public int Minimize_ConjugateGradient(List <ForceField.IForceField> frcflds
, string logpath = ""
, int iterInitial = 0
, double?k = null
, int?max_iteration = null
, double max_atom_movement = 0.1
, double threshold = 0.001
, int randomPurturb = 0
, bool[] atomsMovable = null
, InfoPack extra = null
)
{
IMinimizeLogger logger = new MinimizeLogger_PrintEnergyForceMag(logpath);
return(Minimize_ConjugateGradient_v1(iterInitial, frcflds, k, max_atom_movement, max_iteration, threshold, randomPurturb, atomsMovable, logger, extra, null));
}
public void Start()
{
if (string.IsNullOrEmpty(city) || string.IsNullOrEmpty(key))
{
return;
}
Stop();
cts = new CancellationTokenSource();
Task.Factory.StartNew(async() =>
{
TimeSpan delay = TimeSpan.FromMinutes(10);
var token = cts.Token;
try
{
while (true)
{
token.ThrowIfCancellationRequested();
string url = string.Format(serviceAPI, key, city);
var data = await loadData(url);//load forcast
if (data.Status != ProviderStatusEnum.NA)
{
forcast = data;
}
url = string.Format(serviceAPI_Current, key, city);
data = await loadData(url);//load current weather
if (data.Status != ProviderStatusEnum.NA)
{
current = data;
}
await Task.Delay(delay, token);
}
}
catch (OperationCanceledException)
{
System.Diagnostics.Debug.WriteLine("Xinzhi Weather operation canceled");
}
catch (Exception ex)
{
System.Diagnostics.Debug.WriteLine(ex.ToString());
}
}, cts.Token
);
Status = ProviderStatusEnum.Ready;
}
public static Vector GetBFactor(Matrix hess
, int numIgnoreSmallEigval = 6 // the number to ignore the eigenvalues
, bool zeroForNegEigval = true // set zero for the negative eigen values
)
{
HDebug.Assert(GetBFactorSelfTest());
int n = hess.ColSize / 3;
HDebug.Assert(n * 3 == hess.ColSize);
HDebug.Assert(hess.RowSize == hess.ColSize);
InfoPack lextra = new InfoPack();
Vector[] eigvec;
double[] eigval;
NumericSolver.Eig(hess.ToArray(), out eigvec, out eigval);
double[] abs_eigval = eigval.HAbs();
List <int> idx_sorted_abs_eigval = new List <int>(abs_eigval.HIdxSorted());
for (int i = 0; i < numIgnoreSmallEigval; i++)
{
idx_sorted_abs_eigval.RemoveAt(0);
}
Vector bfactor = new double[n];
foreach (int idx in idx_sorted_abs_eigval)
{
if (eigval[idx] < 0)
{
continue;
}
for (int i = 0; i < n; i++)
{
double dx = eigvec[idx][i * 3 + 0];
double dy = eigvec[idx][i * 3 + 1];
double dz = eigvec[idx][i * 3 + 2];
bfactor[i] += (dx * dx + dy * dy + dz * dz) / eigval[idx];
}
}
return(bfactor);
}
public int MinimizeHydrogens(List <ForceField.IForceField> frcflds
, string logpath = ""
, InfoPack extra = null
)
{
bool[] atomsMovable = new bool[size];
for (int i = 0; i < size; i++)
{
atomsMovable[i] = atoms[i].IsHydrogen();
}
double k = 0.001;
double threshold = 0.001;
double max_atom_movement = 0.1;
IMinimizeLogger logger = new MinimizeLogger_PrintEnergyForceMag(logpath); // null
int randomPurturb = 0; // no random purturbation
return(Minimize_ConjugateGradient_v1(0, frcflds, k, max_atom_movement, null, threshold, randomPurturb, atomsMovable, logger, extra, null));
}
public static bool GetBFactorSelfTest(string pdbpath, double cutoff, double corr, int round, InfoPack extra)
{
if (HFile.Exists(pdbpath) == false)
{
return(false);
}
Pdb pdb = Pdb.FromFile(pdbpath);
for (int i = 0; i < pdb.atoms.Length; i++)
{
HDebug.Assert(pdb.atoms[0].altLoc == pdb.atoms[i].altLoc);
HDebug.Assert(pdb.atoms[0].chainID == pdb.atoms[i].chainID);
}
List <Pdb.Atom> atoms = new List <Pdb.Atom>();
for (int i = 0; i < pdb.atoms.Length; i++)
{
Pdb.Atom atom = pdb.atoms[i];
if (atom.name.Trim().ToUpper() == "CA")
{
atoms.Add(atom);
}
}
List <Vector> coords = atoms.ListCoord();
Matrix hess = Hess.GetHessAnm(coords, cutoff);
InfoPack lextra = new InfoPack();
Vector bfactor = GetBFactor(hess, 0.00000001, null, lextra);
if (extra != null)
{
extra["num_zero_eigvals"] = lextra["num_zero_eigvals"];
extra["eigenvalues"] = lextra["eigenvalues"];
}
double corr_comp = pdb.CorrBFactor(atoms.ListName(), atoms.ListResSeq(), bfactor.ToArray());
corr_comp = Math.Round(corr_comp, round);
HDebug.Assert(corr == corr_comp);
return(corr == corr_comp);
}
public void Minimize(List <ForceField.IForceField> frcflds
, string logpath = ""
, int iterInitial = 0
, double?k = null
, double max_atom_movement = 0.1
, int?max_iteration = null
, double threshold = 0.001
, int randomPurturb = 0
, bool[] atomsMovable = null
, InfoPack extra = null
)
{
Minimize_ConjugateGradient(frcflds
, logpath: logpath
, iterInitial: iterInitial
, k: k
, max_atom_movement: max_atom_movement
, max_iteration: max_iteration
, threshold: threshold
, randomPurturb: randomPurturb
, atomsMovable: atomsMovable
, extra: extra
);
}
public void Minimize_Parallel(List <ForceField.IForceField> frcflds
, string logpath = ""
, int iterInitial = 0
, double?k = null
, double max_atom_movement = 0.1
, int?max_iteration = null
, double threshold = 0.001
, int randomPurturb = 0
, bool[] atomsMovable = null
, InfoPack extra = null
)
{
Minimize_ConjugateGradient_Parallel(frcflds,
k: k,
max_atom_movement: max_atom_movement,
max_iteration: max_iteration,
threshold: threshold,
randomPurturb: randomPurturb,
atomsMovable: atomsMovable,
logger: new MinimizeLogger_PrintEnergyForceMag(logpath),
extra: extra,
doSteepDeescent: null
);
}
public static Vector GetBFactor(Matrix hess, double?thresEigval, int?numZeroEigval, InfoPack extra = null)
{
HDebug.Assert(GetBFactorSelfTest());
int n = hess.ColSize / 3;
HDebug.Assert(n * 3 == hess.ColSize);
