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atom.c File Reference

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <float.h>
#include "atom.h"

Compounds

struct  rnamlATOM

Functions

rnamlAtomrnamlnewAtom ()
 Creates a new rnamlAtom structure.

rnamlAtomrnamlcloneAtom (const rnamlAtom *atom)
 Clones a rnamlAtom struture.

void rnamldeleteAtom (rnamlAtom *atom)
 Frees the rnamlAtom structure.

int rnamlisAtom (const rnamlObject *obj)
 Tells wheter the object is a rnamlAtom.

int rnamlequalsAtom (const rnamlAtom *left, const rnamlAtom *right)
 Tells if left and right are equals.

const char * rnamlgetAtomSerial (const rnamlAtom *atom)
 Gets the atom serial.

void rnamlsetAtomSerial (rnamlAtom *atom, const char *serial)
 Sets the atom serial.

const char * rnamlgetAtomAtomType (const rnamlAtom *atom)
 Gets the atomType from the atom.

void rnamlsetAtomAtomType (rnamlAtom *atom, const char *atomType)
 Sets the atom atomType.

float rnamlgetAtomX (const rnamlAtom *atom)
 Gets the x from the atom.

void rnamlsetAtomX (rnamlAtom *atom, float x)
 Sets the atom x.

float rnamlgetAtomY (const rnamlAtom *atom)
 Gets the y from the atom.

void rnamlsetAtomY (rnamlAtom *atom, float y)
 Sets the atom y.

float rnamlgetAtomZ (const rnamlAtom *atom)
 Gets the z from the atom.

void rnamlsetAtomZ (rnamlAtom *atom, float z)
 Sets the atom z.

float rnamlgetAtomOccupancy (const rnamlAtom *atom)
 Gets the occupancy from the atom.

void rnamlsetAtomOccupancy (rnamlAtom *atom, float occupancy)
 Sets the atom occupancy.

float rnamlgetAtomTempFactor (const rnamlAtom *atom)
 Gets the tempFactor from the atom.

void rnamlsetAtomTempFactor (rnamlAtom *atom, float tempFactor)
 Sets the atom tempFactor.

const char * rnamlgetAtomSegId (const rnamlAtom *atom)
 Gets the segId from the atom.

void rnamlsetAtomSegId (rnamlAtom *atom, const char *segId)
 Sets the atom segId.

const char * rnamlgetAtomElement (const rnamlAtom *atom)
 Gets the element from the atom.

void rnamlsetAtomElement (rnamlAtom *atom, const char *element)
 Sets the atom element.

const char * rnamlgetAtomCharge (const rnamlAtom *atom)
 Gets the charge from the atom.

void rnamlsetAtomCharge (rnamlAtom *atom, const char *charge)
 Sets the atom charge.

xmlcpgObjectrnamltoXMLAtom (const rnamlAtom *atom)
 Translates the rnamlAtom structure into a xmlcpgElement conforming to the RNAML standard.


Function Documentation

rnamlAtom* rnamlcloneAtom const rnamlAtom   atom
 

Clones a rnamlAtom struture.

Parameters:
atom  the structure to clone.
Returns:
the new allocated structure or NULL if something goes wrong.

void rnamldeleteAtom rnamlAtom   atom
 

Frees the rnamlAtom structure.

Parameters:
atom  the rnamlAtom structure to free.

int rnamlequalsAtom const rnamlAtom   left,
const rnamlAtom   right
 

Tells if left and right are equals.

Parameters:
left  the left object to compare.
right  the right object to compare.
Returns:
1 if the objects are equals or 0 otherwise.

const char* rnamlgetAtomAtomType const rnamlAtom   atom
 

Gets the atomType from the atom.

Parameters:
atom  the rnamlAtom structure.
Returns:
the atom atomType string or NULL if atom is NULL or not an rnamlAtom.

const char* rnamlgetAtomCharge const rnamlAtom   atom
 

Gets the charge from the atom.

Parameters:
atom  the rnamlAtom structure.
Returns:
the atom charge string or NULL if atom is NULL or not an rnamlAtom.

const char* rnamlgetAtomElement const rnamlAtom   atom
 

Gets the element from the atom.

Parameters:
atom  the rnamlAtom structure.
Returns:
the atom element string or NULL if atom is NULL or not an rnamlAtom.

float rnamlgetAtomOccupancy const rnamlAtom   atom
 

Gets the occupancy from the atom.

Parameters:
atom  the rnamlAtom structure.
Returns:
the occupancy or 0 if atom is NULL or not an rnamlAtom.

const char* rnamlgetAtomSegId const rnamlAtom   atom
 

Gets the segId from the atom.

