public static void GetPotential_SelfTest(string rootpath, string[] args)
{
if (GetPotential_SelfTest_do == false)
{
return;
}
GetPotential_SelfTest_do = false;
Namd.Psf psf = Namd.Psf.FromFile(rootpath + @"\Sample\alanin.psf");
Pdb pdb = Pdb.FromFile(rootpath + @"\Sample\alanin.pdb");
Namd.Prm prm = Namd.Prm.FromFileXPlor(rootpath + @"\Sample\alanin.params", new TextLogger());
Universe univ = Universe.Build(psf, prm, pdb, false);
List <ForceField.IForceField> frcflds = ForceField.GetMindyForceFields();
Vector[] forces = univ.GetVectorsZero();
MatrixByArr hessian = null;
Dictionary <string, object> cache = new Dictionary <string, object>();
double energy = univ.GetPotential(frcflds, ref forces, ref hessian, cache);
double toler = 0.000005;
HDebug.AssertTolerance(toler, SelfTest_alanin_energy - energy);
HDebug.AssertTolerance(toler, SelfTest_alanin_energy_bonds - (double)cache["energy_bonds "]);
HDebug.AssertTolerance(toler, SelfTest_alanin_energy_angles - (double)cache["energy_angles "]);
HDebug.AssertTolerance(toler, SelfTest_alanin_energy_dihedrals - (double)cache["energy_dihedrals "]);
HDebug.AssertTolerance(toler, SelfTest_alanin_energy_impropers - (double)cache["energy_impropers "]);
HDebug.AssertTolerance(toler, SelfTest_alanin_energy_nonbondeds - (double)cache["energy_nonbondeds"]);
HDebug.AssertTolerance(toler, SelfTest_alanin_energy_unknowns - (double)cache["energy_customs "]);
HDebug.AssertTolerance(toler, SelfTest_alanin_forces.GetLength(0) - forces.Length);
for (int i = 0; i < forces.Length; i++)
{
HDebug.Assert(forces[i].Size == 3);
HDebug.AssertTolerance(toler, SelfTest_alanin_forces[i, 0] - forces[i][0]);
HDebug.AssertTolerance(toler, SelfTest_alanin_forces[i, 1] - forces[i][1]);
HDebug.AssertTolerance(toler, SelfTest_alanin_forces[i, 2] - forces[i][2]);
}
}
public static void SelfTest(string rootpath, string[] args)
{
//{
// Pdb pdb = Pdb.FromFile(rootpath + @"\Sample\1a6g.pdb");
// HTLib2.Bioinfo.Universe.Build(pdb);
//}
GetPotential_SelfTest(rootpath, args);
Universe univ = null;
string sample = null;
//sample = "1a6g_autopsf.unfolded";
//sample = "1a6g_autopsf";
switch (sample)
{
case "alanin":
{
List <ForceField.IForceField> frcflds = ForceField.GetMindyForceFields();
double k = 0.0001;
double threshold = 0.001;
//int iter = univ.Minimize_ConjugateGradient_v0(frcflds, k, threshold);
int randomPurturb = 0; // no random purturbation
bool[] atomsMovable = null; // update all atoms
int iter_conjgrad;
{
Namd.Psf psf = Namd.Psf.FromFile(rootpath + @"\Sample\alanin.psf");
Pdb pdb = Pdb.FromFile(rootpath + @"\Sample\alanin.pdb");
Namd.Prm prm = Namd.Prm.FromFileXPlor(rootpath + @"\Sample\alanin.params", new TextLogger());
univ = Universe.Build(psf, prm, pdb, false);
//frcflds = new List<ForceField.IForceField>();
//frcflds.Add(new ForceField.MindyBond());
//frcflds.Add(new ForceField.MindyAngle());
//frcflds.Add(new ForceField.MindyDihedral());
//frcflds.Add(new ForceField.MindyImproper());
//frcflds.Add(new ForceField.MindyNonbondedLennardJones());
//frcflds.Add(new ForceField.MindyNonbondedElectrostatic());
//iter_conjgrad = univ.Minimize_ConjugateGradient_v1(0, frcflds, k, 0.1, null, threshold, randomPurturb, atomsMovable, new MinimizeLogger_PrintEnergyForceMag(), null, null);
//frcflds = new List<ForceField.IForceField>();
//frcflds.Add(new ForceField.MindyBond());
//frcflds.Add(new ForceField.MindyAngle());
//frcflds.Add(new ForceField.MindyImproper());
//frcflds.Add(new ForceField.MindyNonbondedLennardJones());
//frcflds.Add(new ForceField.MindyNonbondedElectrostatic());
//iter_conjgrad = univ.Minimize_ConjugateGradient_v1(0, frcflds, k*0.1, 0.1, null, threshold, randomPurturb, atomsMovable, new MinimizeLogger_PrintEnergyForceMag(), null, null);
frcflds = new List <ForceField.IForceField>();
if (HDebug.False)
{
frcflds.Add(new ForceField.MindyBond());
}
else
{
frcflds.Add(new ForceField.PwBond());
}
if (HDebug.False)
{
frcflds.Add(new ForceField.MindyAngle());
}
else
{
frcflds.Add(new ForceField.PwAngle());
}
frcflds.Add(new ForceField.MindyDihedral());
if (HDebug.False)
{
frcflds.Add(new ForceField.MindyImproper());
}
else
{
frcflds.Add(new ForceField.PwImproper());
}
if (HDebug.False)
{
frcflds.Add(new ForceField.MindyNonbondedElectrostatic());
}
else
{
frcflds.Add(new ForceField.PwElec());
}
if (HDebug.False)
{
frcflds.Add(new ForceField.MindyNonbondedLennardJones());
}
else
{
frcflds.Add(new ForceField.PwVdw());
}
univ.LoadCoords(@"D:\xxxx.coords");
