bioworld.c
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695 if ((IsAtomInProline(r,bw->m))&&(GetAtomResidue(r,bw->m)==rID[k])&&(GetAtomResidue(l,bw->m)==rID[k]))
1151 Error("Unassigned atom to link in InitWorldFromMolecule (this atom can not be correctly moved)");
1219 if ((!bw->cut)||(PointInBox(NULL,3,&(bw->pos[3*k]),GetBoxDiagonal(NULL,&(bw->cutB))/2,&(bw->cutB))))
1911 void SaveBioWorldBioInfo(Tparameters *p,char *fname,boolean simp,double *conformation,TBioWorld *bw)
boolean HasBond(unsigned int na1, unsigned int na2, TMolecule *ml) Determines is a given bond exists. Definition: babel.cpp:184 boolean PointInBox(boolean *used, unsigned int n, double *v, double tol, Tbox *b) Checks if a point is included in a(sub-) box. Definition: box.c:356 void SetAtomCoordinates(double *pos, TMolecule *ml) Sets the positions of the atoms in the molecule. Definition: babel.cpp:325 void NewSegments(unsigned int n, double *x, double *y, double *z, Tcolor *c, Tpolyhedron *p) Constructor. Definition: polyhedron.c:1098 void DetectLinksAndJoints(TBioWorld *bw) Determines the rigid groups of atoms and the connections between them. Definition: bioworld.c:472 double BioWorldEnergy(Tparameters *p, boolean simp, double *conformation, void *bw) Computes the energy of a given configuration. Definition: bioworld.c:1902 void HTransformApply(double *p_in, double *p_out, THTransform *t) Multiply a homogeneous transform and a vector. Definition: htransform.c:782 unsigned int GetAtomicNumber(unsigned int na, TMolecule *ml) Returns the atomic number of a given atom. Definition: babel.cpp:109 void PrintWorld(char *fname, int argc, char **arg, Tworld *w) Prints the world. Definition: world.c:3902 void GetLinkTransformsFromSolutionPoint(Tparameters *p, boolean simp, double *sol, THTransform **tl, TLinkConf **def, Tworld *w) Define transforms for the links from the a solution point. Definition: world.c:1215 void PrintBioWorld(Tparameters *p, char *fname, int argc, char **arg, TBioWorld *bw) Prints the BioWorld information into a file. Definition: bioworld.c:1919 void SetEquationType(unsigned int type, Tequation *eq) Changes the type of the equation (SYSTEM_EQ, CARTESIAN_EQ, DUMMY_EQ, DERIVED_EQ). ... Definition: equation.c:1076 void GenerateNormEquation(unsigned int vx, unsigned int vy, unsigned int vz, double n, Tequation *eq) Construtor. Generates an equation that is the norm of a 3d vector. Definition: equation.c:1494 Data structure to hold the information about the name of a file. Definition: filename.h:271 void * GetVectorElement(unsigned int i, Tvector *vector) Returns a pointer to a vector element. Definition: vector.c:270 A homgeneous transform in R^3. boolean IsAtomInProline(unsigned int na, TMolecule *ml) Identifies atoms in proline residues. Definition: babel.cpp:155 unsigned int AddVariable2CS(Tvariable *v, TCuikSystem *cs) Adds a variable to the system. Definition: cuiksystem.c:2532 void BioWordSetAtomPositionsFromConformation(Tparameters *p, boolean simp, double *conformation, TBioWorld *bw) Changes the position of the atoms. Definition: bioworld.c:1852 void Atoms2Transforms(Tparameters *p, double *atoms, THTransform *t, TBioWorld *bw) Generates a transform from a gobal frame to a local frame for each link. Definition: bioworld.c:962 void GetAtomCoordinates(double *pos, TMolecule *ml) Gets the positions of the atoms in the molecule. Definition: babel.cpp:308 unsigned int GetCSSystemVars(boolean **sv, TCuikSystem *cs) Identifies the system variables. Definition: cuiksystem.c:2659 void WriteMolecule(char *fname, TMolecule *ml) Writes the molecule information to a file. Definition: babel.cpp:79 void ReadResidueList(char *fname, unsigned int *nr, char *ch, unsigned int **r) Read the list of residues to be considered flexible. Definition: bioworld.c:231 Definition of the Tfilename type and the associated functions. void SetVariableInterval(Tinterval *i, Tvariable *v) Sets the new range for the variable. Definition: variable.c:68 CBLAS_INLINE void Normalize(unsigned int s, double *v) Normalizes a vector. Definition: basic_algebra.c:592 void NewSphere(double r, double *center, Tcolor *c, unsigned int gr, unsigned int bs, Tpolyhedron *p) Constructor. Definition: polyhedron.c:1020 unsigned int GetWorldNumSystemVariables(Tworld *w) Number of system variables in the kinematic subsystem. Definition: world.c:3297 void AddBond(unsigned int na1, unsigned int na2, TMolecule *ml) Adds a bond between two atoms. Definition: babel.cpp:209 void ReadRigidsAndHinges(char *fname, unsigned int **r, unsigned int *nh, unsigned int **h1, unsigned int **h2, boolean **added, TBioWorld *bw) Read the list of rigids and hinges