT

#define KETO_ENOL_TAUT 1 /* include keto-enol tautomerism */

◆ MAX_NUM_STEREO_ATOM_NEIGH

#define MAX_NUM_STEREO_ATOM_NEIGH 4

◆ MAX_NUM_STEREO_BOND_NEIGH

#define MAX_NUM_STEREO_BOND_NEIGH 3

◆ MAX_NUM_STEREO_BONDS

#define MAX_NUM_STEREO_BONDS 3

◆ MIN_NUM_STEREO_BOND_NEIGH

#define MIN_NUM_STEREO_BOND_NEIGH 2

◆ MIN_SB_RING_SIZE

#define MIN_SB_RING_SIZE 8 /* do not assume stereo bonds in rings containing 3..MIN_SB_RING_SIZE-1 atoms */

◆ MOVE_CHARGES

#define MOVE_CHARGES 1 /* 1 => take moveable charges into account */

◆ MOVE_PPLUS_TO_REMOVE_PROTONS

#define MOVE_PPLUS_TO_REMOVE_PROTONS

Value:

0 /* 0=> default; 1=> (disabled) add P/P+ charge group during

* 'hard' proton removal */

◆ MYREALLOC2

#define MYREALLOC2	(	PTRTYPE1,
		PTRTYPE2,
		PTR1,
		PTR2,
		LEN1,
		LEN2,
		ERR
	)

Value:

    do { \
        if( (LEN1) <= (LEN2) ) {\
            PTRTYPE1 * newPTR1 = (PTRTYPE1 *)inchi_calloc( (LEN2)+1, sizeof(PTRTYPE1) );\
            PTRTYPE2 * newPTR2 = (PTRTYPE2 *)inchi_calloc( (LEN2)+1, sizeof(PTRTYPE2) );\
            if ( newPTR1 && newPTR2 ) { \
                if ( (PTR1) && (LEN1) > 0 ) \
                    (memcpy) ( newPTR1, (PTR1), (LEN1) * sizeof(PTRTYPE1) ); \
                if ( (PTR2) && (LEN1) > 0 ) \
                    (memcpy) ( newPTR2, (PTR2), (LEN1) * sizeof(PTRTYPE2) ); \
                if ( PTR1 ) \
                    inchi_free(PTR1);  \
                if ( PTR2 ) \
                    inchi_free(PTR2);  \
                (PTR1) = newPTR1; \
                (PTR2) = newPTR2; \
                (LEN1) = (LEN2);  \
                (ERR)  = 0; \
            } else {        \
                inchi_free(newPTR1); \
                inchi_free(newPTR2); \
                (ERR)  = 1; \
            }               \
        } else { (ERR) = 0; } \
    } while(0)

◆ N_V_STEREOBONDS

#define N_V_STEREOBONDS 1 /* 1=> detect stereobonds incident to N(V); 0 => don't */

◆ NEUTRALIZE_ENDPOINTS

#define NEUTRALIZE_ENDPOINTS 1 /* 1 => before checking whether an H is moveable make 2 endpoints neutral */

◆ NEW_STEREOCENTER_CHECK

#define NEW_STEREOCENTER_CHECK 1 /* 1 => add new stereocenter categories (see bCanInpAtomBeAStereoCenter(...)) */

◆ NORMALIZE_INP_COORD

#define NORMALIZE_INP_COORD 0 /* 0=>keep unchanged, 1 => make atom coordinates integer by normalizing to avg bond len 20 */

◆ ONE_BAD_SB_NEIGHBOR

#define ONE_BAD_SB_NEIGHBOR 1 /* 1 => allow 1 "bad" bond type neighbor to a stereobond atom. 2004-06-02 */

◆ ONLY_DOUBLE_BOND_STEREO

#define ONLY_DOUBLE_BOND_STEREO 0 /* 1=> no alt bond stereo, no taut. bond attachment to stereo bond */

◆ OPPOSITE_CHARGE_IN_CGROUP

#define OPPOSITE_CHARGE_IN_CGROUP 1 /* 1=> allow N(-) in (+) c-group, 0=> disallow */

◆ OUT_N1

#define OUT_N1 0 /* non-tautomeric only */

◆ OUT_NN

#define OUT_NN 4 /* only non-taut representations: non-taut else tautomeric */

◆ OUT_NT

#define OUT_NT 2 /* only non-taut representations of tautomeric */

◆ OUT_T1

#define OUT_T1 1 /* tautomeric if present otherwise non-tautomeric */

◆ OUT_TN

#define OUT_TN

Value:

3 /* tautomeric if present otherwise non-tautomeric;

separately output non-taut representations of tautomeric if present */

◆ OUTPUT_CONNECTED_METAL_ONLY

#define OUTPUT_CONNECTED_METAL_ONLY

Value:

0 /* 0=> default; 1 => (debug) create only reconnected or

* initial struct. output */

◆ POLYMERS_LEGACY

#define POLYMERS_LEGACY 2 /* v. 1.05 mode, no explicit Zz (internally they are here) */

◆ POLYMERS_LEGACY_PLUS

#define POLYMERS_LEGACY_PLUS

Value:

                                   3    /* v. 1.05 mode with an addition of that in all
                                   frame-shiftable-bistar-CRUs their backbone bonds 
                                   are reordered in descending seniority order. 
                                   Used as hidden 1st pass in 1.06 treatment        */

◆ POLYMERS_MODERN

#define POLYMERS_MODERN 1 /* v. 1.06+ way to treat polymers with Zz */

◆ POLYMERS_NO

#define POLYMERS_NO 0 /* ignore polymers */

◆ PROPAGATE_ILL_DEF_STEREO

#define PROPAGATE_ILL_DEF_STEREO 1 /* 1=> if at least one of the pair of constitutionally identical (far) neighbors */

◆ qfree

#define qfree ( X ) do{if(X){inchi_free(X);(X)=NULL;}}while(0)

◆ qmalloc

#define qmalloc ( X ) inchi_malloc(X)

◆ qzfree

#define qzfree ( X ) do{if(X){inchi_free(X);(X)=NULL;}}while(0)

◆ READ_INCHI_KEEP_BALANCE_P

#define READ_INCHI_KEEP_BALANCE_P 0x00000004

◆ READ_INCHI_OUTPUT_INCHI

#define READ_INCHI_OUTPUT_INCHI 0x00000001

◆ READ_INCHI_SPLIT_OUTPUT

#define READ_INCHI_SPLIT_OUTPUT 0x00000002

◆ READ_INCHI_STRING

#define READ_INCHI_STRING 1 /* 1=> input InChI string and process it */

◆ READ_INCHI_TO_STRUCTURE

#define READ_INCHI_TO_STRUCTURE 0x00000008

◆ RECONNECT_METALS

#define RECONNECT_METALS

Value:

0 /* 1=> by default add reconnected layer in case of coord.

* compound disconnection */ /* djb-rwth: default 0 */

◆ REL_RAC_STEREO_IGN_1_SC

#define REL_RAC_STEREO_IGN_1_SC 0 /* 1=> drop from InChI sp3 stereo in components that have a single stereocenter */

◆ RELEASE_IS_FINAL

#define RELEASE_IS_FINAL 1 /* final release */

◆ REMOVE_CALC_NONSTEREO

#define REMOVE_CALC_NONSTEREO 1 /* 1=> check new stereo numberings to remove parities from non-stereogenic elements */

◆ REMOVE_ION_PAIRS_DISC_STRU

#define REMOVE_ION_PAIRS_DISC_STRU 1 /* 1=> new post-preprocessing: remove charhes after metal disconnection */

◆ REMOVE_ION_PAIRS_EARLY

#define REMOVE_ION_PAIRS_EARLY 1 /* 1=> new preprocessing: step 1 before disconnecting metals in fix_odd_things() */

◆ REMOVE_ION_PAIRS_FIX_BONDS

#define REMOVE_ION_PAIRS_FIX_BONDS 1 /* 1=> step2: set unchangeable bonds around removed ion pairs */

◆ REMOVE_ION_PAIRS_ORIG_STRU

#define REMOVE_ION_PAIRS_ORIG_STRU

Value:

                                      0 /* 0=> normal mode (default)
                                      * 1=> testing mode only: remove ion pairs from the original structure
                                      *     to save the changes in the output Molfile (/OutputSDF) or AuxInfo
                                      *     NIP=No Ion Pairs
                                      */

◆ REMOVE_KNOWN_NONSTEREO

#define REMOVE_KNOWN_NONSTEREO 1 /* 1=> check in advance known stereo to remove parities from non-stereogenic elements */