iter_conjgrad = univ.Minimize_ConjugateGradient_v1(0, frcflds, k, 0.01, null, threshold, randomPurturb, atomsMovable, new MinimizeLogger_PrintEnergyForceMag(), null, null);
univ.SaveCoords(@"D:\xxxx.coords");
System.Console.WriteLine("=======================================================================");
System.Console.WriteLine("=======================================================================");
System.Console.WriteLine("=======================================================================");
}
{
//Psf psf = Psf.FromFile(rootpath + @"\Sample\alanin.psf");
//Pdb pdb = Pdb.FromFile(rootpath + @"\Sample\alanin.pdb");
//Prm prm = Prm.FromFileXPlor(rootpath + @"\Sample\alanin.params", new TextLogger());
//univ = Universe.Build(psf, prm, pdb);
//frcflds = new List<ForceField.IForceField>();
//if(true) frcflds.Add(new ForceField.MindyBond()); else frcflds.Add(new ForceField.PwBond());
//if(true) frcflds.Add(new ForceField.MindyAngle()); else frcflds.Add(new ForceField.PwAngle());
//frcflds.Add(new ForceField.MindyDihedral());
//if(true) frcflds.Add(new ForceField.MindyImproper()); else frcflds.Add(new ForceField.PwImproper());
//if(true) frcflds.Add(new ForceField.MindyNonbondedElectrostatic()); else frcflds.Add(new ForceField.PwElec());
//if(true) frcflds.Add(new ForceField.MindyNonbondedLennardJones()); else frcflds.Add(new ForceField.PwVdw());
univ.atoms[0].Coord += new Vector(0.1, 0.1, 0.1);
//iter_conjgrad = univ.Minimize_ConjugateGradient_v1(0, frcflds, k, 0.001, null, threshold, randomPurturb, atomsMovable, new MinimizeLogger_PrintEnergyForceMag(), null, null);
iter_conjgrad = univ.Minimize_ConjugateGradient_AtomwiseUpdate(frcflds,
threshold: threshold,
k: k,
max_atom_movement: 0.001,
max_iteration: null,
atomsMovable: atomsMovable,
logger: new MinimizeLogger_PrintEnergyForceMag()
);
}
k = 0.0005;
HDebug.Assert(false);
//int iter_stepdsnt = univ.Minimize_SteepestDescent(frcflds, k, threshold, System.Console.Error);
}
break;
case "1a6g_autopsf":
{
Namd.Psf psf = Namd.Psf.FromFile(rootpath + @"\Sample\1a6g_autopsf.psf");
Pdb pdb = Pdb.FromFile(rootpath + @"\Sample\1a6g_autopsf.pdb");
Namd.Prm prm = Namd.Prm.FromFile(rootpath + @"\Sample\1a6g_autopsf.prm", new TextLogger());
univ = Universe.Build(psf, prm, pdb, false);
List <ForceField.IForceField> frcflds = ForceField.GetMindyForceFields();
double threshold = 0.001;
string minimize_ver = "v1";
switch (minimize_ver)
{
//case "v2":
// {
// double atom_max_move = 0.03;
// int iter_conjgrad = univ.Minimize_ConjugateGradient_v2(frcflds, atom_max_move, threshold, System.Console.Error);
// break;
// }
case "v1":
{
double k = 0.0001;
int randomPurturb = 0; // no random purturbation
bool[] atomsMovable = null; // update all atoms
int iter_conjgrad = univ.Minimize_ConjugateGradient_v1(0, frcflds, k, 0.1, null, threshold, randomPurturb, atomsMovable, new MinimizeLogger_PrintEnergyForceMag(), null, null);
break;
}
default:
goto case "v1";
}
//atom_max_move = 0.03;
//int iter_stepdsnt = univ.Minimize_SteepestDescent(frcflds, atom_max_move, threshold, System.Console.Error);
}
break;
case "1a6g_autopsf.unfolded":
{
Namd.Psf psf = Namd.Psf.FromFile(rootpath + @"\Sample\1a6g_autopsf.psf");
Pdb pdb = Pdb.FromFile(rootpath + @"\Sample\1a6g_autopsf.pdb");
{
Random rand = new Random(1);
List <Vector> coords = pdb.atoms.ListCoord();
for (int i = 0; i < coords.Count; i++)
{
double x = i * 0.1 + rand.NextDouble() * 0.01;
double y = i * 0.1 + rand.NextDouble() * 0.01;
double z = i * 0.1 + rand.NextDouble() * 0.01;
coords[i] = new Vector(x, y, z);
}
pdb.ToFile(rootpath + @"\Sample\1a6g_autopsf.unfolded.pdb", coords);
pdb = Pdb.FromFile(rootpath + @"\Sample\1a6g_autopsf.unfolded.pdb");
}
Namd.Prm prm = Namd.Prm.FromFile(rootpath + @"\Sample\1a6g_autopsf.prm", new TextLogger());
univ = Universe.Build(psf, prm, pdb, false);
List <ForceField.IForceField> frcflds = ForceField.GetMindyForceFields();
double threshold = 0.01;
string minimize_ver = "v1";
switch (minimize_ver)
{
//case "v2":
// {
// double atom_max_move = 0.1;
// int iter_conjgrad = univ.Minimize_ConjugateGradient_v2(frcflds, atom_max_move, threshold, System.Console.Error);
// break;
// }
case "v1":
{
double k = 0.0001;
int randomPurturb = 100;
bool[] atomsMovable = null; // updates all atoms
int iter_conjgrad = univ.Minimize_ConjugateGradient_v1(0, frcflds, k, 0.1, null, threshold, randomPurturb, atomsMovable, new MinimizeLogger_PrintEnergyForceMag(), null, null);
break;
}
default:
goto case "v1";
