| add_dcd_selection_file(int dcdIndex, char *userDcdFile) | Molecule | |
| add_dcd_selection_freq(int dcdIndex, int freq) | Molecule | |
| alch_unpert_angles | Molecule | |
| alch_unpert_bonds | Molecule | |
| alch_unpert_dihedrals | Molecule | |
| alchDroppedAngles | Molecule | |
| alchDroppedDihedrals | Molecule | |
| alchDroppedImpropers | Molecule | |
| AngleElem class | Molecule | friend |
| AnisoElem class | Molecule | friend |
| atomChainTypes | Molecule | |
| atomcharge(int anum) const | Molecule | inline |
| atommass(int anum) const | Molecule | inline |
| atoms_1to4(unsigned int, unsigned int) | Molecule | |
| atomvdwtype(int anum) const | Molecule | inline |
| BondElem class | Molecule | friend |
| build_alch_unpert_bond_lists(char *) | Molecule | |
| build_constant_forces(char *) | Molecule | |
| build_constorque_params(StringList *, StringList *, StringList *, StringList *, StringList *, StringList *, PDB *, char *) | Molecule | |
| build_constraint_params(StringList *, StringList *, StringList *, PDB *, char *) | Molecule | |
| build_dcd_selection_list_pdb(int dcdIndex, char *userDcdInputFile) | Molecule | |
| build_exPressure_atoms(StringList *, StringList *, PDB *, char *) | Molecule | |
| build_extra_bonds(Parameters *parameters, StringList *file) | Molecule | |
| build_fep_flags(StringList *, StringList *, PDB *, char *, const char *) | Molecule | |
| build_fixed_atoms(StringList *, StringList *, PDB *, char *) | Molecule | |
| build_go_arrays(StringList *, char *) | Molecule | |
| build_go_params(StringList *) | Molecule | |
| build_go_sigmas(StringList *, char *) | Molecule | |
| build_go_sigmas2(StringList *, char *) | Molecule | |
| build_gridforce_params(StringList *, StringList *, StringList *, StringList *, PDB *, char *) | Molecule | |
| build_gro_pair() | Molecule | |
| build_langevin_params(BigReal coupling, BigReal drudeCoupling, Bool doHydrogen) | Molecule | |
| build_langevin_params(StringList *, StringList *, PDB *, char *) | Molecule | |
| build_molecule() | Molecule | |
| build_movdrag_params(StringList *, StringList *, StringList *, PDB *, char *) | Molecule | |
| build_rotdrag_params(StringList *, StringList *, StringList *, StringList *, StringList *, StringList *, PDB *, char *) | Molecule | |
| build_ss_flags(const StringList *ssfile, const StringList *sscol, PDB *initial_pdb, const char *cwd) | Molecule | |
| build_stirred_atoms(StringList *, StringList *, PDB *, char *) | Molecule | |
| checkexcl(int atom1, int atom2) const | Molecule | |
| compute_LJcorrection() | Molecule | |
| compute_LJcorrection_alternative() | Molecule | |
| consForce | Molecule | |
| consForceIndexes | Molecule | |
| consTorqueIndexes | Molecule | |
| consTorqueParams | Molecule | |
| CrosstermElem class | Molecule | friend |
| dcdSelectionAtoms | Molecule | |
| dcdSelectionKeyMap | Molecule | |
| dcdSelectionParams | Molecule | |
| delete_alch_bonded(void) | Molecule | |
| delete_qm_bonded() | Molecule | |
| DihedralElem class | Molecule | friend |
| energyNative | Molecule | |
| energyNonnative | Molecule | |
| ExclElem class | Molecule | friend |
| find_dcd_selection_index(const char *keystr) | Molecule | |
| find_or_create_dcd_selection_index(const char *keystr) | Molecule | |
| freeBFactorData() | Molecule | inline |
