//public static Dictionary<string,AminoAcid> ToDictionaryBy3Letter(this IList<AminoAcid> acids, bool toupper)
//{
// Dictionary<string,AminoAcid> dict = new Dictionary<string,AminoAcid>();
// foreach(AminoAcid acid in acids)
// {
// string name3 = acid.name3;
// if(toupper) name3 = name3.ToUpper();
// dict.Add(name3, acid);
// }
// return dict;
//}
//public static Dictionary<char, AminoAcid> ToDictionaryBy1Letter(this IList<AminoAcid> acids)
//{
// Dictionary<char,AminoAcid> dict = new Dictionary<char, AminoAcid>();
// foreach(AminoAcid acid in acids)
// dict.Add(acid.name1, acid);
// return dict;
//}
//public static string[] HBioinfoConvertTo3Letter( params char [] resis1) { return HBioinfo.AminoAcids.Convert_1Letter_to_3Letter( resis1); }
//public static char [] HBioinfoConvertTo1Letter(bool toupper, params string[] resis3) { return HBioinfo.AminoAcids.Convert_3Letter_to_1Letter(toupper, resis3); }
public static IReadOnlyList <Acid> GerResAminoAcid(this Pdb.Atom atom)
{
string name3 = atom.resName;
HDebug.Assert(name3.Length == 3);
return(Acid.From3Letter(name3));
}
public static List <Top.Atom> SelectMatchToPdb(this IList <Top.Atom> atoms, IList <Pdb.Atom> pdbatoms)
{
Dictionary <int, Pdb.Atom> dict = new Dictionary <int, Pdb.Atom>(pdbatoms.Count);
foreach (Pdb.Atom pdbatom in pdbatoms)
{
dict.Add(pdbatom.serial, pdbatom);
}
List <Top.Atom> select = new List <Top.Atom>();
foreach (Top.Atom atom in atoms)
{
if (dict.ContainsKey(atom.cgnr))
{
Pdb.Atom pdbatom = dict[atom.cgnr];
if ((atom.residu == pdbatom.resName) && (atom.resnr == pdbatom.resSeq))
{
HDebug.AssertOr(atom.atom.Trim() == pdbatom.name.Trim()
, atom.atom.Trim() == (pdbatom.name.Substring(1) + pdbatom.name[0]).Trim() // (top) HG21 <=> 1HG2 (pdb)
);
select.Add(atom);
}
}
}
HDebug.Assert(pdbatoms.Count == select.Count);
return(select);
}
public Pdb CloneWithFixResiToAla()
{
Atom[] atoms = this.atoms;
int numfix = 0;
Dictionary <Element, Atom> atom2natom = new Dictionary <Element, Atom>();
{
var resis = atoms.ListResidue();
foreach (var resi in resis)
{
if (resi.ResName == "ALA")
{
continue;
}
string[] names = resi.atoms.ListName().HTrim().HSort();
if (names.HConcat("-") == "C-CA-CB-N-O")
{
numfix++;
foreach (var atom in resi.atoms)
{
Pdb.Atom natom = Atom.FromData
(
serial: atom.serial,
name: atom.name,
resName: "ALA",
chainID: atom.chainID,
resSeq: atom.resSeq,
x: atom.x,
y: atom.y,
z: atom.z,
altLoc: atom.altLoc,
iCode: atom.iCode,
occupancy: atom.occupancy,
tempFactor: atom.tempFactor,
element: atom.element,
charge: atom.charge
);
atom2natom.Add(atom, natom);
}
}
}
}
//atoms.group();
Element[] newelements = new Element[elements.Length];
for (int i = 0; i < elements.Length; i++)
{
Element element = elements[i];
newelements[i] = element.UpdateElement();
if (atom2natom.ContainsKey(element))
{
newelements[i] = atom2natom[element].UpdateElement();
}
}
return(new Pdb(newelements));
}
public static IEnumerable <List <Pdb.Atom> > BuildWaterBoxExt
(Vector min
, Vector max
, double dist2water = 2.9 //2.8 // 2.7564;
, bool randOrient = true
, string opt = "water in uniform cube"
)
{
double min_x = Math.Min(min[0], max[0]);
double min_y = Math.Min(min[1], max[1]);
double min_z = Math.Min(min[2], max[2]);
double max_x = Math.Max(min[0], max[0]);
double max_y = Math.Max(min[1], max[1]);
double max_z = Math.Max(min[2], max[2]);
double maxx = max_x - min_x;
double maxy = max_y - min_y;
double maxz = max_z - min_z;
Dictionary <int, List <Pdb.Atom> > atoms = new Dictionary <int, List <Pdb.Atom> >();
foreach (var file_atom in EnumAtomsInWaterBox(maxx, maxy, maxz, dist2water, randOrient, opt))
{
int file = file_atom.Item1;
var atom = file_atom.Item2;
double x = atom.x;
double y = atom.y;
double z = atom.z;
Pdb.Atom uatom = Pdb.Atom.FromString(atom.GetUpdatedLine(min_x + x, min_y + y, min_z + z));
if (atoms.ContainsKey(file) == false)
{
if (atoms.Count == 1)
{
yield return(atoms.First().Value);
atoms.Clear();
}
atoms.Add(file, new List <Pdb.Atom>());
}
atoms[file].Add(uatom);
}
if (atoms.Count == 1)
{
yield return(atoms.First().Value);
atoms.Clear();
}
}
public static char?GetResNameSyn(this Pdb.Atom atom)
{
var aa = atom.GerResAminoAcid();
if (aa == null)
{
return(null);
}
if (aa.Count == 1)
{
return(aa[0].name1);
}
throw new NotImplementedException();
}
public static Pdb CopyPdbOccupancyForMergedPsf(Pdb copyto, Pdb copyfrom1, Pdb copyfrom2)
{
KDTreeDLL.KDTree <Pdb.Atom> kdtree = new KDTreeDLL.KDTree <Pdb.Atom>(3);
foreach (var atom in copyfrom1.atoms)
{
kdtree.insert(atom.coord, atom);
}
foreach (var atom in copyfrom2.atoms)
{
kdtree.insert(atom.coord, atom);
}
Pdb pdb = copyto.Clone();
List <string> nlines = new List <string>();
for (int i = 0; i < pdb.elements.Length; i++)
{
var elemi = pdb.elements[i];
if ((elemi is Pdb.Atom) == false)
{
nlines.Add(elemi.line);
}
else
{
var atomi = elemi as Pdb.Atom;
var atomx = kdtree.nearest(atomi.coord);
HDebug.Assert(atomi.coord[0] == atomx.coord[0]);
HDebug.Assert(atomi.coord[1] == atomx.coord[1]);
HDebug.Assert(atomi.coord[2] == atomx.coord[2]);
/// 55 - 60 Real(6.2) occupancy Occupancy.
