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 Universe Build(Pdb pdb, Gromacs.Top top, ITextLogger logger)
{
Universe univ = new Universe();
// atoms
List <Top.Atom> top_atoms = top.elements.SelectSourceExtTop().ListAtom().SelectMatchToPdb(pdb.atoms);
List <Top.Bond> top_bonds = top.elements.SelectSourceExtTop().ListType <Top.Bond>();
List <Top.Pair> top_pairs = top.elements.SelectSourceExtTop().ListType <Top.Pair>(); ///Debug.ToDo("handle pairtype <= nbnd 1-4");
List <Top.Angle> top_angles = top.elements.SelectSourceExtTop().ListType <Top.Angle>();
List <Top.Dihedral> top_dihedral = top.elements.SelectSourceExtTop().ListType <Top.Dihedral>();
List <Top.Atomtypes> top_atomtypes = top.elements.ListAtomtypes();
List <Top.Bondtypes> top_bondtypes = top.elements.ListType <Top.Bondtypes>();
List <Top.Angletypes> top_angletypes = top.elements.ListType <Top.Angletypes>();
List <Top.Dihedraltypes> top_dihedraltypes = top.elements.ListType <Top.Dihedraltypes>();
List <Top.Pairtypes> top_pairtypes = top.elements.ListType <Top.Pairtypes>(); ///Debug.ToDo("handle pairtype <= nbnd 1-4");
{
///Debug.ToDo("handle here");
List <Top.LineElement> elems = new List <Top.LineElement>(top.elements);
foreach (var elem in top_atoms)
{
HDebug.Verify(elems.Remove(elem));
}
foreach (var elem in top_bonds)
{
HDebug.Verify(elems.Remove(elem));
}
foreach (var elem in top_pairs)
{
HDebug.Verify(elems.Remove(elem));
}
foreach (var elem in top_angles)
{
HDebug.Verify(elems.Remove(elem));
}
foreach (var elem in top_dihedral)
{
HDebug.Verify(elems.Remove(elem));
}
foreach (var elem in top_atomtypes)
{
HDebug.Verify(elems.Remove(elem));
}
foreach (var elem in top_bondtypes)
{
HDebug.Verify(elems.Remove(elem));
}
foreach (var elem in top_angletypes)
{
HDebug.Verify(elems.Remove(elem));
}
foreach (var elem in top_dihedraltypes)
{
HDebug.Verify(elems.Remove(elem));
}
foreach (var elem in top_pairtypes)
{
HDebug.Verify(elems.Remove(elem));
}
List <Top.LineElement> srcitp = new List <Top.LineElement>();
List <Top.LineElement> srctop = new List <Top.LineElement>();
for (int i = 0; i < elems.Count; i++)
{
if ((elems[i].source as string).EndsWith(".itp"))
{
srcitp.Add(elems[i]); elems[i] = null; continue;
}
if ((elems[i].source as string).EndsWith(".top"))
{
srctop.Add(elems[i]); elems[i] = null; continue;
}
}
elems = elems.HRemoveAllNull().ToList();
HDebug.Assert(elems.Count == 0);
}
Atoms atoms = new Atoms(univ);
HDebug.Assert(pdb.atoms.Length == top_atoms.Count);
for (int i = 0; i < top_atoms.Count; i++)
{
//Debug.Assert(psf.atoms[i].AtomId == pdb.atoms[i].serial);
//string type0 = psf.atoms[i].AtomType;
//Atom atom = new Atom(psf.atoms[i], prm.FindNonbonded(type0, logger), pdb.atoms[i]);
//atom.Coord = pdb.atoms[i].coord;
//atoms.Add(atom);
Gromacs.Top.Atom atom = top_atoms[i];
HDebug.Assert(i + 1 == atom.cgnr);
HDebug.Assert(atom.cgnr == pdb.atoms[i].serial);
//Gromacs.Top.Atomtypes atomtype = top_atomtypes[atom.type];
List <Gromacs.Top.Atomtypes> atomtypes = FindTypes(top_atomtypes, atom.type);
HDebug.Assert(atomtypes.Count == 1);
Gromacs.Top.Atomtypes atomtype = atomtypes.Last();
//Debug.Assert(atom.charge == atomtype.charge);
//Debug.Assert(atom.mass == atomtype.mass );
Atom uatom = new Atom(atom.cgnr, atom.atom, atom.type, pdb.atoms[i].element.Trim()
