#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)
	Create a new polymer unit.

OAD_PolymerUnit *	OAD_PolymerUnit_CreateCopy (OAD_PolymerUnit *u)
	Create a copy of a polymer unit.

void	OAD_PolymerUnit_Free (OAD_PolymerUnit *unit)
	Free a polymer unit.

int	OAD_PolymerUnit_CompareAtomListsMod (OAD_PolymerUnit u1, OAD_PolymerUnit u2)
	Compare two polymer units based on their atom lists with modifications.

int	OAD_PolymerUnit_CompareAtomLists (OAD_PolymerUnit u1, OAD_PolymerUnit u2)
	Compare two polymer units based on their atom lists.

int	OAD_PolymerUnit_OrderBondAtomsAndBondsThemselves (OAD_PolymerUnit u, int n_star_atoms, int star_atoms)
	Order bond atoms and bonds themselves in a polymer unit.

int	OAD_ValidatePolymerAndPseudoElementData (ORIG_ATOM_DATA orig_at_data, int treat_polymers, int bNPZz, char pStrErr, int bNoWarnings)
	Validate polymer and pseudo-element data in the original atom data.

int	UnMarkRingSystemsInp (inp_ATOM *at, int num_atoms)
	Unmark ring systems in the input atoms.

int	OAD_Polymer_CyclizeCloseableUnits (ORIG_ATOM_DATA orig_at_data, int treat_polymers, char pStrErr, int bNoWarnings)
	Cyclize closeable units in the original atom data.

int	OAD_PolymerUnit_HasMetal (OAD_PolymerUnit u, inp_ATOM at)
	Check if a polymer unit has a specific atom (e.g., metal)

void	OAD_Polymer_Free (OAD_Polymer *pd)
	Free polymer data structure.

void	OAD_PolymerUnit_UnlinkCapsAndConnectEndAtoms (OAD_PolymerUnit unit, ORIG_ATOM_DATA orig_inp_data, int err, char pStrErr)
	Unlink caps and connect end atoms of a polymer unit.

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)
	Find the ends and caps of a polymer unit.

void	OAD_PolymerUnit_SetEndsAndCaps (OAD_PolymerUnit unit, ORIG_ATOM_DATA orig_at_data, int err, char pStrErr)
	Set the ends and caps of a polymer unit.

int	OAD_Polymer_PrepareWorkingSet (OAD_Polymer p, int cano_nums, int compnt_nums, OAD_PolymerUnit units2, int unum)
	Prepare working set for polymer processing (replace original atom numbers in polymer data with (canonical num + 1))

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)
	Find backbones in the original atom data.

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)
	Collect backbone atoms from a polymer unit.

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)
	Find reachable atoms from a given start atom.

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)
	Collect backbone bonds from a polymer unit.

void	OAD_PolymerUnit_DelistIntraRingBackboneBonds (OAD_PolymerUnit unit, ORIG_ATOM_DATA at_data, int err, char pStrErr)
	Collect backbone bonds from a polymer unit and delist intra-ring backbone bonds.

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)
	Find ring systems in the polymer data.

void	OAD_Polymer_SetAtProps (OAD_Polymer pd, inp_ATOM at, int nat, int num_inp_bonds, OAD_AtProps aprops, int *cano_nums)
	Set atom properties for the polymer data.

void	OAD_PolymerUnit_DelistHighOrderBackboneBonds (OAD_PolymerUnit unit, ORIG_ATOM_DATA orig_at_data, COMP_ATOM_DATA composite_norm_data, int err, char *pStrErr)
	Collect high-order backbone bonds from a polymer unit.

void	OAD_PolymerUnit_DebugTrace (OAD_PolymerUnit *u)
	Debug trace for a polymer unit (print the whole polymer unit)

void	OAD_Polymer_DebugTrace (OAD_Polymer *p)
	Debug trace for polymer data structure (print the whole polymer data)

int	OAD_Polymer_GetRepresentation (OAD_Polymer *p)
	Get polymer representation type.

void	OAD_Polymer_SmartReopenCyclizedUnits (OAD_Polymer p, inp_ATOM at, int nat, int *num_inp_bonds)
	Smartly reopen cyclized units in the original atom data (open pre-cyclized CRUs appropriately (i.e., make frame shift))

void	OAD_PolymerUnit_ReopenCyclized (OAD_PolymerUnit u, inp_ATOM at, OAD_AtProps aprops, int nat, int num_inp_bonds)
	Collect backbone atoms from a polymer unit.

