public static IEnumerable <ValueTuple <int, Pdb.Atom> > EnumAtomsInWaterBox
(double maxx
, double maxy
, double maxz
, double dist2water = 2.9 //2.8 // 2.7564;
, bool randOrient = true
, string opt = "water in uniform cube"
)
{
System.Random rand = null;
if (randOrient)
{
rand = new System.Random();
}
//List<Pdb.Atom> atoms = new List<Pdb.Atom>();
int file = 1;
int serial = 1;
int resSeq = 1;
IEnumerable <Vector> enumer = null;
switch (opt)
{
case "water in uniform cube": enumer = Geometry.EnumPointsInVolume_UniformCube(maxx / dist2water, maxy / dist2water, maxz / dist2water); break;
case "water in uniform tetrahedron": enumer = Geometry.EnumPointsInVolume_UniformTetrahedron(maxx / dist2water, maxy / dist2water, maxz / dist2water); break;
}
foreach (Vector pt in enumer)
{
resSeq++;
double x = pt[0] * dist2water;
double y = pt[1] * dist2water;
double z = pt[2] * dist2water;
//var atom = Pdb.Atom.FromData(i+1, "H", "HOH", '1', i+1, pt[0], pt[1], pt[2]);
/// ATOM 8221 OH2 TIP32 547 11.474 41.299 26.099 1.00 0.00 O
/// ATOM 8222 H1 TIP32 547 12.474 41.299 26.099 0.00 0.00 H
/// ATOM 8223 H2 TIP32 547 11.148 42.245 26.099 0.00 0.00 H
Vector[] pthoh = new Vector[]
{
new double[] { 0.000000, 0.000000, 0.000000 },
new double[] { 0.000000, 0.000000, 0.957200 },
new double[] { 0.926627, 0.000000, 0.239987 },
};
if (randOrient != null)
{
Vector axis = new double[]
{ (rand.NextDouble() * 10) % 5
, (rand.NextDouble() * 10) % 5
, (rand.NextDouble() * 10) % 5 };
Trans3 trans = Trans3.FromRotate(axis.UnitVector(), rand.NextDouble() * Math.PI * 4);
trans.DoTransform(pthoh);
}
if ((serial >= 99990) || (resSeq >= 9990))
{
file++;
serial = 1;
resSeq = 1;
}
serial++; Pdb.Atom OH2 = Pdb.Atom.FromData(serial, "OH2", "HOH", '1', resSeq + 1, x + pthoh[0][0], y + pthoh[0][1], z + pthoh[0][2], element: "O"); yield return(new ValueTuple <int, Pdb.Atom>(file, OH2)); //atoms.Add(OH2);
serial++; Pdb.Atom H1 = Pdb.Atom.FromData(serial, "H1", "HOH", '1', resSeq + 1, x + pthoh[1][0], y + pthoh[1][1], z + pthoh[1][2], element: "H"); yield return(new ValueTuple <int, Pdb.Atom>(file, H1)); //atoms.Add(H1 );
serial++; Pdb.Atom H2 = Pdb.Atom.FromData(serial, "H2", "HOH", '1', resSeq + 1, x + pthoh[2][0], y + pthoh[2][1], z + pthoh[2][2], element: "H"); yield return(new ValueTuple <int, Pdb.Atom>(file, H2)); //atoms.Add(H2 );
}
}