public static HessInfo GetHessSsNMA
(Universe univ
, IList <Vector> coords
, double nbondMaxDist // =double.PositiveInfinity
, double?maxAbsSpring = null
//, bool setNanForEmptyAtom // =true
)
{
IEnumerable <Universe.Nonbonded> nonbondeds;
IEnumerable <Universe.Nonbonded14> nonbonded14s;
{
Universe.Nonbondeds _nonbondeds = new Universe.Nonbondeds(univ.atoms, univ.size, nbondMaxDist);
_nonbondeds.UpdateCoords(coords, true);
nonbondeds = _nonbondeds.EnumNonbondeds(true);
nonbonded14s = univ.nonbonded14s.GetEnumerable();
}
return(GetHessSsNMA(univ
, coords, univ.bonds, univ.angles, univ.impropers
, univ.dihedrals, nonbondeds, nonbonded14s
, maxAbsSpring
//, setNanForEmptyAtom
));
}
public IEnumerable <Nonbonded> EnumNonbondeds(Vector[] coords, double cutoff, bool skip_nulls)
{
Universe.Nonbondeds nonbondeds = new Universe.Nonbondeds(atoms, size
, maxdist: cutoff
);
nonbondeds.UpdateCoords(coords, skip_nulls);
return(nonbondeds.EnumNonbondeds(skip_nulls));
}
public static IEnumerable <Universe.Nonbonded> EnumNonbondeds
(Universe.Atoms atoms
, IList <Vector> coords
, int size
, double maxdist // = 12
)
{
Universe.Nonbondeds _nonbondeds;
IEnumerable <Universe.Nonbonded> nonbondeds;
_nonbondeds = new Universe.Nonbondeds(atoms, size, maxdist);
_nonbondeds.UpdateCoords(coords, true);
nonbondeds = _nonbondeds.EnumNonbondeds(true);
return(nonbondeds);
}
public static IEnumerable <Universe.Nonbonded> EnumNonbondeds
(Universe.Atoms atoms
, IList <Vector> coords
, int size
, double maxdist // = 12
, FuncListTip3pHBond func
, string[] options
)
{
bool[] waters = new bool[coords.Count];
KDTree.KDTree <Universe.Atom> kdtree_water = new KDTree.KDTree <Universe.Atom>(3);
foreach (var atom in atoms)
{
if (coords[atom.ID] == null)
{
continue;
}
bool water = atom.IsWater();
waters[atom.ID] = water;
if (water)
{
kdtree_water.insert(coords[atom.ID], atom);
}
}
Universe.Nonbondeds _nonbondeds;
_nonbondeds = new Universe.Nonbondeds(atoms, size, maxdist);
_nonbondeds.UpdateCoords(coords, true);
foreach (var nonbonded in _nonbondeds.EnumNonbondeds(true))
{
HDebug.Assert(nonbonded.atoms.Length == 2);
var atom0 = nonbonded.atoms[0];
var atom1 = nonbonded.atoms[1];
if (waters[atom0.ID] && waters[atom1.ID])
{
continue;
}
yield return(nonbonded);
}
foreach (Universe.Nonbonded nonbonded in func(atoms, coords, waters, kdtree_water, options))
{
yield return(nonbonded);
}
}
public static Nonbonded[] ListWithinNonbondeds(this IList <Atom> atoms, Universe.Nonbondeds nonbondeds)
{
HashSet <Atom> setatoms = new HashSet <Atom>(atoms);
List <Nonbonded> withinnonbondeds = new List <Nonbonded>();
foreach (Nonbonded nbond in nonbondeds.EnumNonbondeds(atoms, false))
{
if (setatoms.Contains(nbond.atoms[0]) == false)
{
continue;
}
if (setatoms.Contains(nbond.atoms[1]) == false)
{
continue;
}
withinnonbondeds.Add(nbond);
}
return(withinnonbondeds.ToArray());
}
public static HessInfo GetHessSsNMA
(Universe univ
, IList <Vector> coords
, double nbondMaxDist // =double.PositiveInfinity
, double?maxAbsSpring
, double?K_r = 340.00
, double?K_theta = 45.00
, double?K_ub = 10.00
, double?K_psi = 70.00
, double?K_chi = 1.00
, double?n = 1
, string k_vdW = "Unif"
//, bool setNanForEmptyAtom // =true
)
{
IEnumerable <Universe.Nonbonded> nonbondeds;
IEnumerable <Universe.Nonbonded14> nonbonded14s;
{
Universe.Nonbondeds _nonbondeds = new Universe.Nonbondeds(univ.atoms, univ.size, nbondMaxDist);
_nonbondeds.UpdateCoords(coords, true);
nonbondeds = _nonbondeds.EnumNonbondeds(true);
nonbonded14s = univ.nonbonded14s.GetEnumerable();
}
return(GetHessSsNMA
(univ
, coords, univ.bonds, univ.angles, univ.impropers
, univ.dihedrals, nonbondeds, nonbonded14s
, maxAbsSpring
, K_r
, K_theta
, K_ub
, K_psi
, K_chi
, n
, k_vdW
));
}