runichi3.c File Reference

#include <stdlib.h>
#include <string.h>
#include <stdarg.h>
#include <errno.h>
#include <limits.h>
#include <math.h>
#include <ctype.h>
#include "mode.h"
#include "ichitime.h"
#include "ichimain.h"
#include "ichi_io.h"
#include "mol_fmt.h"
#include "inchi_api.h"
#include "readinch.h"
#include "inchi_gui.h"
#include "inpdef.h"
#include "bcf_s.h"

Include dependency graph for runichi3.c:

Functions
static int	OrigAtData_bCheckUnusualValences (ORIG_ATOM_DATA *orig_at_data, int bAddIsoH, char *pStrErrStruct, int bNoWarnings)
static void	OAD_PolymerUnit_RemoveLinkFromCRUChain (int at1, int at2, int *nbonds, int **bonds)
int	OrigAtData_Duplicate (ORIG_ATOM_DATA *new_orig_atom, ORIG_ATOM_DATA *orig_atom)
int	PreprocessOneStructure (struct tagINCHI_CLOCK *ic, STRUCT_DATA *sd, INPUT_PARMS *ip, ORIG_ATOM_DATA *orig_inp_data, ORIG_ATOM_DATA *prep_inp_data)
int	CreateCompositeNormAtom (COMP_ATOM_DATA *composite_norm_data, INP_ATOM_DATA2 *all_inp_norm_data, int num_components)
void	OrigAtData_DebugTrace (ORIG_ATOM_DATA *d)
OAD_PolymerUnit *	OAD_PolymerUnit_New (int maxatoms, int maxbonds, int id, int label, int type, int subtype, int conn, char *smt, int na, INT_ARRAY *alist, int nb, INT_ARRAY *blist, int nbkbonds, int **bkbonds)
OAD_PolymerUnit *	OAD_PolymerUnit_CreateCopy (OAD_PolymerUnit *u)
void	OAD_PolymerUnit_Free (OAD_PolymerUnit *unit)
int	OAD_PolymerUnit_CompareAtomListsMod (OAD_PolymerUnit *u1, OAD_PolymerUnit *u2)
int	OAD_PolymerUnit_CompareAtomLists (OAD_PolymerUnit *u1, OAD_PolymerUnit *u2)
int	OAD_PolymerUnit_OrderBondAtomsAndBondsThemselves (OAD_PolymerUnit *u, int n_star_atoms, int *star_atoms)
int	OAD_ValidatePolymerAndPseudoElementData (ORIG_ATOM_DATA *orig_at_data, int treat_polymers, int bNPZz, char *pStrErr, int bNoWarnings)
int	UnMarkRingSystemsInp (inp_ATOM *at, int num_atoms)
int	OAD_Polymer_CyclizeCloseableUnits (ORIG_ATOM_DATA *orig_at_data, int treat_polymers, char *pStrErr, int bNoWarnings)
int	OAD_PolymerUnit_HasMetal (OAD_PolymerUnit *u, inp_ATOM *at)
void	OAD_Polymer_Free (OAD_Polymer *pd)
void	OAD_PolymerUnit_UnlinkCapsAndConnectEndAtoms (OAD_PolymerUnit *unit, ORIG_ATOM_DATA *orig_inp_data, int *err, char *pStrErr)
void	OAD_PolymerUnit_FindEndsAndCaps (OAD_PolymerUnit *unit, ORIG_ATOM_DATA *orig_at_data, int *end1, int *cap1, int *cap1_is_star, int *end2, int *cap2, int *cap2_is_star, int *err, char *pStrErr)
void	OAD_PolymerUnit_SetEndsAndCaps (OAD_PolymerUnit *unit, ORIG_ATOM_DATA *orig_at_data, int *err, char *pStrErr)
int	OAD_Polymer_PrepareWorkingSet (OAD_Polymer *p, int *cano_nums, int *compnt_nums, OAD_PolymerUnit **units2, int *unum)
int	OrigAtData_RemoveHalfBond (int this_atom, int other_atom, inp_ATOM *at, int *bond_type, int *bond_stereo)
int	OrigAtData_RemoveAtom (ORIG_ATOM_DATA *orig_at_data, int iatom)
int	OrigAtData_RemoveBond (int this_atom, int other_atom, inp_ATOM *at, int *bond_type, int *bond_stereo, int *num_inp_bonds)