HDebug.Assert(hess.RowSize == hess.ColSize);
InfoPack lextra = new InfoPack();
Matrix invhess = NumericSolver.InvEig(hess, thresEigval, numZeroEigval, lextra);
//Matrix invhess = NumericSolver.InvEig(hess, 0.00000001, null, lextra);
Vector bfactor = new double[n];
for (int i = 0; i < n; i++)
{
bfactor[i] = invhess[i * 3 + 0, i *3 + 0] + invhess[i * 3 + 1, i *3 + 1] + invhess[i * 3 + 2, i *3 + 2];
}
if (extra != null)
{
extra["num_zero_eigvals"] = lextra["num_zero_eigvals"];
extra["eigenvalues"] = lextra["eigenvalues"];
}
return(bfactor);
}
public static Vector GetBFactor(Matrix hess, Vector mass, double?thresEigval, int?numZeroEigval, InfoPack extra = null)
{
HDebug.Assert(GetBFactorSelfTest());
HDebug.Assert(hess.ColSize == hess.RowSize);
HDebug.Assert(hess.ColSize % 3 == 0);
HDebug.Assert(hess.ColSize / 3 == mass.Size);
Matrix mhess = GetMassWeightedHess(hess, mass);
// ei : mass weighted eigenvector
// wi2 : mass weighted eigenvalue
// Ui' : ei*ei/wi2 = diag(eigenvec * 1/eigenval * eigenvec')
Vector bfactor = GetBFactor(mhess, thresEigval, numZeroEigval, extra);
// vi : mass free eigenvector
// Ui := (Kb T) * (vi * vi / wi2)
// = (Kb T / mi) * ((vi*mi^-2) * (vi*mi^-2) / wi2)
// = (Kb T / mi) * (ei * ei / wi2)
// = (Kb T / mi) * Ui'
int n = mass.Size;
for (int i = 0; i < n; i++)
{
// assume Kb, T are constant (=1)
bfactor[i] = bfactor[i] / mass[i];
}
return(bfactor);
}
public int Minimize_ConjugateGradient_v1(int iterInitial,
List <ForceField.IForceField> frcflds,
double?k,
double max_atom_movement,
int?max_iteration,
double threshold,
int randomPurturb,
bool[] atomsMovable,
IMinimizeLogger logger,
InfoPack extra,
bool?doSteepDeescent // null or true for default
)
{
if (doSteepDeescent == null)
{
doSteepDeescent = true;
}
if (k == null)
{
k = double.MaxValue;
foreach (ForceField.IForceField frcfld in frcflds)
{
double?kk = frcfld.GetDefaultMinimizeStep();
if (kk.HasValue)
{
k = Math.Min(k.Value, kk.Value);
}
}
}
// double k = 0.0001;
int iter = iterInitial;
// 0. Initial configuration of atoms
Vectors coords = GetCoords();
if (atomsMovable == null)
{
atomsMovable = new bool[size];
for (int i = 0; i < size; i++)
{
atomsMovable[i] = true;
}
}
Vectors h = GetVectorsZero();
Vectors forces = null;
Dictionary <string, object> cache = new Dictionary <string, object>();
double energy = GetPotential(frcflds, coords, out forces, cache);
double forces_NormInf = NormInf(forces, atomsMovable);
double forces_Norm1 = Norm(1, forces, atomsMovable);
double forces_Norm2 = Norm(2, forces, atomsMovable);
Vectors forces0 = forces;
double energy0 = energy;
while (true)
{
if (forces.IsComputable == false)
{
System.Console.Error.WriteLine("non-computable components while doing steepest-descent");
HEnvironment.Exit(0);
}
if (logger != null)
{
logger.log(iter, coords, energy, forces, atomsMovable);
logger.logTrajectory(this, iter, coords);
//if(iter %10 == 0)
//{
// System.IO.Directory.CreateDirectory("output");
// string pdbname = string.Format("mini.conju.{0:D5}.pdb", iter);
// pdb.ToFile("output\\"+pdbname, coords.ToArray());
// System.IO.File.AppendAllLines("output\\mini.conju.[animation].pml", new string[] { "load "+pdbname+", 1A6G" });
//}
}
// 1. Save the position of atoms
// 2. Calculate the potential energy of system and the net forces on atoms
// 3. Check if every force reaches to zero,
// , and END if yes
bool stopIteration = false;
if (forces_NormInf < threshold)
{
stopIteration = true;
}
if ((max_iteration != null) && (iter >= max_iteration.Value))
{
stopIteration = true;
}
if (stopIteration)
{
// double check
cache = new Dictionary <string, object>(); // reset cache
energy = GetPotential(frcflds, coords, out forces, cache);
forces_NormInf = NormInf(forces, atomsMovable);
forces_Norm1 = Norm(1, forces, atomsMovable);
forces_Norm2 = Norm(2, forces, atomsMovable);
// This is already checked by "if(forces_NormInf < threshold) stopIteration = true;"
//if(forces_NormInf < threshold)
/////////////////////////////////////////////////////
{
if (iter != 1)
{
SetCoords((Vector[])coords);
}
//{
// string pdbname = string.Format("mini.conju.{0:D5}.pdb", iter);
// pdb.ToFile("output\\"+pdbname, coords.ToArray());
// System.IO.File.AppendAllLines("output\\mini.conju.[animation].pml", new string[] { "load "+pdbname+", 1A6G" });
//}
if (extra != null)
{
extra.SetValue("energy", energy);
extra.SetValue("forces", forces);
extra.SetValue("forces norm-1", forces_Norm1);
extra.SetValue("forces norm-2", forces_Norm2);
extra.SetValue("forces norm-inf", forces_NormInf);
extra.SetValue("iter", iter);
}
return(iter);
}
}
// 4. Move atoms with conjugated gradient
Vectors coords_prd;
{
if ((iter > 0) && (iter % 100 == 0))
{
cache = new Dictionary <string, object>(); // reset cache
}
if ((randomPurturb > 0) && (iter % randomPurturb == 0))
{
Vectors dcoords = GetVectorsRandom();
dcoords *= max_atom_movement;
coords = AddConditional(coords, dcoords, atomsMovable);
}
if (iter > 1)
{
HDebug.Assert(forces0 != null);
double r = Vectors.VtV(forces, forces).Sum() / Vectors.VtV(forces0, forces0).Sum();
h = forces + r * h;
double kk = k.Value;
double hNormInf = NormInf(h, atomsMovable);
if (kk * hNormInf > max_atom_movement)
{
// make the maximum movement as atomsMovable
kk = max_atom_movement / (hNormInf);
}
//double kk = (k*h.NormsInf().NormInf() < max_atom_movement) ? k : (max_atom_movement/h.NormsInf().NormInf());
//double kk = (k.Value*NormInf(h,atomsMovable) < max_atom_movement)? k.Value : (max_atom_movement/NormInf(h,atomsMovable));