int	OAD_PolymerUnit_SetReopeningDetails (OAD_PolymerUnit u, inp_ATOM at)
	Set reopening details for a polymer unit.

void	OAD_PolymerUnit_SortBackboneBondsAndSetSeniors (OAD_PolymerUnit u, inp_ATOM at, OAD_AtProps aprops, int senior_bond)
	Sort backbone bonds and set seniors for a polymer unit.

void	OAD_PolymerUnit_SortBackboneBonds (OAD_PolymerUnit u, OAD_AtProps aprops, int *bnum)
	Collect backbone bonds from a polymer unit and sort them.

int	OAD_Polymer_CompareBackboneBondsSeniority (int b1, int b2, OAD_AtProps *aprops)
	Compare backbone bonds seniority (for sorting SRU cyclizing bonds (PS=='frame-shift') in descending order)

int	OAD_Polymer_CompareRanksOfTwoAtoms (int atom1, int atom2, OAD_AtProps *aprops)
	Compare ranks of two atoms (compare seniority of two atoms in polymer SRU)

int	OAD_Polymer_IsFirstAtomRankLower (int atom1, int atom2, OAD_AtProps *aprops)
	Check if the first atom has a lower rank than the second atom (check seniority of two atoms in polymer SRU)

void	OAD_ValidateAndSortOutPseudoElementAtoms (ORIG_ATOM_DATA orig_at_data, int treat_polymers, int bNPZz, int err, char *pStrErr)
	Validate and sort out pseudo-element atoms in the original atom data.

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
	)

Collect backbone atoms from a polymer unit.

Parameters

at_data	Pointer to the original atom data
na	The number of atoms
alist	Array of atom indices
end_atom1	The first end atom
end_atom2	The second end atom
nbkatoms	Pointer to the number of backbone atoms
bkatoms	Pointer to the array of backbone atoms
err	Pointer to the error status
pStrErr	Pointer to the error string

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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
	)

Collect backbone bonds from a polymer unit.

Parameters

at_data	Pointer to the original atom data
na	The number of atoms
alist	Array of atom indices
end_atom1	The first end atom
end_atom2	The second end atom
nbkbonds	Pointer to the number of backbone bonds
bkbonds	Pointer to the array of backbone bonds
err	Pointer to the error status
pStrErr	Pointer to the error string

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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_bonds,
		int *	n_reachable,
		int *	reachable,
		int *	err,
		char *	pStrErr
	)

Find reachable atoms from a given start atom.

Parameters

orig_at_data	Pointer to the original atom data
start_atom	The starting atom
nforbidden_bonds	The number of forbidden bonds
forbidden_bonds	Array of forbidden bonds
n_reachable	Pointer to the number of reachable atoms
reachable	Pointer to the array of reachable atoms
err	Pointer to the error status
pStrErr	Pointer to the error string

Returns: int Status code

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◆ OAD_Polymer_CompareBackboneBondsSeniority()

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

Compare backbone bonds seniority (for sorting SRU cyclizing bonds (PS=='frame-shift') in descending order)

Parameters

b1	Pointer to first backbone bond
b2	Pointer to second backbone bond
aprops	Pointer to atom properties structure

Returns: int Comparison result (-1 if b1 < b2, 0 if equal, 1 if b1 > b2)

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◆ OAD_Polymer_CompareRanksOfTwoAtoms()

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

Compare ranks of two atoms (compare seniority of two atoms in polymer SRU)

Parameters

atom1	Index of the first atom
atom2	Index of the second atom
aprops	Pointer to atom properties structure

Returns: int Comparison result

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◆ OAD_Polymer_CyclizeCloseableUnits()

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

Cyclize closeable units in the original atom data.

Parameters

orig_at_data	Pointer to original atom data structure
use_zz	Flag indicating whether to use Zz atoms
pStrErr	Pointer to error string
bNoWarnings	Flag indicating whether to suppress warnings

Returns: int Status code

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◆ OAD_Polymer_DebugTrace()

void OAD_Polymer_DebugTrace ( OAD_Polymer * p )

Debug trace for polymer data structure (print the whole polymer data)

Parameters

p	Pointer to polymer data structure

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◆ OAD_Polymer_FindBackbones()

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

Find backbones in the original atom data.