int	OrigAtData_AddBond (int this_atom, int other_atom, inp_ATOM *at, int bond_type, int bond_stereo, int *num_bonds)
int	OrigAtData_AddSingleStereolessBond (int this_atom, int other_atom, inp_ATOM *at, int *num_bonds)
int	OrigAtData_IncreaseBondOrder (int this_atom, int other_atom, inp_ATOM *at)
int	OrigAtData_DecreaseBondOrder (int this_atom, int other_atom, inp_ATOM *at)
void	OAD_CollectFragmentBondsAndAtoms (ORIG_ATOM_DATA *orig_at_data, int nforbidden, int *forbidden_orig, int *n_fragbonds, int **fragbonds, int *n_fragatoms, int *fragatoms, int *err, char *pStrErr)
void	OAD_Polymer_FindBackbones (ORIG_ATOM_DATA *at_data, COMP_ATOM_DATA *composite_norm_data, int *err, char *pStrErr)
void	OAD_CollectBackboneAtoms (ORIG_ATOM_DATA *at_data, int na, int *alist, int end_atom1, int end_atom2, int *nbkatoms, int *bkatoms, int *err, char *pStrErr)
int	OAD_CollectReachableAtoms (ORIG_ATOM_DATA *orig_at_data, int start_atom, int nforbidden_bonds, int *forbidden_bond_atoms, int *n_reachable, int *reachable, int *err, char *pStrErr)
void	OAD_CollectBackboneBonds (ORIG_ATOM_DATA *at_data, int na, int *alist, int end_atom1, int end_atom2, int *nbkbonds, int **bkbonds, int *err, char *pStrErr)
void	OAD_PolymerUnit_DelistIntraRingBackboneBonds (OAD_PolymerUnit *unit, ORIG_ATOM_DATA *at_data, int *err, char *pStrErr)
int	OAD_Polymer_FindRingSystems (OAD_Polymer *pd, inp_ATOM *at, int nat, int *num_inp_bonds, int *num_ring_sys, int *size_ring_sys, int start)
void	OAD_Polymer_SetAtProps (OAD_Polymer *pd, inp_ATOM *at, int nat, int *num_inp_bonds, OAD_AtProps *aprops, int *cano_nums)
void	OAD_PolymerUnit_DelistHighOrderBackboneBonds (OAD_PolymerUnit *unit, ORIG_ATOM_DATA *orig_at_data, COMP_ATOM_DATA *composite_norm_data, int *err, char *pStrErr)
void	OAD_PolymerUnit_DebugTrace (OAD_PolymerUnit *u)
void	OAD_Polymer_DebugTrace (OAD_Polymer *p)
int	OAD_Polymer_GetRepresentation (OAD_Polymer *p)
void	OAD_Polymer_SmartReopenCyclizedUnits (OAD_Polymer *p, inp_ATOM *at, int nat, int *num_inp_bonds)
void	OAD_PolymerUnit_ReopenCyclized (OAD_PolymerUnit *u, inp_ATOM *at, OAD_AtProps *aprops, int nat, int *num_inp_bonds)
int	OAD_PolymerUnit_SetReopeningDetails (OAD_PolymerUnit *u, inp_ATOM *at)
void	OAD_PolymerUnit_SortBackboneBondsAndSetSeniors (OAD_PolymerUnit *u, inp_ATOM *at, OAD_AtProps *aprops, int *senior_bond)
void	OAD_PolymerUnit_SortBackboneBonds (OAD_PolymerUnit *u, OAD_AtProps *aprops, int *bnum)
int	OAD_Polymer_CompareBackboneBondsSeniority (int *b1, int *b2, OAD_AtProps *aprops)
int	OAD_Polymer_CompareRanksOfTwoAtoms (int atom1, int atom2, OAD_AtProps *aprops)
int	OAD_Polymer_IsFirstAtomRankLower (int atom1, int atom2, OAD_AtProps *aprops)
void	OAD_ValidateAndSortOutPseudoElementAtoms (ORIG_ATOM_DATA *orig_at_data, int treat_polymers, int bNPZz, int *err, char *pStrErr)
int	Inp_Atom_GetBondType (inp_ATOM *at, int iatom1, int iatom2)