coords_prd = AddConditional(coords, kk * h, atomsMovable);
}
else
{
// same to the steepest descent for the first iteration
h = forces;
double kk = k.Value;
double hNormInf = NormInf(h, atomsMovable);
if (kk * hNormInf > max_atom_movement)
{
// make the maximum movement as atomsMovable
kk = max_atom_movement / (hNormInf);
}
//double kk = (k*h.NormsInf().NormInf() < max_atom_movement) ? k : (max_atom_movement/h.NormsInf().NormInf());
//double kk = (k.Value*NormInf(h,atomsMovable) < max_atom_movement)? k.Value : (max_atom_movement/NormInf(h, atomsMovable));
coords_prd = AddConditional(coords, kk * h, atomsMovable);
}
}
// 5. Predict energy or forces on atoms
Vectors forces_prd;
double energy_prd = GetPotential(frcflds, coords_prd, out forces_prd, cache); iter++;
double forces_prd_NormInf = NormInf(forces_prd, atomsMovable);
double forces_prd_Norm1 = Norm(1, forces_prd, atomsMovable);
double forces_prd_Norm2 = Norm(2, forces_prd, atomsMovable);
// 6. Check if the predicted forces or energy will exceed over the limit
// , and goto 1 if no
doSteepDeescent = true;
//if((doSteepDeescent == false) || ((energy_prd <= energy) && (forces_prd_NormInf < forces_NormInf+1.0))
if ((energy_prd < energy + 0.1) && (forces_prd_NormInf < forces_NormInf + 0.0001))
{
energy0 = energy;
forces0 = forces;
coords = coords_prd;
forces = forces_prd;
energy = energy_prd;
forces_NormInf = forces_prd_NormInf;
forces_Norm1 = forces_prd_Norm1;
forces_Norm2 = forces_prd_Norm2;
continue;
}
if (logger != null)
{
logger.log(iter, coords_prd, energy_prd, forces_prd, atomsMovable, "will do steepest");
}
// 7. Back to saved configuration
// 8. Move atoms with simple gradient
{
// same to the steepest descent
h = forces;
double kk = k.Value;
double hNormInf = NormInf(h, atomsMovable);
if (kk * hNormInf > max_atom_movement)
{
// make the maximum movement as atomsMovable
kk = max_atom_movement / (hNormInf);
}
//double kk = (k*h.NormsInf().NormInf() < max_atom_movement) ? k : (max_atom_movement/h.NormsInf().NormInf());
//double kk = (k.Value*NormInf(h,atomsMovable) < max_atom_movement)? k.Value : (max_atom_movement/NormInf(h, atomsMovable));
coords_prd = AddConditional(coords, kk * h, atomsMovable);
//if(randomPurturb)
//{
// Vectors dcoords = GetForcesRandom();
// dcoords *= (0.1*max_atom_movement);
// coords += dcoords;
//}
}
energy_prd = GetPotential(frcflds, coords_prd, out forces_prd, cache);
forces_prd_NormInf = NormInf(forces_prd, atomsMovable);
forces_prd_Norm1 = Norm(1, forces_prd, atomsMovable);
forces_prd_Norm2 = Norm(2, forces_prd, atomsMovable);
energy0 = energy;
forces0 = forces;
coords = coords_prd;
forces = forces_prd;
energy = energy_prd;
forces_NormInf = forces_prd_NormInf;
forces_Norm1 = forces_prd_Norm1;
forces_Norm2 = forces_prd_Norm2;
// 9. goto 1
}
}
public int Minimize_ConjugateGradient_AtomwiseUpdate(
List <ForceField.IForceField> frcflds
, double threshold = 0.001 // * threshold for forces.NormInf
, double?k = null // * step step
// 0.0001
, double max_atom_movement = 0.1 // * maximum atom movement
, int?max_iteration = null // null for the infinite iteration until converged
, bool[] atomsMovable = null // * selection of movable atoms
// move all atoms if (atomsMovable == null) or (atomsMovable[all] == true)
// move only atom whose (atomsMovable[id] == true)
, IMinimizeLogger logger = null // * write log
// = new MinimizeLogger_PrintEnergyForceMag()
, InfoPack extra = null // get extra information
, bool?doSteepDeescent = null // null or true for default
, HPack <double> optOutEnergy = null // optional output for final energy
, List <Vector> optOutForces = null // optional output for final force vectors
, HPack <double> optOutForcesNorm1 = null // optional output for norm of final force vectors
, HPack <double> optOutForcesNorm2 = null // optional output for norm of final force vectors
, HPack <double> optOutForcesNormInf = null // optional output for norm of final force vectors
)
{
if (doSteepDeescent == null)
{
doSteepDeescent = true;
}
if (k == null)
{
k = double.MaxValue;
foreach (ForceField.IForceField frcfld in frcflds)
{
double?kk = frcfld.GetDefaultMinimizeStep();
if (kk.HasValue)
{
k = Math.Min(k.Value, kk.Value);
}
}
}
int iter = 0;
// 0. Initial configuration of atoms
Vector[] coords = GetCoords();
if (atomsMovable == null)
{
atomsMovable = new bool[size];
for (int i = 0; i < size; i++)
{
atomsMovable[i] = true;
}
}
Vectors h = GetVectorsZero();
Vectors forces = Vector.NewVectors(size, new double[3]);
Vectors moves = Vector.NewVectors(size, new double[3]);
Nonbondeds_v1 nonbondeds = null;
// Dictionary<string,object> cache = new Dictionary<string, object>();
double energy = GetPotentialUpdated(frcflds, null, null, null, coords, forces, ref nonbondeds);
double forces_NormInf = NormInf(forces, atomsMovable);
double forces_Norm1 = Norm(1, forces, atomsMovable);
double forces_Norm2 = Norm(2, forces, atomsMovable);
Vector[] forces0 = forces;
double energy0 = energy;
Vectors moves0 = moves;
double leastMove = 0.000001;
while (true)
{
if (forces.IsComputable == false)
{
System.Console.Error.WriteLine("non-computable components while doing steepest-descent");
HEnvironment.Exit(0);
}
if (logger != null)
{
logger.log(iter, coords, energy, forces, atomsMovable);
logger.logTrajectory(this, iter, coords);
}
// 1. Save the position of atoms
// 2. Calculate the potential energy of system and the net forces on atoms
// 3. Check if every force reaches to zero,