| freeOccupancyData() | Molecule | inline |
| gA | Molecule | |
| get_acceptor(int dnum) const | Molecule | inline |
| get_angle(int anum) const | Molecule | inline |
| get_angles_for_atom(int anum) | Molecule | inline |
| get_atom_dcd_status(const int index) | Molecule | inline |
| get_atom_from_index_in_residue(const char *segid, int resid, int index) const | Molecule | |
| get_atom_from_name(const char *segid, int resid, const char *aname) const | Molecule | |
| get_atom_index_from_dcd_selection(const int index, const int atomIndex) | Molecule | inline |
| get_atomtype(int anum) const | Molecule | inline |
| get_bond(int bnum) const | Molecule | inline |
| get_bonds_for_atom(int anum) | Molecule | inline |
| get_cluster(int anum) const | Molecule | inline |
| get_clusterSize(int anum) const | Molecule | inline |
| get_cons_params(Real &k, Vector &refPos, int atomnum) const | Molecule | inline |
| get_constorque_params(BigReal &v, Vector &a, Vector &p, int atomnum) const | Molecule | inline |
| get_crossterm(int inum) const | Molecule | inline |
| get_crossterms_for_atom(int anum) | Molecule | inline |
| get_cSMDcoffs() | Molecule | inline |
| get_cSMDindex() | Molecule | inline |
| get_cSMDindxLen() | Molecule | inline |
| get_cSMDKs() | Molecule | inline |
| get_cSMDnumInst() | Molecule | inline |
| get_cSMDpairs() | Molecule | inline |
| get_cSMDVels() | Molecule | inline |
| get_dcd_selection_index_from_atom_id(const int index, const int atomIndex) | Molecule | inline |
| get_dcd_selection_size(const int index) | Molecule | inline |
| get_dihedral(int dnum) const | Molecule | inline |
| get_dihedrals_for_atom(int anum) | Molecule | inline |
| get_donor(int dnum) const | Molecule | inline |
| get_excl_check_for_atom(int anum) const | Molecule | inline |
| get_exclusion(int ex) const | Molecule | inline |
| get_exclusions_for_atom(int anum) | Molecule | inline |
| get_fep_bonded_type(const int *atomID, unsigned int order) const | Molecule | inline |
| get_fep_type(int anum) const | Molecule | inline |
| get_full_exclusions_for_atom(int anum) const | Molecule | inline |
| get_go_cutoff(int chain1, int chain2) | Molecule | inline |
| get_go_epsilon(int chain1, int chain2) | Molecule | inline |
| get_go_epsilonRep(int chain1, int chain2) | Molecule | inline |
| get_go_exp_a(int chain1, int chain2) | Molecule | inline |
| get_go_exp_b(int chain1, int chain2) | Molecule | inline |
| get_go_exp_rep(int chain1, int chain2) | Molecule | inline |
| get_go_force(BigReal, int, int, BigReal *, BigReal *) const | Molecule | |
| get_go_force2(BigReal, BigReal, BigReal, int, int, BigReal *, BigReal *) const | Molecule | |
| get_go_force_new(BigReal, int, int, BigReal *, BigReal *) const | Molecule | |
| get_go_sigmaRep(int chain1, int chain2) | Molecule | inline |
| get_gridfrc_grid(int gridnum) const | Molecule | inline |
| get_gridfrc_params(Real &k, Charge &q, int atomnum, int gridnum) const | Molecule | inline |
| get_gro_force(BigReal, BigReal, BigReal, int, int) const | Molecule | |
| get_gro_force2(BigReal, BigReal, BigReal, int, int, BigReal *, BigReal *) const | Molecule | |
| get_groupSize(int) | Molecule | |
| get_improper(int inum) const | Molecule | inline |
| get_impropers_for_atom(int anum) | Molecule | inline |