Function Documentation

CreateCompositeNormAtom()

int CreateCompositeNormAtom	(	COMP_ATOM_DATA *	composite_norm_data,
		INP_ATOM_DATA2 *	all_inp_norm_data,
		int	num_components
	)

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Inp_Atom_GetBondType()

int Inp_Atom_GetBondType	(	inp_ATOM *	at,
		int	iatom1,
		int	iatom2
	)

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OAD_CollectBackboneAtoms()

void OAD_CollectBackboneAtoms	(	ORIG_ATOM_DATA *	at_data,
		int	na,
		int *	alist,
		int	end_atom1,
		int	end_atom2,
		int *	nbkatoms,
		int *	bkatoms,
		int *	err,
		char *	pStrErr
	)

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OAD_CollectBackboneBonds()

void OAD_CollectBackboneBonds	(	ORIG_ATOM_DATA *	at_data,
		int	na,
		int *	alist,
		int	end_atom1,
		int	end_atom2,
		int *	nbkbonds,
		int **	bkbonds,
		int *	err,
		char *	pStrErr
	)

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OAD_CollectFragmentBondsAndAtoms()

void OAD_CollectFragmentBondsAndAtoms	(	ORIG_ATOM_DATA *	orig_at_data,
		int	nforbidden,
		int *	forbidden_orig,
		int *	n_fragbonds,
		int **	fragbonds,
		int *	n_fragatoms,
		int *	fragatoms,
		int *	err,
		char *	pStrErr
	)

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OAD_CollectReachableAtoms()

int OAD_CollectReachableAtoms	(	ORIG_ATOM_DATA *	orig_at_data,
		int	start_atom,
		int	nforbidden_bonds,
		int *	forbidden_bond_atoms,
		int *	n_reachable,
		int *	reachable,
		int *	err,
		char *	pStrErr
	)

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OAD_Polymer_CompareBackboneBondsSeniority()

int OAD_Polymer_CompareBackboneBondsSeniority	(	int *	b1,
		int *	b2,
		OAD_AtProps *	aprops
	)

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OAD_Polymer_CompareRanksOfTwoAtoms()

int OAD_Polymer_CompareRanksOfTwoAtoms	(	int	atom1,
		int	atom2,
		OAD_AtProps *	aprops
	)

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OAD_Polymer_CyclizeCloseableUnits()

int OAD_Polymer_CyclizeCloseableUnits	(	ORIG_ATOM_DATA *	orig_at_data,
		int	treat_polymers,
		char *	pStrErr,
		int	bNoWarnings
	)

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OAD_Polymer_DebugTrace()

void OAD_Polymer_DebugTrace

(

OAD_Polymer *

p

)

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OAD_Polymer_FindBackbones()

void OAD_Polymer_FindBackbones	(	ORIG_ATOM_DATA *	at_data,
		COMP_ATOM_DATA *	composite_norm_data,
		int *	err,
		char *	pStrErr
	)

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OAD_Polymer_FindRingSystems()

int OAD_Polymer_FindRingSystems	(	OAD_Polymer *	pd,
		inp_ATOM *	at,
		int	nat,
		int *	num_inp_bonds,
		int *	num_ring_sys,
		int *	size_ring_sys,
		int	start
	)

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OAD_Polymer_Free()

void OAD_Polymer_Free

(

OAD_Polymer *

pd

)

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OAD_Polymer_GetRepresentation()

int OAD_Polymer_GetRepresentation

(

OAD_Polymer *

p

)

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OAD_Polymer_IsFirstAtomRankLower()

int OAD_Polymer_IsFirstAtomRankLower	(	int	atom1,
		int	atom2,
		OAD_AtProps *	aprops
	)

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OAD_Polymer_PrepareWorkingSet()

int OAD_Polymer_PrepareWorkingSet	(	OAD_Polymer *	p,
		int *	cano_nums,
		int *	compnt_nums,
		OAD_PolymerUnit **	units2,
		int *	unum
	)

