mol2atom.c File Reference

#include <stdlib.h>
#include <string.h>
#include <math.h>
#include "mode.h"
#include "mol_fmt.h"
#include "ichierr.h"
#include "util.h"
#include "strutil.h"
#include "inchi_api.h"
#include "bcf_s.h"
#include "logging.h"

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Functions
int	ReadMolfileToInpAtoms (INCHI_IOSTREAM *inp_file, int bDoNotAddH, inp_ATOM **at, MOL_COORD **szCoord, OAD_Polymer **polymer, OAD_V3000 **v3000, int treat_polymers, int treat_NPZz, int max_num_at, int *num_dimensions, int *num_bonds, const char *pSdfLabel, char *pSdfValue, unsigned long *Id, long *lMolfileNumber, INCHI_MODE *pInpAtomFlags, int *err, char *pStrErr, int bNoWarnings)
inp_ATOM *	MakeInpAtomsFromMolfileData (MOL_FMT_DATA *mfdata, int *num_atoms, int *num_bonds, inp_ATOM *at_inp, int bDoNotAddH, int *err, char *pStrErr)
int	SetInpAtomsXYZ (MOL_FMT_DATA *mfdata, int num_atoms, inp_ATOM *at, int *err, char *pStrErr)
void	calculate_valences (MOL_FMT_DATA *mfdata, inp_ATOM *at, int *num_atoms, int bDoNotAddH, int *err, char *pStrErr)
int	SetExtOrigAtDataByMolfileExtInput (MOL_FMT_DATA *mfdata, OAD_Polymer **polymer, OAD_V3000 **v3000, char *pStrErr)
int	CreateOrigInpDataFromMolfile (INCHI_IOSTREAM *inp_file, ORIG_ATOM_DATA *orig_at_data, int bMergeAllInputStructures, int bGetOrigCoord, int bDoNotAddH, int treat_polymers, int treat_NPZz, const char *pSdfLabel, char *pSdfValue, unsigned long *lSdfId, long *lMolfileNumber, INCHI_MODE *pInpAtomFlags, int *err, char *pStrErr, int bNoWarnings)
inp_ATOM *	CreateInpAtom (int num_atoms)
void	FreeInpAtom (inp_ATOM **at)
void	FreeInpAtomData (INP_ATOM_DATA *inp_at_data)
int	CreateInpAtomData (INP_ATOM_DATA *inp_at_data, int num_atoms, int create_at_fixed_bonds)
void	FreeCompAtomData (COMP_ATOM_DATA *inp_at_data)
int	CreateCompAtomData (COMP_ATOM_DATA *inp_at_data, int num_atoms, int num_components, int bIntermediateTaut)
void	FreeOrigAtData (ORIG_ATOM_DATA *orig_at_data)
void	FreeExtOrigAtData (OAD_Polymer *pd, OAD_V3000 *v3k)

Function Documentation

calculate_valences()

void calculate_valences	(	MOL_FMT_DATA *	mfdata,
		inp_ATOM *	at,
		int *	num_atoms,
		int	bDoNotAddH,
		int *	err,
		char *	pStrErr
	)

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CreateCompAtomData()

int CreateCompAtomData	(	COMP_ATOM_DATA *	inp_at_data,
		int	num_atoms,
		int	num_components,
		int	bIntermediateTaut
	)

CreateInpAtom()

inp_ATOM * CreateInpAtom

(

int

num_atoms

)

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CreateInpAtomData()

int CreateInpAtomData	(	INP_ATOM_DATA *	inp_at_data,
		int	num_atoms,
		int	create_at_fixed_bonds
	)

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CreateOrigInpDataFromMolfile()

int CreateOrigInpDataFromMolfile	(	INCHI_IOSTREAM *	inp_file,
		ORIG_ATOM_DATA *	orig_at_data,
		int	bMergeAllInputStructures,
		int	bGetOrigCoord,
		int	bDoNotAddH,
		int	treat_polymers,
		int	treat_NPZz,
		const char *	pSdfLabel,
		char *	pSdfValue,
		unsigned long *	lSdfId,
		long *	lMolfileNumber,
		INCHI_MODE *	pInpAtomFlags,
		int *	err,
		char *	pStrErr,
		int	bNoWarnings
	)

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FreeCompAtomData()

void FreeCompAtomData

(

COMP_ATOM_DATA *

inp_at_data

)

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FreeExtOrigAtData()

void FreeExtOrigAtData	(	OAD_Polymer *	pd,
		OAD_V3000 *	v3k
	)

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FreeInpAtom()

void FreeInpAtom

(

inp_ATOM **

at

)

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FreeInpAtomData()

void FreeInpAtomData

(

INP_ATOM_DATA *

inp_at_data

)

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FreeOrigAtData()

void FreeOrigAtData

(

ORIG_ATOM_DATA *

orig_at_data

)

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MakeInpAtomsFromMolfileData()

inp_ATOM * MakeInpAtomsFromMolfileData	(	MOL_FMT_DATA *	mfdata,
		int *	num_atoms,
		int *	num_bonds,
		inp_ATOM *	at_inp,
		int	bDoNotAddH,
		int *	err,
		char *	pStrErr
	)

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ReadMolfileToInpAtoms()

int ReadMolfileToInpAtoms	(	INCHI_IOSTREAM *	inp_file,
		int	bDoNotAddH,
		inp_ATOM **	at,
		MOL_COORD **	szCoord,
		OAD_Polymer **	polymer,
		OAD_V3000 **	v3000,
		int	treat_polymers,
		int	treat_NPZz,
		int	max_num_at,
		int *	num_dimensions,
		int *	num_bonds,
		const char *	pSdfLabel,
		char *	pSdfValue,
		unsigned long *	Id,
		long *	lMolfileNumber,
		INCHI_MODE *	pInpAtomFlags,
		int *	err,
		char *	pStrErr,
		int	bNoWarnings
	)

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SetExtOrigAtDataByMolfileExtInput()

int SetExtOrigAtDataByMolfileExtInput	(	MOL_FMT_DATA *	mfdata,
		OAD_Polymer **	polymer,
		OAD_V3000 **	v3000,
		char *	pStrErr
	)

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SetInpAtomsXYZ()

int SetInpAtomsXYZ	(	MOL_FMT_DATA *	mfdata,
		int	num_atoms,
		inp_ATOM *	at,
		int *	err,
		char *	pStrErr
	)

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