// , and END if yes
bool stopIteration = false;
if (forces_NormInf < threshold)
{
stopIteration = true;
}
if ((max_iteration != null) && (iter >= max_iteration.Value))
{
stopIteration = true;
}
if (stopIteration)
{
// double check
//cache = new Dictionary<string, object>(); // reset cache
//energy = GetPotential(frcflds, coords, out forces, cache);
nonbondeds = null;
energy = GetPotentialUpdated(frcflds, null, null, null, coords, forces, ref nonbondeds);
forces_NormInf = NormInf(forces, atomsMovable);
forces_Norm1 = Norm(1, forces, atomsMovable);
forces_Norm2 = Norm(2, forces, atomsMovable);
if (forces_NormInf < threshold)
{
if (iter != 1)
{
SetCoords(coords);
}
{
if (optOutEnergy != null)
{
optOutEnergy.value = energy;
}
if (optOutForces != null)
{
optOutForces.Clear(); optOutForces.AddRange(forces.ToArray());
}
if (optOutForcesNorm1 != null)
{
optOutForcesNorm1.value = forces_Norm1;
}
if (optOutForcesNorm2 != null)
{
optOutForcesNorm2.value = forces_Norm2;
}
if (optOutForcesNormInf != null)
{
optOutForcesNormInf.value = forces_NormInf;
}
}
return(iter);
}
}
// 4. Move atoms with conjugated gradient
Vectors coords_prd;
double kk;
{
if ((iter > 0) && (iter % 100 == 0))
{
//cache = new Dictionary<string, object>(); // reset cache
nonbondeds = null;
}
if (iter > 1)
{
HDebug.Assert(forces0 != null);
double r = Vectors.VtV(forces, forces).Sum() / Vectors.VtV(forces0, forces0).Sum();
h = forces + r * h;
kk = k.Value;
double hNormInf = NormInf(h, atomsMovable);
if (kk * hNormInf > max_atom_movement)
{
// make the maximum movement as atomsMovable
kk = max_atom_movement / (hNormInf);
}
moves = moves0.Clone();
coords_prd = AddConditional(coords, atomsMovable, moves, kk * h, leastMove);
}
else
{
// same to the steepest descent for the first iteration
h = forces;
kk = k.Value;
double hNormInf = NormInf(h, atomsMovable);
if (kk * hNormInf > max_atom_movement)
{
// make the maximum movement as atomsMovable
kk = max_atom_movement / (hNormInf);
}
//double kk = (k*h.NormsInf().NormInf() < max_atom_movement) ? k : (max_atom_movement/h.NormsInf().NormInf());
//double kk = (k.Value*NormInf(h,atomsMovable) < max_atom_movement)? k.Value : (max_atom_movement/NormInf(h, atomsMovable));
moves = moves0.Clone();
coords_prd = AddConditional(coords, atomsMovable, moves, kk * h, leastMove);
}
}
// 5. Predict energy or forces on atoms
Vectors forces_prd = forces.Clone();
double energy_prd = GetPotentialUpdated(frcflds, energy, coords, forces, coords_prd, forces_prd, ref nonbondeds); iter++;
//double energy_prd = GetPotential(frcflds, coords_prd, out forces_prd, cache); iter++;
double forces_prd_NormInf = NormInf(forces_prd, atomsMovable);
double forces_prd_Norm1 = Norm(1, forces_prd, atomsMovable);
double forces_prd_Norm2 = Norm(2, forces_prd, atomsMovable);
// 6. Check if the predicted forces or energy will exceed over the limit
// , and goto 1 if no
doSteepDeescent = true;
//if((doSteepDeescent == false) || ((energy_prd <= energy) && (forces_prd_NormInf < forces_NormInf+1.0))
if ((energy_prd < energy + 0.1) && (forces_prd_NormInf < forces_NormInf + 0.0001))
{
energy0 = energy;
forces0 = forces;
moves0 = moves;
coords = coords_prd;
forces = forces_prd;
energy = energy_prd;
forces_NormInf = forces_prd_NormInf;
forces_Norm1 = forces_prd_Norm1;
forces_Norm2 = forces_prd_Norm2;
continue;
}
if (logger != null)
{
logger.log(iter, coords_prd, energy_prd, forces_prd, atomsMovable, "will do steepest");
}
// 7. Back to saved configuration
// 8. Move atoms with simple gradient
{
// same to the steepest descent
h = forces;
kk = k.Value;
double hNormInf = NormInf(h, atomsMovable);
if (kk * hNormInf > max_atom_movement)
{
// make the maximum movement as atomsMovable
kk = max_atom_movement / (hNormInf);
}
moves = moves0.Clone();
coords_prd = AddConditional(coords, atomsMovable, moves, kk * h, leastMove);
}
//energy_prd = GetPotential(frcflds, coords_prd, out forces_prd, cache);
energy_prd = GetPotentialUpdated(frcflds, energy, coords, forces, coords_prd, forces_prd, ref nonbondeds);
forces_prd_NormInf = NormInf(forces_prd, atomsMovable);
forces_prd_Norm1 = Norm(1, forces_prd, atomsMovable);
forces_prd_Norm2 = Norm(2, forces_prd, atomsMovable);
energy0 = energy;
forces0 = forces;
moves0 = moves;
coords = coords_prd;
forces = forces_prd;
energy = energy_prd;
forces_NormInf = forces_prd_NormInf;
forces_Norm1 = forces_prd_Norm1;
forces_Norm2 = forces_prd_Norm2;
// 9. goto 1
}
}
public void Add3(int id0, int id1, int id2, Vector[] lcoords, Vector[] lforces)
{
if (forceij == null)
{
return;
}
Vector ud01 = (lcoords[1] - lcoords[0]).UnitVector();
Vector ud12 = (lcoords[2] - lcoords[1]).UnitVector();
Vector ud20 = (lcoords[0] - lcoords[2]).UnitVector();
// [ ud01_x, 0, -ud20_x] [f01] [lf0x]
// [-ud01_x, ud12_x, 0] [f12] [lf1x]
// [ 0, -ud12_x, ud20_x] * [f20] = [lf2x]
//
// [ ud01_y, 0, -ud20_y] [lf0y]
// [-ud01_y, ud12_y, 0] [lf1y]
// [ 0, -ud12_y, ud20_y] [lf2y]
//
// [ ud01_z, 0, -ud20_z] [lf0z]
// [-ud01_z, ud12_z, 0] [lf1z]
// [ 0, -ud12_z, ud20_z] [lf2z]
/////////////////////////////////////////////////
// A * x = b
MatrixByArr A = new double[9, 3];
Vector b = new double[9];
for (int i = 0; i < 3; i++)
{
A[i + 3 * 0, 0] = ud01[i]; A[i + 3 * 0, 1] = 0; A[i + 3 * 0, 2] = -ud20[i]; b[i + 3 * 0] = lforces[0][i];
A[i + 3 * 1, 0] = -ud01[i]; A[i + 3 * 1, 1] = ud12[i]; A[i + 3 * 1, 2] = 0; b[i + 3 * 1] = lforces[1][i];
A[i + 3 * 2, 0] = 0; A[i + 3 * 2, 1] = -ud12[i]; A[i + 3 * 2, 2] = ud20[i]; b[i + 3 * 2] = lforces[2][i];