char[] line = atomi.line.ToCharArray();
line[55 - 1] = atomx.line[55 - 1];
line[56 - 1] = atomx.line[56 - 1];
line[57 - 1] = atomx.line[57 - 1];
line[58 - 1] = atomx.line[58 - 1];
line[59 - 1] = atomx.line[59 - 1];
line[60 - 1] = atomx.line[60 - 1];
string nline = line.HToString();
nlines.Add(nline);
Pdb.Atom natomi = Pdb.Atom.FromString(nline);
pdb.elements[i] = natomi;
}
}
return(pdb);
}
static Tuple <string, string, double, double, double, int> UnivAtomToTinkKey(Universe.Atom uatom)
{
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;
var key = new Tuple <string, string, double, double, double, int>(name + "-" + resn, type, rmin2, eps, chrg, valnc);
return(key);
}
public static List <Atom[]> GroupByResidue(this IList <Atom> atoms)
{
Dictionary <string, Atom[]> resi2atoms = new Dictionary <string, Atom[]>();
foreach (var atom in atoms)
{
string key;
if (atom._ResidueId != null)
{
key = atom._ResidueId;
}
else
{
Pdb.Atom pdbatom = atom.correspond_PdbAtom();
if (pdbatom != null)
{
key = string.Format("[{0},{1},{2}]", pdbatom.chainID, pdbatom.resSeq, pdbatom.iCode);
}
else
{
// if corresponding PDB atom cannot be found, then
// * if it is not hydrogen, then use AtomId
// * if it is hydrogen, then use its connected atom's AtomId
Atom key_atom = null;
if (atom.AtomElem == "H")
{
key_atom = atom.Inter12.First();
}
else
{
key_atom = atom;
}
key = string.Format("ID-{0}", key_atom.AtomId);
}
}
if (resi2atoms.ContainsKey(key) == false)
{
resi2atoms.Add(key, new Atom[0]);
}
resi2atoms[key] = resi2atoms[key].HAdd(atom);
}
return(resi2atoms.Values.ToList());
}
public int GetValence()
{
HDebug.Assert(false);
Pdb.Atom PdbAtom = null;
switch (PdbAtom.element)
{
case " H": return(1);
case " N": return(3);
case " C": return(4);
case " O": return(2);
//case " S": return
}
HDebug.Assert(false);
return(-1);
}
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 static Dictionary <Pdb.Atom, HashSet <Pdb.Atom> > BuildBonds(params Pdb.Atom[] atoms)
{
int resSeq = atoms[0].resSeq;
string resName = atoms[0].resName;
List <Tuple <string, string> > list_name1_name2 = BuildBonds(resName);
Dictionary <Pdb.Atom, HashSet <Pdb.Atom> > bonds = new Dictionary <Pdb.Atom, HashSet <Pdb.Atom> >();
foreach (Tuple <string, string> name1_name2 in list_name1_name2)
{
string name1 = name1_name2.Item1;
string name2 = name1_name2.Item2;
List <Pdb.Atom> atom1s = atoms.SelectByName(name1.Trim());
List <Pdb.Atom> atom2s = atoms.SelectByName(name2.Trim());
if (atom1s.Count == 0 || atom2s.Count == 0)
{
continue;
}
HDebug.Assert(atom1s.Count == 1, atom2s.Count == 1);
Pdb.Atom atom1 = atom1s[0];
Pdb.Atom atom2 = atom2s[0];
HDebug.Assert(atom1.resSeq == atom2.resSeq);
HDebug.Assert(atom1.resName == atom2.resName);
if (bonds.ContainsKey(atom1) == false)
{
bonds.Add(atom1, new HashSet <Pdb.Atom>());
}
if (bonds.ContainsKey(atom2) == false)
{
bonds.Add(atom2, new HashSet <Pdb.Atom>());
}
bonds[atom1].Add(atom2);
bonds[atom2].Add(atom1);
}
HDebug.Assert(bonds.Count == atoms.Length);
return(bonds);
}
public Atom(Namd.Psf.Atom PsfAtom, Namd.Prm.Nonbonded Nonbonded, Pdb.Atom PdbAtom)
{
//Debug.Assert(ID <= MaxID);
//this._ID = ID;
//this.PdbAtom = PdbAtom;
//this.PsfAtom = PsfAtom;
//this.PrmNonbonded = Nonbonded;
this.AtomId = PsfAtom.AtomId;
this.AtomName = PsfAtom.AtomName;
this.AtomType = PsfAtom.AtomType;
this.AtomElem = PdbAtom.element.Trim();
this._ResidueId = string.Format("({0},{1},{2})", PsfAtom.SegmentName, PsfAtom.ResidueId.Item1, PsfAtom.ResidueId.Item2);
this.ResidueName = PsfAtom.ResidueName;
this.Charge = PsfAtom.Charge;
this.Mass = PsfAtom.Mass;
this.epsilon = Nonbonded.epsilon;
this.Rmin2 = Nonbonded.Rmin2;
this.eps_14 = Nonbonded.eps_14;
this.Rmin2_14 = Nonbonded.Rmin2_14;
this.sources = new object[] { PdbAtom, PsfAtom, Nonbonded };
/// this.IsVirtual = (PdbAtom.occupancy < 0) ? true : false;
}
public Pdb.Atom correspond_PdbAtom()
{
Pdb.Atom pdbatom = sources_PdbAtom();
if (pdbatom != null)
{
return(pdbatom);
}
HashSet <Atom> visiteds = new HashSet <Atom>();
visiteds.Add(this);
List <Atom> tovisit = new List <Atom>();
tovisit.AddRange(Inter12);
tovisit.AddRange(Inter123);
tovisit.AddRange(Inter14);
foreach (var link in tovisit)
{
if (visiteds.Contains(link))
{
continue;
}
pdbatom = link.sources_PdbAtom();
if (pdbatom != null)
{
return(pdbatom);
}
visiteds.Add(link);
}
return(null);
//HDebug.Assert(false);
throw new NotImplementedException();
}
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 );
}
}
public static Universe Build(Tinker.Xyz xyz, Tinker.Prm prm, Pdb pdb
, double?tolCoordPdbXyz // 0.002 for default distance
// (0.001 * sqrt(3) = 0.0017321, which is the largest tolerance between pdb and xyz)
// null for not ordering by distance;
)
{
Universe univ = new Universe();
Dictionary <int, Prm.Atom> prm_id2atom = prm.atoms.ToIdDictionary();
Dictionary <int, Prm.Vdw> prm_cls2vdw = prm.vdws.ToClassDictionary();
Dictionary <int, Prm.Vdw14> prm_cls2vdw14 = prm.vdw14s.ToClassDictionary();
Dictionary <Tuple <int, int>, Prm.Bond> prm_cls2bond = prm.bonds.ToClassDictionary();
Dictionary <Tuple <int, int, int>, Prm.Angle> prm_cls2angle = prm.angles.ToClassDictionary();
Dictionary <Tuple <int, int, int>, Prm.Ureybrad> prm_cls2ureybrad = prm.ureybrads.ToClassDictionary();
