| activateResidue(int Rid1, int Rid2) | PChain | |
| AddResidue(const string &resName) | PChain | |
| AddResidue(const string &resName, PResidueSpec &resSpec) | PChain | |
| AddRotateEventHandler(PRotateEventHandler *handler) | PChain | |
| AntiMultiRotate(vector< ChainMove > &moves) | PChain | |
| Clone() | PProtein | |
| CloneResiduesIntoChain(PChain *other) | PChain | [protected] |
| CreateResidue(const string &name) | PProtein | [inline, protected, virtual] |
| CreateResidue(const string &name, PResidueSpec &spec) | PProtein | [inline, protected, virtual] |
| CreateResidue(const string &name, PResidue *res) | PProtein | [inline, protected, virtual] |
| CreateResidue(const string &name, PResidueSpec &spec, PResidue *res) | PProtein | [inline, protected, virtual] |
| DetachBlocks(const string &blockType, const string &blockTypeToDetachFrom) | PChain | |
| DetachBlocks(const string &blockType, const string &blockTypeToDetachFrom, int resStartIndex, int resEndIndex) | PChain | |
| DisableSidechains() | PProtein | |
| DisableSidechains(int resIndex1, int resIndex2) | PProtein | |
| EnableSidechains() | PProtein | |
| EnableSidechains(int resIndex1, int resIndex2) | PProtein | |
| finalize() | PChain | |
| FindAnyCollision() | PChain | |
| FindAnyCollision(int resIndex1, int resIndex2) | PChain | |
| FindSelfCollision() | PChain | [virtual] |
| FindSelfCollision(int resIndex1, int resIndex2) | PChain | [virtual] |
| FindStaticCollision() | PChain | |
| FindStaticCollision(int resIndex1, int resIndex2) | PChain | |
| getAllCollidingEither() | PChain | |
| getAllCollidingEither(int resIndex1, int resIndex2) | PChain | |
| getAllCollidingSelf() | PChain | [virtual] |
| getAllCollidingSelf(int resIndex1, int resIndex2) | PChain | [virtual] |
| getAllCollidingStatic() | PChain | |
| getAllCollidingStatic(int resIndex1, int resIndex2) | PChain | |
| GetAnchors(ProteinSide side, PAtom *&endAnchor, PAtom *&endPriorAnchor) | PProtein | |
| getAtom(const string &blockType, int index) | PChain | |
| getAtomAtRes(const string &atomID, int resNum) | PChain | [virtual] |
| getAtomPos(const string &blockType, int index) | PChain | |
| GetBlockTypes() const | PChain | |
| getBond(int res_index, const string &id1, const string &id2) | PChain | |
| getBond(int res_index1, const string &id1, int res_index2, const string &id2) | PChain | |
| GetDOFs(const string &blockType) | PChain | |
| GetEndEffectors(ProteinSide side, PAtom *&endAtom, PAtom *&endPriorAtom) | PProtein | |
| getParent() | PProtein | [inline] |
| PChain::getParent() const | PChain | |
| getResidue(int localIndex) | PProtein | [inline, virtual] |
| getResidueByPdbIndex(int pdbIndex) | PProtein | |
| getResidueGlobalIndex(PResidue *res) | PChain | |
| getResidueIndex(const PAtom *atom) | PChain | |
| getResidueLocalIndex(PResidue *res) | PChain | |
| getShortestPath(const PAtom *a1, ConstAtomSet a2Set, int maxLength) | PChain | |
| getShortestPath(const PAtom *a1, const PAtom *a2, int maxLength) | PChain | |
| getShortestPath(const PAtom *a1, ConstAtomSet a2Set, int maxLength, int extendNum) | PChain | |
| getSpaceManager() | PChain | [inline, virtual] |
| getSubchainByPdbIndices(int startPdbIndex, int endPdbIndex) | PProtein | |
| getTopLevelChain() | PChain | |
| getTopLevelIndices() const | PChain | |
| getTopLevelProtein() | PProtein | |
| inactivateResidue(int Rid1, int Rid2) | PChain | |
| InAnyCollision() | PChain | |
| InAnyCollision(int resIndex1, int resIndex2) | PChain | |
| InSelfCollision() | PChain | [virtual] |
| InSelfCollision(int resIndex1, int resIndex2) | PChain | [virtual] |
| InStaticCollision() | PChain | |
| InStaticCollision(int resIndex1, int resIndex2) | PChain | |
| IsSubChainOf(const PChain *other) const | PChain | |
| MultiRotate(vector< ChainMove > &moves) | PChain | |
| NumAtoms(const string &blockType) const | PChain | |
| NumBackboneDOFs() const | PProtein | |
| NumDOF(const string &blockType) const | PChain | |
| NumSidechainDOFs() const | PProtein | |
| Obliterate() | PChain | |
| PAtom class | PChain | [friend] |
| PChain() | PChain | |
| PChain(const string &firstResidueName) | PChain | |
| PChain(const string &firstResidueName, PResidueSpec &firstResidueSpec) | PChain | |
| PChain(PChain *protein, int resStartIndex, int resEndIndex) | PChain | |
| PProtein() | PProtein | |
| PProtein(const string &firstResidueName) | PProtein | |
| PProtein(const string &firstResidueName, PResidueSpec &firstResidueSpec) | PProtein | |
| PProtein(PProtein *protein, int resStartIndex, int resEndIndex) | PProtein | |
| PProtein(int numResidues) | PProtein | |
| RandomizeAllSidechains() | PProtein | |
| RandomizeBackbone() | PProtein | |
| RandomizeDOFs(BondDirection dir) | PChain | |
| RandomizeSidechainAtRes(int resIndex) | PProtein | |
| ReattachAllBlocks() | PChain | |
| ReattachAllBlocks(int resStartIndex, int resEndIndex) | PChain | |
| ReattachBlocks(const string &blockType) | PChain | |
| ReattachBlocks(const string &blockType, int resStartIndex, int resEndIndex) | PChain | |
| RemoveRotateEventHandler(PRotateEventHandler *handler) | PChain | |
| revertAtomColorAtRes(const string &atomID, int resNum) | PChain | [inline, virtual] |
| RotateBackbone(int DOF_index, BondDirection dir, Real numDegrees) | PProtein | |
| RotateChain(const string &blockType, int DOFindex, BondDirection dir, float degrees) | PChain | |
| RotateChain(const ChainMove &move) | PChain | |
| RotateSidechain(int DOF_index, float numDegrees) | PProtein | |
| setAtomColorAtRes(const string &atomID, int resNum, GLColor setColor) | PChain | [inline, virtual] |
| size() const | PChain | [virtual] |
| traverseFromStart(AtomFunctor *atomFn) | PChain | [inline] |
| traverseFromStart(BondFunctor *bondFn) | PChain | [inline] |
| traverseFromStart(AtomFunctor *atomFn, BondFunctor *bondFn) | PChain | |
| ~PChain() | PChain | |