| get_lphost(int atomid) const | Molecule | inline |
| get_mod_exclusions_for_atom(int anum) const | Molecule | inline |
| get_mother_atom(int) const | Molecule | |
| get_movdrag_params(Vector &v, int atomnum) const | Molecule | inline |
| get_noPC() | Molecule | inline |
| get_numQMAtoms() | Molecule | inline |
| get_qmAtmChrg() | Molecule | inline |
| get_qmAtmIndx() | Molecule | inline |
| get_qmAtomGroup() const | Molecule | inline |
| get_qmAtomGroup(int indx) const | Molecule | inline |
| get_qmcSMD() | Molecule | inline |
| get_qmCustomPCIdxs() | Molecule | inline |
| get_qmCustPCSizes() | Molecule | inline |
| get_qmDummyBondVal() | Molecule | inline |
| get_qmDummyElement() | Molecule | inline |
| get_qmElements() | Molecule | inline |
| get_qmGrpBonds() | Molecule | inline |
| get_qmGrpChrg() | Molecule | inline |
| get_qmGrpID() | Molecule | inline |
| get_qmGrpMult() | Molecule | inline |
| get_qmGrpNumBonds() | Molecule | inline |
| get_qmGrpSizes() | Molecule | inline |
| get_qmLSSFreq() | Molecule | inline |
| get_qmLSSIdxs() | Molecule | inline |
| get_qmLSSMass() | Molecule | inline |
| get_qmLSSRefIDs() | Molecule | inline |
| get_qmLSSRefMass() | Molecule | inline |
| get_qmLSSRefSize() | Molecule | inline |
| get_qmLSSResSize() | Molecule | inline |
| get_qmLSSSize() | Molecule | inline |
| get_qmMeMMindx() | Molecule | inline |
| get_qmMeNumBonds() | Molecule | inline |
| get_qmMeQMGrp() | Molecule | inline |
| get_qmMMBond() | Molecule | inline |
| get_qmMMBondedIndx() | Molecule | inline |
| get_qmMMChargeTarget() | Molecule | inline |
| get_qmMMNumTargs() | Molecule | inline |
| get_qmMMSolv() | Molecule | inline |
| get_qmNumBonds() | Molecule | inline |
| get_qmNumGrps() const | Molecule | inline |
| get_qmPCFreq() | Molecule | inline |
| get_qmReplaceAll() | Molecule | inline |
| get_qmTotCustPCs() | Molecule | inline |
| get_residue_size(const char *segid, int resid) const | Molecule | |
| get_rotdrag_params(BigReal &v, Vector &a, Vector &p, int atomnum) const | Molecule | inline |
| get_ss_type(int anum) const | Molecule | inline |
| get_stir_refPos(Vector &refPos, int atomnum) const | Molecule | inline |
| get_stir_startTheta(int atomnum) const | Molecule | inline |
| getAllAcceptors() const | Molecule | inline |
| getAllAngles() const | Molecule | inline |
| getAllBonds() const | Molecule | inline |
| getAllCrossterms() const | Molecule | inline |
| getAllDihedrals() const | Molecule | inline |
| getAllDonors() const | Molecule | inline |
| getAllImpropers() const | Molecule | inline |
| getAllLphosts() const | Molecule | inline |
| GetAtomAlpha(int i) const | Molecule | inline |
| getAtomNames() const | Molecule | inline |
| getAtoms() const | Molecule | inline |
| getAtomSegResInfo() const | Molecule | inline |
| getBFactorData() | Molecule | inline |
| getEnergyTailCorr(const BigReal, const int) | Molecule | |
| getFepAtomFlags() const | Molecule | inline |
| getLcpoParamType() | Molecule | inline |
| getOccupancyData() | Molecule | inline |
| getVirialTailCorr(const BigReal) | Molecule | |
| giSigma1 | Molecule | |
| giSigma2 | Molecule | |
| gMu1 | Molecule | |
| gMu2 | Molecule | |
| go_array | Molecule | |
| go_indices | Molecule | |
| go_restricted(int, int, int) | Molecule | |
| goCoordinates | Molecule | |