Dictionary <Tuple <int, int, int, int>, Prm.Improper> prm_cls2improper = prm.impropers.ToClassDictionary();
Dictionary <Tuple <int, int, int, int>, Prm.Torsion> prm_cls2torsion = prm.torsions.ToClassDictionary();
Dictionary <int, Prm.Charge> prm_id2charge = prm.charges.ToIdDictionary();
Prm.Biotype[] prm_biotypes = prm.biotypes;
Xyz.Atom[] xyz_atoms = xyz.atoms;
Pdb.Atom[] pdb_atoms = (pdb != null) ? pdb.atoms : null;
Dictionary <int, Xyz.Atom> xyz_id2atom = xyz_atoms.ToIdDictionary();
KDTree.KDTree <Tuple <int, Pdb.Atom> > coord2pdbatom = null;
{
if (pdb_atoms != null)
{
coord2pdbatom = new KDTree.KDTree <Tuple <int, Pdb.Atom> >(3);
for (int ia = 0; ia < pdb_atoms.Length; ia++)
{
Pdb.Atom pdb_atom = pdb_atoms[ia];
Vector coord = pdb_atom.coord;
coord2pdbatom.insert(coord.ToArray(), new Tuple <int, Pdb.Atom>(ia, pdb_atom));
}
}
}
Atoms atoms = new Atoms(univ);
/// Debug.Assert(pdb.atoms.Length == top_atoms.Count);
for (int i = 0; i < xyz_atoms.Length; i++)
{
Xyz.Atom xyz_atom = xyz_atoms[i];
Pdb.Atom pdb_atom = null; // = (pdb_atoms != null) ? (pdb_atoms[i]) : null;
if (coord2pdbatom != null)
{
Vector xyz_coord = xyz_atom.Coord;
Tuple <int, Pdb.Atom> ia_atom = coord2pdbatom.nearest(xyz_coord);
Vector pdb_coord = ia_atom.Item2.coord;
if (tolCoordPdbXyz == null)
{
pdb_atom = pdb_atoms[i];
}
else
{
if ((xyz_coord - pdb_coord).Dist < tolCoordPdbXyz)
{
pdb_atom = ia_atom.Item2;
}
else
{
//HDebug.Assert(false);
pdb_atom = null;
}
}
}
if (pdb_atom != null)
{
string pdb_atom_type = pdb_atom.element.Trim();
string xyz_atom_type = xyz_atom.AtomType.Trim();
if (HDebug.IsDebuggerAttached && pdb_atom_type.Length > 0) // sometimes element is blank: " "
{
HDebug.AssertIf(pdb_atom_type[0] == xyz_atom_type[0]);
}
if (tolCoordPdbXyz != null)
{
HDebug.AssertTolerance(tolCoordPdbXyz.Value, xyz_atom.Coord - pdb_atom.coord);
}
}
//if(pdb_atom != null) Debug.Assert(xyz_atom.Id == pdb_atom.serial);
HDebug.Assert(i + 1 == xyz_atom.Id);
Prm.Atom prm_atom = prm_id2atom [xyz_atom.AtomId];
Prm.Charge prm_charge = prm_id2charge[xyz_atom.AtomId];
Prm.Vdw prm_vdw = null;
Prm.Vdw14 prm_vdw14 = null;
if (prm_cls2vdw.ContainsKey(prm_atom.Class))
{
prm_vdw = prm_cls2vdw [prm_atom.Class];
}
if (prm_cls2vdw14.ContainsKey(prm_atom.Class))
{
prm_vdw14 = prm_cls2vdw14[prm_atom.Class];
}
if (pdb_atom != null)
{
if (pdb_atom.element.Trim() != "")
{
if (pdb_atom.element.Trim() != prm_atom.AtomElem)
{
throw new Exception();
}
}
}
Atom uatom = new Atom(AtomId: xyz_atom.Id
, AtomName: ((pdb_atom != null) ? (pdb_atom.name.Trim()) : ("?" + prm_atom.Type)) /// fix later
, AtomType: prm_atom.Type
, AtomElem: prm_atom.AtomElem
, ResidueId: ((pdb_atom != null) ? (pdb_atom.resSeq) : (-1)) /// fix later
, ResidueName: ((pdb_atom != null) ? (pdb_atom.resName.Trim()) : ("?res")) /// fix later
, Charge: prm_charge.pch
, Mass: prm_atom.Mass
, epsilon: ((prm_vdw != null) ? prm_vdw.Epsilon : 0)
, Rmin2: ((prm_vdw != null) ? prm_vdw.Rmin2 : 0)
, eps_14: ((prm_vdw14 != null) ? prm_vdw14.Eps_14 : double.NaN)
, Rmin2_14: ((prm_vdw14 != null) ? prm_vdw14.Rmin2_14 : double.NaN)
, sources: new object[] { xyz_atom, pdb_atom, prm_atom, prm_charge }
);
uatom.Coord = xyz_atom.Coord;
atoms.Add(uatom);
}
// bonds
Bonds bonds;
{
Dictionary <Tuple <Atom, Atom>, Bond> lbonds = new Dictionary <Tuple <Atom, Atom>, Bond>();
for (int i = 0; i < xyz_atoms.Length; i++)
{
int id0 = xyz_atoms[i].Id; HDebug.Assert(id0 == i + 1);
int atm0 = xyz_atoms[i].AtomId;
int cls0 = prm_id2atom[atm0].Class;
Atom atom0 = atoms[id0 - 1]; HDebug.Assert(atom0.AtomId == id0);
Tuple <int, int> cls;
foreach (int id1 in xyz_atoms[i].BondedIds)
{
int atm1 = xyz_id2atom[id1].AtomId;
int cls1 = prm_id2atom[atm1].Class;
Atom atom1 = atoms[id1 - 1]; HDebug.Assert(atom1.AtomId == id1);
HashSet <Prm.Bond> bondtypes = new HashSet <Prm.Bond>();
Atom[] iatom = null;
cls = new Tuple <int, int>(cls0, cls1); if (prm_cls2bond.ContainsKey(cls))
{
bondtypes.Add(prm_cls2bond[cls]); iatom = new Atom[] { atom0, atom1 };
}
cls = new Tuple <int, int>(cls1, cls0); if (prm_cls2bond.ContainsKey(cls))
{
bondtypes.Add(prm_cls2bond[cls]); iatom = new Atom[] { atom1, atom0 };
}
HDebug.Assert(bondtypes.Count == 1);
if (bondtypes.Count >= 1)
{
Prm.Bond bondtype = bondtypes.Last();
HDebug.Assert(bondtype != null);
// sort atom id, in order to avoid duplication of bonds such that (0,1) and (1,0)
if (iatom.First().ID > iatom.Last().ID)
{
iatom = iatom.Reverse().ToArray();
}
var key = new Tuple <Atom, Atom>(iatom[0], iatom[1]);
Bond bond = new Bond(iatom[0], iatom[1], bondtype.Kb, bondtype.b0, bondtype);
if (lbonds.ContainsKey(key) == false)
{
lbonds.Add(key, bond);
}
else
{
HDebug.Assert(bond.Kb == lbonds[key].Kb);
HDebug.Assert(bond.b0 == lbonds[key].b0);
}
}
}
}
bonds = new Bonds();
foreach (Bond bond in lbonds.Values)
{
HDebug.Assert(bond.atoms.Length == 2);
HDebug.Assert(bond.atoms[0].ID < bond.atoms[1].ID);
bonds.Add(bond);
Atom atom0 = bond.atoms[0];
Atom atom1 = bond.atoms[1];
atom0.Bonds.Add(bond); atom0.Inter123.Add(atom1); atom0.Inter12.Add(atom1);
atom1.Bonds.Add(bond); atom1.Inter123.Add(atom0); atom1.Inter12.Add(atom0);
}
}
HashSet <Atom>[] inter12 = new HashSet <Atom> [xyz_atoms.Length];
HashSet <Tuple <Atom, Atom> >[] inter123 = new HashSet <Tuple <Atom, Atom> > [xyz_atoms.Length];
HashSet <Tuple <Atom, Atom, Atom> >[] inter1234 = new HashSet <Tuple <Atom, Atom, Atom> > [xyz_atoms.Length];