}
//atom_max_move = 0.03;
//int iter_stepdsnt = univ.Minimize_SteepestDescent(frcflds, atom_max_move, threshold, System.Console.Error);
}
break;
default:
goto case "alanin";
}
}
public static Tuple <Xyz, Prm> FromNamd(Pdb pdb, Namd.Psf psf, Namd.Prm prm)
{
return(BuilderFromNamd.BuildFromNamd(pdb, psf, prm));
}
public static Tuple <Xyz, Prm> BuildFromNamd(Pdb pdb, Namd.Psf psf, Namd.Prm prm)
{
var univ = Universe.BuilderNamd.Build(psf, prm, pdb, null, null);
/// Atom(Id,Class,Type,Desc,Mass)
/// * Id : Vdw(Id,Rmin2,Epsilon)
/// Charge(Id,pch)
/// Biotype(BioId,Name,Resi,Id)
/// * Class: Vdw14(Class,Rmin2_14,Eps_14)
/// Bond(Class1,Class2,Kb,b0)
/// Angle(Class1,Class2,Class3,Ktheta,Theta0)
/// Ureybrad(Class1,Class2,Class3,Kub,S0)
/// Improper(Class1,Class2,Class3,Class4,Kpsi,psi0)
/// Torsion(Class1,Class2,Class3,Class4,Kchi0,delta0,n0,Kchi1,delta1,n1,Kchi2,delta2,n2)
/// Type :
Dictionary <Tuple <string, string, double, double, double, int>, int> key_id = new Dictionary <Tuple <string, string, double, double, double, int>, int>();
Dictionary <string, int> type_cls = new Dictionary <string, int>();
Dictionary <int, Prm.Atom> id_atom = new Dictionary <int, Prm.Atom>();
Dictionary <int, Prm.Vdw> cls_vdw = new Dictionary <int, Prm.Vdw>();
Dictionary <int, Prm.Charge> id_charge = new Dictionary <int, Prm.Charge>();
Dictionary <int, Prm.Biotype> id_biotype = new Dictionary <int, Prm.Biotype>();
Dictionary <int, Prm.Vdw14> cls_vdw14 = new Dictionary <int, Prm.Vdw14>();
Dictionary <int, Tuple <string, Vector, int, List <int> > > xyzid_info = new Dictionary <int, Tuple <string, Vector, int, List <int> > >();
/// 1 NH3
/// ------------------------------------------------------------------------------------------------------------------
/// pdb: "ATOM 1 N GLY A 2 24.776 -0.687 28.652 1.00 0.00 A N"
/// namd-psf: " 1 A 2 GLY N NH3 -0.300000 14.0070 0"
/// namd-prm: "NH3 0.000000 -0.200000 1.850000 ! ALLOW POL"
/// tink-xyz: " 1 NH3 24.776000 -0.687000 28.652000 65 2 5 6 7"
/// tink-prm: "atom 65 26 NH3 "Ammonium Nitrogen" 7 14.007 4"
foreach (var uatom in univ.atoms)
{
HDebug.Assert(uatom.sources.Length == 3);
Pdb.Atom pdbatom = uatom.sources.HFirstByType(null as Pdb.Atom); HDebug.Assert(pdbatom != null);
Namd.Psf.Atom psfatom = uatom.sources.HFirstByType(null as Namd.Psf.Atom); HDebug.Assert(psfatom != null);
Namd.Prm.Nonbonded prmnbnd = uatom.sources.HFirstByType(null as Namd.Prm.Nonbonded); HDebug.Assert(prmnbnd != null);
string name = psfatom.AtomName.Trim();
string resn = psfatom.ResidueName.Trim();
string type = psfatom.AtomType.Trim();
double rmin2 = prmnbnd.Rmin2;
double eps = prmnbnd.epsilon;
double chrg = psfatom.Charge;
int valnc = uatom.Bonds.Count;
string desc = string.Format("{0}({1})-{2}", name, type, resn);
var key = UnivAtomToTinkKey(uatom);
if (key_id.ContainsKey(key) == false)
{
key_id.Add(key, key_id.Count + 1);
}
if (type_cls.ContainsKey(type) == false)
{
type_cls.Add(type, type_cls.Count + 1);
}
int tink_id = key_id[key];
int tink_cls = type_cls[type];
string tink_type = type;
if (id_atom.ContainsKey(tink_id) == false)
{
Prm.Atom tink_atom = Prm.Atom.FromData
(Id: tink_id
, Class: tink_cls
, Type: tink_type
, Description: desc
, AtomicNumber: null
, Mass: psfatom.Mass
, Valence: valnc
);
id_atom.Add(tink_id, tink_atom);
}
else
{
Prm.Atom tink_atom = id_atom[tink_id];
tink_id = tink_atom.Id;
tink_cls = tink_atom.Class;
HDebug.Exception(tink_atom.Type == tink_type);
HDebug.Exception(tink_atom.Description == desc);
HDebug.Exception(Math.Abs(tink_atom.Mass - psfatom.Mass) < 0.001);
HDebug.Exception(tink_atom.Valence == valnc);
}
if (cls_vdw.ContainsKey(tink_cls) == false)
{
Prm.Vdw tink_vdw = Prm.Vdw.FromData
(Class: tink_cls
, Rmin2: prmnbnd.Rmin2
, Epsilon: prmnbnd.epsilon
);
cls_vdw.Add(tink_cls, tink_vdw);
}
else
{
Prm.Vdw tink_vdw = cls_vdw[tink_cls];
HDebug.Exception(tink_vdw.Rmin2 == prmnbnd.Rmin2);
HDebug.Exception(tink_vdw.Epsilon == prmnbnd.epsilon);
}
HDebug.AssertIf(double.IsNaN(prmnbnd.Rmin2_14) == true, double.IsNaN(prmnbnd.eps_14) == true);
HDebug.AssertIf(double.IsNaN(prmnbnd.Rmin2_14) == false, double.IsNaN(prmnbnd.eps_14) == false);
if (double.IsNaN(prmnbnd.Rmin2_14) == false && double.IsNaN(prmnbnd.eps_14) == false)
{
if (cls_vdw14.ContainsKey(tink_cls) == false)
{
Prm.Vdw14 tink_vdw14 = Prm.Vdw14.FromData
(Class: tink_cls
, Rmin2_14: prmnbnd.Rmin2_14
, Eps_14: prmnbnd.eps_14
);
cls_vdw14.Add(tink_cls, tink_vdw14);
}
else
{