}
InfoPack extra = HDebug.IsDebuggerAttached ? new InfoPack() : null;
Matrix pinvA = NumericSolver.Pinv(A, extra);
HDebug.Assert(extra.GetValueInt("rank") == 3);
Vector x = LinAlg.MV(pinvA, b);
Vector f01 = ud01 * x[0];
Vector f12 = ud12 * x[1];
Vector f20 = ud20 * x[2];
if (HDebug.IsDebuggerAttached)
{
// check net force
Vector sumforces = lforces[0];
for (int i = 1; i < lforces.Length; i++)
{
sumforces += lforces[i];
}
HDebug.AssertTolerance(0.00000001, sumforces);
Vector f0 = f01 - f20;
Vector f1 = f12 - f01;
Vector f2 = -f12 + f20;
HDebug.AssertTolerance(0.00000001, f0 - lforces[0]);
HDebug.AssertTolerance(0.00000001, f1 - lforces[1]);
HDebug.AssertTolerance(0.00000001, f2 - lforces[2]);
}
this[id0, id1] += f01; this[id1, id2] += f12; this[id2, id0] += f20;
this[id1, id0] += -f01; this[id2, id1] += -f12; this[id0, id2] += -f20;
}
public static bool SelfTest_1AAC()
{
Pdb.Atom[] atoms_ca = new Pdb.Atom[]
{
#region 1AAC text of CA atoms
Pdb.Atom.FromString("ATOM 2 CA ASP A 1 25.378 -18.141 21.012 1.00 23.28 C "),
Pdb.Atom.FromString("ATOM 10 CA LYS A 2 24.390 -18.799 17.407 1.00 12.32 C "),
Pdb.Atom.FromString("ATOM 19 CA ALA A 3 25.772 -15.617 15.840 1.00 10.31 C "),
Pdb.Atom.FromString("ATOM 24 CA THR A 4 28.837 -13.442 16.439 1.00 9.47 C "),
Pdb.Atom.FromString("ATOM 31 CA ILE A 5 28.913 -9.665 15.865 1.00 7.94 C "),
Pdb.Atom.FromString("ATOM 39 CA PRO A 6 31.906 -8.243 13.886 1.00 8.02 C "),
Pdb.Atom.FromString("ATOM 46 CA SER A 7 31.049 -4.632 14.810 1.00 7.70 C "),
Pdb.Atom.FromString("ATOM 52 CA GLU A 8 28.768 -3.589 17.658 1.00 10.01 C "),
Pdb.Atom.FromString("ATOM 73 CA PRO A 10 26.932 0.412 12.498 1.00 7.09 C "),
Pdb.Atom.FromString("ATOM 80 CA PHE A 11 29.488 1.217 9.844 1.00 6.81 C "),
Pdb.Atom.FromString("ATOM 91 CA ALA A 12 29.431 2.815 6.390 1.00 6.76 C "),
Pdb.Atom.FromString("ATOM 96 CA ALA A 13 28.012 1.036 3.320 1.00 8.60 C "),
Pdb.Atom.FromString("ATOM 101 CA ALA A 14 31.392 1.654 1.659 1.00 11.18 C "),
Pdb.Atom.FromString("ATOM 106 CA GLU A 15 33.092 -0.407 4.404 1.00 9.76 C "),
Pdb.Atom.FromString("ATOM 115 CA VAL A 16 31.115 -3.590 3.763 1.00 12.85 C "),
Pdb.Atom.FromString("ATOM 122 CA ALA A 17 33.429 -6.584 3.205 1.00 20.32 C "),
Pdb.Atom.FromString("ATOM 127 CA ASP A 18 34.080 -7.894 -0.306 1.00 27.64 C "),
Pdb.Atom.FromString("ATOM 135 CA GLY A 19 31.708 -10.634 -1.313 1.00 26.92 C "),
Pdb.Atom.FromString("ATOM 139 CA ALA A 20 29.393 -9.683 1.528 1.00 19.57 C "),
Pdb.Atom.FromString("ATOM 144 CA ILE A 21 25.881 -11.238 1.583 1.00 11.70 C "),
Pdb.Atom.FromString("ATOM 152 CA VAL A 22 23.847 -8.061 1.553 1.00 7.77 C "),
Pdb.Atom.FromString("ATOM 159 CA VAL A 23 20.196 -7.501 2.410 1.00 6.37 C "),
Pdb.Atom.FromString("ATOM 166 CA ASP A 24 19.093 -3.982 1.466 1.00 6.66 C "),
Pdb.Atom.FromString("ATOM 174 CA ILE A 25 16.500 -2.121 3.513 1.00 7.21 C "),
Pdb.Atom.FromString("ATOM 182 CA ALA A 26 14.398 0.375 1.556 1.00 8.41 C "),
Pdb.Atom.FromString("ATOM 187 CA LYS A 27 10.724 1.489 1.214 1.00 9.80 C "),
Pdb.Atom.FromString("ATOM 201 CA MET A 28 10.147 0.295 4.838 1.00 8.69 C "),
Pdb.Atom.FromString("ATOM 209 CA LYS A 29 10.882 -3.362 4.004 1.00 9.09 C "),
Pdb.Atom.FromString("ATOM 223 CA TYR A 30 13.753 -5.845 4.132 1.00 6.32 C "),
Pdb.Atom.FromString("ATOM 235 CA GLU A 31 14.275 -6.364 0.381 1.00 9.00 C "),
Pdb.Atom.FromString("ATOM 244 CA THR A 32 15.144 -10.026 0.769 1.00 7.30 C "),
Pdb.Atom.FromString("ATOM 251 CA PRO A 33 12.722 -11.107 3.546 1.00 8.68 C "),
Pdb.Atom.FromString("ATOM 258 CA GLU A 34 13.757 -14.780 3.406 1.00 9.28 C "),
Pdb.Atom.FromString("ATOM 267 CA LEU A 35 17.468 -15.255 2.972 1.00 7.34 C "),
Pdb.Atom.FromString("ATOM 275 CA HIS A 36 19.181 -18.672 2.822 1.00 6.97 C "),
Pdb.Atom.FromString("ATOM 285 CA VAL A 37 22.841 -18.828 3.840 1.00 7.29 C "),
Pdb.Atom.FromString("ATOM 292 CA LYS A 38 25.361 -21.456 5.044 1.00 9.55 C "),
Pdb.Atom.FromString("ATOM 306 CA VAL A 39 26.828 -21.965 8.529 1.00 9.09 C "),
Pdb.Atom.FromString("ATOM 313 CA GLY A 40 29.717 -19.533 8.887 1.00 8.81 C "),
Pdb.Atom.FromString("ATOM 317 CA ASP A 41 28.343 -16.891 6.520 1.00 8.19 C "),
Pdb.Atom.FromString("ATOM 325 CA THR A 42 28.196 -13.227 7.468 1.00 7.95 C "),
Pdb.Atom.FromString("ATOM 332 CA VAL A 43 24.989 -11.395 6.512 1.00 6.02 C "),
Pdb.Atom.FromString("ATOM 339 CA THR A 44 25.158 -7.607 6.224 1.00 5.34 C "),
Pdb.Atom.FromString("ATOM 346 CA TRP A 45 22.054 -5.421 6.244 1.00 4.51 C "),
Pdb.Atom.FromString("ATOM 360 CA ILE A 46 22.453 -1.974 4.623 1.00 5.55 C "),
Pdb.Atom.FromString("ATOM 368 CA ASN A 47 19.890 0.774 5.248 1.00 6.52 C "),
Pdb.Atom.FromString("ATOM 376 CA ARG A 48 19.350 2.559 1.939 1.00 10.21 C "),
Pdb.Atom.FromString("ATOM 387 CA GLU A 49 16.823 5.111 3.196 1.00 12.44 C "),
Pdb.Atom.FromString("ATOM 396 CA ALA A 50 16.764 8.058 5.564 1.00 13.39 C "),
Pdb.Atom.FromString("ATOM 401 CA MET A 51 14.386 6.508 8.133 1.00 12.52 C "),
Pdb.Atom.FromString("ATOM 409 CA PRO A 52 16.509 4.566 10.725 1.00 9.20 C "),
Pdb.Atom.FromString("ATOM 416 CA HIS A 53 16.032 0.778 10.889 1.00 6.43 C "),
Pdb.Atom.FromString("ATOM 426 CA ASN A 54 17.658 -2.107 12.766 1.00 5.06 C "),
Pdb.Atom.FromString("ATOM 434 CA VAL A 55 17.296 -5.891 13.052 1.00 5.44 C "),
Pdb.Atom.FromString("ATOM 441 CA HIS A 56 15.979 -7.379 16.316 1.00 4.53 C "),
Pdb.Atom.FromString("ATOM 451 CA PHE A 57 15.920 -11.061 17.243 1.00 5.94 C "),
Pdb.Atom.FromString("ATOM 462 CA VAL A 58 13.932 -11.794 20.435 1.00 7.60 C "),
