|
int | DisplayTheWholeStructure (struct tagCANON_GLOBALS *pCG, struct tagINCHI_CLOCK *ic, struct tagStructData *sd, INPUT_PARMS *ip, char *szTitle, INCHI_IOSTREAM *inp_file, INCHI_IOSTREAM *log_file, ORIG_ATOM_DATA *orig_inp_data, long num_inp, int iINChI, int bShowStruct, int bINCHI_LIB_Flag) |
|
int | DisplayStructure (struct tagCANON_GLOBALS *pCG, inp_ATOM *at, int num_at, OAD_Polymer *polymer, int num_removed_H, int bAdd_DT_to_num_H, int nNumRemovedProtons, NUM_H *nNumRemovedProtonsIsotopic, int bIsotopic, int j, INChI **cur_INChI, INChI_Aux **cur_INChI_Aux, int bAbcNumbers, DRAW_PARMS *dp, INCHI_MODE nMode, char *szTitle) |
|
int | ReadInChICoord (INCHI_IOSTREAM *pInp, SEGM_LINE *pLine, int *pState, INChI *pInpInChI[INCHI_NUM][TAUT_NUM], int nNumComponents[INCHI_NUM][TAUT_NUM]) |
|
static int | DoOneStructureEarlyPreprocessing (INCHI_CLOCK *ic, CANON_GLOBALS *pCG, long num_inp, STRUCT_DATA *sd, INPUT_PARMS *ip, INCHI_IOSTREAM *inp_file, INCHI_IOSTREAM *log_file, INCHI_IOSTREAM *out_file, INCHI_IOSTREAM *prb_file, ORIG_ATOM_DATA *orig_inp_data, ORIG_ATOM_DATA *prep_inp_data) |
|
int | ProcessOneStructureExCore (struct tagINCHI_CLOCK *ic, struct tagCANON_GLOBALS *CG, STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle, PINChI2 *pINChI2[INCHI_NUM], PINChI_Aux2 *pINChI_Aux2[INCHI_NUM], INCHI_IOSTREAM *inp_file, INCHI_IOSTREAM *log_file, INCHI_IOSTREAM *out_file, INCHI_IOSTREAM *prb_file, ORIG_ATOM_DATA *orig_inp_data, ORIG_ATOM_DATA *prep_inp_data, long num_inp, INCHI_IOS_STRING *strbuf, unsigned char save_opt_bits) |
|
static ORIG_STRUCT * | OrigAtData_StoreNativeInput (CANON_GLOBALS *pCG, int *nRet, STRUCT_DATA *sd, INPUT_PARMS *ip, ORIG_ATOM_DATA *orig_inp_data, ORIG_STRUCT *pOrigStruct) |
|
static void | PrepareSaveOptBits (unsigned char *save_opt_bits, INPUT_PARMS *ip) |
|
static void | DisplayOrigAndResultStructuresAndComponents (int nRet, INCHI_CLOCK *ic, CANON_GLOBALS *pCG, STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle, PINChI2 *pINChI[INCHI_NUM], PINChI_Aux2 *pINChI_Aux[INCHI_NUM], INCHI_IOSTREAM *inp_file, INCHI_IOSTREAM *log_file, INCHI_IOSTREAM *out_file, ORIG_ATOM_DATA *orig_inp_data, ORIG_ATOM_DATA *prep_inp_data, long num_inp, int maxINChI, COMP_ATOM_DATA composite_norm_data[INCHI_NUM][TAUT_NUM+1]) |
|
static void | SaveOkProcessedMolfile (int nRet, STRUCT_DATA *sd, INPUT_PARMS *ip, INCHI_IOSTREAM *prb_file, INCHI_IOSTREAM *inp_file) |
|
static int | mark_atoms_to_delete_or_renumber (ORIG_ATOM_DATA *orig_at_data, OAD_StructureEdits *ed, int *at_renum) |
|
static int | set_renumbered_or_delete (int *number, int *buf, int nelems, int *renum, int base) |
|
static void | swap_atoms_xyz (ORIG_ATOM_DATA *orig_at_data, int ia1, int ia2) |
|
int | ProcessOneStructure (INCHI_CLOCK *ic, CANON_GLOBALS *pCG, STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle, PINChI2 *pINChI[INCHI_NUM], PINChI_Aux2 *pINChI_Aux[INCHI_NUM], INCHI_IOSTREAM *inp_file, INCHI_IOSTREAM *log_file, INCHI_IOSTREAM *out_file, INCHI_IOSTREAM *prb_file, ORIG_ATOM_DATA *orig_inp_data, ORIG_ATOM_DATA *prep_inp_data, long num_inp, INCHI_IOS_STRING *strbuf, unsigned char save_opt_bits) |
|
int | OrigAtData_SaveMolfile (ORIG_ATOM_DATA *orig_inp_data, STRUCT_DATA *sd, INPUT_PARMS *ip, long num_inp, INCHI_IOSTREAM *out_file) |
|