| goIndxLJA | Molecule | |
| goIndxLJB | Molecule | |
| goInit() | Molecule | |
| goNumLJPair | Molecule | |
| goPDB | Molecule | |
| goResidIndices | Molecule | |
| goResids | Molecule | |
| goSigmaIndices | Molecule | |
| goSigmaPairA | Molecule | |
| goSigmaPairB | Molecule | |
| goSigmas | Molecule | |
| goWithinCutoff | Molecule | |
| gRepulsive | Molecule | |
| gromacsPair_type | Molecule | |
| GromacsPairElem class | Molecule | friend |
| hydrogenGroup | Molecule | |
| ImproperElem class | Molecule | friend |
| indxGaussA | Molecule | |
| indxGaussB | Molecule | |
| indxLJA | Molecule | |
| indxLJB | Molecule | |
| initialize() | Molecule | |
| is_atom_constorqued(int atomnum) const | Molecule | inline |
| is_atom_constrained(int atomnum) const | Molecule | inline |
| is_atom_dcd_selection(int atomnum, int tag) const | Molecule | inline |
| is_atom_exPressure(int atomnum) const | Molecule | inline |
| is_atom_fixed(int atomnum) const | Molecule | inline |
| is_atom_gridforced(int atomnum, int gridnum) const | Molecule | inline |
| is_atom_movdragged(int atomnum) const | Molecule | inline |
| is_atom_rotdragged(int atomnum) const | Molecule | inline |
| is_atom_stirred(int atomnum) const | Molecule | inline |
| is_drude(int) const | Molecule | |
| is_drude_psf | Molecule | |
| is_group_fixed(int atomnum) const | Molecule | inline |
| is_hydrogen(int) | Molecule | |
| is_hydrogenGroupParent(int) | Molecule | |
| is_lonepairs_psf | Molecule | |
| is_lp(int) | Molecule | |
| is_oxygen(int) | Molecule | |
| is_water(int) | Molecule | |
| isBFactorValid | Molecule | |
| isOccupancyValid | Molecule | |
| langevin_param(int atomnum) const | Molecule | inline |
| maxHydrogenGroupSize | Molecule | |
| maxMigrationGroupSize | Molecule | |
| Molecule(SimParameters *, Parameters *param) | Molecule | |
| Molecule(SimParameters *, Parameters *param, char *filename, ConfigList *cfgList=NULL) | Molecule | |
| Molecule(SimParameters *simParams, Parameters *param, molfile_plugin_t *pIOHdl, void *pIOFileHdl, int natoms) | Molecule | |
| Molecule(SimParameters *, Parameters *, Ambertoppar *) | Molecule | |
| Molecule(SimParameters *, Parameters *, AmberParm7Reader::Ambertoppar *) | Molecule | |
| Molecule(SimParameters *, Parameters *, const GromacsTopFile *) | Molecule | |
| moleculeAtom | Molecule | |
| moleculeStartIndex | Molecule | |
| num_alch_unpert_Angles | Molecule | |
| num_alch_unpert_Bonds | Molecule | |
| num_alch_unpert_Dihedrals | Molecule | |
| num_deg_freedom(int isInitialReport=0) const | Molecule | inline |
| num_fixed_atoms() const | Molecule | inline |
| num_fixed_groups() const | Molecule | inline |
| num_group_deg_freedom() const | Molecule | inline |
| numAcceptors | Molecule | |
| numAngles | Molecule | |
| numAnisos | Molecule | |
| numAtoms | Molecule | |
| numBonds | Molecule | |
| numCalcAngles | Molecule | |
| numCalcAnisos | Molecule | |
| numCalcBonds | Molecule | |
| numCalcCrossterms | Molecule | |
| numCalcDihedrals | Molecule | |
| numCalcExclusions | Molecule | |
| numCalcFullExclusions | Molecule | |
| numCalcImpropers | Molecule | |
| numCalcLJPair | Molecule | |
| numCalcOneFourNbTholes | Molecule | |
| numCalcTholes | Molecule | |
| numConsForce | Molecule | |
| numConsTorque | Molecule | |
