NAMD
Molecule Member List

This is the complete list of members for Molecule, including all inherited members.

alch_unpert_anglesMolecule
alch_unpert_bondsMolecule
alch_unpert_dihedralsMolecule
alchDroppedAnglesMolecule
alchDroppedDihedralsMolecule
alchDroppedImpropersMolecule
AngleElem classMoleculefriend
AnisoElem classMoleculefriend
atomChainTypesMolecule
atomcharge(int anum) const Moleculeinline
atommass(int anum) const Moleculeinline
atoms_1to4(unsigned int, unsigned int)Molecule
atomvdwtype(int anum) const Moleculeinline
BondElem classMoleculefriend
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_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 classMoleculefriend
delete_alch_bonded(void)Molecule
delete_qm_bonded()Molecule
DihedralElem classMoleculefriend
energyNativeMolecule
energyNonnativeMolecule
ExclElem classMoleculefriend
freeBFactorData()Moleculeinline
freeOccupancyData()Moleculeinline
gAMolecule
get_acceptor(int dnum) const Moleculeinline
get_angle(int anum) const Moleculeinline
get_angles_for_atom(int anum)Moleculeinline
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 Moleculeinline
get_bond(int bnum) const Moleculeinline
get_bonds_for_atom(int anum)Moleculeinline
get_cluster(int anum) const Moleculeinline
get_clusterSize(int anum) const Moleculeinline
get_cons_params(Real &k, Vector &refPos, int atomnum) const Moleculeinline
get_constorque_params(BigReal &v, Vector &a, Vector &p, int atomnum) const Moleculeinline
get_crossterm(int inum) const Moleculeinline
get_crossterms_for_atom(int anum)Moleculeinline
get_cSMDcoffs()Moleculeinline
get_cSMDindex()Moleculeinline
get_cSMDindxLen()Moleculeinline
get_cSMDKs()Moleculeinline
get_cSMDnumInst()Moleculeinline
get_cSMDpairs()Moleculeinline
get_cSMDVels()Moleculeinline
get_dihedral(int dnum) const Moleculeinline
get_dihedrals_for_atom(int anum)Moleculeinline
get_donor(int dnum) const Moleculeinline
get_excl_check_for_atom(int anum) const Moleculeinline
get_exclusion(int ex) const Moleculeinline
get_exclusions_for_atom(int anum)Moleculeinline
get_fep_bonded_type(const int *atomID, unsigned int order) const Moleculeinline
get_fep_type(int anum) const Moleculeinline
get_full_exclusions_for_atom(int anum) const Moleculeinline
get_go_cutoff(int chain1, int chain2)Moleculeinline
get_go_epsilon(int chain1, int chain2)Moleculeinline
get_go_epsilonRep(int chain1, int chain2)Moleculeinline
get_go_exp_a(int chain1, int chain2)Moleculeinline
get_go_exp_b(int chain1, int chain2)Moleculeinline
get_go_exp_rep(int chain1, int chain2)Moleculeinline
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)Moleculeinline
get_gridfrc_grid(int gridnum) const Moleculeinline
get_gridfrc_params(Real &k, Charge &q, int atomnum, int gridnum) const Moleculeinline
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 Moleculeinline
get_impropers_for_atom(int anum)Moleculeinline
get_lphost(int atomid) const Moleculeinline
get_mod_exclusions_for_atom(int anum) const Moleculeinline
get_mother_atom(int)Molecule
get_movdrag_params(Vector &v, int atomnum) const Moleculeinline
get_noPC()Moleculeinline
get_numQMAtoms()Moleculeinline
get_qmAtmChrg()Moleculeinline
get_qmAtmIndx()Moleculeinline
get_qmAtomGroup() const Moleculeinline
get_qmAtomGroup(int indx) const Moleculeinline
get_qmcSMD()Moleculeinline
get_qmCustomPCIdxs()Moleculeinline
get_qmCustPCSizes()Moleculeinline
get_qmDummyBondVal()Moleculeinline
get_qmDummyElement()Moleculeinline
get_qmElements()Moleculeinline
get_qmGrpBonds()Moleculeinline
