| CloseAlmostClosedLoop(PProtein *lp, Vector3 endPriorGoal, Vector3 endGoal, Vector3 endNextGoal) | PTools | [static] |
| ComputeJacobian(PProtein *loop, vector< int > ind, double **Jac, Vector3 p, bool forward) | PTools | [static] |
| ComputeJacobian(PProtein *loop, vector< int > ind, double **Jac, bool forward) | PTools | [static] |
| ComputeJacobian(PProtein *loop, double **Jac) | PTools | [static] |
| ComputeNullSpace(double **Jac, int dim, bool SixDimensional, NullSpaceRet *Ret) | PTools | [static] |
| ComputePseudoInverse(double **A, int m, int n, double **Ainv) | PTools | [static] |
| CopyBackbone(PProtein *lpS, PProtein *lpD, int startS, int startD, int numRes) | PTools | [static] |
| CopyBackbone(PProtein *lpS, PProtein *lpD) | PTools | [static] |
| CreateSlimProtein(PProtein *protein) | PTools | [static] |
| CreateSlimProtein(PProtein *protein, int startRes, int endRes) | PTools | [static] |
| EffectorAnchorDist(PProtein *loop, ProteinSide side) | PTools | [static] |
| getBackboneAtomIndex(int resIndex, const string &atomID) | PTools | [static] |
| GetBBDofs(vector< PProtein * > loops) | PTools | [static] |
| GetClusters(const PConformationSpace &space, ConformationDistFn distFn, Real threshold) | PTools | [static] |
| GetGoals(PAtom *anchorPrior, PAtom *anchorEnd, PAtom *effectorPrior, PAtom *effectorEnd, Real len, Real angle1, Real angle2, Vector3 &goalPrior, Vector3 &goalEnd) | PTools | [static] |
| GetGoals(PProtein *protein, ProteinSide side, Vector3 &goalPrior, Vector3 &goalEnd) | PTools | [static] |
| GetGoals(PProtein *protein, Vector3 &goalPrior, Vector3 &goalEnd) | PTools | [static] |
| gsl_test() | PTools | [static] |
| LowestCommonChain(PChain *c1, PChain *c2) | PTools | [static] |
| ProjectOnNullSpace(PProtein *loop, vector< int > ind, bool forward, double ToProject[], double AfterProject[]) | PTools | [static] |
| RandomNullSpacePerturb(PProtein *lp, double pert_mag) | PTools | [static] |
| RandomNullSpacePerturb(PProtein *lp, vector< vector< CDof > > Dofs, double pert_mag) | PTools | [static] |
| RMSDAllAtom(PProtein *protein0, PProtein *protein1, int loopstart, int loopend) | PTools | [static] |
| RMSDBackbone(PProtein *protein0, PProtein *protein1, int loopstart, int loopend) | PTools | [static] |