Prm.Vdw14 tink_vdw14 = cls_vdw14[tink_cls];
HDebug.Exception(tink_vdw14.Rmin2_14 == prmnbnd.Rmin2_14);
HDebug.Exception(tink_vdw14.Eps_14 == prmnbnd.eps_14);
}
}
else
{
HDebug.Exception(cls_vdw14.ContainsKey(tink_cls) == false);
}
if (id_charge.ContainsKey(tink_id) == false)
{
Prm.Charge tink_charge = Prm.Charge.FromData
(Id: tink_id
, pch: psfatom.Charge
);
id_charge.Add(tink_id, tink_charge);
}
else
{
Prm.Charge tink_charge = id_charge[tink_id];
HDebug.Exception(tink_charge.pch == psfatom.Charge);
}
if (id_biotype.ContainsKey(tink_id) == false)
{
Prm.Biotype tink_biotype = Prm.Biotype.FromData
(BioId: id_biotype.Count + 1
, Name: name
, Resn: string.Format("{0}({1})-{2}", name, type, resn)
, Id: tink_id
);
id_biotype.Add(tink_id, tink_biotype);
}
else
{
Prm.Biotype tink_biotype = id_biotype[tink_id];
HDebug.Exception(tink_biotype.Name == name);
HDebug.Exception(tink_biotype.Resn == string.Format("{0}({1})-{2}", name, type, resn));
HDebug.Exception(tink_biotype.Id == tink_id);
}
var xyzid = uatom.AtomId;
var xyzinfo = new Tuple <string, Vector, int, List <int> >
(tink_type // AtomType
, uatom.Coord // X, Y, Z
, tink_id // AtomId
, new List <int>()
);
xyzid_info.Add(xyzid, xyzinfo);
}
Dictionary <Tuple <int, int>, Prm.Bond> cls_bond = new Dictionary <Tuple <int, int>, Prm.Bond>();
foreach (var ubond in univ.bonds)
{
var key0 = UnivAtomToTinkKey(ubond.atoms[0]); string type0 = key0.Item2; int cls0 = type_cls[type0];
var key1 = UnivAtomToTinkKey(ubond.atoms[1]); string type1 = key1.Item2; int cls1 = type_cls[type1];
Tuple <int, int> cls01;
if (cls0 < cls1)
{
cls01 = new Tuple <int, int>(cls0, cls1);
}
else
{
cls01 = new Tuple <int, int>(cls1, cls0);
}
if (cls_bond.ContainsKey(cls01) == false)
{
Prm.Bond tink_bond01 = Prm.Bond.FromData
(Class1: cls01.Item1
, Class2: cls01.Item2
, Kb: ubond.Kb
, b0: ubond.b0
);
cls_bond.Add(cls01, tink_bond01);
}
else
{
Prm.Bond tink_bond01 = cls_bond[cls01];
HDebug.Exception(Math.Abs(tink_bond01.Kb - ubond.Kb) < 0.01);
HDebug.Exception(tink_bond01.b0 == ubond.b0);
}
int xyzid0 = ubond.atoms[0].AtomId;
int xyzid1 = ubond.atoms[1].AtomId;
xyzid_info[xyzid0].Item4.Add(xyzid1);
xyzid_info[xyzid1].Item4.Add(xyzid0);
}
Dictionary <Tuple <int, int, int>, Prm.Angle> cls_angle = new Dictionary <Tuple <int, int, int>, Prm.Angle>();
Dictionary <Tuple <int, int, int>, Prm.Ureybrad> cls_ureybrad = new Dictionary <Tuple <int, int, int>, Prm.Ureybrad>();
foreach (var uangle in univ.angles)
{
var key0 = UnivAtomToTinkKey(uangle.atoms[0]); string type0 = key0.Item2; int cls0 = type_cls[type0];
var key1 = UnivAtomToTinkKey(uangle.atoms[1]); string type1 = key1.Item2; int cls1 = type_cls[type1];
var key2 = UnivAtomToTinkKey(uangle.atoms[2]); string type2 = key2.Item2; int cls2 = type_cls[type2];
Tuple <int, int, int> cls012;
if (cls0 < cls2)
{
cls012 = new Tuple <int, int, int>(cls0, cls1, cls2);
}
else
{
cls012 = new Tuple <int, int, int>(cls2, cls1, cls0);
}
double uangle_Theta0 = 180.0 * uangle.Theta0 / Math.PI;
if (cls_angle.ContainsKey(cls012) == false)
{
Prm.Angle tink_angle012 = Prm.Angle.FromData
(Class1: cls012.Item1
, Class2: cls012.Item2
, Class3: cls012.Item3
, Ktheta: uangle.Ktheta
, Theta0: uangle_Theta0
);
cls_angle.Add(cls012, tink_angle012);
HDebug.Exception(cls_ureybrad.ContainsKey(cls012) == false);
if (uangle.Kub != 0)
{
Prm.Ureybrad tink_ureybrad = Prm.Ureybrad.FromData
(Class1: cls012.Item1
, Class2: cls012.Item2
, Class3: cls012.Item3
, Kub: uangle.Kub
, S0: uangle.S0
);
cls_ureybrad.Add(cls012, tink_ureybrad);
}
}
else
{
Prm.Angle tink_angle012 = cls_angle[cls012];
HDebug.Exception(tink_angle012.Ktheta == uangle.Ktheta);
HDebug.Exception(Math.Abs(tink_angle012.Theta0 - uangle_Theta0) < 0.01);
if (uangle.Kub != 0)
{
Prm.Ureybrad tink_ureybrad = cls_ureybrad[cls012];
HDebug.Exception(tink_ureybrad.Kub == uangle.Kub);
HDebug.Exception(tink_ureybrad.S0 == uangle.S0);
}
else
{
HDebug.Exception(cls_ureybrad.ContainsKey(cls012) == false);
}
}
}
Dictionary <Tuple <int, int, int, int>, Prm.Improper> cls_improper = new Dictionary <Tuple <int, int, int, int>, Prm.Improper>();
foreach (var improper in univ.impropers)
{
var key0 = UnivAtomToTinkKey(improper.atoms[0]); string type0 = key0.Item2; int cls0 = type_cls[type0];
var key1 = UnivAtomToTinkKey(improper.atoms[1]); string type1 = key1.Item2; int cls1 = type_cls[type1];
var key2 = UnivAtomToTinkKey(improper.atoms[2]); string type2 = key2.Item2; int cls2 = type_cls[type2];