| numConstraints | Molecule | |
| numCrossterms | Molecule | |
| numDihedrals | Molecule | |
| numDonors | Molecule | |
| numDrudeAtoms | Molecule | |
| numExclusions | Molecule | |
| numExPressureAtoms | Molecule | |
| numFepFinal | Molecule | |
| numFepInitial | Molecule | |
| numFixedAtoms | Molecule | |
| numFixedGroups | Molecule | |
| numFixedRigidBonds | Molecule | |
| numGaussPair | Molecule | |
| numGoAtoms | Molecule | |
| NumGoChains | Molecule | |
| numGridforceGrids | Molecule | |
| numGridforces | Molecule | |
| numHydrogenGroups | Molecule | |
| numImpropers | Molecule | |
| numLargeMolecules | Molecule | |
| numLJPair | Molecule | |
| numLonepairs | Molecule | |
| numLphosts | Molecule | |
| numMigrationGroups | Molecule | |
| numMolecules | Molecule | |
| numMovDrag | Molecule | |
| numMultipleDihedrals | Molecule | |
| numMultipleImpropers | Molecule | |
| numOneFourNbTholes | Molecule | |
| numPair | Molecule | |
| numRealBonds | Molecule | |
| numRigidBonds | Molecule | |
| numRotDrag | Molecule | |
| numStirredAtoms | Molecule | |
| numTholes | Molecule | |
| numTotalExclusions | Molecule | |
| numZeroMassAtoms | Molecule | |
| OneFourNbTholeElem class | Molecule | friend |
| pairC12 | Molecule | |
| pairC6 | Molecule | |
| parse_dcd_selection_params(ConfigList *configList) | Molecule | |
| pointerToGaussBeg | Molecule | |
| pointerToGaussEnd | Molecule | |
| pointerToGoBeg | Molecule | |
| pointerToGoEnd | Molecule | |
| pointerToLJBeg | Molecule | |
| pointerToLJEnd | Molecule | |
| prepare_qm(const char *pdbFileName, Parameters *params, ConfigList *cfgList) | Molecule | |
| print_atoms(Parameters *) | Molecule | |
| print_bonds(Parameters *) | Molecule | |
| print_exclusions() | Molecule | |
| print_go_params() | Molecule | |
| print_go_sigmas() | Molecule | |
| put_stir_startTheta(Real theta, int atomnum) const | Molecule | inline |
| r_ohc | Molecule | |
| r_om | Molecule | |
| read_alch_unpert_angles(FILE *) | Molecule | |
| read_alch_unpert_bonds(FILE *) | Molecule | |
| read_alch_unpert_dihedrals(FILE *) | Molecule | |
| read_go_file(char *) | Molecule | |
| read_parm(Ambertoppar *) | Molecule | |
| read_parm(AmberParm7Reader::Ambertoppar *) | Molecule | |
| receive_GoMolecule(MIStream *) | Molecule | |
| receive_Molecule(MIStream *) | Molecule | |
| reloadCharges(float charge[], int n) | Molecule | |
| rigid_bond_length(int atomnum) const | Molecule | inline |
| send_GoMolecule(MOStream *) | Molecule | |
| send_Molecule(MOStream *) | Molecule | |
| set_gridfrc_grid(int gridnum, GridforceGrid *grid) | Molecule | inline |
| set_qm_replaceAll(Bool newReplaceAll) | Molecule | inline |
| setBFactorData(molfile_atom_t *atomarray) | Molecule | |
| setOccupancyData(molfile_atom_t *atomarray) | Molecule | |
| ss_index | Molecule | |
| ss_num_vdw_params | Molecule | |
| ss_vdw_type | Molecule | |
| suspiciousAlchBonds | Molecule | |
| tail_corr_dUdl_1 | Molecule | |
| tail_corr_dUdl_2 | Molecule | |
| tail_corr_ener | Molecule | |
| tail_corr_virial | Molecule | |
| tail_corr_virial_1 | Molecule | |
| tail_corr_virial_2 | Molecule | |
| TholeElem class | Molecule | friend |
| updateAtomDcdSelection(int atomIdx, uint16 bits) | Molecule | inline |
| WorkDistrib class | Molecule | friend |
| ~Molecule() | Molecule | |