Parameters

where_to_look	Pointer to original atom data structure
composite_norm_data	Pointer to composite atom data structure
err	Pointer to error code
pStrErr	Pointer to error string

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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
	)

Find ring systems in the polymer data.

Parameters

pd	Pointer to polymer data structure
at	Array of input atoms
nat	Number of input atoms
num_inp_bonds	Pointer to number of input bonds
num_ring_sys	Pointer to number of ring systems found
size_ring_sys	Pointer to size of ring systems found
start	Starting atom index

Returns: int Status code

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◆ OAD_Polymer_Free()

void OAD_Polymer_Free ( OAD_Polymer * p )

Free polymer data structure.

Parameters

p	Pointer to polymer data structure

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◆ OAD_Polymer_GetRepresentation()

int OAD_Polymer_GetRepresentation ( OAD_Polymer * p )

Get polymer representation type.

Parameters

p	Pointer to polymer data structure

Returns: int Polymer representation type (NO_POLYMER, POLYMER_REPRESENTATION_SOURCE_BASED, POLYMER_REPRESENTATION_STRUCTURE_BASED, POLYMER_REPRESENTATION_MIXED,POLYMER_REPRESENTATION_UNRECOGNIZED)

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◆ OAD_Polymer_IsFirstAtomRankLower()

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

Check if the first atom has a lower rank than the second atom (check seniority of two atoms in polymer SRU)

Parameters

atom1	Index of the first atom
atom2	Index of the second atom
aprops	Pointer to atom properties structure

Returns: int 1 if atom1 has a lower rank than atom2, 0 otherwise

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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
	)

Prepare working set for polymer processing (replace original atom numbers in polymer data with (canonical num + 1))

Parameters

p	Pointer to polymer data structure
cano_nums	Pointer to canonical numbers array
compnt_nums	Pointer to component numbers array
units2	Pointer to array of polymer units (a copy of original polymer units with updated atom numbers)
unum	Pointer to number of polymer units

Returns: int Status code

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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
	)

Set atom properties for the polymer data.

Parameters

pd	Pointer to polymer data structure
at	Array of input atoms
nat	Number of input atoms
num_inp_bonds	Pointer to number of input bonds
aprops	Pointer to atom properties structure
cano_nums	Pointer to canonical numbers array

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◆ OAD_Polymer_SmartReopenCyclizedUnits()

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

Smartly reopen cyclized units in the original atom data (open pre-cyclized CRUs appropriately (i.e., make frame shift))

Parameters

p	Pointer to polymer data structure
at	Pointer to input atom data
nat	Number of input atoms
num_inp_bonds	Pointer to number of input bonds

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◆ OAD_PolymerUnit_CompareAtomLists()

int OAD_PolymerUnit_CompareAtomLists	(	OAD_PolymerUnit *	u1,
		OAD_PolymerUnit *	u2
	)

Compare two polymer units based on their atom lists.

Parameters

u1	Pointer to the first polymer unit
u2	Pointer to the second polymer unit

Returns: int comparison result (-1, 0, 1)

◆ OAD_PolymerUnit_CompareAtomListsMod()

int OAD_PolymerUnit_CompareAtomListsMod	(	OAD_PolymerUnit *	u1,
		OAD_PolymerUnit *	u2
	)

Compare two polymer units based on their atom lists with modifications.

Parameters

u1	Pointer to the first polymer unit
u2	Pointer to the second polymer unit

Returns: int comparison result (-1, 0, 1)

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◆ OAD_PolymerUnit_CreateCopy()

OAD_PolymerUnit * OAD_PolymerUnit_CreateCopy ( OAD_PolymerUnit * u )

Create a copy of a polymer unit.

Parameters

u	Pointer to the original polymer unit

Returns: OAD_PolymerUnit* Pointer to the new polymer unit

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◆ OAD_PolymerUnit_DebugTrace()

void OAD_PolymerUnit_DebugTrace ( OAD_PolymerUnit * unit )

Debug trace for a polymer unit (print the whole polymer unit)

Parameters

unit	Pointer to the polymer unit

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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
	)

Collect high-order backbone bonds from a polymer unit.