var key3 = UnivAtomToTinkKey(improper.atoms[3]); string type3 = key3.Item2; int cls3 = type_cls[type3];
Tuple <int, int, int, int> cls0123 = new Tuple <int, int, int, int>(cls0, cls1, cls2, cls3);
//if(cls0 < cls2) cls0123 = new Tuple<int, int, int, int>(cls0, cls1, cls2, cls3);
//else cls0123 = new Tuple<int, int, int, int>(cls3, cls2, cls1, cls0);
double improper_psi0 = 180.0 * improper.psi0 / Math.PI;
if (cls_improper.ContainsKey(cls0123) == false)
{
Prm.Improper tink_improper = Prm.Improper.FromData
(Class1: cls0
, Class2: cls1
, Class3: cls2
, Class4: cls3
, Kpsi: improper.Kpsi
, psi0: improper_psi0
);
cls_improper.Add(cls0123, tink_improper);
}
else
{
Prm.Improper tink_improper = cls_improper[cls0123];
HDebug.Exception(tink_improper.Kpsi == improper.Kpsi);
HDebug.Exception(Math.Abs(tink_improper.psi0 - improper_psi0) < 0.01);
}
}
Dictionary <Tuple <int, int, int, int>, List <Universe.Dihedral> > cls_dihedrals = new Dictionary <Tuple <int, int, int, int>, List <Universe.Dihedral> >();
foreach (var atom in univ.atoms)
{
var inter1234s = atom.ListInterAtom1234();
foreach (var inter1234 in inter1234s)
{
HDebug.Assert(inter1234.Count == 4);
var key0 = UnivAtomToTinkKey(inter1234[0]); string type0 = key0.Item2; int cls0 = type_cls[type0];
var key1 = UnivAtomToTinkKey(inter1234[1]); string type1 = key1.Item2; int cls1 = type_cls[type1];
var key2 = UnivAtomToTinkKey(inter1234[2]); string type2 = key2.Item2; int cls2 = type_cls[type2];
var key3 = UnivAtomToTinkKey(inter1234[3]); string type3 = key3.Item2; int cls3 = type_cls[type3];
Tuple <int, int, int, int> cls0123 = new Tuple <int, int, int, int>(cls0, cls1, cls2, cls3);
Tuple <int, int, int, int> cls3210 = new Tuple <int, int, int, int>(cls3, cls2, cls1, cls0);
if (cls_dihedrals.ContainsKey(cls0123) == false)
{
cls_dihedrals.Add(cls0123, new List <Universe.Dihedral>());
}
if (cls_dihedrals.ContainsKey(cls3210) == false)
{
cls_dihedrals.Add(cls3210, new List <Universe.Dihedral>());
}
}
}
foreach (var dihedral in univ.dihedrals)
{
var key0 = UnivAtomToTinkKey(dihedral.atoms[0]); string type0 = key0.Item2; int cls0 = type_cls[type0];
var key1 = UnivAtomToTinkKey(dihedral.atoms[1]); string type1 = key1.Item2; int cls1 = type_cls[type1];
var key2 = UnivAtomToTinkKey(dihedral.atoms[2]); string type2 = key2.Item2; int cls2 = type_cls[type2];
var key3 = UnivAtomToTinkKey(dihedral.atoms[3]); string type3 = key3.Item2; int cls3 = type_cls[type3];
Tuple <int, int, int, int> cls0123 = new Tuple <int, int, int, int>(cls0, cls1, cls2, cls3);
Tuple <int, int, int, int> cls3210 = new Tuple <int, int, int, int>(cls3, cls2, cls1, cls0);
cls_dihedrals[cls0123].Add(dihedral);
cls_dihedrals[cls3210].Add(dihedral);
}
Dictionary <Tuple <int, int, int, int>, Prm.Torsion> cls_torsion = new Dictionary <Tuple <int, int, int, int>, Prm.Torsion>();
foreach (var cls0123 in cls_dihedrals.Keys)
{
Universe.Dihedral[] dihedrals = cls_dihedrals[cls0123].ToArray();
Dictionary <Tuple <double, double>, List <double> > delta_n_Kchis = new Dictionary <Tuple <double, double>, List <double> >();
foreach (var dihedral in dihedrals)
{
double dihedral_delta = 180.0 * dihedral.delta / Math.PI;
var delta_n = new Tuple <double, double>(dihedral_delta, dihedral.n);
if (delta_n_Kchis.ContainsKey(delta_n) == false)
{
delta_n_Kchis.Add(delta_n, new List <double>());
}
delta_n_Kchis[delta_n].Add(dihedral.Kchi);
}
Tuple <double, double>[] lst_delta_n = delta_n_Kchis.Keys.ToArray();
HDebug.Exception(lst_delta_n.Length <= 3);
double?Kchi0 = null; if (lst_delta_n.Length >= 1)
{
Kchi0 = delta_n_Kchis[lst_delta_n[0]].Mean();
}
double?delta0 = null; if (lst_delta_n.Length >= 1)
{
delta0 = lst_delta_n[0].Item1;
}
double?n0 = null; if (lst_delta_n.Length >= 1)
{
n0 = lst_delta_n[0].Item2;
}
double?Kchi1 = null; if (lst_delta_n.Length >= 2)
{
Kchi1 = delta_n_Kchis[lst_delta_n[1]].Mean();
}
double?delta1 = null; if (lst_delta_n.Length >= 2)
{
delta1 = lst_delta_n[1].Item1;
}
double?n1 = null; if (lst_delta_n.Length >= 2)
{
n1 = lst_delta_n[1].Item2;
}
double?Kchi2 = null; if (lst_delta_n.Length >= 3)
{
Kchi2 = delta_n_Kchis[lst_delta_n[2]].Mean();
}
double?delta2 = null; if (lst_delta_n.Length >= 3)
{
delta2 = lst_delta_n[2].Item1;
}
double?n2 = null; if (lst_delta_n.Length >= 3)
{
n2 = lst_delta_n[2].Item2;
}
Prm.Torsion tink_torsion = Prm.Torsion.FromData
(Class1: cls0123.Item1
, Class2: cls0123.Item2
, Class3: cls0123.Item3
, Class4: cls0123.Item4
, Kchi0: Kchi0
, delta0: delta0
, n0: n0
, Kchi1: Kchi1
, delta1: delta1
, n1: n1