, atom.resnr, atom.residu
, atom.charge, atom.mass
, atomtype.epsilon, atomtype.sigma
, double.NaN, double.NaN
, atom, atomtype
);
uatom.Coord = pdb.atoms[i].coord;
atoms.Add(uatom);
}
// bonds
Bonds bonds = new Bonds();
for (int i = 0; i < top_bonds.Count; i++)
{
int idx0 = top_bonds[i].ai - 1; Atom atom0 = atoms[idx0]; string type0 = atom0.AtomType;
int idx1 = top_bonds[i].aj - 1; Atom atom1 = atoms[idx1]; string type1 = atom1.AtomType;
List <Gromacs.Top.Bondtypes> bondtypes = FindTypes(top_bondtypes, type0, type1);
//Debug.Assert(bondtypes.Count == 1);
Gromacs.Top.Bondtypes bondtype = bondtypes.Last();
//Gromacs.Top.Bondtypes bondtype = top_bondtypes[Gromacs.Top.Bondtypes.GetStringKey(type0,type1)];
Bond bond = new Bond(atom0, atom1, bondtype.kb, bondtype.b0, bondtype);
bonds.Add(bond);
atom0.Bonds.Add(bond); atom0.Inter123.Add(atom1); atom0.Inter12.Add(atom1);
atom1.Bonds.Add(bond); atom1.Inter123.Add(atom0); atom1.Inter12.Add(atom0);
}
// angles
Angles angles = new Angles();
for (int i = 0; i < top_angles.Count; i++)
{
int idx0 = top_angles[i].ai - 1; Atom atom0 = atoms[idx0]; string type0 = atom0.AtomType;
int idx1 = top_angles[i].aj - 1; Atom atom1 = atoms[idx1]; string type1 = atom1.AtomType;
int idx2 = top_angles[i].ak - 1; Atom atom2 = atoms[idx2]; string type2 = atom2.AtomType;
List <Gromacs.Top.Angletypes> angletypes = FindTypes(top_angletypes, type0, type1, type2);
//Debug.Assert(angletypes.Count == 1);
Gromacs.Top.Angletypes angletype = angletypes.Last();
//Gromacs.Top.Angletypes angletype = top_angletypes[Gromacs.Top.Bondtypes.GetStringKey(type0, type1, type2)];
Angle angle = new Angle(atom0, atom1, atom2
, angletype.cth, angletype.th0, angletype.cub, angletype.ub0
, angletype
);
angles.Add(angle);
atom0.Angles.Add(angle); atom0.Inter123.Add(atom1); atom0.Inter123.Add(atom2);
atom1.Angles.Add(angle); atom1.Inter123.Add(atom2); atom1.Inter123.Add(atom0);
atom2.Angles.Add(angle); atom2.Inter123.Add(atom0); atom2.Inter123.Add(atom1);
}
// dihedrals
Dihedrals dihedrals = new Dihedrals();
Impropers impropers = new Impropers();
for (int i = 0; i < top_dihedral.Count; i++)
{
int idx0 = top_dihedral[i].ai - 1; Atom atom0 = atoms[idx0]; string type0 = atom0.AtomType;
int idx1 = top_dihedral[i].aj - 1; Atom atom1 = atoms[idx1]; string type1 = atom1.AtomType;
int idx2 = top_dihedral[i].ak - 1; Atom atom2 = atoms[idx2]; string type2 = atom2.AtomType;
int idx3 = top_dihedral[i].al - 1; Atom atom3 = atoms[idx3]; string type3 = atom3.AtomType;
int funct = top_dihedral[i].funct;
List <Gromacs.Top.Dihedraltypes> dihedraltypes = FindTypes(top_dihedraltypes, type0, type1, type2, type3);
{
List <Gromacs.Top.Dihedraltypes> ldihedraltypes = new List <Top.Dihedraltypes>(dihedraltypes);
// select funct matching to its query
for (int j = 0; j < ldihedraltypes.Count;)
{
if (ldihedraltypes[j].func == funct)
{
j++;
}
else
{
ldihedraltypes.RemoveAt(j);
}
}
// if there are no matching query but improper, select the improper
if ((ldihedraltypes.Count == 0) && (dihedraltypes[0].func == 2))
{
ldihedraltypes.Add(dihedraltypes[0]);
}
dihedraltypes = new List <Top.Dihedraltypes>(ldihedraltypes);
}
//{
// // if dihedral(func==9) and improper(func==2) are mixed
// // select only improper