◆ REMOVE_TGROUP_CHARGE

#define REMOVE_TGROUP_CHARGE 0 /* 0: do not remove charge information from tautomeric groups */

◆ REPLACE_ALT_WITH_TAUT

#define REPLACE_ALT_WITH_TAUT 1 /* 1 => replace alt bonds with tautomeric bonds in case of standard t-groups */

◆ RING2CHAIN

#define RING2CHAIN 1 /* open rings R-C(-OH)-O-R => R-C(=O) OH-R */

◆ S_VI_O_PLUS_METAL_FIX_BOND

#define S_VI_O_PLUS_METAL_FIX_BOND 1 /* 1=> count double bond M-O(+)=S as O=S in S(VI) ans S(VIII) fixing bonds */

◆ SALT_WITH_PROTONS

#define SALT_WITH_PROTONS 1 /* 1=> (new new) include proton migrarion C-SH, =C-OH, NH+ */

◆ SDF_OUTPUT_DT

#define SDF_OUTPUT_DT 1 /* 1=> all option -SdfAtomsDT to output D and T into SDfile */

◆ SDF_OUTPUT_V2000

#define SDF_OUTPUT_V2000 1 /* 1=>always output V2000 SDfile, 0=>only if needed */

◆ SINGLET_IS_TRIPLET

#define SINGLET_IS_TRIPLET

Value:

1 /* 'singlet' means two electrons make a lone pair instead of 2 bonds

its effect on valence is same as the effect of a triplet */

◆ STEREO_AT_MARK

#define STEREO_AT_MARK 8 /* > MAX_NUM_STEREO_BONDS */

◆ STEREO_AT_ZZ

#define STEREO_AT_ZZ 0

◆ STEREO_CENTER_BOND4_NORM

#define STEREO_CENTER_BOND4_NORM 0 /* set length of the added bond around a stereocenter = 1 before getting the parity */

◆ STEREO_CENTER_BONDS_NORM

#define STEREO_CENTER_BONDS_NORM 1 /* set length of the bonds around a stereocenter = 1 before getting the parity */

◆ STEREO_WEDGE_ONLY [1/2]

#define STEREO_WEDGE_ONLY 1 /* 1=> only pointed ends stereo bonds define stereo; 0=> both ends */

◆ STEREO_WEDGE_ONLY [2/2]

#define STEREO_WEDGE_ONLY 1 /* 1=> only pointed ends stereo bonds define stereo; 0=> both ends 1.12Beta */

◆ TARGET_PLATFORM

#define TARGET_PLATFORM "Linux"

◆ TAUT_15_NON_RING

#define TAUT_15_NON_RING 1 /* 1,5 tautomerism with endpoints not in ring */

◆ TAUT_4PYRIDINOL_RINGS

#define TAUT_4PYRIDINOL_RINGS 1 /* 1=> OH-C5H4N rings tautomerism */

◆ TAUT_IGNORE_EQL_ENDPOINTS

#define TAUT_IGNORE_EQL_ENDPOINTS

Value:

                                              0  /* 0=> even though 2 endpoints belong to same t-group check
                                              them to find more alt bonds (new)
                                          1=> ignore and do not check (old mode) */

◆ TAUT_INI

#define TAUT_INI 2 /* 2 => intermediate tautomeric structure */

◆ TAUT_NON

#define TAUT_NON 0 /* 0 => normal structure */

◆ TAUT_NUM

#define TAUT_NUM 2 /* = array size; member indexes: */

◆ TAUT_OTHER

#define TAUT_OTHER 1

◆ TAUT_PT_06_00

#define TAUT_PT_06_00 1 /* tautomerism rule PT_06_00 */

◆ TAUT_PT_13_00

#define TAUT_PT_13_00 1 /* tautomerism rule PT_13_00 */

◆ TAUT_PT_16_00

#define TAUT_PT_16_00 1 /* tautomerism rule PT_16_00 */

◆ TAUT_PT_18_00

#define TAUT_PT_18_00 1 /* tautomerism rule PT_18_00 */

◆ TAUT_PT_22_00

#define TAUT_PT_22_00 1 /* tautomerism rule PT_22_00 */

◆ TAUT_PT_39_00

#define TAUT_PT_39_00 1 /* tautomerism rule PT_39_00 */

◆ TAUT_PYRAZOLE_RINGS

#define TAUT_PYRAZOLE_RINGS 1 /* 1=> tautomerizm in pyrazole rings */

◆ TAUT_RINGS_ATTACH_CHAIN

#define TAUT_RINGS_ATTACH_CHAIN 1 /* 1=> allow only chain attachments to tautomeric endpoints */