get_qmGrpChrg()Moleculeinline
get_qmGrpID()Moleculeinline
get_qmGrpMult()Moleculeinline
get_qmGrpNumBonds()Moleculeinline
get_qmGrpSizes()Moleculeinline
get_qmLSSFreq()Moleculeinline
get_qmLSSIdxs()Moleculeinline
get_qmLSSMass()Moleculeinline
get_qmLSSRefIDs()Moleculeinline
get_qmLSSRefMass()Moleculeinline
get_qmLSSRefSize()Moleculeinline
get_qmLSSResSize()Moleculeinline
get_qmLSSSize()Moleculeinline
get_qmMeMMindx()Moleculeinline
get_qmMeNumBonds()Moleculeinline
get_qmMeQMGrp()Moleculeinline
get_qmMMBond()Moleculeinline
get_qmMMBondedIndx()Moleculeinline
get_qmMMChargeTarget()Moleculeinline
get_qmMMNumTargs()Moleculeinline
get_qmMMSolv()Moleculeinline
get_qmNumBonds()Moleculeinline
get_qmNumGrps() const Moleculeinline
get_qmPCFreq()Moleculeinline
get_qmReplaceAll()Moleculeinline
get_qmTotCustPCs()Moleculeinline
get_residue_size(const char *segid, int resid) const Molecule
get_rotdrag_params(BigReal &v, Vector &a, Vector &p, int atomnum) const Moleculeinline
get_ss_type(int anum) const Moleculeinline
get_stir_refPos(Vector &refPos, int atomnum) const Moleculeinline
get_stir_startTheta(int atomnum) const Moleculeinline
getAllAcceptors() const Moleculeinline
getAllAngles() const Moleculeinline
getAllBonds() const Moleculeinline
getAllCrossterms() const Moleculeinline
getAllDihedrals() const Moleculeinline
getAllDonors() const Moleculeinline
getAllImpropers() const Moleculeinline
getAllLphosts() const Moleculeinline
GetAtomAlpha(int i) const Moleculeinline
getAtomNames() const Moleculeinline
getAtoms() const Moleculeinline
getAtomSegResInfo() const Moleculeinline
getBFactorData()Moleculeinline
getEnergyTailCorr(const BigReal, const int)Molecule
getLcpoParamType()Moleculeinline
getOccupancyData()Moleculeinline
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 classMoleculefriend
hydrogenGroupMolecule
ImproperElem classMoleculefriend
indxGaussAMolecule
indxGaussBMolecule
indxLJAMolecule
indxLJBMolecule
initialize()Molecule
is_atom_constorqued(int atomnum) const Moleculeinline
is_atom_constrained(int atomnum) const Moleculeinline
is_atom_exPressure(int atomnum) const Moleculeinline
is_atom_fixed(int atomnum) const Moleculeinline
is_atom_gridforced(int atomnum, int gridnum) const Moleculeinline
is_atom_movdragged(int atomnum) const Moleculeinline
is_atom_rotdragged(int atomnum) const Moleculeinline
is_atom_stirred(int atomnum) const Moleculeinline
is_drude(int)Molecule
is_drude_psfMolecule
is_group_fixed(int atomnum) const Moleculeinline
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 Moleculeinline
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_alch_unpert_AnglesMolecule
num_alch_unpert_BondsMolecule
num_alch_unpert_DihedralsMolecule
num_deg_freedom(int isInitialReport=0) const Moleculeinline
num_fixed_atoms() const Moleculeinline
num_fixed_groups() const Moleculeinline
num_group_deg_freedom() const Moleculeinline
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 Moleculeinline
r_ohcMolecule
r_omMolecule
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
receive_GoMolecule(MIStream *)Molecule
receive_Molecule(MIStream *)Molecule
reloadCharges(float charge[], int n)Molecule
rigid_bond_length(int atomnum) const Moleculeinline
send_GoMolecule(MOStream *)Molecule
send_Molecule(MOStream *)Molecule
set_gridfrc_grid(int gridnum, GridforceGrid *grid)Moleculeinline
set_qm_replaceAll(Bool newReplaceAll)Moleculeinline
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 classMoleculefriend
WorkDistrib classMoleculefriend
~Molecule()Molecule