{
HDebug.Assert(xyz_atoms.Length == atoms.Count);
foreach (Atom atom in atoms)
{
inter12 [atom.ID] = new HashSet <Atom>(atom.Inter12);
inter123 [atom.ID] = new HashSet <Tuple <Atom, Atom> >();
inter1234[atom.ID] = new HashSet <Tuple <Atom, Atom, Atom> >();
}
// build inter123 and inter1234
for (int i = 0; i < xyz_atoms.Length; i++)
{
Atom atom0 = atoms[i];
HDebug.Assert(atom0.ID == i);
foreach (Atom atom1 in inter12[atom0.ID])
{
HDebug.Assert(atom0 != atom1);
foreach (Atom atom2 in inter12[atom1.ID])
{
HDebug.Assert(atom1 != atom2);
if (atom0 == atom2)
{
continue;
}
inter123[atom0.ID].Add(new Tuple <Atom, Atom>(atom1, atom2));
foreach (Atom atom3 in inter12[atom2.ID])
{
HDebug.Assert(atom2 != atom3);
if (atom0 == atom2)
{
continue;
}
if (atom0 == atom3)
{
continue;
}
if (atom1 == atom3)
{
continue;
}
inter1234[atom0.ID].Add(new Tuple <Atom, Atom, Atom>(atom1, atom2, atom3));
}
}
}
}
}
// angles
Angles angles;
{
Dictionary <Tuple <Atom, Atom, Atom>, Angle> langles = new Dictionary <Tuple <Atom, Atom, Atom>, Angle>();
foreach (Atom atom0 in atoms)
{
int id0 = xyz_atoms[atom0.ID].Id; HDebug.Assert(id0 == atom0.ID + 1);
int atm0 = xyz_atoms[atom0.ID].AtomId;
int cls0 = prm_id2atom[atm0].Class;
foreach (var atom123 in inter123[atom0.ID])
{
Atom atom1 = atom123.Item1; int atm1 = xyz_atoms[atom1.ID].AtomId; int cls1 = prm_id2atom[atm1].Class;
Atom atom2 = atom123.Item2; int atm2 = xyz_atoms[atom2.ID].AtomId; int cls2 = prm_id2atom[atm2].Class;
Tuple <int, int, int> cls;
Atom[] iatom = null;
HashSet <Prm.Angle> angs = new HashSet <Prm.Angle>();
HashSet <Prm.Ureybrad> urbs = new HashSet <Prm.Ureybrad>();
cls = new Tuple <int, int, int>(cls0, cls1, cls2); if (prm_cls2angle.ContainsKey(cls))
{
angs.Add(prm_cls2angle[cls]); iatom = new Atom[] { atom0, atom1, atom2 };
}
if (prm_cls2ureybrad.ContainsKey(cls))
{
urbs.Add(prm_cls2ureybrad[cls]);
}
cls = new Tuple <int, int, int>(cls2, cls1, cls0); if (prm_cls2angle.ContainsKey(cls))
{
angs.Add(prm_cls2angle[cls]); iatom = new Atom[] { atom2, atom1, atom0 };
}
if (prm_cls2ureybrad.ContainsKey(cls))
{
urbs.Add(prm_cls2ureybrad[cls]);
}
HDebug.Assert(angs.Count == 1);
HDebug.Assert(urbs.Count <= angs.Count);
if (angs.Count >= 1)
{
Prm.Angle ang = angs.Last();
HDebug.Assert(ang != null);
Prm.Ureybrad urb = null;
if (urbs.Count >= 1)
{
urb = urbs.Last();
}
// sort atom id, in order to avoid duplication of bonds such that (0,1) and (1,0)
if (iatom.First().ID > iatom.Last().ID)
{
iatom = iatom.Reverse().ToArray();
}
var key = new Tuple <Atom, Atom, Atom>(iatom[0], iatom[1], iatom[2]);
Angle angle = new Angle(iatom[0], iatom[1], iatom[2]
, Ktheta: ang.Ktheta
, Theta0: ang.Theta0
, Kub: ((urb != null) ? urb.Kub : 0)
, S0: ((urb != null) ? urb.S0 : 0)
, sources: new object[] { ang, urb }
);
if (langles.ContainsKey(key) == false)
{
langles.Add(key, angle);
}
else
{
HDebug.Assert(langles[key].Ktheta == angle.Ktheta
, langles[key].Theta0 == angle.Theta0
, langles[key].Kub == angle.Kub
, langles[key].S0 == angle.S0
);
}
}
}
}
angles = new Angles();
foreach (Angle angle in langles.Values)
{
HDebug.Assert(angle.atoms.Length == 3);
HDebug.Assert(angle.atoms[0].ID < angle.atoms[2].ID);
angles.Add(angle);
Atom atom0 = angle.atoms[0];
Atom atom1 = angle.atoms[1];
Atom atom2 = angle.atoms[2];
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;
{
Dictionary <Tuple <Atom, Atom, Atom, Atom>, List <Dihedral> > ldihedrals = new Dictionary <Tuple <Atom, Atom, Atom, Atom>, List <Dihedral> >();
foreach (Atom atom0 in atoms)
{
int id0 = xyz_atoms[atom0.ID].Id; HDebug.Assert(id0 == atom0.ID + 1);
int atm0 = xyz_atoms[atom0.ID].AtomId;
int cls0 = prm_id2atom[atm0].Class;
Tuple <int, int, int, int> cls;
foreach (var atom1234 in inter1234[atom0.ID])
{
Atom atom1 = atom1234.Item1; int atm1 = xyz_atoms[atom1.ID].AtomId; int cls1 = prm_id2atom[atm1].Class;
Atom atom2 = atom1234.Item2; int atm2 = xyz_atoms[atom2.ID].AtomId; int cls2 = prm_id2atom[atm2].Class;
Atom atom3 = atom1234.Item3; int atm3 = xyz_atoms[atom3.ID].AtomId; int cls3 = prm_id2atom[atm3].Class;
HashSet <Prm.Torsion> tors = new HashSet <Prm.Torsion>();
Atom[] iatom = null;
cls = new Tuple <int, int, int, int>(cls0, cls1, cls2, cls3); if (prm_cls2torsion.ContainsKey(cls))
{
tors.Add(prm_cls2torsion[cls]); iatom = new Atom[] { atom0, atom1, atom2, atom3 };
}
cls = new Tuple <int, int, int, int>(cls3, cls2, cls1, cls0); if (prm_cls2torsion.ContainsKey(cls))
{
tors.Add(prm_cls2torsion[cls]); iatom = new Atom[] { atom3, atom2, atom1, atom0 };
}
HDebug.Assert(tors.Count == 1);
if (tors.Count >= 1)
{
// sort atom id, in order to avoid duplication of bonds such that (0,1) and (1,0)
if (iatom.First().ID > iatom.Last().ID)
{
iatom = iatom.Reverse().ToArray();
}
var key = new Tuple <Atom, Atom, Atom, Atom>(iatom[0], iatom[1], iatom[2], iatom[3]);
if (ldihedrals.ContainsKey(key) == false)
{
ldihedrals.Add(key, new List <Dihedral>());
Prm.Torsion tor = tors.Last();
foreach (var tordat in tor.GetListData())
{
Dihedral dihedral = new Dihedral(iatom[0], iatom[1], iatom[2], iatom[3]
, Kchi: tordat.Kchi
, n: tordat.n
, delta: tordat.delta
, sources: new object[] { tor }
);
ldihedrals[key].Add(dihedral);
HDebug.Assert(dihedral.n != 0);
}
}
else
{
// do not check its contents because ...