◆ TAUT_TROPOLONE_5

#define TAUT_TROPOLONE_5 1 /* 1=> taut. similar to tropolone, 5-member ring */

◆ TAUT_TROPOLONE_7

#define TAUT_TROPOLONE_7 1 /* 1=> tautomeric 7-member rings ON */

◆ TAUT_YES

#define TAUT_YES 1 /* 1 => tautomeric */

◆ TEST_REMOVE_S_ATOMS

#define TEST_REMOVE_S_ATOMS

Value:

                                        1  /* 1=>default: after merging into one group test &
                                        *    remove unreachable,
                                        * 0=> old version: test only before merging into one t-group */

◆ TG_FLAG_1_5_TAUT

#define TG_FLAG_1_5_TAUT 0x00100000 /* turn on 1,5 tautomerism detection */

◆ TG_FLAG_ALL_SALT_DONE

#define TG_FLAG_ALL_SALT_DONE

Value:

                                        (TG_FLAG_TEST_TAUT__SALTS_DONE | \
                                        TG_FLAG_TEST_TAUT2_SALTS_DONE | \
                                        TG_FLAG_MERGE_TAUT_SALTS_DONE )

◆ TG_FLAG_ALL_TAUTOMERIC

#define TG_FLAG_ALL_TAUTOMERIC

Value:

                                         (TG_FLAG_TEST_TAUT__ATOMS| \
                                         TG_FLAG_TEST_TAUT__SALTS| \
                                         TG_FLAG_TEST_TAUT2_SALTS| \
                                         TG_FLAG_MERGE_TAUT_SALTS)

◆ TG_FLAG_ALLOW_NO_NEGTV_O

#define TG_FLAG_ALLOW_NO_NEGTV_O 0x00000020 /* CHARGED_SALTS_ONLY=0 (debug) find long-range H-only tautomerism on =C-OH, >C=O */

◆ TG_FLAG_ALLOW_NO_NEGTV_O_DONE

#define TG_FLAG_ALLOW_NO_NEGTV_O_DONE 0x00000040

◆ TG_FLAG_ARSINE_STEREO

#define TG_FLAG_ARSINE_STEREO 0x00010000 /* add arsine sp3 stereo */

◆ TG_FLAG_CHECK_VALENCE_COORD

#define TG_FLAG_CHECK_VALENCE_COORD 0x00000200 /* do not disconnect "coord. centers" with usual valence */

◆ TG_FLAG_CHECK_VALENCE_COORD_DONE

#define TG_FLAG_CHECK_VALENCE_COORD_DONE 0x00000200 /* did not disconnect "coord. centers" with usual valence */

◆ TG_FLAG_DISCONNECT_COORD

#define TG_FLAG_DISCONNECT_COORD 0x00000080 /* find "coord. centers" and disconnect them */

◆ TG_FLAG_DISCONNECT_COORD_DONE

#define TG_FLAG_DISCONNECT_COORD_DONE 0x00000100 /* found and disconnected "coord. centers" */

◆ TG_FLAG_DISCONNECT_SALTS

#define TG_FLAG_DISCONNECT_SALTS 0x00000002 /* DISCONNECT_SALTS disconnect */

◆ TG_FLAG_DISCONNECT_SALTS_DONE

#define TG_FLAG_DISCONNECT_SALTS_DONE 0x00000004

◆ TG_FLAG_FIX_ISO_FIXEDH_BUG

#define TG_FLAG_FIX_ISO_FIXEDH_BUG 0x00200000 /* fix bug found after v.102b (isotopic H representation) */

◆ TG_FLAG_FIX_ODD_THINGS_DONE

#define TG_FLAG_FIX_ODD_THINGS_DONE 0x00000800 /* fixed drawing ambiguities in fix_odd_things */

◆ TG_FLAG_FIX_SP3_BUG

#define TG_FLAG_FIX_SP3_BUG 0x00040000 /* fix sp3 stereo bug: overlapping 2D stereo bond & coordinate scaling */

◆ TG_FLAG_FIX_TERM_H_CHRG_BUG

#define TG_FLAG_FIX_TERM_H_CHRG_BUG 0x00400000 /* fix bug found after v.102b (moving H charge in 'remove_terminal_HDT') */