Pdb.Atom.FromString("ATOM 469 CA ALA A 59 15.316 -13.765 23.405 1.00 7.37 C "),
Pdb.Atom.FromString("ATOM 474 CA GLY A 60 16.074 -17.393 22.787 1.00 9.00 C "),
Pdb.Atom.FromString("ATOM 478 CA VAL A 61 16.521 -17.029 18.997 1.00 8.51 C "),
Pdb.Atom.FromString("ATOM 485 CA LEU A 62 20.244 -16.290 18.543 1.00 9.65 C "),
Pdb.Atom.FromString("ATOM 493 CA GLY A 63 21.156 -16.644 22.197 1.00 10.26 C "),
Pdb.Atom.FromString("ATOM 497 CA GLU A 64 19.729 -16.413 25.651 1.00 9.18 C "),
Pdb.Atom.FromString("ATOM 506 CA ALA A 65 19.129 -12.671 25.468 1.00 8.86 C "),
Pdb.Atom.FromString("ATOM 511 CA ALA A 66 17.408 -10.687 22.723 1.00 7.22 C "),
Pdb.Atom.FromString("ATOM 516 CA LEU A 67 19.808 -9.283 20.128 1.00 9.01 C "),
Pdb.Atom.FromString("ATOM 524 CA LYS A 68 18.504 -5.777 19.473 1.00 10.06 C "),
Pdb.Atom.FromString("ATOM 533 CA GLY A 69 20.805 -4.416 16.788 1.00 8.06 C "),
Pdb.Atom.FromString("ATOM 537 CA PRO A 70 21.868 -0.715 16.656 1.00 8.23 C "),
Pdb.Atom.FromString("ATOM 544 CA MET A 71 19.807 1.769 14.640 1.00 8.56 C "),
Pdb.Atom.FromString("ATOM 552 CA MET A 72 21.337 2.189 11.156 1.00 8.26 C "),
Pdb.Atom.FromString("ATOM 560 CA LYS A 73 21.086 5.638 9.601 1.00 9.59 C "),
Pdb.Atom.FromString("ATOM 574 CA LYS A 74 21.097 6.084 5.777 1.00 9.46 C "),
Pdb.Atom.FromString("ATOM 588 CA GLU A 75 23.892 4.149 4.097 1.00 9.45 C "),
Pdb.Atom.FromString("ATOM 602 CA GLN A 76 24.997 2.451 7.267 1.00 6.02 C "),
Pdb.Atom.FromString("ATOM 611 CA ALA A 77 25.416 -1.310 7.631 1.00 5.75 C "),
Pdb.Atom.FromString("ATOM 616 CA TYR A 78 25.448 -3.978 10.318 1.00 4.90 C "),
Pdb.Atom.FromString("ATOM 628 CA SER A 79 26.700 -7.612 10.117 1.00 5.13 C "),
Pdb.Atom.FromString("ATOM 634 CA LEU A 80 26.024 -10.884 11.899 1.00 5.65 C "),
Pdb.Atom.FromString("ATOM 642 CA THR A 81 27.969 -14.123 11.320 1.00 6.53 C "),
Pdb.Atom.FromString("ATOM 649 CA PHE A 82 25.693 -17.171 11.780 1.00 5.24 C "),
Pdb.Atom.FromString("ATOM 660 CA THR A 83 27.363 -20.163 13.449 1.00 6.79 C "),
Pdb.Atom.FromString("ATOM 667 CA GLU A 84 24.599 -22.785 13.726 1.00 6.27 C "),
Pdb.Atom.FromString("ATOM 676 CA ALA A 85 21.975 -24.045 11.260 1.00 7.61 C "),
Pdb.Atom.FromString("ATOM 681 CA GLY A 86 18.324 -23.142 11.886 1.00 7.35 C "),
Pdb.Atom.FromString("ATOM 685 CA THR A 87 15.680 -20.519 11.055 1.00 8.50 C "),
Pdb.Atom.FromString("ATOM 692 CA TYR A 88 16.009 -17.145 12.731 1.00 7.35 C "),
Pdb.Atom.FromString("ATOM 704 CA ASP A 89 13.191 -14.620 12.557 1.00 7.28 C "),
Pdb.Atom.FromString("ATOM 712 CA TYR A 90 13.740 -10.922 13.122 1.00 5.26 C "),
Pdb.Atom.FromString("ATOM 724 CA HIS A 91 11.902 -7.619 12.935 1.00 4.80 C "),
Pdb.Atom.FromString("ATOM 734 CA CYS A 92 12.663 -3.894 13.049 1.00 5.44 C "),
Pdb.Atom.FromString("ATOM 740 CA THR A 93 12.228 -2.579 16.647 1.00 6.60 C "),
Pdb.Atom.FromString("ATOM 747 CA PRO A 94 10.460 0.815 15.821 1.00 7.51 C "),
Pdb.Atom.FromString("ATOM 754 CA HIS A 95 8.594 -0.728 12.857 1.00 7.46 C "),
Pdb.Atom.FromString("ATOM 764 CA PRO A 96 7.518 -4.286 13.932 1.00 7.59 C "),
Pdb.Atom.FromString("ATOM 771 CA PHE A 97 5.480 -4.778 10.739 1.00 7.30 C "),
Pdb.Atom.FromString("ATOM 782 CA MET A 98 8.923 -5.104 8.994 1.00 6.57 C "),
Pdb.Atom.FromString("ATOM 790 CA ARG A 99 9.707 -8.821 9.391 1.00 7.91 C "),
Pdb.Atom.FromString("ATOM 808 CA GLY A 100 12.343 -11.105 7.827 1.00 6.39 C "),
Pdb.Atom.FromString("ATOM 812 CA LYS A 101 14.085 -14.438 8.459 1.00 7.31 C "),
Pdb.Atom.FromString("ATOM 826 CA VAL A 102 17.523 -15.900 7.870 1.00 6.58 C "),
Pdb.Atom.FromString("ATOM 833 CA VAL A 103 17.552 -19.658 7.157 1.00 7.20 C "),
Pdb.Atom.FromString("ATOM 840 CA VAL A 104 21.061 -21.012 7.897 1.00 7.28 C "),
Pdb.Atom.FromString("ATOM 847 CA GLU A 105 21.699 -24.347 6.221 1.00 13.74 C "),
#endregion
};
Pdb.Atom[] atoms_r6 = new Pdb.Atom[]
{
Pdb.Atom.FromString("ATOM 42 CB PRO A 6 31.929 -8.271 12.386 1.00 7.98 C "),
Pdb.Atom.FromString("ATOM 43 CG PRO A 6 30.972 -9.378 12.022 1.00 9.48 C "),
Pdb.Atom.FromString("ATOM 44 CD PRO A 6 29.880 -9.313 13.099 1.00 8.27 C "),
};
{
HessMatrix hess = GetHessCa(atoms_ca.ListCoord());
InfoPack extra = new InfoPack();
//Vector bfactors = ENM.BFactorFromHessian(hess, null, 6, extra);
Vector bfactors = Hess.GetBFactor(hess, null, 6, extra);
Vector eigvals = (double[])extra["eigenvalues"];
int[] idxsorted_eigvals = eigvals.ToArray().HAbs().HIdxSorted();
for (int i = 0; i < 6; i++)
{
eigvals[idxsorted_eigvals[i]] = 0;
}
for (int i = 0; i < eigvals.Size; i++)
{
if (eigvals[i] < 0)
{
// return false, if there exists negative eigenvalue
HDebug.Assert(false);
return(false);
}
}
}
{
List <Pdb.Atom> atoms = new List <Pdb.Atom>();
atoms.AddRange(atoms_ca);
atoms.AddRange(atoms_r6);
HDebug.Assert(atoms[5].resSeq == 6);
List <int> idxs_ca = new List <int>(); for (int i = 0; i < atoms_ca.Length; i++)
{
idxs_ca.Add(i);
}
List <int> idxs_r6 = new List <int>(); for (int i = atoms_ca.Length; i < atoms.Count; i++)
{
idxs_r6.Add(i);
}
idxs_r6.InsertRange(0, new int[] { 3, 4, 5 });
List <Tuple <int, int> > list12 = new List <Tuple <int, int> >();
for (int i = 1; i < idxs_ca.Count; i++)
{
list12.Add(new Tuple <int, int>(idxs_ca[i - 1], idxs_ca[i]));
}
for (int i = 3; i < idxs_r6.Count; i++)
{
list12.Add(new Tuple <int, int>(idxs_r6[i - 1], idxs_r6[i]));
}
List <Tuple <int, int, int> > list123 = new List <Tuple <int, int, int> >();
for (int i = 2; i < idxs_ca.Count; i++)
{
list123.Add(new Tuple <int, int, int>(idxs_ca[i - 2], idxs_ca[i - 1], idxs_ca[i]));
}