// bool has_func_2 = false;
// for(int j=0; j<dihedraltypes.Count; j++)
// if(dihedraltypes[j].func == 2)
// has_func_2 = true;
// if(has_func_2)
// {
// for(int j=0; j<dihedraltypes.Count; )
// {
// if(dihedraltypes[j].func == 2)
// j++;
// else
// dihedraltypes.RemoveAt(j);
// }
// }
//}
if (dihedraltypes[0].func == 9)
{
// dihedral
for (int j = 1; j < dihedraltypes.Count; j++)
{
HDebug.Assert(dihedraltypes[0].func == dihedraltypes[j].func);
HDebug.Assert(dihedraltypes[0].i.Trim() == dihedraltypes[j].i.Trim());
HDebug.Assert(dihedraltypes[0].j.Trim() == dihedraltypes[j].j.Trim());
HDebug.Assert(dihedraltypes[0].k.Trim() == dihedraltypes[j].k.Trim());
HDebug.Assert(dihedraltypes[0].l.Trim() == dihedraltypes[j].l.Trim());
}
Gromacs.Top.Dihedraltypes dihedraltype = dihedraltypes.Last();
Dihedral dihedral = new Dihedral(atom0, atom1, atom2, atom3
, dihedraltype.cp, dihedraltype.mult, dihedraltype.phi0
, dihedraltype
);
dihedrals.Add(dihedral);
atom0.Dihedrals.Add(dihedral); //atom0.Inter123.Add(atom1); atom0.Inter123.Add(atom2); atom0.Inter123.Add(atom3);
atom1.Dihedrals.Add(dihedral); //atom1.Inter123.Add(atom2); atom1.Inter123.Add(atom3); atom1.Inter123.Add(atom0);
atom2.Dihedrals.Add(dihedral); //atom2.Inter123.Add(atom3); atom2.Inter123.Add(atom0); atom2.Inter123.Add(atom1);
atom3.Dihedrals.Add(dihedral); //atom3.Inter123.Add(atom0); atom3.Inter123.Add(atom1); atom3.Inter123.Add(atom2);
continue;
}
if (dihedraltypes[0].func == 2)
{
// improper
for (int j = 1; j < dihedraltypes.Count; j++)
{
HDebug.Assert(dihedraltypes[0].func == dihedraltypes[j].func);
HDebug.Assert(dihedraltypes[0].i.Trim() == dihedraltypes[j].i.Trim());
HDebug.Assert(dihedraltypes[0].j.Trim() == dihedraltypes[j].j.Trim());
HDebug.Assert(dihedraltypes[0].k.Trim() == dihedraltypes[j].k.Trim());
HDebug.Assert(dihedraltypes[0].l.Trim() == dihedraltypes[j].l.Trim());
}
Gromacs.Top.Dihedraltypes impropertype = dihedraltypes.Last();
Improper improper = new Improper(atom0, atom1, atom2, atom3
, impropertype.cp, impropertype.phi0
, impropertype
);
impropers.Add(improper);
atom0.Impropers.Add(improper); //atom0.Inter123.Add(atom1); atom0.Inter123.Add(atom2); atom0.Inter123.Add(atom3);
atom1.Impropers.Add(improper); //atom1.Inter123.Add(atom2); atom1.Inter123.Add(atom3); atom1.Inter123.Add(atom0);
atom2.Impropers.Add(improper); //atom2.Inter123.Add(atom3); atom2.Inter123.Add(atom0); atom2.Inter123.Add(atom1);
atom3.Impropers.Add(improper); //atom3.Inter123.Add(atom0); atom3.Inter123.Add(atom1); atom3.Inter123.Add(atom2);
continue;
}
HDebug.Assert(false);
//Debug.Assert(dihedraltypes.Count == 1);
//
//for(int j=0; j<dihedraltypes.Count; j++)
// if(dihedraltypes[j].func != 2)
// dihedraltype = dihedraltypes[j];
//Debug.Assert(dihedraltype != null);
//List<Gromacs.Top.Dihedraltypes> dihedraltypes = top_dihedraltypes[Gromacs.Top.Dihedraltypes.GetStringKey(type0, type1, type2, type3)];
}
// 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("top", top);
univ.atoms = atoms;
univ.bonds = bonds;
univ.angles = angles;
univ.dihedrals = dihedrals;
univ.impropers = impropers;
//univ.nonbondeds = nonbondeds ; // do not make this list in advance, because it depends on the atom positions
univ.nonbonded14s = nonbonded14s;