}
}
}
}
dihedrals = new Dihedrals();
foreach (var ldihedral in ldihedrals.Values)
{
foreach (Dihedral dihedral in ldihedral)
{
HDebug.Assert(dihedral.atoms.Length == 4);
HDebug.Assert(dihedral.atoms[0].ID < dihedral.atoms[3].ID);
dihedrals.Add(dihedral);
dihedral.atoms[0].Dihedrals.Add(dihedral);
dihedral.atoms[1].Dihedrals.Add(dihedral);
dihedral.atoms[2].Dihedrals.Add(dihedral);
dihedral.atoms[3].Dihedrals.Add(dihedral);
}
}
}
// impropers
Impropers impropers = new Impropers();
{
Dictionary <Tuple <Atom, Atom, Atom, Atom>, Improper> limpropers = new Dictionary <Tuple <Atom, Atom, Atom, Atom>, Improper>();
foreach (Atom atom0 in atoms)
{
/// ####################################
/// ## ##
/// ## Improper Dihedral Parameters ##
/// ## ##
/// ####################################
///
/// ##################################################################
/// ## ##
/// ## Following CHARMM style, the improper for a trigonal atom ##
/// ## D bonded to atoms A, B and C could be input as improper ##
/// ## dihedral angle D-A-B-C. The actual angle computed by the ##
/// ## program is then literally the dihedral D-A-B-C, which will ##
/// ## always have as its ideal value zero degrees. In general ##
/// ## D-A-B-C is different from D-B-A-C; the order of the three ##
/// ## peripheral atoms matters. In the original CHARMM parameter ##
/// ## files, the trigonal atom is often listed last; ie, as ##
/// ## C-B-A-D instead of D-A-B-C. ##
/// ## ##
/// ## Some of the improper angles are "double counted" in the ##
/// ## CHARMM protein parameter set. Since TINKER uses only one ##
/// ## improper parameter per site, we have doubled these force ##
/// ## constants in the TINKER version of the CHARMM parameters. ##
/// ## Symmetric parameters, which are the origin of the "double ##
/// ## counted" CHARMM values, are handled in the TINKER package ##
/// ## by assigning all symmetric states and using the TINKER ##
/// ## force constant divided by the symmetry number. ##
/// ## ##
/// ## ... ##
/// ##################################################################
int id0 = xyz_atoms[atom0.ID].Id; HDebug.Assert(id0 == atom0.ID + 1);
int atm0 = xyz_atoms[atom0.ID].AtomId;
int cls0 = prm_id2atom[atm0].Class;
bool bAtom0InImpropers = false;
foreach (var cls in prm_cls2improper.Keys)
{
if (cls.Item1 == cls0)
{
bAtom0InImpropers = true;
}
}
if (bAtom0InImpropers == false)
{
continue;
}
Atom[] bondeds0 = inter12[atom0.ID].ToArray();
if (bondeds0.Length < 3)
{
continue;
}
for (int i = 0; i < bondeds0.Length - 2; i++)
{
Atom atom1 = bondeds0[i];
int atm1 = xyz_atoms[atom1.ID].AtomId;
int cls1 = prm_id2atom[atm1].Class;
for (int j = i + 1; j < bondeds0.Length - 1; j++)
{
Atom atom2 = bondeds0[j];
int atm2 = xyz_atoms[atom2.ID].AtomId;
int cls2 = prm_id2atom[atm2].Class;
for (int k = j + 1; k < bondeds0.Length; k++)
{
Atom atom3 = bondeds0[k];
int atm3 = xyz_atoms[atom3.ID].AtomId;
int cls3 = prm_id2atom[atm3].Class;
Tuple <int, int, int, int> cls;
HashSet <Prm.Improper> imps = new HashSet <Prm.Improper>();
Atom[] iatom = null;
cls = new Tuple <int, int, int, int>(cls0, cls1, cls2, cls3); if (prm_cls2improper.ContainsKey(cls))
{
imps.Add(prm_cls2improper[cls]); iatom = new Atom[] { atom0, atom1, atom2, atom3 };
}
cls = new Tuple <int, int, int, int>(cls3, cls2, cls1, cls0); if (prm_cls2improper.ContainsKey(cls))
{
imps.Add(prm_cls2improper[cls]); iatom = new Atom[] { atom3, atom2, atom1, atom0 };
}
cls = new Tuple <int, int, int, int>(cls0, cls1, cls3, cls2); if (prm_cls2improper.ContainsKey(cls))
{
imps.Add(prm_cls2improper[cls]); iatom = new Atom[] { atom0, atom1, atom3, atom2 };
}
cls = new Tuple <int, int, int, int>(cls2, cls3, cls1, cls0); if (prm_cls2improper.ContainsKey(cls))
{
imps.Add(prm_cls2improper[cls]); iatom = new Atom[] { atom2, atom3, atom1, atom0 };
}
cls = new Tuple <int, int, int, int>(cls0, cls2, cls1, cls3); if (prm_cls2improper.ContainsKey(cls))
{
imps.Add(prm_cls2improper[cls]); iatom = new Atom[] { atom0, atom2, atom1, atom3 };
}
cls = new Tuple <int, int, int, int>(cls3, cls1, cls2, cls0); if (prm_cls2improper.ContainsKey(cls))
{
imps.Add(prm_cls2improper[cls]); iatom = new Atom[] { atom3, atom1, atom2, atom0 };
}
cls = new Tuple <int, int, int, int>(cls0, cls2, cls3, cls1); if (prm_cls2improper.ContainsKey(cls))
{
imps.Add(prm_cls2improper[cls]); iatom = new Atom[] { atom0, atom2, atom3, atom1 };
}
cls = new Tuple <int, int, int, int>(cls1, cls3, cls2, cls0); if (prm_cls2improper.ContainsKey(cls))
{
imps.Add(prm_cls2improper[cls]); iatom = new Atom[] { atom1, atom3, atom2, atom0 };
}
cls = new Tuple <int, int, int, int>(cls0, cls3, cls1, cls2); if (prm_cls2improper.ContainsKey(cls))
{
imps.Add(prm_cls2improper[cls]); iatom = new Atom[] { atom0, atom3, atom1, atom2 };
}
cls = new Tuple <int, int, int, int>(cls2, cls1, cls3, cls0); if (prm_cls2improper.ContainsKey(cls))
{
imps.Add(prm_cls2improper[cls]); iatom = new Atom[] { atom2, atom1, atom3, atom0 };
}
cls = new Tuple <int, int, int, int>(cls0, cls3, cls2, cls1); if (prm_cls2improper.ContainsKey(cls))
{
imps.Add(prm_cls2improper[cls]); iatom = new Atom[] { atom0, atom3, atom2, atom1 };
}
cls = new Tuple <int, int, int, int>(cls1, cls2, cls3, cls0); if (prm_cls2improper.ContainsKey(cls))
{
imps.Add(prm_cls2improper[cls]); iatom = new Atom[] { atom1, atom2, atom3, atom0 };
}
HDebug.Assert(imps.Count <= 1); // for example, H-C-HHH has C-HHH connectivity but it is not improper...
