newanalysis.helpers

Functions

`NQRdipTen`
`NQRself`
`NQRselfAndB`
`SphereinCube`
`applyRotationMatrix`	calcRotationMatrix(coor,coorA,coorB)
`atomicCurrent`
`calcAngularDisplacement`
`calcAngularMomentum`
`calcDipDipEnergyAtomic`	energy = calcDipDipEnergyAtomic(coms, dipol, resnum_solute, nmolecules)
`calcEnergyAA`	energy = calcEnergyAA(xyz, charges, atoms_per_residue, residue_first_atom, resnum_solute, nmolecules)
`calcEnergyAASep`	Calculates the solvation energy of a solute in an ionic liquid for a given frame.
`calcEnergyAAhisto`	energy = calcEnergyAAhisto(xyz, coms, charges, atoms_per_residue, residue_first_atom, resnum_solute, nmolecules, min_histo, max_histo, bins_hist,array indices, array indices 2)
`calcEnergyAAhisto1`	energy = calcEnergyAAhisto(xyz, coms, charges, atoms_per_residue, residue_first_atom, resnum_solute, nmolecules, min_histo, max_histo, bins_hist,array indices)
`calcEnergyAApermind`	energy = calcEnergyAA(xyz, coms, charges, atoms_per_residue, residue_first_atom, resnum_solute, resnum_from, resnum_to, drude_list)
`calcEnergyAApermindhisto`	energy = calcEnergyAA(xyz, coms, charges, atoms_per_residue, residue_first_atom, resnum_solute, resnum_from, resnum_to, drude_list, min_histo, max_histo, bins_histo)
`calcEnergyAtomic`	energy = calcEnergyAtomic(xyz, charges, atoms_per_residue, residue_first_atom, resnum_solute, nmolecules)
`calcEnergyAtomicVoro`	energy = calcEnergyAtomic(xyz, charges, atoms_per_residue, residue_first_atom, resnum_solute, nmolecules, delaunay_shell)
`calcEnergyDouble`	energy = calcEnergyDouble(xyz, charges_1, charges_2, atoms_per_residue, residue_first_atom, resnum_solute, nmolecules,start_res,end_res)
`calcEnergyMuA`	energy = calcEnergyMuA(xyz, charges, atoms_per_residue, residue_first_atom, resnum_solute, nmolecules,mu_solute)
`calcFourierLaplaceTransform`
`calcInertiaTensor`
`calcOctant`	In a box, that is centered on a specific residue and rotated to its body-fixed frame, this determines in which octant around this molecule each other molecule is centered.
`calcResidenceTimeseries`
`calcRotationMatrix`	Applies the Berthold-Horn-algorithm to a set of coordinates xyz, inplace.
`centerOrientBox`	Centers the box to the center of mass of a given molecule and rotates the box so that two sets of coordinates are as identical as possible.
`centerToPointOrientBox`	centerOrientToPointBox(com, xyz, center, boxlength, atoms_per_residue, residue_first_atom, coorA, coorB)
`checkHBond`
`collectiveDipoleMomentWaterShells`
`comByResidue`	Calculates the center-of-mass coordinates for a given selection.
`dipByResidue`	Calculates the molecular dipole moments, each referenced to the respective center of mass, for a given selection.
`dipTen`	Calculates the dipole T-tensor (see Daniel's NMR code).
`dipTenCorrel`
`dipTenInit`
`dipoleMomentNeutralSelection`
`findDS`
`findNearestAtom`
`sphHarmMatrix`
`sumMDCage`
`sumMDCageSingle`
`velcomByResidue`	Calculates the center-of-mass velocities for a given selection.
`waterRotationMatrix`