for (int i = 3; i < idxs_r6.Count; i++)
{
list123.Add(new Tuple <int, int, int>(idxs_r6[i - 2], idxs_r6[i - 1], idxs_r6[i]));
}
List <Tuple <int, int, int, int> > list1234 = new List <Tuple <int, int, int, int> >();
for (int i = 3; i < idxs_ca.Count; i++)
{
list1234.Add(new Tuple <int, int, int, int>(idxs_ca[i - 3], idxs_ca[i - 2], idxs_ca[i - 1], idxs_ca[i]));
}
for (int i = 3; i < idxs_r6.Count; i++)
{
list1234.Add(new Tuple <int, int, int, int>(idxs_r6[i - 3], idxs_r6[i - 2], idxs_r6[i - 1], idxs_r6[i]));
}
List <Tuple <int, int> > listNonbond = new List <Tuple <int, int> >();
for (int i = 0; i < idxs_ca.Count; i++)
{
for (int j = i + 4; j < idxs_ca.Count; j++)
{
listNonbond.Add(new Tuple <int, int>(idxs_ca[i], idxs_ca[j]));
}
}
for (int i = 0; i < idxs_r6.Count; i++)
{
for (int j = i + 4; j < idxs_r6.Count; j++)
{
listNonbond.Add(new Tuple <int, int>(idxs_r6[i], idxs_r6[j]));
}
}
List <Vector> coords = atoms.ListCoord();
HessMatrix hessian = HessMatrixSparse.ZerosSparse(atoms.Count * 3, atoms.Count * 3);
double Epsilon = 0.36;
double K_r = 100 * Epsilon;
double K_theta = 20 * Epsilon;
double K_phi1 = 1 * Epsilon;
double K_phi3 = 0.5 * Epsilon;
for (int i = 0; i < list12.Count; i++)
{
FirstTerm(coords, K_r, hessian, list12[i].Item1, list12[i].Item2);
}
for (int i = 0; i < list123.Count; i++)
{
SecondTerm(coords, K_theta, hessian, list123[i].Item1, list123[i].Item2, list123[i].Item3);
}
for (int i = 0; i < list1234.Count; i++)
{
ThirdTerm(coords, K_phi1, K_phi3, hessian, list1234[i].Item1, list1234[i].Item2, list1234[i].Item3, list1234[i].Item4);
}
for (int i = 0; i < listNonbond.Count; i++)
{
FourthTerm(coords, Epsilon, hessian, listNonbond[i].Item1, listNonbond[i].Item2);
}
InfoPack extra = new InfoPack();
//Vector bfactors = ENM.BFactorFromHessian(hessian, null, 6, extra);
Vector bfactors = Hess.GetBFactor(hessian, null, 6, extra);
Vector eigvals = (double[])extra["eigenvalues"];
int[] idxsorted_eigvals = eigvals.ToArray().HAbs().HIdxSorted();
for (int i = 0; i < 6; i++)
{
eigvals[idxsorted_eigvals[i]] = 0;
}
for (int i = 0; i < eigvals.Size; i++)
{
if (eigvals[i] < 0)
{
// return false, if there exists negative eigenvalue
HDebug.Assert(false);
return(false);
}
}
}
//{
// Debug.Assert(atoms_ca[5].resSeq == 6);
// Pdb.Atom[] atoms_resi6 = new Pdb.Atom[]
// {
// atoms_ca[5],
// Pdb.Atom.FromString("ATOM 42 CB PRO A 6 31.929 -8.271 12.386 1.00 7.98 C "),
// Pdb.Atom.FromString("ATOM 43 CG PRO A 6 30.972 -9.378 12.022 1.00 9.48 C "),
// Pdb.Atom.FromString("ATOM 44 CD PRO A 6 29.880 -9.313 13.099 1.00 8.27 C "),
// };
// Matrix hess_ca = GetHessCa(atoms_ca.ListCoord());
// Matrix hess_resi6 = GetHessCa(atoms_resi6.ListCoord());
//
// int size_ca = atoms_ca.Length;
// int size_r6 = atoms_resi6.Length - 1;
// Matrix hess = new double[(size_ca+size_r6)*3,(size_ca+size_r6)*3];
// for(int c = 0; c < hess.ColSize; c++)
// for(int r = 0; r < hess.RowSize; r++)
// hess[c, r] = double.NaN;
// for(int c = 0; c < hess_ca.ColSize; c++)
// for(int r = 0; r < hess_ca.RowSize; r++)
// hess[c, r] = hess_ca[c, r];
// for(int c = 0; c < hess_resi6.ColSize; c++)
// for(int r = 0; r < hess_resi6.RowSize; r++)
// {
// if(c < 3 && r < 3) { int c0=5 *3+ c ; int r0=5 *3+ r ; Debug.Assert(double.IsNaN(hess[c0, r0]) ==false); hess[c0, r0] = hess_resi6[c, r]; }
// else if(c < 3 && r >= 3) { int c0=5 *3+ c ; int r0=size_ca*3+(r-3); Debug.Assert(double.IsNaN(hess[c0, r0]) == true); hess[c0, r0] = hess_resi6[c, r]; }
// else if(c >= 3 && r < 3) { int c0=size_ca*3+(c-3); int r0=5 *3+ r ; Debug.Assert(double.IsNaN(hess[c0, r0]) == true); hess[c0, r0] = hess_resi6[c, r]; }
// else if(c >= 3 && r >= 3) { int c0=size_ca*3+(c-3); int r0=size_ca*3+(r-3); Debug.Assert(double.IsNaN(hess[c0, r0]) == true); hess[c0, r0] = hess_resi6[c, r]; }
// else Debug.Assert(false);
// }
// for(int j = size_ca * 3; j < (size_ca + size_r6) * 3; j++)
// {
// for(int i = 0; i < 5*3; i++)
// {
// Debug.Assert(double.IsNaN(hess[i, j]) == true); hess[i, j] = 0;
// Debug.Assert(double.IsNaN(hess[j, i]) == true); hess[j, i] = 0;
// }
// for(int i = 6*3; i < size_ca * 3; i++)
// {
// Debug.Assert(double.IsNaN(hess[i, j]) == true); hess[i, j] = 0;
// Debug.Assert(double.IsNaN(hess[j, i]) == true); hess[j, i] = 0;
// }
// }
// for(int c = 0; c < hess.ColSize; c++)
// for(int r = 0; r < hess.RowSize; r++)
// Debug.Assert(double.IsNaN(hess[c, r]) == false);
//
// InfoPack extra = new InfoPack();
// Vector bfactors = ENM.BFactorFromHessian(hess, null, 6, extra);
// Vector eigvals = (double[])extra["eigenvalues"];
// int[] idxsorted_eigvals = eigvals.ToArray().Abs().IdxSorted();
// for(int i = 0; i < 6; i++) eigvals[idxsorted_eigvals[i]] = 0;
// for(int i = 0; i < eigvals.Size; i++)
// if(eigvals[i] < 0)
// {
// // return false, if there exists negative eigenvalue
// Debug.Assert(false);
// return false;
// }
//}
return(true);
}
private static MatrixByArr[,] GetMassWeightedHess(MatrixByArr[,] hess, Vector mass, InfoPack extra = null)
{
//HDebug.Depreciated();
HDebug.Assert(hess.GetLength(0) == hess.GetLength(1));
int n = hess.GetLength(0);
// mass weighted hessian
// MH = M^(-1/2) * H * M^(-1/2)
// MH_ij = H_IJ * sqrt(M[i] * M[j])
MatrixByArr[,] mwhess = new MatrixByArr[n, n];
{
// mass weighted block hessian
//Matrix[,] mbhess = new Matrix[n, n];
for (int i = 0; i < n; i++)
{
//mbhess[i, i] = new double[3, 3];
for (int j = 0; j < n; j++)
{
//if(i == j) continue;
HDebug.Assert(hess[i, j].ColSize == 3, hess[i, j].RowSize == 3);