HDebug.Assert(univ.Verify());
return(univ);
}
static Universe BuildUnion(Universe univ1, Universe univ2)
{
Universe univ = new Universe();
Atoms atoms = new Atoms(univ);
//int maxresi = int.MinValue;
//foreach(var atom in univ1.atoms)
//{
// if(atom._ResidueId != null)
// maxresi = Math.Max(maxresi, atom._ResidueId.Value);
// atoms.Add(atom);
//}
//foreach(var atom in univ2.atoms)
//{
// if(atom._ResidueId != null)
// atom._ResidueId = (atom._ResidueId + maxresi + 100);
// atoms.Add(atom);
//}
foreach (var atom in univ1.atoms)
{
atoms.Add(atom);
}
foreach (var atom in univ2.atoms)
{
atoms.Add(atom);
}
Bonds bonds = new Bonds();
foreach (var bond in univ1.bonds)
{
bonds.Add(bond);
Atom atom0 = bond.atoms[0];
Atom atom1 = bond.atoms[1];
HDebug.Assert(atom0.Bonds.Contains(bond)); HDebug.Assert(atom0.Inter123.Contains(atom1)); HDebug.Assert(atom0.Inter12.Contains(atom1));
HDebug.Assert(atom1.Bonds.Contains(bond)); HDebug.Assert(atom1.Inter123.Contains(atom0)); HDebug.Assert(atom1.Inter12.Contains(atom0));
}
foreach (var bond in univ2.bonds)
{
bonds.Add(bond);
Atom atom0 = bond.atoms[0];
Atom atom1 = bond.atoms[1];
HDebug.Assert(atom0.Bonds.Contains(bond)); HDebug.Assert(atom0.Inter123.Contains(atom1)); HDebug.Assert(atom0.Inter12.Contains(atom1));
HDebug.Assert(atom1.Bonds.Contains(bond)); HDebug.Assert(atom1.Inter123.Contains(atom0)); HDebug.Assert(atom1.Inter12.Contains(atom0));
}
Angles angles = new Angles();
foreach (Angle angle in univ1.angles)
{
angles.Add(angle);
Atom atom0 = angle.atoms[0];
Atom atom1 = angle.atoms[1];
Atom atom2 = angle.atoms[2];
HDebug.Assert(atom0.Angles.Contains(angle)); HDebug.Assert(atom0.Inter123.Contains(atom1)); HDebug.Assert(atom0.Inter123.Contains(atom2));
HDebug.Assert(atom1.Angles.Contains(angle)); HDebug.Assert(atom1.Inter123.Contains(atom2)); HDebug.Assert(atom1.Inter123.Contains(atom0));
HDebug.Assert(atom2.Angles.Contains(angle)); HDebug.Assert(atom2.Inter123.Contains(atom0)); HDebug.Assert(atom2.Inter123.Contains(atom1));
}
foreach (Angle angle in univ2.angles)
{
angles.Add(angle);
Atom atom0 = angle.atoms[0];
Atom atom1 = angle.atoms[1];
Atom atom2 = angle.atoms[2];
HDebug.Assert(atom0.Angles.Contains(angle)); HDebug.Assert(atom0.Inter123.Contains(atom1)); HDebug.Assert(atom0.Inter123.Contains(atom2));
HDebug.Assert(atom1.Angles.Contains(angle)); HDebug.Assert(atom1.Inter123.Contains(atom2)); HDebug.Assert(atom1.Inter123.Contains(atom0));
HDebug.Assert(atom2.Angles.Contains(angle)); HDebug.Assert(atom2.Inter123.Contains(atom0)); HDebug.Assert(atom2.Inter123.Contains(atom1));
}
Dihedrals dihedrals = new Dihedrals();
foreach (Dihedral dihedral in univ1.dihedrals)
{
dihedrals.Add(dihedral);
HDebug.Assert(dihedral.atoms[0].Dihedrals.Contains(dihedral));
HDebug.Assert(dihedral.atoms[1].Dihedrals.Contains(dihedral));
HDebug.Assert(dihedral.atoms[2].Dihedrals.Contains(dihedral));
HDebug.Assert(dihedral.atoms[3].Dihedrals.Contains(dihedral));
}
foreach (Dihedral dihedral in univ2.dihedrals)
{
dihedrals.Add(dihedral);
HDebug.Assert(dihedral.atoms[0].Dihedrals.Contains(dihedral));
HDebug.Assert(dihedral.atoms[1].Dihedrals.Contains(dihedral));
HDebug.Assert(dihedral.atoms[2].Dihedrals.Contains(dihedral));
HDebug.Assert(dihedral.atoms[3].Dihedrals.Contains(dihedral));
}