, Kchi2: Kchi2
, delta2: delta2
, n2: n2
);
cls_torsion.Add(cls0123, tink_torsion);
}
List <string> prmlines;
#region build lines
{
List <string> lines = new List <string>();
lines.Add("");
lines.Add(" ##############################");
lines.Add(" ## ##");
lines.Add(" ## Force Field Definition ##");
lines.Add(" ## ##");
lines.Add(" ##############################");
lines.Add("");
lines.Add("");
lines.Add("forcefield CHARMM22");
lines.Add("");
lines.Add("vdwtype LENNARD-JONES");
lines.Add("radiusrule ARITHMETIC");
lines.Add("radiustype R-MIN");
lines.Add("radiussize RADIUS");
lines.Add("epsilonrule GEOMETRIC");
lines.Add("vdw-14-scale 1.0");
lines.Add("chg-14-scale 1.0");
lines.Add("electric 332.0716");
lines.Add("dielectric 1.0");
lines.Add("");
lines.Add("");
lines.Add(" #############################");
lines.Add(" ## ##");
lines.Add(" ## Atom Type Definitions ##");
lines.Add(" ## ##");
lines.Add(" #############################");
lines.Add("");
lines.Add("");
foreach (int id in id_atom.Keys.ToArray().HSort())
{
lines.Add(id_atom[id].line);
}
lines.Add("");
lines.Add("");
lines.Add(" ################################");
lines.Add(" ## ##");
lines.Add(" ## Van der Waals Parameters ##");
lines.Add(" ## ##");
lines.Add(" ################################");
lines.Add("");
lines.Add("");
foreach (int cls in cls_vdw.Keys.ToArray().HSort())
{
lines.Add(cls_vdw[cls].line);
}
lines.Add("");
lines.Add("");
lines.Add(" ####################################");
lines.Add(" ## ##");
lines.Add(" ## 1-4 Van der Waals Parameters ##");
lines.Add(" ## ##");
lines.Add(" ####################################");
lines.Add("");
lines.Add("");
foreach (int cls in cls_vdw14.Keys.ToArray().HSort())
{
lines.Add(cls_vdw14[cls].line);
}
lines.Add("");
lines.Add("");
lines.Add(" ##################################");
lines.Add(" ## ##");
lines.Add(" ## Bond Stretching Parameters ##");
lines.Add(" ## ##");
lines.Add(" ##################################");
lines.Add("");
lines.Add("");
foreach (var bond in cls_bond)
{
lines.Add(bond.Value.line);
}
lines.Add("");
lines.Add("");
lines.Add(" ################################");
lines.Add(" ## ##");
lines.Add(" ## Angle Bending Parameters ##");
lines.Add(" ## ##");
lines.Add(" ################################");
lines.Add("");
lines.Add("");
foreach (var angle in cls_angle)
{
lines.Add(angle.Value.line);
}
lines.Add("");
lines.Add("");
lines.Add(" ###############################");
lines.Add(" ## ##");
lines.Add(" ## Urey-Bradley Parameters ##");
lines.Add(" ## ##");
lines.Add(" ###############################");
lines.Add("");
lines.Add("");
foreach (var ureybrad in cls_ureybrad)
{
lines.Add(ureybrad.Value.line);
}
lines.Add("");
lines.Add("");
lines.Add(" ####################################");
lines.Add(" ## ##");
lines.Add(" ## Improper Dihedral Parameters ##");
lines.Add(" ## ##");
lines.Add(" ####################################");
lines.Add("");
lines.Add("");
foreach (var improper in cls_improper)
{
lines.Add(improper.Value.line);
}
lines.Add("");
lines.Add("");
lines.Add(" ############################");
lines.Add(" ## ##");
lines.Add(" ## Torsional Parameters ##");
lines.Add(" ## ##");
lines.Add(" ############################");
lines.Add("");
lines.Add("");
foreach (var torsion in cls_torsion)
{
lines.Add(torsion.Value.line);
}
lines.Add("");
lines.Add("");
lines.Add(" ########################################");
lines.Add(" ## ##");
lines.Add(" ## Atomic Partial Charge Parameters ##");
lines.Add(" ## ##");
lines.Add(" ########################################");
lines.Add("");
lines.Add("");
foreach (int id in id_charge.Keys.ToArray().HSort())
{
lines.Add(id_charge[id].line);
}
lines.Add("");
lines.Add("");
lines.Add(" ########################################");
lines.Add(" ## ##");
lines.Add(" ## Biopolymer Atom Type Conversions ##");
lines.Add(" ## ##");
lines.Add(" ########################################");
lines.Add("");
lines.Add("");
foreach (int id in id_biotype.Keys.ToArray().HSort())
{
lines.Add(id_biotype[id].line);
}
lines.Add("");
prmlines = lines;
}
#endregion
Dictionary <string, string> atomtype_natomtype;
{
atomtype_natomtype = xyzid_info.Values.ToArray().HListItem1().HToHashSet().HToDictionaryAsKey("");
foreach (string atomtype in atomtype_natomtype.Keys.ToArray())
{
string natomtype = atomtype;
if (natomtype.Length > 3)
{
Dictionary <char, char> map = new Dictionary <char, char>
{
{ '0', '1' }, { '1', '2' }, { '2', '3' }, { '3', '4' }, { '4', '5' },