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OAD_Polymer_SetAtProps()

void OAD_Polymer_SetAtProps	(	OAD_Polymer *	pd,
		inp_ATOM *	at,
		int	nat,
		int *	num_inp_bonds,
		OAD_AtProps *	aprops,
		int *	cano_nums
	)

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OAD_Polymer_SmartReopenCyclizedUnits()

void OAD_Polymer_SmartReopenCyclizedUnits	(	OAD_Polymer *	p,
		inp_ATOM *	at,
		int	nat,
		int *	num_inp_bonds
	)

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OAD_PolymerUnit_CompareAtomLists()

int OAD_PolymerUnit_CompareAtomLists	(	OAD_PolymerUnit *	u1,
		OAD_PolymerUnit *	u2
	)

OAD_PolymerUnit_CompareAtomListsMod()

int OAD_PolymerUnit_CompareAtomListsMod	(	OAD_PolymerUnit *	u1,
		OAD_PolymerUnit *	u2
	)

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OAD_PolymerUnit_CreateCopy()

OAD_PolymerUnit * OAD_PolymerUnit_CreateCopy

(

OAD_PolymerUnit *

u

)

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OAD_PolymerUnit_DebugTrace()

void OAD_PolymerUnit_DebugTrace

(

OAD_PolymerUnit *

u

)

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OAD_PolymerUnit_DelistHighOrderBackboneBonds()

void OAD_PolymerUnit_DelistHighOrderBackboneBonds	(	OAD_PolymerUnit *	unit,
		ORIG_ATOM_DATA *	orig_at_data,
		COMP_ATOM_DATA *	composite_norm_data,
		int *	err,
		char *	pStrErr
	)

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OAD_PolymerUnit_DelistIntraRingBackboneBonds()

void OAD_PolymerUnit_DelistIntraRingBackboneBonds	(	OAD_PolymerUnit *	unit,
		ORIG_ATOM_DATA *	at_data,
		int *	err,
		char *	pStrErr
	)

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OAD_PolymerUnit_FindEndsAndCaps()

void OAD_PolymerUnit_FindEndsAndCaps	(	OAD_PolymerUnit *	unit,
		ORIG_ATOM_DATA *	orig_at_data,
		int *	end1,
		int *	cap1,
		int *	cap1_is_star,
		int *	end2,
		int *	cap2,
		int *	cap2_is_star,
		int *	err,
		char *	pStrErr
	)

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OAD_PolymerUnit_Free()

void OAD_PolymerUnit_Free

(

OAD_PolymerUnit *

unit

)

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OAD_PolymerUnit_HasMetal()

int OAD_PolymerUnit_HasMetal	(	OAD_PolymerUnit *	u,
		inp_ATOM *	at
	)

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OAD_PolymerUnit_New()

OAD_PolymerUnit * OAD_PolymerUnit_New	(	int	maxatoms,
		int	maxbonds,
		int	id,
		int	label,
		int	type,
		int	subtype,
		int	conn,
		char *	smt,
		int	na,
		INT_ARRAY *	alist,
		int	nb,
		INT_ARRAY *	blist,
		int	nbkbonds,
		int **	bkbonds
	)

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OAD_PolymerUnit_OrderBondAtomsAndBondsThemselves()

int OAD_PolymerUnit_OrderBondAtomsAndBondsThemselves	(	OAD_PolymerUnit *	u,
		int	n_star_atoms,
		int *	star_atoms
	)

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OAD_PolymerUnit_RemoveLinkFromCRUChain()

void OAD_PolymerUnit_RemoveLinkFromCRUChain ( int  at1, int  at2, int *  nbonds, int **  bonds  )

static

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OAD_PolymerUnit_ReopenCyclized()

void OAD_PolymerUnit_ReopenCyclized	(	OAD_PolymerUnit *	u,
		inp_ATOM *	at,
		OAD_AtProps *	aprops,
		int	nat,
		int *	num_inp_bonds
	)

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OAD_PolymerUnit_SetEndsAndCaps()

void OAD_PolymerUnit_SetEndsAndCaps	(	OAD_PolymerUnit *	unit,
		ORIG_ATOM_DATA *	orig_at_data,
		int *	err,
		char *	pStrErr
	)