of a molecule. Definition: bioworld.c:277 void DeleteLinkTransforms(THTransform *tl, TLinkConf *def, Tworld *w) Deletes transforms for each link. Definition: world.c:1336 void GetAtomPositions(char *fname, double *pos, TBioWorld *bw) Initializes the atom positions in a BioWorld. Definition: bioworld.c:437 void SetEquationValue(double v, Tequation *eq) Changes the right-hand value of the equation. Definition: equation.c:1089 void AddMonomial(Tmonomial *f, Tequation *eq) Adds a new monomial to the equation. Definition: equation.c:1419 unsigned int GetAtomResidue(unsigned int na, TMolecule *ml) Returns the residue of a given atom. Definition: babel.cpp:121 void CheckAllCollisions(unsigned int fl, unsigned int fo, Tworld *w) Activates all the possible collision between links and links and obstacles. Definition: world.c:2097 unsigned int GetSolutionPointFromLinkTransforms(Tparameters *p, THTransform *tl, TLinkConf *def, double **sol, Tworld *w) Determines the mechanisms configuration from the pose of all links. Definition: world.c:1261 void HTransformFromVectors(double *x, double *y, double *z, double *h, THTransform *t) Defines a homogeneous transform from 4 vectors. Definition: htransform.c:341 void SetEquationCmp(unsigned int cmp, Tequation *eq) Changes the relational operator (LEQ, GEQ, EQU) of the equation. Definition: equation.c:1081 double Distance(unsigned int s, double *v1, double *v2) Computes the distance of two points. Definition: basic_algebra.c:438 double DotProduct(double *v1, double *v2) Computes the dot product of two 3d vectors. Definition: geom.c:652 void HTransformInverse(THTransform *t, THTransform *ti) Inverse of a homogeneous transform. Definition: htransform.c:503 void RemoveBond(unsigned int na1, unsigned int na2, TMolecule *ml) Removes a bond between two atoms. Definition: babel.cpp:218 void DeleteBondIterator(TBondIterator *it) Deletes the bond iterator defined in GetFirstNeighbour. Definition: babel.cpp:299 void GenerateWorldEquations(Tparameters *p, Tworld *w) Generates all the cuiksystems derived from the world information. Definition: world.c:2431 unsigned int GetNextNeighbour(unsigned int na, boolean *fix, TBondIterator *it, TMolecule *ml) Gets the identifier of the next neighbour for a given atom in a molecule. Definition: babel.cpp:271 void AdjustBioWorldGeometry(Tparameters *p, TBioWorld *bw) Enforces all bond lengths and angles to be the same. Definition: bioworld.c:1475 unsigned int AddLink2World(Tlink *l, boolean object, Tworld *w) Adds a link to the mechanism in the world. Definition: world.c:1383 void InitVector(unsigned int ele_size, void(*Copy)(void *, void *), void(*Delete)(void *), unsigned int max_ele, Tvector *vector) Constructor. Definition: vector.c:100 unsigned int BioWorldNAtoms(TBioWorld *bw) Number of atoms in the molecule. Definition: bioworld.c:1812 Definition of the Tjoint type and the associated functions. void DifferenceVector(unsigned int s, double *v1, double *v2, double *v) Substracts two vectors. Definition: basic_algebra.c:264 void NewRevoluteJoint(unsigned int id, unsigned int r, unsigned int linkID1, Tlink *link1, unsigned int linkID2, Tlink *link2, double **points, boolean hasLimits, Tinterval *range, double **rPoints, boolean avoidLimits, double avoidLimitsWeight, Tjoint *coupled, Tjoint *j) Constructor. Definition: joint.c:124 Minimalistic Cuik-OpenBabel interface. void DetectLinksAndJointsFromResidues(unsigned int nr, char ch, unsigned int *rID, TBioWorld *bw) Determines the rigid groups of atoms and the connections between them. Definition: bioworld.c:553 char GetAtomChain(unsigned int na, TMolecule *ml) Returns a char identifying the chain of the atom. Definition: babel.cpp:138 TMolecule * ReadMolecule(char *fname) Reads the molecule information from a file. Definition: babel.cpp:46 boolean InitBioWorld(Tparameters *p, char *filename, unsigned int maxAtomsLink, double **conformation, TBioWorld *bw) Initializes a world form a biomolecule. Definition: bioworld.c:1394 void AddEquation2CS(Tparameters *p, Tequation *eq, TCuikSystem *cs) Adds an equation to the system. Definition: cuiksystem.c:2502 A table of parameters. void CreateFileName(char *path, char *name, char *suffix, char *ext, Tfilename *fn) Constructor. Definition: filename.c:22 void NewCylinder(double r, double *p1, double *p2, Tcolor *c, unsigned int gr, unsigned int bs, Tpolyhedron *p) Constructor. Definition: polyhedron.c:1044 unsigned int AddJoint2World(Tjoint *j, Tworld *w) Adds a joint to the mechanism in the world. Definition: world.c:1436 A bridge between world structures and biological information. double GetBoxDiagonal(boolean *used, Tbox *b) Computes