Parameters

unit	Pointer to the polymer unit
orig_at_data	Pointer to the original atom data
composite_norm_data	Pointer to the composite atom data
err	Pointer to the error status
pStrErr	Pointer to the error string

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◆ OAD_PolymerUnit_DelistIntraRingBackboneBonds()

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

Collect backbone bonds from a polymer unit and delist intra-ring backbone bonds.

Parameters

unit	Pointer to the polymer unit
orig_at_data	Pointer to the original atom data
err	Pointer to the error status
pStrErr	Pointer to the error string

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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_undef,
		int *	end2,
		int *	cap2,
		int *	cap2_is_undef,
		int *	err,
		char *	pStrErr
	)

Find the ends and caps of a polymer unit.

Parameters

unit	Pointer to the polymer unit
orig_at_data	Pointer to the original atom data
end1	Pointer to the first end atom
cap1	Pointer to the first cap atom
cap1_is_undef	Pointer to the first cap atom's undefined status
end2	Pointer to the second end atom
cap2	Pointer to the second cap atom
cap2_is_undef	Pointer to the second cap atom's undefined status
err	Pointer to the error status
pStrErr	Pointer to the error string

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◆ OAD_PolymerUnit_Free()

void OAD_PolymerUnit_Free ( OAD_PolymerUnit * unit )

Free a polymer unit.

Parameters

unit	Pointer to the polymer unit to free

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◆ OAD_PolymerUnit_HasMetal()

int OAD_PolymerUnit_HasMetal	(	OAD_PolymerUnit *	u,
		inp_ATOM *	at
	)

Check if a polymer unit has a specific atom (e.g., metal)

Parameters

u	Pointer to the polymer unit
at	Pointer to the atom data

Returns: int Status code (1 if an atom is found, 0 otherwise)

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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
	)

Create a new polymer unit.

Parameters

maxatoms	Maximum number of atoms
maxbonds	Maximum number of bonds
id	Unique identifier for the polymer unit
label	Label for the polymer unit
type	Type of the polymer unit
subtype	Subtype of the polymer unit
conn	Connection type
smt	SMARTS pattern?
na	Number of atoms
alist	Pointer to the atom list
nb	Number of bonds
blist	Pointer to the bond list
nbkbonds	Number of backbone bonds
bkbonds	Pointer to the backbone bond list

Returns: OAD_PolymerUnit* Pointer to the new polymer unit

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◆ OAD_PolymerUnit_OrderBondAtomsAndBondsThemselves()

int OAD_PolymerUnit_OrderBondAtomsAndBondsThemselves	(	OAD_PolymerUnit *	u,
		int	n_stars,
		int *	stars
	)

Order bond atoms and bonds themselves in a polymer unit.

Parameters

u	Pointer to the polymer unit
n_stars	Pointer to the number of stars
stars	Pointer to the array of star atoms

Returns: int

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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
	)

Collect backbone atoms from a polymer unit.

Parameters

u	Pointer to the polymer unit
at	Pointer to the atom data
aprops	Pointer to the atom properties
nat	Pointer to the number of atoms
num_inp_bonds	Pointer to the number of input 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
	)

Set the ends and caps of a polymer unit.

Parameters

unit	Pointer to the polymer unit
orig_at_data	Pointer to the original atom data
err	Pointer to the error status
pStrErr	Pointer to the error string

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◆ OAD_PolymerUnit_SetReopeningDetails()

int OAD_PolymerUnit_SetReopeningDetails	(	OAD_PolymerUnit *	u,
		inp_ATOM *	at
	)

Set reopening details for a polymer unit.

Parameters

u	Pointer to polymer unit
at	Array of input atoms

Returns: int Number of breakable bonds

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◆ OAD_PolymerUnit_SortBackboneBonds()

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

Collect backbone bonds from a polymer unit and sort them.

Parameters

u	Pointer to the polymer unit
aprops	Pointer to the atom properties
bnum	Pointer to the number of backbone bonds

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◆ OAD_PolymerUnit_SortBackboneBondsAndSetSeniors()

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

Sort backbone bonds and set seniors for a polymer unit.

Parameters

u	Pointer to polymer unit
at	Array of input atoms
aprops	Pointer to atom properties structure
senior_bond	Pointer to array to store senior bond indices

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◆ OAD_PolymerUnit_UnlinkCapsAndConnectEndAtoms()

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

Unlink caps and connect end atoms of a polymer unit.