◆ TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE

#define TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE 0x00008000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */

◆ TG_FLAG_FOUND_ISOTOPIC_H_DONE

#define TG_FLAG_FOUND_ISOTOPIC_H_DONE 0x00004000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */

◆ TG_FLAG_FOUND_SALT_CHARGES_DONE

#define TG_FLAG_FOUND_SALT_CHARGES_DONE 0x00002000 /* not assigned: preprocessing detected possibility of salt-type tautomerism */

◆ TG_FLAG_H_ALREADY_REMOVED

#define TG_FLAG_H_ALREADY_REMOVED 0x00020000 /* processing structure restored from InChI */

◆ TG_FLAG_HARD_ADD_REM_PROTONS

#define TG_FLAG_HARD_ADD_REM_PROTONS 0x00001000 /* add/remove protons to neutralize in hard way */

◆ TG_FLAG_KETO_ENOL_TAUT

#define TG_FLAG_KETO_ENOL_TAUT 0x00080000 /* turn on keto-enol tautomerism detection */

◆ TG_FLAG_MERGE_TAUT_SALTS

#define TG_FLAG_MERGE_TAUT_SALTS 0x00000040 /* DISCONNECT_SALTS merge all "salt"-t-groups and other =C-OH into one t-group */

◆ TG_FLAG_MERGE_TAUT_SALTS_DONE

#define TG_FLAG_MERGE_TAUT_SALTS_DONE 0x00000080 /* added non-taut O to taut groups */

◆ TG_FLAG_MOVE_CHARGE_COORD_DONE

#define TG_FLAG_MOVE_CHARGE_COORD_DONE 0x00000400 /* changed charge of a disconnected ligand to fit its valence */

◆ TG_FLAG_MOVE_HPLUS2NEUTR

#define TG_FLAG_MOVE_HPLUS2NEUTR 0x00000400 /* move protons to neutralize */

◆ TG_FLAG_MOVE_HPLUS2NEUTR_DONE

#define TG_FLAG_MOVE_HPLUS2NEUTR_DONE 0x00000001 /* protons have been moved to neutralize */

◆ TG_FLAG_MOVE_POS_CHARGES

#define TG_FLAG_MOVE_POS_CHARGES 0x00000008 /* MOVE_CHARGES allow long-range movement of N(+), P(+) charges */

◆ TG_FLAG_MOVE_POS_CHARGES_DONE

#define TG_FLAG_MOVE_POS_CHARGES_DONE 0x00000010

◆ TG_FLAG_PHOSPHINE_STEREO

#define TG_FLAG_PHOSPHINE_STEREO 0x00008000 /* add phosphine sp3 stereo */

◆ TG_FLAG_POINTED_EDGE_STEREO

#define TG_FLAG_POINTED_EDGE_STEREO 0x00002000 /* only pointed edge of stereo bond defines stereo */

◆ TG_FLAG_PT_06_00

#define TG_FLAG_PT_06_00 0x02000000

◆ TG_FLAG_PT_13_00

#define TG_FLAG_PT_13_00 0x08000000

◆ TG_FLAG_PT_16_00

#define TG_FLAG_PT_16_00 0x01000000

◆ TG_FLAG_PT_18_00

#define TG_FLAG_PT_18_00 0x10000000

◆ TG_FLAG_PT_22_00

#define TG_FLAG_PT_22_00 0x00800000

◆ TG_FLAG_PT_39_00

#define TG_FLAG_PT_39_00 0x04000000

◆ TG_FLAG_RECONNECT_COORD

#define TG_FLAG_RECONNECT_COORD 0x00000100 /* reconnect disconnected "coord. centers" */

◆ TG_FLAG_TEST_TAUT2_SALTS

#define TG_FLAG_TEST_TAUT2_SALTS 0x00000010 /* TEST_REMOVE_S_ATOMS multi-attachement long-range H/(-) taut. on =C-OH, >C=O */

◆ TG_FLAG_TEST_TAUT2_SALTS_DONE

#define TG_FLAG_TEST_TAUT2_SALTS_DONE 0x00000020 /* merged t-groups */

◆ TG_FLAG_TEST_TAUT3_SALTS_DONE

#define TG_FLAG_TEST_TAUT3_SALTS_DONE 0x00001000 /* merged t-groups + non-O taut atoms */