the diagonal of a (sub-)box. Definition: box.c:678 Definition of a local chart on a manifold. char * GetFileFullName(Tfilename *fn) Gets the file full name (paht+name+extension). Definition: filename.c:151 void InitWorldFromMolecule(Tparameters *p, double **conformation, unsigned int maxAtomsLink, TBioWorld *bw) Defines a world from molecular information. Definition: bioworld.c:1130 double VdWRadius(unsigned int na, TMolecule *ml) Returns the Van der Waals radius for a given atom. Definition: babel.cpp:172 Definition of the Tpolyhedron type and the associated functions. #define MEM_DUP(_var, _n, _type) Duplicates a previously allocated memory space. Definition: defines.h:414 A cuiksystem, i.e., a set of variables and equations defining a position analysis problem... Definition: cuiksystem.h:181 #define NO_UINT Used to denote an identifier that has not been initialized. Definition: defines.h:435 CBLAS_INLINE void SumVectorScale(unsigned int s, double *v1, double w, double *v2, double *v) Adds two vectors with a scale. Definition: basic_algebra.c:86 void InitBoxFromPoint(unsigned int dim, double *p, Tbox *b) Initializes a box from a point. Definition: box.c:43 void AddVariable2Monomial(unsigned int fn, unsigned int varid, unsigned int p, Tmonomial *f) Adds a power variable to the monomial. Definition: monomial.c:171 unsigned int GetFirstNeighbour(unsigned int na, boolean *fix, TBondIterator **it, TMolecule *ml) Gets the identifier of the first neighbour for a given atom in a molecule. Definition: babel.cpp:244 void PrintCuikSystem(Tparameters *p, FILE *f, TCuikSystem *cs) Prints a cuiksystem. Definition: cuiksystem.c:5359 unsigned int BioWordConformationFromAtomPositions(Tparameters *p, double *atoms, double **conformation, TBioWorld *bw) Produces the internal coordinates from the atom positions. Definition: bioworld.c:1882 void GetCSVariableNames(char **varNames, TCuikSystem *cs) Gets points to the variable names. Definition: cuiksystem.c:2555 void PrintBoxSubset(FILE *f, boolean *used, char **varNames, Tbox *b) Prints a (sub-)box. Definition: box.c:1162 Tlink * GetWorldLink(unsigned int linkID, Tworld *w) Gets a link from its identifier. Definition: world.c:1842 #define MEM_EXPAND(_var, _n, _type) Expands a previously allocated memory space. Definition: defines.h:404 double GetParameter(unsigned int n, Tparameters *p) Gets the value for a particular parameter. Definition: parameters.c:93 void ExpandBox(double *p, Tbox *b) Expands a box so that it includes a given point. Definition: box.c:67 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:1911 #define HINGE_EXT File extension for files storing the hinges of a molecule. Definition: filename.h:245 Auxiliary functions to deal with sets of samples. Definition of the Tlink type and the associated functions. unsigned int GetCSVariableID(char *name, TCuikSystem *cs) Gets the numerical identifier of a variable given its name. Definition: cuiksystem.c:2607 #define RIGID_EXT File extension for files storing rigid part of molecules. Definition: filename.h:237 void HTransformPrint(FILE *f, THTransform *t) Prints the a homogeneous transform to a file. Definition: htransform.c:822 double ComputeEnergy(TMolecule *ml) Computes the potential energy of a molecule. Definition: babel.cpp:334 Tworld * BioWorldWorld(TBioWorld *bw) Returns a pointer to the world generated from the bio-information. Definition: bioworld.c:1807 void CrossProduct(double *v1, double *v2, double *v3) Computes the cross product of two 3d vectors. Definition: geom.c:639 void DetectLinksAndJointsFromRigidsAndHinges(unsigned int *rg, unsigned int nh, unsigned int *h1, unsigned int *h2, TBioWorld *bw) Determines the rigid groups of atoms and the connections between them. Definition: bioworld.c:766 void GetMoleculeBasicInfo(TBioWorld *bw) Collects the basic information about the molecule. Definition: bioworld.c:398 void GenerateDotProductEquation(unsigned int v1x, unsigned int v1y, unsigned int v1z, unsigned int v2x, unsigned int v2y, unsigned int v2z, unsigned int vc, double c, Tequation *eq) Construtor. Generates the equation of the dot product of two unitary vectors. Definition: equation.c:1588 void BioWordGetAtomPositionsFromConformation(Tparameters *p, boolean simp, double *conformation, double *pos, TBioWorld *bw) Computes the position of the atoms. Definition: bioworld.c:1822 unsigned int NewVectorElement(void *e, Tvector *vector) Adds an element to the vector. Definition: vector.c:216 unsigned int BioWorldConformationSize(TBioWorld *bw) Number of variables used to represent a conformation. Definition: bioworld.c:1817 |
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