bioworld.h

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#ifndef BIOWORLDH
#define BIOWORLDH

#include "parameters.h"
#include "world.h"
#include "babel.h"
#include "vector.h"
#include "htransform.h"
#include "box.h"

typedef struct {
  Tworld w;               
  TMolecule *m;           
  unsigned int na;        
  unsigned int nb;        
  unsigned int nba;       
  double *localPos;       
  double *pos;            
  unsigned int *nbAtom;   
  unsigned int nl;        
  Tvector links;          
  unsigned int *linkID;   
  unsigned int nj;        
  Tvector joint1;         
  Tvector joint2;         
  unsigned int *linkList; 
  THTransform *g2l;       
  boolean cut;            
  Tbox cutB;              
} TBioWorld;

boolean InitBioWorld(Tparameters *p,char *filename,unsigned int maxAtomsLink,
                     double **conformation,
                     TBioWorld *bw);

void AdjustBioWorldGeometry(Tparameters *p,TBioWorld *bw);

Tworld *BioWorldWorld(TBioWorld *bw);

unsigned int BioWorldNAtoms(TBioWorld *bw);

unsigned int BioWorldConformationSize(TBioWorld *bw);

void BioWordGetAtomPositionsFromConformation(Tparameters *p,boolean simp,double *conformation,
                                             double *pos,TBioWorld *bw);

void BioWordSetAtomPositionsFromConformation(Tparameters *p,boolean simp,
                                             double *conformation,TBioWorld *bw);

double BioWorldRMSE(double *pos,TBioWorld *bw);

unsigned int BioWordConformationFromAtomPositions(Tparameters *p,double *atoms,
                                                  double **conformation,TBioWorld *bw);

double BioWorldEnergy(Tparameters *p,boolean simp,double *conformation,void *bw);

void SaveBioWorldBioInfo(Tparameters *p,char *fname,boolean simp,double *conformation,
                         TBioWorld *bw);

void PrintBioWorld(Tparameters *p,char *fname,int argc,char **arg,TBioWorld *bw);

void DeleteBioWorld(TBioWorld *bw);

#endif