Molecule Member List

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

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_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
consForce	Molecule
consForceIndexes	Molecule
consTorqueIndexes	Molecule
consTorqueParams	Molecule
CrosstermElem class	Molecule	friend
delete_alch_bonded(void)	Molecule
delete_qm_bonded()	Molecule
DihedralElem class	Molecule	friend
energyNative	Molecule
energyNonnative	Molecule
ExclElem class	Molecule	friend
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_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
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_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_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
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
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
numLJPair	Molecule
numLonepairs	Molecule
numLphosts	Molecule
numMigrationGroups	Molecule
numMovDrag	Molecule
numMultipleDihedrals	Molecule
numMultipleImpropers	Molecule
numPair	Molecule
numRealBonds	Molecule
numRigidBonds	Molecule
numRotDrag	Molecule
numStirredAtoms	Molecule
numTholes	Molecule
numTotalExclusions	Molecule
numZeroMassAtoms	Molecule
pairC12	Molecule
pairC6	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
WorkDistrib class	Molecule	friend
~Molecule()	Molecule