// so imps.count <= 1
if (imps.Count >= 1)
{
Prm.Improper imp = imps.Last(); // because iatoms contains the last case only.
///////////////////////////////////////////////////////////////////////////////////////
// This bug was raised by Jae-Kyun Song at 2016-04-01 //
// In 1AAC, (1501,C)-(1503,NC2)-(1502,NC2)-(1500,NC2) is reordered //
// as (1500,NC2)-(1502,NC2)-(1503,NC2)-(1501,C) //
// This bug was originally copied from dihedral code that is added to prevent adding //
// duplicated interactions such as 1-2-3-4 and 4-3-2-1. //
///////////////////////////////////////////////////////////////////////////////////////
/// old code
// // sort atom id, in order to avoid duplication of bonds such that (0,1) and (1,0)
// if(iatom.First().ID > iatom.Last().ID)
// iatom = iatom.Reverse().ToArray();
// var key = new Tuple<Atom, Atom, Atom, Atom>(iatom[0], iatom[1], iatom[2], iatom[3]);
///////////////////////////////////////////////////////////////////////////////////////
/// new code
Tuple <Atom, Atom, Atom, Atom> key;
{
Atom key0 = iatom[0];
Atom[] key123 = (new Atom[] { iatom[1], iatom[2], iatom[3] }).SortByIDs();
key = new Tuple <Atom, Atom, Atom, Atom>(key0, key123[0], key123[1], key123[2]);
}
///////////////////////////////////////////////////////////////////////////////////////
Improper improper = new Improper(iatom[0], iatom[1], iatom[2], iatom[3]
, Kpsi: imp.Kpsi
, psi0: imp.psi0
, sources: new object[] { imp }
);
if (limpropers.ContainsKey(key) == false)
{
limpropers.Add(key, improper);
}
else
{
HDebug.Assert(limpropers[key].Kpsi == improper.Kpsi
, limpropers[key].psi0 == improper.psi0
);
}
}
}
}
}
}
foreach (var improper in limpropers.Values)
{
HDebug.Assert(improper.atoms.Length == 4);
//HDebug.Assert(improper.atoms[0].ID < improper.atoms[3].ID);
impropers.Add(improper);
improper.atoms[0].Impropers.Add(improper);
improper.atoms[1].Impropers.Add(improper);
improper.atoms[2].Impropers.Add(improper);
improper.atoms[3].Impropers.Add(improper);
}
}
// 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("xyz", xyz);
univ.refs.Add("prm", prm);
univ.refs.Add("pdb", pdb);
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());
if (HDebug.False)
{
List <Tuple <double, string, Bond> > lbnds = new List <Tuple <double, string, Bond> >();
foreach (Bond bnd in bonds)
{
lbnds.Add(new Tuple <double, string, Bond>(bnd.Kb
, bnd.atoms[0].AtomType + "-" + bnd.atoms[1].AtomType
, bnd));
}
lbnds = lbnds.HSelectByIndex(lbnds.HListItem1().HIdxSorted().Reverse().ToArray()).ToList();
double avgKb = lbnds.HListItem1().Average();
List <Tuple <double, string, Angle> > langs = new List <Tuple <double, string, Angle> >();
List <Tuple <double, string, Angle> > langubs = new List <Tuple <double, string, Angle> >();
foreach (Angle ang in angles)
{
langs.Add(new Tuple <double, string, Angle>(ang.Ktheta
, ang.atoms[0].AtomType + "-" + ang.atoms[1].AtomType + "-" + ang.atoms[2].AtomType
, ang));
if (ang.Kub != 0)
{
langubs.Add(new Tuple <double, string, Angle>(ang.Kub
, ang.atoms[0].AtomType + "-" + ang.atoms[1].AtomType + "-" + ang.atoms[2].AtomType
, ang));
}
}
langs = langs.HSelectByIndex(langs.HListItem1().HIdxSorted().Reverse().ToArray()).ToList();
langubs = langubs.HSelectByIndex(langubs.HListItem1().HIdxSorted().Reverse().ToArray()).ToList();
double avgKtheta = langs.HListItem1().Average();
double avgKub = langubs.HListItem1().Average();
List <Tuple <double, string, Improper> > limps = new List <Tuple <double, string, Improper> >();
foreach (Improper imp in impropers)
{
limps.Add(new Tuple <double, string, Improper>(imp.Kpsi
, imp.atoms[0].AtomType + "-" + imp.atoms[1].AtomType + "-" + imp.atoms[2].AtomType + "-" + imp.atoms[3].AtomType
, imp));
}
limps = limps.HSelectByIndex(limps.HListItem1().HIdxSorted().Reverse().ToArray()).ToList();
double avgKpsi = limps.HListItem1().Average();
List <Tuple <double, string, Dihedral> > ldihs = new List <Tuple <double, string, Dihedral> >();
foreach (Dihedral dih in dihedrals)
{
ldihs.Add(new Tuple <double, string, Dihedral>(dih.Kchi
, dih.atoms[0].AtomType + "-" + dih.atoms[1].AtomType + "-" + dih.atoms[2].AtomType + "-" + dih.atoms[3].AtomType
, dih));
}
ldihs = ldihs.HSelectByIndex(ldihs.HListItem1().HIdxSorted().Reverse().ToArray()).ToList();
double avgKchi = ldihs.HListItem1().Average();
}
return(univ);
}
public static HessInfoCoarseResiIter GetHessCoarseResiIter
(Hess.HessInfo hessinfo
, Vector[] coords
, FuncGetIdxKeepListRemv GetIdxKeepListRemv
, ILinAlg ila
, double thres_zeroblk = 0.001
, IterOption iteropt = IterOption.Matlab_experimental
, string[] options = null
)
{
bool rediag = true;
HessMatrix H = null;
List <int>[] lstNewIdxRemv = null;
int numca = 0;
double[] reMass = null;
object[] reAtoms = null;
Vector[] reCoords = null;
Tuple <int[], int[][]> idxKeepRemv = null;
//System.Console.WriteLine("begin re-indexing hess");
{
object[] atoms = hessinfo.atoms;
idxKeepRemv = GetIdxKeepListRemv(atoms, coords);
int[] idxKeep = idxKeepRemv.Item1;
int[][] idxsRemv = idxKeepRemv.Item2;
{
List <int> check = new List <int>();
check.AddRange(idxKeep);
foreach (int[] idxRemv in idxsRemv)
{
check.AddRange(idxRemv);
}
check = check.HToHashSet().ToList();
if (check.Count != coords.Length)
{
throw new Exception("the re-index contains the duplicated atoms or the missing atoms");
}
}
List <int> idxs = new List <int>();
idxs.AddRange(idxKeep);
foreach (int[] idxRemv in idxsRemv)
{
idxs.AddRange(idxRemv);
}
HDebug.Assert(idxs.Count == idxs.HToHashSet().Count);
H = hessinfo.hess.ReshapeByAtom(idxs);
numca = idxKeep.Length;
reMass = hessinfo.mass.ToArray().HSelectByIndex(idxs);
reAtoms = hessinfo.atoms.ToArray().HSelectByIndex(idxs);
reCoords = coords.HSelectByIndex(idxs);
int nidx = idxKeep.Length;
lstNewIdxRemv = new List <int> [idxsRemv.Length];
for (int i = 0; i < idxsRemv.Length; i++)
{
lstNewIdxRemv[i] = new List <int>();
foreach (var idx in idxsRemv[i])
{
lstNewIdxRemv[i].Add(nidx);
nidx++;
}
}
HDebug.Assert(nidx == lstNewIdxRemv.Last().Last() + 1);
HDebug.Assert(nidx == idxs.Count);
}
GC.Collect(0);
HDebug.Assert(numca == H.ColBlockSize - lstNewIdxRemv.HListCount().Sum());
//if(bool.Parse("false"))
{
if (bool.Parse("false"))
#region
{
int[] idxKeep = idxKeepRemv.Item1;
int[][] idxsRemv = idxKeepRemv.Item2;
Pdb.Atom[] pdbatoms = hessinfo.atomsAsUniverseAtom.ListPdbAtoms();
Pdb.ToFile(@"C:\temp\coarse-keeps.pdb", pdbatoms.HSelectByIndex(idxKeep), false);
if (HFile.Exists(@"C:\temp\coarse-graining.pdb"))
{
HFile.Delete(@"C:\temp\coarse-graining.pdb");
}
foreach (int[] idxremv in idxsRemv.Reverse())
{
List <Pdb.Element> delatoms = new List <Pdb.Element>();
foreach (int idx in idxremv)
{
if (pdbatoms[idx] == null)
{
continue;
}
string line = pdbatoms[idx].GetUpdatedLine(coords[idx]);
Pdb.Atom delatom = Pdb.Atom.FromString(line);
delatoms.Add(delatom);
}
Pdb.ToFile(@"C:\temp\coarse-graining.pdb", delatoms.ToArray(), true);
}
}
#endregion
if (bool.Parse("false"))
#region
{
// export matrix to matlab, so the matrix can be checked in there.