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OAD_PolymerUnit_SetReopeningDetails()

int OAD_PolymerUnit_SetReopeningDetails	(	OAD_PolymerUnit *	u,
		inp_ATOM *	at
	)

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OAD_PolymerUnit_SortBackboneBonds()

void OAD_PolymerUnit_SortBackboneBonds	(	OAD_PolymerUnit *	u,
		OAD_AtProps *	aprops,
		int *	bnum
	)

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OAD_PolymerUnit_SortBackboneBondsAndSetSeniors()

void OAD_PolymerUnit_SortBackboneBondsAndSetSeniors	(	OAD_PolymerUnit *	u,
		inp_ATOM *	at,
		OAD_AtProps *	aprops,
		int *	senior_bond
	)

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OAD_PolymerUnit_UnlinkCapsAndConnectEndAtoms()

void OAD_PolymerUnit_UnlinkCapsAndConnectEndAtoms	(	OAD_PolymerUnit *	unit,
		ORIG_ATOM_DATA *	orig_inp_data,
		int *	err,
		char *	pStrErr
	)

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OAD_ValidateAndSortOutPseudoElementAtoms()

void OAD_ValidateAndSortOutPseudoElementAtoms	(	ORIG_ATOM_DATA *	orig_at_data,
		int	treat_polymers,
		int	bNPZz,
		int *	err,
		char *	pStrErr
	)

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OAD_ValidatePolymerAndPseudoElementData()

int OAD_ValidatePolymerAndPseudoElementData	(	ORIG_ATOM_DATA *	orig_at_data,
		int	treat_polymers,
		int	bNPZz,
		char *	pStrErr,
		int	bNoWarnings
	)

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OrigAtData_AddBond()

int OrigAtData_AddBond	(	int	this_atom,
		int	other_atom,
		inp_ATOM *	at,
		int	bond_type,
		int	bond_stereo,
		int *	num_bonds
	)

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OrigAtData_AddSingleStereolessBond()

int OrigAtData_AddSingleStereolessBond	(	int	this_atom,
		int	other_atom,
		inp_ATOM *	at,
		int *	num_bonds
	)

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OrigAtData_bCheckUnusualValences()

int OrigAtData_bCheckUnusualValences ( ORIG_ATOM_DATA *  orig_at_data, int  bAddIsoH, char *  pStrErrStruct, int  bNoWarnings  )

static

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OrigAtData_DebugTrace()

void OrigAtData_DebugTrace

(

ORIG_ATOM_DATA *

d

)

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OrigAtData_DecreaseBondOrder()

int OrigAtData_DecreaseBondOrder	(	int	this_atom,
		int	other_atom,
		inp_ATOM *	at
	)

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OrigAtData_Duplicate()

int OrigAtData_Duplicate	(	ORIG_ATOM_DATA *	new_orig_atom,
		ORIG_ATOM_DATA *	orig_atom
	)

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OrigAtData_IncreaseBondOrder()

int OrigAtData_IncreaseBondOrder	(	int	this_atom,
		int	other_atom,
		inp_ATOM *	at
	)

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OrigAtData_RemoveAtom()

int OrigAtData_RemoveAtom	(	ORIG_ATOM_DATA *	orig_at_data,
		int	iatom
	)

OrigAtData_RemoveBond()

int OrigAtData_RemoveBond	(	int	this_atom,
		int	other_atom,
		inp_ATOM *	at,
		int *	bond_type,
		int *	bond_stereo,
		int *	num_inp_bonds
	)

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OrigAtData_RemoveHalfBond()

int OrigAtData_RemoveHalfBond	(	int	this_atom,
		int	other_atom,
		inp_ATOM *	at,
		int *	bond_type,
		int *	bond_stereo
	)

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PreprocessOneStructure()

int PreprocessOneStructure	(	struct tagINCHI_CLOCK *	ic,
		STRUCT_DATA *	sd,
		INPUT_PARMS *	ip,
		ORIG_ATOM_DATA *	orig_inp_data,
		ORIG_ATOM_DATA *	prep_inp_data
	)

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UnMarkRingSystemsInp()

int UnMarkRingSystemsInp	(	inp_ATOM *	at,
		int	num_atoms
	)

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