mwhess[i, j] = hess[i, j] / Math.Sqrt(mass[i] * mass[j]);
//mbhess[i, i] -= mbhess[i, j];
}
}
}
return(mwhess);
}
public int MinimizeHydrogens(List <ForceField.IForceField> frcflds, double?k, double threshold, int randomPurturb, InfoPack extra)
{
bool[] atomsMovable = new bool[size];
for (int i = 0; i < size; i++)
{
atomsMovable[i] = atoms[i].IsHydrogen();
}
IMinimizeLogger logger = null;
double max_atom_movement = 0.1;
return(Minimize_ConjugateGradient_v1(0, frcflds, k, max_atom_movement, null, threshold, randomPurturb, atomsMovable, logger, extra, null));
}
public void Add3(int id0, int id1, int id2, int id3, Vector[] lcoords, Vector[] lforces)
{
if (forceij == null)
{
return;
}
Vector ud01 = (lcoords[1] - lcoords[0]).UnitVector();
Vector ud02 = (lcoords[2] - lcoords[0]).UnitVector();
Vector ud03 = (lcoords[3] - lcoords[0]).UnitVector();
Vector ud12 = (lcoords[2] - lcoords[1]).UnitVector();
Vector ud13 = (lcoords[3] - lcoords[1]).UnitVector();
Vector ud23 = (lcoords[3] - lcoords[2]).UnitVector();
// f01 f02 f03 f12 f13 f23
// [ ud01_x, ud02_x, ud03_x, 0, 0, 0] [f01] [lf0x]
// [-ud01_x, 0, 0, ud12_x, ud13_x, 0] [f02] [lf1x]
// [ 0, -ud02_x, 0, -ud12_x, 0, ud23_x] * [f03] = [lf2x]
// [ 0, 0, -ud03_x, 0, -ud13_x, -ud23_x] * [f03] = [lf3x]
// [f12]
// [ ud01_y, ud02_y, ud03_y, 0, 0, 0] [f13] [lf0y]
// [-ud01_y, 0, 0, ud12_y, ud13_y, 0] [f23] [lf1y]
// [ 0, -ud02_y, 0, -ud12_y, 0, ud23_y] [lf2y]
// [ 0, 0, -ud03_y, 0, -ud13_y, -ud23_y] [lf3y]
//
// [ ud01_z, ud02_z, ud03_z, 0, 0, 0] [lf0z]
// [-ud01_z, 0, 0, ud12_z, ud13_z, 0] [lf1z]
// [ 0, -ud02_z, 0, -ud12_z, 0, ud23_z] [lf2z]
// [ 0, 0, -ud03_z, 0, -ud13_z, -ud23_z] [lf3z]
/////////////////////////////////////////////////
// A * x = b
MatrixByArr A = new double[12, 6];
Vector b = new double[12];
for (int i = 0; i < 3; i++)
{
A[i + 3 * 0, 0] = ud01[i]; A[i + 3 * 0, 1] = ud02[i]; A[i + 3 * 0, 2] = ud03[i]; A[i + 3 * 0, 3] = 0; A[i + 3 * 0, 4] = 0; A[i + 3 * 0, 5] = 0; b[i + 3 * 0] = lforces[0][i];
A[i + 3 * 1, 0] = -ud01[i]; A[i + 3 * 1, 1] = 0; A[i + 3 * 1, 2] = 0; A[i + 3 * 1, 3] = ud12[i]; A[i + 3 * 1, 4] = ud13[i]; A[i + 3 * 1, 5] = 0; b[i + 3 * 1] = lforces[1][i];
A[i + 3 * 2, 0] = 0; A[i + 3 * 2, 1] = -ud02[i]; A[i + 3 * 2, 2] = 0; A[i + 3 * 2, 3] = -ud12[i]; A[i + 3 * 2, 4] = 0; A[i + 3 * 2, 5] = ud23[i]; b[i + 3 * 2] = lforces[2][i];
A[i + 3 * 3, 0] = 0; A[i + 3 * 3, 1] = 0; A[i + 3 * 3, 2] = -ud03[i]; A[i + 3 * 3, 3] = 0; A[i + 3 * 3, 4] = -ud13[i]; A[i + 3 * 3, 5] = -ud23[i]; b[i + 3 * 3] = lforces[3][i];
}
InfoPack extra = HDebug.IsDebuggerAttached ? new InfoPack() : null;
Matrix pinvA = NumericSolver.Pinv(A, extra);
HDebug.Assert(extra.GetValueInt("rank") == 6);
Vector x = LinAlg.MV(pinvA, b);
Vector f01 = ud01 * x[0];
Vector f02 = ud02 * x[1];
Vector f03 = ud03 * x[2];
Vector f12 = ud12 * x[3];
Vector f13 = ud13 * x[4];
Vector f23 = ud23 * x[5];
if (HDebug.IsDebuggerAttached)
{
// check net force
Vector sumforces = lforces[0];
for (int i = 1; i < lforces.Length; i++)
{
sumforces += lforces[i];
}
HDebug.AssertTolerance(0.00000001, sumforces);
Vector f0 = f01 + f02 + f03;
Vector f1 = -f01 + f12 + f13;
Vector f2 = -f02 - f12 + f23;
Vector f3 = -f03 - f13 - f23;
HDebug.AssertTolerance(0.00000001, f0 - lforces[0]);
HDebug.AssertTolerance(0.00000001, f1 - lforces[1]);
HDebug.AssertTolerance(0.00000001, f2 - lforces[2]);
HDebug.AssertTolerance(0.00000001, f3 - lforces[3]);
}
this[id0, id1] += f01; this[id0, id2] += f02; this[id0, id3] += f03; this[id1, id2] += f12; this[id1, id3] += f13; this[id2, id3] += f23;
this[id1, id0] += -f01; this[id2, id0] += -f02; this[id3, id0] += -f03; this[id2, id1] += -f12; this[id3, id1] += -f13; this[id3, id2] += -f23;
}
public double CorrBFactor(IList <string> name, IList <int> resSeq, IList <double> BFactor, char selAltLoc = 'A', InfoPack extre = null, bool ignoreHydrogen = true)
{
List <double> bfactor_pdb = new List <double>();
List <double> bfactor_input = new List <double>();
HDebug.Assert(name.Count == resSeq.Count);
HDebug.Assert(name.Count == BFactor.Count);
int count = name.Count;
for (int i = 0; i < count; i++)
{
List <Atom> found = atoms.FindAtoms(name[i], resSeq[i]);
if (found.Count == 0)
{
continue;
}
int idx = -1;
for (int j = 0; j < found.Count; j++)
{
if (found[j].altLoc == ' ')
{
idx = j;
}
}
for (int j = 0; j < found.Count; j++)
{
if (found[j].altLoc == selAltLoc)
{
idx = j;
}
}
HDebug.Assert(idx != -1); // only one atom should be found
// handle altLoc later
if (ignoreHydrogen)
{
if (found[idx].IsHydrogen())
{
continue;
}
}
bfactor_pdb.Add(found[idx].tempFactor);
bfactor_input.Add(BFactor[i]);
}
double corr = NumericSolver.Corr(bfactor_pdb.ToArray(), bfactor_input.ToArray());
if (extre != null)
{
MatrixByArr A = new double[bfactor_input.Count, 2];
for (int i = 0; i < bfactor_input.Count; i++)
{
A[i, 0] = bfactor_input[i];
A[i, 1] = 1;
}
Vector b = bfactor_pdb.ToArray();
Matrix pinvA = NumericSolver.Pinv(A);
Vector x = LinAlg.MV(pinvA, b);
extre["bfactor_pdb"] = bfactor_pdb;
extre["bfactor_input"] = bfactor_input;
extre["info1"] = "approx (bfactor_input * scale1 + shift1 = bfactor_pdb)";
extre["scale1"] = x[0];
extre["shift1"] = x[1];
extre["info2"] = "approx (bfactor_input * scale2 = bfactor_pdb)";
extre["scale2"] = LinAlg.VtV(bfactor_input.ToArray(), bfactor_pdb.ToArray()) // x = (A' * A)^-1 * (A' * b) <= a,b: column vector
/ LinAlg.VtV(bfactor_input.ToArray(), bfactor_input.ToArray()); // (a' * a) / (a' * a) <= A : matrix
}
return(corr);
}