Parameters

unit	Pointer to the polymer unit
orig_at_data	Pointer to the original atom data
err	Pointer to the error status
pStrErr	Pointer to the error string

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◆ OAD_ValidateAndSortOutPseudoElementAtoms()

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

Validate and sort out pseudo-element atoms in the original atom data.

Parameters

orig_at_data	Pointer to original atom data structure
treat_polymers	Flag indicating how to treat polymers (POLYMER_NO, POLYMER_MODERN, POLYMER_LEGACY, POLYMER_LEGACY_PLUS)
use_zz	Flag indicating whether to use Zz atoms
err	Pointer to error code
pStrErr	Pointer to error string

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◆ OAD_ValidatePolymerAndPseudoElementData()

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

Validate polymer and pseudo-element data in the original atom data.

Parameters

orig_at_data	Pointer to original atom data structure
treat_polymers	Flag indicating how to treat polymers
bNPZz	Flag indicating whether to treat non-polymeric Zz atoms
pStrErr	Pointer to error string
bNoWarnings	Flag indicating whether to suppress warnings

Returns: int Status code

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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
	)

Unmark ring systems in the input atoms.

Parameters

at	Array of input atoms
num_atoms	Number of input atoms

Returns: int Status code

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Functions

Function Documentation

◆ CreateCompositeNormAtom()

◆ Inp_Atom_GetBondType()

◆ OAD_CollectBackboneAtoms()

◆ OAD_CollectBackboneBonds()

◆ OAD_CollectFragmentBondsAndAtoms()

◆ OAD_CollectReachableAtoms()

◆ OAD_Polymer_CompareBackboneBondsSeniority()

◆ OAD_Polymer_CompareRanksOfTwoAtoms()

◆ OAD_Polymer_CyclizeCloseableUnits()

◆ OAD_Polymer_DebugTrace()

◆ OAD_Polymer_FindBackbones()

◆ OAD_Polymer_FindRingSystems()

◆ OAD_Polymer_Free()

◆ OAD_Polymer_GetRepresentation()

◆ OAD_Polymer_IsFirstAtomRankLower()

◆ OAD_Polymer_PrepareWorkingSet()

◆ OAD_Polymer_SetAtProps()

◆ OAD_Polymer_SmartReopenCyclizedUnits()

◆ OAD_PolymerUnit_CompareAtomLists()

◆ OAD_PolymerUnit_CompareAtomListsMod()

◆ OAD_PolymerUnit_CreateCopy()

◆ OAD_PolymerUnit_DebugTrace()

◆ OAD_PolymerUnit_DelistHighOrderBackboneBonds()

◆ OAD_PolymerUnit_DelistIntraRingBackboneBonds()

◆ OAD_PolymerUnit_FindEndsAndCaps()

◆ OAD_PolymerUnit_Free()

◆ OAD_PolymerUnit_HasMetal()

◆ OAD_PolymerUnit_New()

◆ OAD_PolymerUnit_OrderBondAtomsAndBondsThemselves()

◆ OAD_PolymerUnit_RemoveLinkFromCRUChain()

◆ OAD_PolymerUnit_ReopenCyclized()

◆ OAD_PolymerUnit_SetEndsAndCaps()

◆ OAD_PolymerUnit_SetReopeningDetails()

◆ OAD_PolymerUnit_SortBackboneBonds()

◆ OAD_PolymerUnit_SortBackboneBondsAndSetSeniors()

◆ OAD_PolymerUnit_UnlinkCapsAndConnectEndAtoms()

◆ OAD_ValidateAndSortOutPseudoElementAtoms()

◆ OAD_ValidatePolymerAndPseudoElementData()

◆ OrigAtData_AddBond()

◆ OrigAtData_AddSingleStereolessBond()

◆ OrigAtData_bCheckUnusualValences()

◆ OrigAtData_DebugTrace()

◆ OrigAtData_DecreaseBondOrder()

◆ OrigAtData_Duplicate()

◆ OrigAtData_IncreaseBondOrder()

◆ OrigAtData_RemoveAtom()

◆ OrigAtData_RemoveBond()

◆ OrigAtData_RemoveHalfBond()

◆ PreprocessOneStructure()

◆ UnMarkRingSystemsInp()