int[] idxca = HEnum.HEnumCount(numca).ToArray();
int[] idxoth = HEnum.HEnumFromTo(numca, coords.Length - 1).ToArray();
Matlab.Register(@"C:\temp\");
Matlab.PutSparseMatrix("H", H.GetMatrixSparse(), 3, 3);
Matlab.Execute("figure; spy(H)");
Matlab.Clear();
}
#endregion
if (bool.Parse("false"))
#region
{
HDirectory.CreateDirectory(@"K:\temp\$coarse-graining\");
{ // export original hessian matrix
List <int> cs = new List <int>();
List <int> rs = new List <int>();
foreach (ValueTuple <int, int, MatrixByArr> bc_br_bval in hessinfo.hess.EnumBlocks())
{
cs.Add(bc_br_bval.Item1);
rs.Add(bc_br_bval.Item2);
}
Matlab.Clear();
Matlab.PutVector("cs", cs.ToArray());
Matlab.PutVector("rs", rs.ToArray());
Matlab.Execute("hess = sparse(cs+1, rs+1, ones(size(cs)));");
Matlab.Execute("hess = float(hess);");
Matlab.Execute("figure; spy(hess)");
Matlab.Execute("cs = int32(cs+1);");
Matlab.Execute("rs = int32(rs+1);");
Matlab.Execute(@"save('K:\temp\$coarse-graining\hess-original.mat', 'cs', 'rs', '-v6');");
Matlab.Clear();
}
{ // export reshuffled hessian matrix
List <int> cs = new List <int>();
List <int> rs = new List <int>();
foreach (ValueTuple <int, int, MatrixByArr> bc_br_bval in H.EnumBlocks())
{
cs.Add(bc_br_bval.Item1);
rs.Add(bc_br_bval.Item2);
}
Matlab.Clear();
Matlab.PutVector("cs", cs.ToArray());
Matlab.PutVector("rs", rs.ToArray());
Matlab.Execute("H = sparse(cs+1, rs+1, ones(size(cs)));");
Matlab.Execute("H = float(H);");
Matlab.Execute("figure; spy(H)");
Matlab.Execute("cs = int32(cs+1);");
Matlab.Execute("rs = int32(rs+1);");
Matlab.Execute(@"save('K:\temp\$coarse-graining\hess-reshuffled.mat', 'cs', 'rs', '-v6');");
Matlab.Clear();
}
}
#endregion
if (bool.Parse("false"))
#region
{
int[] idxca = HEnum.HEnumCount(numca).ToArray();
int[] idxoth = HEnum.HEnumFromTo(numca, coords.Length - 1).ToArray();
HessMatrix A = H.SubMatrixByAtoms(false, idxca, idxca);
HessMatrix B = H.SubMatrixByAtoms(false, idxca, idxoth);
HessMatrix C = H.SubMatrixByAtoms(false, idxoth, idxca);
HessMatrix D = H.SubMatrixByAtoms(false, idxoth, idxoth);
Matlab.Clear();
Matlab.PutSparseMatrix("A", A.GetMatrixSparse(), 3, 3);
Matlab.PutSparseMatrix("B", B.GetMatrixSparse(), 3, 3);
Matlab.PutSparseMatrix("C", C.GetMatrixSparse(), 3, 3);
Matlab.PutSparseMatrix("D", D.GetMatrixSparse(), 3, 3);
Matlab.Clear();
}
#endregion
}
List <HessCoarseResiIterInfo> iterinfos = null;
{
object[] atoms = reAtoms; // reAtoms.HToType(null as Universe.Atom[]);
CGetHessCoarseResiIterImpl info = null;
switch (iteropt)
{
case IterOption.ILinAlg_20150329: info = GetHessCoarseResiIterImpl_ILinAlg_20150329(H, lstNewIdxRemv, thres_zeroblk, ila, false); break;
case IterOption.ILinAlg: info = GetHessCoarseResiIterImpl_ILinAlg(H, lstNewIdxRemv, thres_zeroblk, ila, false); break;
case IterOption.Matlab: info = GetHessCoarseResiIterImpl_Matlab(atoms, H, lstNewIdxRemv, thres_zeroblk, ila, false, options); break;
case IterOption.Matlab_experimental: info = GetHessCoarseResiIterImpl_Matlab_experimental(atoms, H, lstNewIdxRemv, thres_zeroblk, ila, false, options); break;
case IterOption.Matlab_IterLowerTri: info = GetHessCoarseResiIterImpl_Matlab_IterLowerTri(atoms, H, lstNewIdxRemv, thres_zeroblk, ila, false, options); break;
case IterOption.LinAlg_IterLowerTri: info = GetHessCoarseResiIterImpl_LinAlg_IterLowerTri.Do(atoms, H, lstNewIdxRemv, thres_zeroblk, ila, false, options); break;
}
;
H = info.H;
iterinfos = info.iterinfos;
}
//{
// var info = GetHessCoarseResiIterImpl_Matlab(H, lstNewIdxRemv, thres_zeroblk);
// H = info.H;
//}
GC.Collect(0);
if (HDebug.IsDebuggerAttached)
{
int nidx = 0;
int[] ikeep = idxKeepRemv.Item1;
foreach (int idx in ikeep)
{
bool equal = object.ReferenceEquals(hessinfo.atoms[idx], reAtoms[nidx]);
if (equal == false)
{
HDebug.Assert(false);
}
HDebug.Assert(equal);
nidx++;
}
}
if (rediag)
{
H = H.CorrectHessDiag();
}
//System.Console.WriteLine("finish fixing diag");
return(new HessInfoCoarseResiIter
{
hess = H,
mass = reMass.HSelectCount(numca),
atoms = reAtoms.HSelectCount(numca),
coords = reCoords.HSelectCount(numca),
numZeroEigval = 6,
iterinfos = iterinfos,
});
}
public List <Tuple <int, int> > GetIndex(Pdb pdb, char selAltLoc = 'A', bool includeHydrogen = true)
{
List <Tuple <int, int> > idxs = new List <Tuple <int, int> >();
// (idx in univ.atoms, idx in pdb)
List <int> lidxs = new List <int>();
for (int i = 0; i < atoms.Count; i++)
{
Atom atm0 = atoms[i];
if (includeHydrogen == false && atm0.IsHydrogen())
{
continue;
}
lidxs.Clear();
for (int j = 0; j < pdb.atoms.Length; j++)
{
Pdb.Atom atm1 = pdb.atoms[j];
if (atm0.AtomName != atm1.name)
{
continue;
}
if (atm0.ResiduePdbId != atm1.resSeq)
{
continue;
}
lidxs.Add(j);
}
if (lidxs.Count == 1)
{
int j = lidxs.First();