int | CreateOneStructureINChI (CANON_GLOBALS *pCG, INCHI_CLOCK *ic, STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle, PINChI2 *pINChI2[INCHI_NUM], PINChI_Aux2 *pINChI_Aux2[INCHI_NUM], int iINChI, INCHI_IOSTREAM *inp_file, INCHI_IOSTREAM *log_file, INCHI_IOSTREAM *out_file, INCHI_IOSTREAM *prb_file, ORIG_ATOM_DATA *orig_inp_data, ORIG_ATOM_DATA *prep_inp_data, COMP_ATOM_DATA composite_norm_data2[][TAUT_NUM+1], long num_inp, INCHI_IOS_STRING *strbuf, NORM_CANON_FLAGS *pncFlags) |
|
int | CreateOneComponentINChI (CANON_GLOBALS *pCG, INCHI_CLOCK *ic, STRUCT_DATA *sd, INPUT_PARMS *ip, INP_ATOM_DATA *inp_cur_data, ORIG_ATOM_DATA *orig_inp_data, PINChI2 *pINChI, PINChI_Aux2 *pINChI_Aux, int iINChI, int i, long num_inp, INP_ATOM_DATA **inp_norm_data, NORM_CANON_FLAGS *pncFlags, INCHI_IOSTREAM *log_file) |
|
int | ProcessOneStructureEx (struct tagINCHI_CLOCK *ic, struct tagCANON_GLOBALS *CG, STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle, PINChI2 *pINChI2[INCHI_NUM], PINChI_Aux2 *pINChI_Aux2[INCHI_NUM], INCHI_IOSTREAM *inp_file, INCHI_IOSTREAM *log_file, INCHI_IOSTREAM *out_file, INCHI_IOSTREAM *prb_file, ORIG_ATOM_DATA *orig_inp_data, ORIG_ATOM_DATA *prep_inp_data, long num_inp, INCHI_IOS_STRING *strbuf, unsigned char save_opt_bits) |
|
int | PreprocessPolymerCRUData (struct tagINCHI_CLOCK *ic, struct tagCANON_GLOBALS *CG, STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle, PINChI2 *pINChI2[INCHI_NUM], PINChI_Aux2 *pINChI_Aux2[INCHI_NUM], INCHI_IOSTREAM *inp_file, INCHI_IOSTREAM *log_file, INCHI_IOSTREAM *out_file, INCHI_IOSTREAM *prb_file, ORIG_ATOM_DATA *orig_inp_data, ORIG_ATOM_DATA *prep_inp_data, long num_inp, INCHI_IOS_STRING *strbuf, unsigned char save_opt_bits, char **sinchi_noedits, char **saux_noedits) |
|
int | OAD_StructureEdits_Apply (STRUCT_DATA *sd, INPUT_PARMS *ip, ORIG_ATOM_DATA *orig_at_data, OAD_StructureEdits *ed, int *ret) |
|
int | ValidateAndPreparePolymerAndPseudoatoms (struct tagINCHI_CLOCK *ic, struct tagCANON_GLOBALS *CG, STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle, PINChI2 *pINChI2[INCHI_NUM], PINChI_Aux2 *pINChI_Aux2[INCHI_NUM], INCHI_IOSTREAM *inp_file, INCHI_IOSTREAM *log_file, INCHI_IOSTREAM *out_file, INCHI_IOSTREAM *prb_file, ORIG_ATOM_DATA *orig_inp_data, ORIG_ATOM_DATA *prep_inp_data, long num_inp, INCHI_IOS_STRING *strbuf, unsigned char save_opt_bits, int *mind_polymers) |
|
int | OAD_ProcessOneStructureNoEdits (struct tagINCHI_CLOCK *ic, struct tagCANON_GLOBALS *CG, STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle, PINChI2 *pINChI2[INCHI_NUM], PINChI_Aux2 *pINChI_Aux2[INCHI_NUM], INCHI_IOSTREAM *inp_file, INCHI_IOSTREAM *log_file, INCHI_IOSTREAM *out_file, INCHI_IOSTREAM *prb_file, ORIG_ATOM_DATA *orig_inp_data, ORIG_ATOM_DATA *prep_inp_data, long num_inp, INCHI_IOS_STRING *strbuf, unsigned char save_opt_bits, int *n_pzz, char **sinchi, char **saux) |
|
int | OAD_ProcessOneStructure105Plus (struct tagINCHI_CLOCK *ic, struct tagCANON_GLOBALS *CG, STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle, PINChI2 *pINChI2[INCHI_NUM], PINChI_Aux2 *pINChI_Aux2[INCHI_NUM], INCHI_IOSTREAM *inp_file, INCHI_IOSTREAM *log_file, INCHI_IOSTREAM *out_file, INCHI_IOSTREAM *prb_file, ORIG_ATOM_DATA *orig_inp_data, ORIG_ATOM_DATA *prep_inp_data, long num_inp, INCHI_IOS_STRING *strbuf, unsigned char save_opt_bits, char **sinchi, char **saux) |
|