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1 #ifndef BIOWORLDH
2 #define BIOWORLDH
4 #include "parameters.h"
5 #include "world.h"
6 #include "babel.h"
7 #include "vector.h"
8 #include "htransform.h"
9 #include "box.h"
28 typedef struct {
31  unsigned int na;
32  unsigned int nb;
33  unsigned int nba;
34  double *localPos;
35  double *pos;
36  unsigned int *nbAtom;
37  unsigned int nl;
39  unsigned int *linkID;
41  unsigned int nj;
45  unsigned int *linkList;
50  boolean cut;
53 } TBioWorld;
74 void InitBioWorld(Tparameters *p,char *filename,unsigned int maxAtomsLink,
75  double **conformation,
76  TBioWorld *bw);
117 unsigned int BioWorldNAtoms(TBioWorld *bw);
134 unsigned int BioWorldConformationSize(TBioWorld *bw);
152 void BioWordGetAtomPositionsFromConformation(Tparameters *p,boolean simp,double *conformation,
153  double *pos,TBioWorld *bw);
170  double *conformation,TBioWorld *bw);
190 double BioWorldRMSE(double *pos,TBioWorld *bw);
209 unsigned int BioWordConformationFromAtomPositions(Tparameters *p,double *atoms,
210  double **conformation,TBioWorld *bw);
225 double BioWorldEnergy(Tparameters *p,boolean simp,double *conformation,void *bw);
241 void SaveBioWorldBioInfo(Tparameters *p,char *fname,boolean simp,double *conformation,
242  TBioWorld *bw);
264 void PrintBioWorld(Tparameters *p,char *fname,int argc,char **arg,TBioWorld *bw);
273 void DeleteBioWorld(TBioWorld *bw);
275 #endif
unsigned int * linkList
Definition: bioworld.h:45
unsigned int nba
Definition: bioworld.h:33
unsigned int nl
Definition: bioworld.h:37
unsigned int na
Definition: bioworld.h:31
A homgeneous transform in R^3.
unsigned int BioWorldConformationSize(TBioWorld *bw)
Number of variables used to represent a conformation.
Definition: bioworld.c:1812
void SaveBioWorldBioInfo(Tparameters *p, char *fname, boolean simp, double *conformation, TBioWorld *bw)
Stores the BioWorld information in a molecular format (eg. pdb).
Definition: bioworld.c:1905
void AdjustBioWorldGeometry(Tparameters *p, TBioWorld *bw)
Enforces all bond lengths and angles to be the same.
Definition: bioworld.c:1470
All the necessary information to generate equations for mechanisms.
Definition: world.h:124
unsigned int BioWordConformationFromAtomPositions(Tparameters *p, double *atoms, double **conformation, TBioWorld *bw)
Produces the internal coordinates from the atom positions.
Definition: bioworld.c:1876
Tvector joint1
Definition: bioworld.h:42
Definition of the Tworld type and the associated functions.
Tworld w
Definition: bioworld.h:29
Tvector links
Definition: bioworld.h:38
double BioWorldRMSE(double *pos, TBioWorld *bw)
Computes the RMSE.
Definition: bioworld.c:1854
unsigned int nb
Definition: bioworld.h:32
double * localPos
Definition: bioworld.h:34
Tbox cutB
Definition: bioworld.h:52
void DeleteBioWorld(TBioWorld *bw)
Definition: bioworld.c:1918
Definition of the Tbox type and the associated functions.
double BioWorldEnergy(Tparameters *p, boolean simp, double *conformation, void *bw)
Computes the energy of a given configuration.
Definition: bioworld.c:1896
Tworld * BioWorldWorld(TBioWorld *bw)
Returns a pointer to the world generated from the bio-information.
Definition: bioworld.c:1802
void PrintBioWorld(Tparameters *p, char *fname, int argc, char **arg, TBioWorld *bw)
Prints the BioWorld information into a file.
Definition: bioworld.c:1913
Minimalistic Cuik-OpenBabel interface.
A table of parameters.
void BioWordGetAtomPositionsFromConformation(Tparameters *p, boolean simp, double *conformation, double *pos, TBioWorld *bw)
Computes the position of the atoms.
Definition: bioworld.c:1817
boolean cut
Definition: bioworld.h:50
Definition of the THTransform type and the associated functions.
void BioWordSetAtomPositionsFromConformation(Tparameters *p, boolean simp, double *conformation, TBioWorld *bw)
Changes the position of the atoms.
Definition: bioworld.c:1846
A generic vector.
Definition: vector.h:227
void InitBioWorld(Tparameters *p, char *filename, unsigned int maxAtomsLink, double **conformation, TBioWorld *bw)
Initializes a world form a biomolecule.
Definition: bioworld.c:1394
double * pos
Definition: bioworld.h:35
A box.
Definition: box.h:83
THTransform * g2l
Definition: bioworld.h:47
Tvector joint2
Definition: bioworld.h:43
Definition of the Tvector type and the associated functions.
void TMolecule
The molecule handler type.
Definition: babel.h:33
Structure with the molecular and the mechanical information.
Definition: bioworld.h:28
unsigned int nj
Definition: bioworld.h:41
Definition of the Tparameters type and the associated functions.
unsigned int BioWorldNAtoms(TBioWorld *bw)
Number of atoms in the molecule.
Definition: bioworld.c:1807
unsigned int * linkID
Definition: bioworld.h:39
unsigned int * nbAtom
Definition: bioworld.h:36
TMolecule * m
Definition: bioworld.h:30