◆ TG_FLAG_TEST_TAUT__ATOMS

#define TG_FLAG_TEST_TAUT__ATOMS 0x00000001 /* find regular tautomerism */

◆ TG_FLAG_TEST_TAUT__ATOMS_DONE

#define TG_FLAG_TEST_TAUT__ATOMS_DONE 0x00000002

◆ TG_FLAG_TEST_TAUT__SALTS

#define TG_FLAG_TEST_TAUT__SALTS 0x00000004 /* DISCONNECT_SALTS if possible find long-range H/(-) taut. on =C-OH, >C=O */

◆ TG_FLAG_TEST_TAUT__SALTS_DONE

#define TG_FLAG_TEST_TAUT__SALTS_DONE 0x00000008 /* multiple H tautomerism */

◆ TG_FLAG_VARIABLE_PROTONS

#define TG_FLAG_VARIABLE_PROTONS 0x00000800 /* add/remove protons to neutralize */

◆ TRACE_MEMORY_LEAKS

#define TRACE_MEMORY_LEAKS 0 /* 0: do not change */

◆ UNDERIV_ADD_EXPLICIT_H

#define UNDERIV_ADD_EXPLICIT_H /* Underiv: add removed explict H after underivatization */

◆ UNDERIV_OOB_nButyl

#define UNDERIV_OOB_nButyl /* 4r2c1 DERIV_RING_O_OUTSIDE_PRECURSOR: 5 at, n-Butyl */

◆ UNDERIV_PYRROLIDIDES

#define UNDERIV_PYRROLIDIDES /* 7r1c1 DERIV_RING2_PRRLDD_OUTSIDE_PRECUR */

◆ UNDERIV_RN_AcMe

#define UNDERIV_RN_AcMe /* 2r1c3 R-N(-X)--C(=O)Me => R-N(-X)H: DERIV_BRIDGE_tN, X is not H */

◆ UNDERIV_RNH_AcMe

#define UNDERIV_RNH_AcMe /* 2r1c3 R-NH--C(=O)Me => R-NH2: DERIV_BRIDGE_NH */

◆ UNDERIV_RO_COX_BENZOATES

#define UNDERIV_RO_COX_BENZOATES /* 3r1c2 create alcohols from benzoates DERIV_RO_COX */

◆ UNDERIV_RO_COX_Me

#define UNDERIV_RO_COX_Me /* 3r1c1 RO-C(=O)Me => ROH: create alcohols from acetates DERIV_RO_COX */

◆ UNDERIV_RO_COX_PENTAFLOUROBENZOATES

#define UNDERIV_RO_COX_PENTAFLOUROBENZOATES /* 3r1c3 create alcohols from pentafluorobenzoates DERIV_RO_COX -C(=O)C6F5*/

◆ UNDERIV_X_OXIME_TBDMS

#define UNDERIV_X_OXIME_TBDMS /* 5r2c3 DERIV_X_OXIME: >C=N--O-TBDMS */

◆ UNDERIV_X_OXIME_TMS

#define UNDERIV_X_OXIME_TMS /* 5r2c2 DERIV_X_OXIME: >C=N--O-TMS */

◆ UNDERIVATIZE

#define UNDERIVATIZE 1 /* split to possible underivatized fragments */

◆ UNDERIVATIZE_REPORT

#define UNDERIVATIZE_REPORT 1 /* if SdfValue found, add to SdfValue a list of removed deriv. agents */

◆ USE_ALLOCA

#define USE_ALLOCA 0

◆ USE_AUX_RANKING

#define USE_AUX_RANKING 1 /* 1=> get auxiliary ranking to accelerate canonicalization of H layers */

◆ USE_AUX_RANKING_ALL

#define USE_AUX_RANKING_ALL 1 /* 1=> include all vertices in CellGetMinNode() selection 0=> only vertices with highest ranks */

◆ USE_DISTANCES_FOR_RANKING

#define USE_DISTANCES_FOR_RANKING 0 /* 1 => rank ring systems according to distances from terminal */

◆ USE_ISO_SORT_KEY_HFIXED

#define USE_ISO_SORT_KEY_HFIXED

Value:

                                           0  /* 0=> normal mode: merge isotopic taut H to isotopic atom sorting key in
                                           taut H-fixed canonicalization;
                                       1=> add one more "string" iso_sort_Hfixed to the canonicalization */