Pdb.Atom atm1 = pdb.atoms[j];
HDebug.Assert(atm1.altLoc == ' ' || atm1.altLoc == 'A');
idxs.Add(new Tuple <int, int>(i, j));
}
else if (lidxs.Count >= 2)
{
// get index of the matching altLoc
int sel = -1;
foreach (int lidx in lidxs)
{
if (pdb.atoms[lidx].altLoc == selAltLoc)
{
sel = lidx;
}
else if (pdb.atoms[lidx].altLoc == '1' && selAltLoc == 'A')
{
sel = lidx;
}
else if (pdb.atoms[lidx].altLoc == '2' && selAltLoc == 'B')
{
sel = lidx;
}
else if (pdb.atoms[lidx].altLoc == '3' && selAltLoc == 'C')
{
sel = lidx;
}
}
// put it into idxs
HDebug.Assert(sel != -1);
int j = sel;
Pdb.Atom atm1 = pdb.atoms[j];
HDebug.Assert(atm1.altLoc == selAltLoc);
idxs.Add(new Tuple <int, int>(i, j));
}
}
return(idxs);
}
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);
}
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 CPsfgenExt PsfgenExt
(IList <Tuple <string, string, Pdb.IAtom[]> > lstSegFileAtoms
, string[] toplines
, string[] parlines
, Pdb alignto
, string[] psfgen_lines
, IList <string> minimize_conf_lines = null
, HOptions options = null
)
{
if (options == null)
{
options = new HOptions((string)null);
}
string tempbase = @"C:\temp\";
string psfgen_workdir = null;
string topname = "prot.top";
string parname = "prot.par";
List <string> psf_lines = null;
List <string> pdb_lines = null;
using (var temp = new HTempDirectory(tempbase, null))
{
temp.EnterTemp();
HFile.WriteAllLines(topname, toplines);
HFile.WriteAllLines(parname, parlines);
if ((HFile.Exists("prot.pdb") == false) || (HFile.Exists("prot.psf") == false))
{
var psfgen = Namd.RunPsfgen
(lstSegFileAtoms, tempbase, null, "2.10"
, new string[] { topname }
, new string[] {}
, topname
, psfgen_lines: psfgen_lines
, psfgen_workdir: psfgen_workdir
, options: options
);
psf_lines = psfgen.psf_lines;
pdb_lines = psfgen.pdb_lines;
if (alignto != null)
{
HDebug.Exception("check!!!");
////////////////////////////
Pdb prot = Pdb.FromLines(pdb_lines);
prot = PsfgenExt_AlignTo(prot, alignto);
pdb_lines = prot.ToLines().ToList();
}
HFile.WriteAllLines("prot.pdb", pdb_lines);
HFile.WriteAllLines("prot.psf", psf_lines);
}
if (options.Contains("nomin") == false)
{
if ((HFile.Exists("protmin.coor") == false) || (HFile.Exists("protmin.pdb") == false))
{
List <string> psfgen_pdb_lines = System.IO.File.ReadLines("prot.pdb").ToList();
List <string> psfgen_psf_lines = System.IO.File.ReadLines("prot.psf").ToList();
List <string> prm_lines = System.IO.File.ReadLines(parname).ToList();
string Namd2_opt = null;
if (options.HSelectStartsWith("minimize option:").Length >= 1)
{
Namd2_opt = options.HSelectStartsWith("minimize option:").First().Replace("minimize option:", "");
}
var minpdb = Namd.Run.Namd2
(psfgen_pdb_lines
, psfgen_psf_lines
, prm_lines
, tempbase
, "2.10"
, ((Namd2_opt == null) ? "+p3" : Namd2_opt)
, conf_lines: minimize_conf_lines
);
HFile.WriteAllLines("protmin.coor", minpdb.coor_lines);
Pdb prot0 = Pdb.FromLines(psfgen_pdb_lines);
Pdb prot1 = Pdb.FromLines(minpdb.coor_lines);
HDebug.Exception(prot0.atoms.Length == prot1.atoms.Length);
HDebug.Exception(prot0.elements.Length == prot1.elements.Length);
// update conformation to minimized conformation
for (int i = 0; i < prot0.elements.Length; i++)
{
if (prot0.elements[i].GetType() != prot1.elements[i].GetType())
{
throw new HException("prot0.elements[i].GetType() != prot1.elements[i].GetType()");
}
if ((prot0.elements[i] is Pdb.IAtom) == false)
{
continue;
}
Pdb.IAtom iatom0 = prot0.elements[i] as Pdb.IAtom;
Pdb.IAtom iatom1 = prot1.elements[i] as Pdb.IAtom;
Vector coord0 = iatom0.coord;
Vector coord1 = iatom1.coord;
double dist = (coord0 - coord1).Dist;
if (iatom0.occupancy != 0)
{
if (dist != 0)
{
throw new HException("iatom0.coord - iatom1.coord != 0");
}
}
if (dist != 0)
{
if (iatom0 is Pdb.Atom)
{
string nline0 = (iatom0 as Pdb.Atom).GetUpdatedLine(coord1);
Pdb.Atom natom0 = Pdb.Atom.FromString(nline0);
prot0.elements[i] = natom0;
continue;
}
if (iatom0 is Pdb.Hetatm)
{
string nline0 = (iatom0 as Pdb.Hetatm).GetUpdatedLine(coord1);
Pdb.Hetatm natom0 = Pdb.Hetatm.FromString(nline0);
prot0.elements[i] = natom0;
continue;
}
}
}
if ((prot0.elements[0] is Pdb.Remark) && (prot1.elements[0] is Pdb.Remark))
{
prot0.elements[0] = Pdb.Remark.FromString(prot1.elements[0].line);
}
prot0.ToFile("protmin.pdb");
pdb_lines = System.IO.File.ReadLines("protmin.pdb").ToList();
}
}
//{
// Pdb confpdb = GetConfPdb(options);
// var psf = Namd.Psf.FromFile("prot.psf");
// var prm = Namd.Prm.FromFile(parname);
// List<string> log = new List<string>();
// Universe univ = Universe.BuilderNamd.Build(psf, prm, confpdb, true, new TextLogger(log));
// return univ;
//}
temp.QuitTemp();
}
return(new CPsfgenExt
{
psflines = psf_lines,
pdblines = pdb_lines,
});
}