Molecule Member List

This is the complete list of members for Molecule, including all inherited members.
alchDroppedAnglesMolecule
alchDroppedDihedralsMolecule
alchDroppedImpropersMolecule
AngleElem classMolecule [friend]
AnisoElem classMolecule [friend]
atomChainTypesMolecule
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 classMolecule [friend]
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_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_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
consForceMolecule
consForceIndexesMolecule
consTorqueIndexesMolecule
consTorqueParamsMolecule
CrosstermElem classMolecule [friend]
delete_alch_bonded(void)Molecule
delete_qm_bonded()Molecule
DihedralElem classMolecule [friend]
energyNativeMolecule
energyNonnativeMolecule
ExclElem classMolecule [friend]
freeBFactorData()Molecule [inline]
freeOccupancyData()Molecule [inline]
gAMolecule
get_acceptor(int dnum) const Molecule [inline]
get_angle(int anum) const Molecule [inline]
get_angles_for_atom(int anum)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_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_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)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
getLcpoParamType()Molecule [inline]
getOccupancyData()Molecule [inline]
getVirialTailCorr(const BigReal)Molecule
giSigma1Molecule
giSigma2Molecule
gMu1Molecule
gMu2Molecule
go_arrayMolecule
go_indicesMolecule
go_restricted(int, int, int)Molecule
goCoordinatesMolecule
goIndxLJAMolecule
goIndxLJBMolecule
goInit()Molecule
goNumLJPairMolecule
goPDBMolecule
goResidIndicesMolecule
goResidsMolecule
goSigmaIndicesMolecule
goSigmaPairAMolecule
goSigmaPairBMolecule
goSigmasMolecule
goWithinCutoffMolecule
gRepulsiveMolecule
gromacsPair_typeMolecule
GromacsPairElem classMolecule [friend]
hydrogenGroupMolecule
ImproperElem classMolecule [friend]
indxGaussAMolecule
indxGaussBMolecule
indxLJAMolecule
indxLJBMolecule
initialize()Molecule
is_atom_constorqued(int atomnum) const Molecule [inline]
is_atom_constrained(int atomnum) 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)Molecule
is_drude_psfMolecule
is_group_fixed(int atomnum) const Molecule [inline]
is_hydrogen(int)Molecule
is_hydrogenGroupParent(int)Molecule
is_lonepairs_psfMolecule
is_lp(int)Molecule
is_oxygen(int)Molecule
is_water(int)Molecule
isBFactorValidMolecule
isOccupancyValidMolecule
langevin_param(int atomnum) const Molecule [inline]
maxHydrogenGroupSizeMolecule
maxMigrationGroupSizeMolecule
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 *, const GromacsTopFile *)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]
numAcceptorsMolecule
numAnglesMolecule
numAnisosMolecule
numAtomsMolecule
numBondsMolecule
numCalcAnglesMolecule
numCalcAnisosMolecule
numCalcBondsMolecule
numCalcCrosstermsMolecule
numCalcDihedralsMolecule
numCalcExclusionsMolecule
numCalcFullExclusionsMolecule
numCalcImpropersMolecule
numCalcLJPairMolecule
numCalcTholesMolecule
numConsForceMolecule
numConsTorqueMolecule
numConstraintsMolecule
numCrosstermsMolecule
numDihedralsMolecule
numDonorsMolecule
numDrudeAtomsMolecule
numExclusionsMolecule
numExPressureAtomsMolecule
numFepFinalMolecule
numFepInitialMolecule
numFixedAtomsMolecule
numFixedGroupsMolecule
numFixedRigidBondsMolecule
numGaussPairMolecule
numGoAtomsMolecule
NumGoChainsMolecule
numGridforceGridsMolecule
numGridforcesMolecule
numHydrogenGroupsMolecule
numImpropersMolecule
numLJPairMolecule
numLonepairsMolecule
numLphostsMolecule
numMigrationGroupsMolecule
numMovDragMolecule
numMultipleDihedralsMolecule
numMultipleImpropersMolecule
numPairMolecule
numRealBondsMolecule
numRigidBondsMolecule
numRotDragMolecule
numStirredAtomsMolecule
numTholesMolecule
numTotalExclusionsMolecule
numZeroMassAtomsMolecule
pairC12Molecule
pairC6Molecule
pointerToGaussBegMolecule
pointerToGaussEndMolecule
pointerToGoBegMolecule
pointerToGoEndMolecule
pointerToLJBegMolecule
pointerToLJEndMolecule
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_ohcMolecule
r_omMolecule
read_go_file(char *)Molecule
read_parm(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_indexMolecule
ss_num_vdw_paramsMolecule
ss_vdw_typeMolecule
suspiciousAlchBondsMolecule
tail_corr_dUdl_1Molecule
tail_corr_dUdl_2Molecule
tail_corr_enerMolecule
tail_corr_virialMolecule
tail_corr_virial_1Molecule
tail_corr_virial_2Molecule
TholeElem classMolecule [friend]
WorkDistrib classMolecule [friend]
~Molecule()Molecule

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