◆ USE_SYMMETRY_TO_ACCELERATE

#define USE_SYMMETRY_TO_ACCELERATE 1 /*1 => for fast CT canonicalization, to avoid full enumeration */

◆ WORSE_PARITY

#define WORSE_PARITY 2

Typedef Documentation

◆ INCHI_IOS_STRING

typedef struct tagOutputString INCHI_IOS_STRING

◆ INCHI_IOSTREAM

typedef struct tagOutputStream INCHI_IOSTREAM

Data Structures

Macros

Typedefs

Macro Definition Documentation

◆ ABC_CT_NUM_CLOSURES

◆ ADD_6MEMB_AROM_BOND_PARITY

◆ ADD_ChCh_STEREO_CANON_CHK

◆ ADD_CMLPP

◆ ADD_MOVEABLE_O_PLUS

◆ ALL_ALT_AS_AROMATIC

◆ ALLOW_EMPTY_INCHI_AS_INPUT

◆ ALLOW_SUBSTRUCTURE_FILTERING

◆ ALLOW_TAUT_ATTACHMENTS_TO_STEREO_BONDS

◆ ALT_TAUT

◆ ALWAYS_ADD_TG_ON_THE_FLY

◆ ANY_ATOM_IN_ALT_CYCLE

◆ APPLY_IMPLICIT_H_DOWN_RULE

◆ BEST_PARITY

◆ BNS_MARK_EDGE_2_DISCONNECT

◆ BNS_PROTECT_FROM_TAUT

◆ BNS_RAD_SEARCH

◆ bOUTPUT_ONE_STRUCT_TIME [1/2]

◆ bOUTPUT_ONE_STRUCT_TIME [2/2]

◆ BREAK_ALSO_NEIGH_TIE

◆ BREAK_ALSO_NEIGH_TIE_ROTATE

◆ BREAK_ONE_MORE_SC_TIE

◆ bRELEASE_VERSION

◆ bREUSE_INCHI

◆ BUILD_WITH_AMI

◆ BUILD_WITH_ENG_OPTIONS

◆ CANON_FIXH_TRANS

◆ CANON_MODE_CT

◆ CANON_MODE_ISO

◆ CANON_MODE_ISO_STEREO

◆ CANON_MODE_MASK

◆ CANON_MODE_STEREO

◆ CANON_MODE_TAUT

◆ CANON_TAUTOMERS

◆ CHARGED_SALTS_ONLY

◆ CHECK_AROMBOND2ALT

◆ CHECK_C2v_S4_SYMM

◆ CHECK_METAL_VALENCE

◆ CHECK_STRTOL_ATNUMB

◆ CMODE_CT

◆ CMODE_ISO

◆ CMODE_ISO_OUT

◆ CMODE_ISO_STEREO

◆ CMODE_NO_ALT_SBONDS

◆ CMODE_NOEQ_STEREO

◆ CMODE_RACEMIC_STEREO

◆ CMODE_REDNDNT_STEREO

◆ CMODE_RELATIVE_STEREO

◆ CMODE_SB_IGN_ALL_UU

◆ CMODE_SC_IGN_ALL_UU

◆ CMODE_STEREO

◆ CMODE_TAUT

◆ COMPILE_ANSI_ONLY

◆ CT_ATOMID

◆ CT_ATOMID_DONTINCLUDE

◆ CT_ATOMID_IS_CURRANK

◆ CT_ATOMID_IS_INITRANK

◆ CT_GREATER_THAN

◆ CT_INITVALUE

◆ CT_NEIGH_INCREASE

◆ CT_NEIGH_SMALLER

◆ CT_NEIGH_SMALLER_THAN

◆ CT_SMALLEST

◆ DEBUG_POLYMERS

◆ DISABLE_READ_COMPRESSED_INCHI

◆ DISCONNECT_METALS

◆ DISCONNECT_SALTS

◆ DISPLAY_DEBUG_DATA_C_POINT

◆ DISPLAY_ORIG_AT_NUMBERS

◆ DISPLAY_RING_SYSTEMS

◆ DISPLAY_ZZ_AS_STAR

◆ DOUBLE_BOND_NEIGH_LIST

◆ DRAW_AROM_TAUT

◆ EMBED_REC_METALS_INCHI

◆ EQL_H_NUM_TOGETHER

◆ EXCL_ALL_AROM_BOND_PARITY