{ '5', '6' }, { '6', '7' }, { '7', '8' }, { '8', '9' }, { '9', 'A' },
{ 'A', 'B' }, { 'B', 'C' }, { 'C', 'D' }, { 'D', 'E' }, { 'E', 'F' },
{ 'F', 'G' }, { 'G', 'H' }, { 'H', 'I' }, { 'I', 'J' }, { 'J', 'K' },
{ 'K', 'L' }, { 'L', 'M' }, { 'M', 'N' }, { 'N', 'O' }, { 'O', 'P' },
{ 'P', 'Q' }, { 'Q', 'R' }, { 'R', 'S' }, { 'S', 'T' }, { 'T', 'U' },
{ 'U', 'V' }, { 'V', 'W' }, { 'W', 'X' }, { 'X', 'Y' }, { 'Y', 'Z' },
{ 'Z', '0' },
};
string temptype = atomtype.Substring(0, 3);
foreach (var key in map.Keys.ToArray())
{
if (map[key] == temptype[2])
{
map[key] = ' '; // marking ending point as ' '
}
}
while (true)
{
if (temptype[2] == ' ')
{
HDebug.Exception();
}
if ((atomtype_natomtype.ContainsKey(temptype) == false) && (atomtype_natomtype.ContainsValue(temptype) == false))
{
natomtype = temptype;
break;
}
temptype = temptype.Substring(0, 2) + map[temptype[2]];
}
}
atomtype_natomtype[atomtype] = natomtype;
}
}
List <string> xyzlines;
{
xyzlines = new List <string>();
xyzlines.Add(Xyz.Header.FromData(xyzid_info.Count, "", "", "").line);
foreach (var xyzid in xyzid_info.Keys.ToArray().HSort())
{
int id = xyzid;
string atomtype = xyzid_info[xyzid].Item1;
atomtype = atomtype_natomtype[atomtype];
double x = xyzid_info[xyzid].Item2[0];
double y = xyzid_info[xyzid].Item2[1];
double z = xyzid_info[xyzid].Item2[2];
int atomid = xyzid_info[xyzid].Item3;
int[] bondedids = xyzid_info[xyzid].Item4.ToArray();
xyzlines.Add(Xyz.Atom.FromData(id, atomtype, x, y, z, atomid, bondedids).line);
}
}
{
for (int i = 0; i < prmlines.Count; i++)
{
if (prmlines[i].StartsWith("atom "))
{
var atom = Prm.Atom.FromLine(prmlines[i]);
var natom = Prm.Atom.FromData
(Id: atom.Id
, Class: atom.Class
, Type: atomtype_natomtype[atom.Type]
, Description: atom.Description
, AtomicNumber: atom.AtomicNumber
, Mass: atom.Mass
, Valence: atom.Valence
);
prmlines[i] = natom.line;
}
}
}
Prm tink_prm = Prm.FromLines(prmlines);
Xyz tink_xyz = Xyz.FromLines(xyzlines);
return(new Tuple <Xyz, Prm>(tink_xyz, tink_prm));
}
public static Universe Build(Namd.Psf psf, Namd.Prm prm, Pdb pdb, bool?ignore_neg_occupancy, ITextLogger logger)
{
return(BuilderNamd.Build(psf, prm, pdb, ignore_neg_occupancy, logger));
}
public static Universe Build(Namd.Psf psf, Namd.Prm prm, Pdb pdb, bool?ignore_neg_occupancy, ITextLogger logger)
{
Universe univ = new Universe();
// atoms
Atoms atoms = new Atoms(univ);
Dictionary <int, Atom> id_atom = new Dictionary <int, Atom>();
Pdb.Atom[] pdb_atoms = pdb.atoms;
HDebug.Assert(psf.atoms.Length == pdb_atoms.Length);
for (int i = 0; i < psf.atoms.Length; i++)
{
HDebug.Assert(pdb_atoms[i].try_serial == null || psf.atoms[i].AtomId == pdb_atoms[i].serial); // when num atoms in pdb is too large (>99999), it is marked as *****
string type0 = psf.atoms[i].AtomType;
Atom atom = new Atom(psf.atoms[i], prm.FindNonbonded(type0, logger), pdb_atoms[i]);
atom.Coord = pdb_atoms[i].coord;
{
if (ignore_neg_occupancy == null)
{
if (pdb_atoms[i].occupancy < 0)
{
throw new HException("unhandled negative occupancy during building universe");
}
}
else
{
if (ignore_neg_occupancy.Value && pdb_atoms[i].occupancy < 0)
{
continue;
}
}
}
atoms.Add(atom);
id_atom.Add(psf.atoms[i].AtomId, atom);
}
// bonds
Bonds bonds = new Bonds();
for (int i = 0; i < psf.bonds.GetLength(0); i++)
{
int id0 = psf.bonds[i, 0]; if (id_atom.ContainsKey(id0) == false)
{
continue;
}
Atom atom0 = id_atom[id0]; string type0 = atom0.AtomType;
int id1 = psf.bonds[i, 1]; if (id_atom.ContainsKey(id1) == false)
{
continue;
}
Atom atom1 = id_atom[id1]; string type1 = atom1.AtomType;
Bond bond = new Bond(atom0, atom1, prm.FindBond(type0, type1, logger));
bonds.Add(bond);
atom0.Bonds.Add(bond); atom0.Inter123.Add(atom1); atom0.Inter12.Add(atom1);
atom1.Bonds.Add(bond); atom1.Inter123.Add(atom0); atom1.Inter12.Add(atom0);
}
// angles
Angles angles = new Angles();
for (int i = 0; i < psf.angles.GetLength(0); i++)
{
int id0 = psf.angles[i, 0]; if (id_atom.ContainsKey(id0) == false)
{
continue;
}
Atom atom0 = id_atom[id0]; string type0 = atom0.AtomType;
int id1 = psf.angles[i, 1]; if (id_atom.ContainsKey(id1) == false)
{
continue;
}
Atom atom1 = id_atom[id1]; string type1 = atom1.AtomType;
int id2 = psf.angles[i, 2]; if (id_atom.ContainsKey(id2) == false)
{
continue;
}
Atom atom2 = id_atom[id2]; string type2 = atom2.AtomType;
var prm_angle = prm.FindAngle(type0, type1, type2, logger);
if (prm_angle == null)
{
HDebug.Assert(false);
logger.Log(string.Format