Parameters:
atom  the rnamlAtom structure.
Returns:
the atom segId string or NULL if atom is NULL or not an rnamlAtom.

const char* rnamlgetAtomSerial const rnamlAtom   atom
 

Gets the atom serial.

Parameters:
atom  the rnamlAtom structure.
Returns:
the atom serial string or NULL if atom is NULL or not an rnamlAtom.

float rnamlgetAtomTempFactor const rnamlAtom   atom
 

Gets the tempFactor from the atom.

Parameters:
atom  the rnamlAtom structure.
Returns:
the tempFactor or 0 if atom is NULL or not an rnamlAtom.

float rnamlgetAtomX const rnamlAtom   atom
 

Gets the x from the atom.

Parameters:
atom  the rnamlAtom structure.
Returns:
the x or 0 if atom is NULL or not an rnamlAtom.

float rnamlgetAtomY const rnamlAtom   atom
 

Gets the y from the atom.

Parameters:
atom  the rnamlAtom structure.
Returns:
the y or 0 if atom is NULL or not an rnamlAtom.

float rnamlgetAtomZ const rnamlAtom   atom
 

Gets the z from the atom.

Parameters:
atom  the rnamlAtom structure.
Returns:
the z or 0 if atom is NULL or not an rnamlAtom.

int rnamlisAtom const rnamlObject   obj
 

Tells wheter the object is a rnamlAtom.

Parameters:
obj  the rnamlObject to test.
Returns:
1 if the object is a rnamlAtom, 0 otherwise.

rnamlAtom* rnamlnewAtom  
 

Creates a new rnamlAtom structure.

Returns:
the new allocated structure or NULL if something goes wrong.

void rnamlsetAtomAtomType rnamlAtom   atom,
const char *    atomType
 

Sets the atom atomType.

The previous atom atomType is freed and a copy of atomType is generated.

Parameters:
atom  the rnamlAtom structure.
atomType  the atom atomType.

void rnamlsetAtomCharge rnamlAtom   atom,
const char *    charge
 

Sets the atom charge.

The previous atom charge is freed and a copy of charge is generated.

Parameters:
atom  the rnamlAtom structure.
charge  the atom charge.

void rnamlsetAtomElement rnamlAtom   atom,
const char *    element
 

Sets the atom element.

The previous atom element is freed and a copy of element is generated.

Parameters:
atom  the rnamlAtom structure.
element  the atom element.

void rnamlsetAtomOccupancy rnamlAtom   atom,
float    occupancy
 

Sets the atom occupancy.

The previous atom occupancy is freed and a copy of occupancy is generated.

Parameters:
atom  the rnamlAtom structure.
occupancy  the atom occupancy.

void rnamlsetAtomSegId rnamlAtom   atom,
const char *    segId
 

Sets the atom segId.

The previous atom segId is freed and a copy of segId is generated.

Parameters:
atom  the rnamlAtom structure.
segId  the atom segId.

void rnamlsetAtomSerial rnamlAtom   atom,
const char *    serial
 

Sets the atom serial.

The previous atom serial is freed and a copy of serial is generated.

Parameters:
atom  the rnamlAtom structure.
serial  the atom serial.

void rnamlsetAtomTempFactor rnamlAtom   atom,
float    tempFactor
 

Sets the atom tempFactor.

The previous atom tempFactor is freed and a copy of tempFactor is generated.

Parameters:
atom  the rnamlAtom structure.
tempFactor  the atom tempFactor.

void rnamlsetAtomX rnamlAtom   atom,
float    x
 

Sets the atom x.

The previous atom x is freed and a copy of x is generated.

Parameters:
atom  the rnamlAtom structure.
x  the atom x.

void rnamlsetAtomY rnamlAtom   atom,
float    y
 

Sets the atom y.

The previous atom y is freed and a copy of y is generated.

Parameters:
atom  the rnamlAtom structure.
y  the atom y.

void rnamlsetAtomZ rnamlAtom   atom,
float    z
 

Sets the atom z.

The previous atom z is freed and a copy of z is generated.

Parameters:
atom  the rnamlAtom structure.
z  the atom z.

xmlcpgObject* rnamltoXMLAtom const rnamlAtom   atom
 

Translates the rnamlAtom structure into a xmlcpgElement conforming to the RNAML standard.

Parameters:
molecule  the rnamlAtom structure to translate.
Returns:
the xmlcpgObject or NULL if something goes wrong.


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