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)
	Create original input data from molfile.
inp_ATOM *	CreateInpAtom (int num_atoms)
	Create/allocate a Inp Atom structure.
void	FreeInpAtom (inp_ATOM **at)
	Free input atom array.
void	FreeInpAtomData (INP_ATOM_DATA *inp_at_data)
	Free input atom data.
int	CreateInpAtomData (INP_ATOM_DATA *inp_at_data, int num_atoms, int create_at_fixed_bonds)
	Create a Inp Atom Data structure.
void	FreeCompAtomData (COMP_ATOM_DATA *inp_at_data)
	Free composite atom data.
int	CreateCompAtomData (COMP_ATOM_DATA *inp_at_data, int num_atoms, int num_components, int bIntermediateTaut)
	Create a Comp Atom Data structure.
void	FreeOrigAtData (ORIG_ATOM_DATA *orig_at_data)
	Free original atom data.
void	FreeExtOrigAtData (OAD_Polymer *pd, OAD_V3000 *v3k)
	Free extended original atom data (polymers and V3000)

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
	)

Create a Comp Atom Data structure.

Parameters

inp_at_data	Pointer to the Comp Atom Data structure
num_atoms	Number of atoms
num_components	Number of components
bIntermediateTaut	Flag for intermediate tautomer

Returns

int Status code (1 if successful, 0 otherwise)

CreateInpAtom()

inp_ATOM * CreateInpAtom

(

int

num_atoms

)

Create/allocate a Inp Atom structure.

Parameters

num_atoms

Number of atoms

Returns

inp_ATOM* Pointer to the created Inp Atom structure

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CreateInpAtomData()

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

Create a Inp Atom Data structure.

Parameters

inp_at_data	Pointer to the Inp Atom Data structure
num_atoms	Number of atoms
create_at_fixed_bonds	Flag to create fixed bonds

Returns

int Status code (1 if successful, 0 otherwise)

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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
	)

Create original input data from molfile.

Parameters

inp_file	Input file stream
orig_at_data	Pointer to original atom data structure to be filled
bMergeAllInputStructures	Flag indicating whether to merge all input structures
bGetOrigCoord	Flag indicating whether to get original coordinates
bDoNotAddH	Flag indicating whether to avoid adding hydrogens
treat_polymers	Flag indicating how to treat polymers
treat_NPZz	Flag indicating how to treat non-polymeric Zz atoms
pSdfLabel	Pointer to SDF label
pSdfValue	Pointer to SDF value
lSdfId	Pointer to SDF ID
lMolfileNumber	Pointer to molfile number
pInpAtomFlags	Pointer to input atom flags
err	Pointer to error code
pStrErr	Pointer to error string
bNoWarnings	Flag indicating whether to suppress warnings

Returns

int Status code

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FreeCompAtomData()

void FreeCompAtomData

(

COMP_ATOM_DATA *

inp_at_data

)

Free composite atom data.

Parameters

inp_at_data

Pointer to composite atom data structure

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FreeExtOrigAtData()

void FreeExtOrigAtData	(	OAD_Polymer *	pd,
		OAD_V3000 *	v3k
	)

Free extended original atom data (polymers and V3000)

Parameters

pd	Pointer to polymer data structure
v3k	Pointer to V3000 data structure

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FreeInpAtom()

void FreeInpAtom

(

inp_ATOM **

at

)

Free input atom array.

Parameters

at	Pointer to input atom array

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FreeInpAtomData()

void FreeInpAtomData

(

INP_ATOM_DATA *

inp_at_data

)

Free input atom data.

Parameters

inp_at_data

Pointer to input atom data structure

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FreeOrigAtData()

void FreeOrigAtData

(

ORIG_ATOM_DATA *

orig_at_data

)

Free original atom data.

Parameters

orig_at_data

Pointer to original atom data structure

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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
	)

@nnuk: GHI#252 addressed and redundant logic removed

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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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