("try to add non-existing angle (({0}, prm {1})-({2}, prm {3})-({4}, prm {5})) in prm"
, atom0, type0, atom1, type1, atom2, type2
));
continue;
}
Angle angle = new Angle(atom0, atom1, atom2, prm_angle);
angles.Add(angle);
atom0.Angles.Add(angle); atom0.Inter123.Add(atom1); atom0.Inter123.Add(atom2);
atom1.Angles.Add(angle); atom1.Inter123.Add(atom2); atom1.Inter123.Add(atom0);
atom2.Angles.Add(angle); atom2.Inter123.Add(atom0); atom2.Inter123.Add(atom1);
}
// dihedrals
Dihedrals dihedrals = new Dihedrals();
for (int i = 0; i < psf.dihedrals.GetLength(0); i++)
{
int id0 = psf.dihedrals[i, 0]; if (id_atom.ContainsKey(id0) == false)
{
continue;
}
Atom atom0 = id_atom[id0]; string type0 = atom0.AtomType;
int id1 = psf.dihedrals[i, 1]; if (id_atom.ContainsKey(id1) == false)
{
continue;
}
Atom atom1 = id_atom[id1]; string type1 = atom1.AtomType;
int id2 = psf.dihedrals[i, 2]; if (id_atom.ContainsKey(id2) == false)
{
continue;
}
Atom atom2 = id_atom[id2]; string type2 = atom2.AtomType;
int id3 = psf.dihedrals[i, 3]; if (id_atom.ContainsKey(id3) == false)
{
continue;
}
Atom atom3 = id_atom[id3]; string type3 = atom3.AtomType;
var prm_dihedrals = prm.FindDihedral(type0, type1, type2, type3, logger);
if (prm_dihedrals.Length == 0)
{
HDebug.Assert(false);
logger.Log(string.Format
("try to add non-existing dihedral (({0}, prm {1})-({2}, prm {3})-({4}, prm {5})-({6}, prm {7})) in prm"
, atom0, type0, atom1, type1, atom2, type2, atom3, type3
));
continue;
}
foreach (var prm_dihedral in prm_dihedrals)
{
Dihedral dihedral;
if (atom0.ID < atom3.ID)
{
dihedral = new Dihedral(atom0, atom1, atom2, atom3, prm_dihedral);
}
else
{
dihedral = new Dihedral(atom3, atom2, atom1, atom0, prm_dihedral);
}
dihedrals.Add(dihedral);
atom0.Dihedrals.Add(dihedral); //atom0.Inter123.Add(atom1); atom0.Inter123.Add(atom2); atom0.Inter123.Add(atom3);
atom1.Dihedrals.Add(dihedral); //atom1.Inter123.Add(atom2); atom1.Inter123.Add(atom3); atom1.Inter123.Add(atom0);
atom2.Dihedrals.Add(dihedral); //atom2.Inter123.Add(atom3); atom2.Inter123.Add(atom0); atom2.Inter123.Add(atom1);
atom3.Dihedrals.Add(dihedral); //atom3.Inter123.Add(atom0); atom3.Inter123.Add(atom1); atom3.Inter123.Add(atom2);
}
}
// impropers
Impropers impropers = new Impropers();
for (int i = 0; i < psf.impropers.GetLength(0); i++)
{
int id0 = psf.impropers[i, 0]; if (id_atom.ContainsKey(id0) == false)
{
continue;
}
Atom atom0 = id_atom[id0]; string type0 = atom0.AtomType;
int id1 = psf.impropers[i, 1]; if (id_atom.ContainsKey(id1) == false)
{
continue;
}
Atom atom1 = id_atom[id1]; string type1 = atom1.AtomType;
int id2 = psf.impropers[i, 2]; if (id_atom.ContainsKey(id2) == false)
{
continue;
}
Atom atom2 = id_atom[id2]; string type2 = atom2.AtomType;
int id3 = psf.impropers[i, 3]; if (id_atom.ContainsKey(id3) == false)
{
continue;
}
Atom atom3 = id_atom[id3]; string type3 = atom3.AtomType;
Improper improper = new Improper(atom0, atom1, atom2, atom3, prm.FindImproper(type0, type1, type2, type3, logger));
impropers.Add(improper);
atom0.Impropers.Add(improper); //atom0.Inter123.Add(atom1); atom0.Inter123.Add(atom2); atom0.Inter123.Add(atom3);
atom1.Impropers.Add(improper); //atom1.Inter123.Add(atom2); atom1.Inter123.Add(atom3); atom1.Inter123.Add(atom0);
atom2.Impropers.Add(improper); //atom2.Inter123.Add(atom3); atom2.Inter123.Add(atom0); atom2.Inter123.Add(atom1);
atom3.Impropers.Add(improper); //atom3.Inter123.Add(atom0); atom3.Inter123.Add(atom1); atom3.Inter123.Add(atom2);
}
// 1-4 interactions
for (int i = 0; i < atoms.Count; i++)
{
HashSet <Atom> Inter14 = new HashSet <Atom>();
BuildInter1toN(atoms[i], 4, Inter14); // find all atoms for 1-4 interaction
Inter14.Remove(atoms[i]); // remove self
foreach (Atom atom in atoms[i].Inter123)
{
Inter14.Remove(atom); // remove all 1-2, 1-3 interactions
}
atoms[i].Inter14 = Inter14;
}
Nonbonded14s nonbonded14s = new Nonbonded14s();
nonbonded14s.Build(atoms);
//// nonbondeds
//// do not make this list in advance, because it depends on the atom positions
//Nonbondeds nonbondeds = new Nonbondeds();
//nonbondeds.Build(atoms);
//Universe univ = new Universe();
univ.pdb = pdb;
univ.refs.Add("psf", psf);
univ.refs.Add("prm", prm);
univ.atoms = atoms;
univ.bonds = bonds;
univ.angles = angles;
univ.dihedrals = dihedrals;
univ.impropers = impropers;
//univ.nonbondeds = nonbondeds ; // do not make this list in advance, because it depends on the atom positions
univ.nonbonded14s = nonbonded14s;
HDebug.Assert(univ.Verify());
return(univ);
}