Impropers impropers = new Impropers();
foreach (var improper in univ1.impropers)
{
impropers.Add(improper);
HDebug.Assert(improper.atoms[0].Impropers.Contains(improper));
HDebug.Assert(improper.atoms[1].Impropers.Contains(improper));
HDebug.Assert(improper.atoms[2].Impropers.Contains(improper));
HDebug.Assert(improper.atoms[3].Impropers.Contains(improper));
}
foreach (var improper in univ2.impropers)
{
impropers.Add(improper);
HDebug.Assert(improper.atoms[0].Impropers.Contains(improper));
HDebug.Assert(improper.atoms[1].Impropers.Contains(improper));
HDebug.Assert(improper.atoms[2].Impropers.Contains(improper));
HDebug.Assert(improper.atoms[3].Impropers.Contains(improper));
}
Nonbonded14s nonbonded14s = new Nonbonded14s();
nonbonded14s.Build(atoms);
Pdb pdb;
{
List <Pdb.Element> elements = new List <Pdb.Element>();
elements.AddRange(univ1.pdb.atoms);
elements.AddRange(univ2.pdb.atoms);
pdb = new Pdb(elements);
}
//Universe univ = new Universe();
univ.pdb = pdb;
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;
return(univ);
}
public static Universe Build(Namd.Psf psf, Namd.Prm prm, Pdb pdb, bool?ignore_neg_occupancy, ITextLogger logger)
{
Universe univ = new Universe();
// atoms
Atoms atoms = new Atoms(univ);
Dictionary <int, Atom> id_atom = new Dictionary <int, Atom>();
Pdb.Atom[] pdb_atoms = pdb.atoms;
HDebug.Assert(psf.atoms.Length == pdb_atoms.Length);
for (int i = 0; i < psf.atoms.Length; i++)
{
HDebug.Assert(pdb_atoms[i].try_serial == null || psf.atoms[i].AtomId == pdb_atoms[i].serial); // when num atoms in pdb is too large (>99999), it is marked as *****
string type0 = psf.atoms[i].AtomType;
Atom atom = new Atom(psf.atoms[i], prm.FindNonbonded(type0, logger), pdb_atoms[i]);
atom.Coord = pdb_atoms[i].coord;
{
if (ignore_neg_occupancy == null)
{
if (pdb_atoms[i].occupancy < 0)
{
throw new HException("unhandled negative occupancy during building universe");
}
}
else
{
if (ignore_neg_occupancy.Value && pdb_atoms[i].occupancy < 0)
{
continue;
}
}
}
atoms.Add(atom);
id_atom.Add(psf.atoms[i].AtomId, atom);
}
// bonds
Bonds bonds = new Bonds();
for (int i = 0; i < psf.bonds.GetLength(0); i++)
{
int id0 = psf.bonds[i, 0]; if (id_atom.ContainsKey(id0) == false)
{
continue;
}
Atom atom0 = id_atom[id0]; string type0 = atom0.AtomType;
int id1 = psf.bonds[i, 1]; if (id_atom.ContainsKey(id1) == false)
{
continue;
}
Atom atom1 = id_atom[id1]; string type1 = atom1.AtomType;
Bond bond = new Bond(atom0, atom1, prm.FindBond(type0, type1, logger));
bonds.Add(bond);
atom0.Bonds.Add(bond); atom0.Inter123.Add(atom1); atom0.Inter12.Add(atom1);
atom1.Bonds.Add(bond); atom1.Inter123.Add(atom0); atom1.Inter12.Add(atom0);
}
// angles
Angles angles = new Angles();
for (int i = 0; i < psf.angles.GetLength(0); i++)
{
int id0 = psf.angles[i, 0]; if (id_atom.ContainsKey(id0) == false)
{
continue;
}
Atom atom0 = id_atom[id0]; string type0 = atom0.AtomType;
int id1 = psf.angles[i, 1]; if (id_atom.ContainsKey(id1) == false)
{
continue;
}
Atom atom1 = id_atom[id1]; string type1 = atom1.AtomType;
int id2 = psf.angles[i, 2]; if (id_atom.ContainsKey(id2) == false)
{
continue;
}
Atom atom2 = id_atom[id2]; string type2 = atom2.AtomType;
var prm_angle = prm.FindAngle(type0, type1, type2, logger);
if (prm_angle == null)
{
HDebug.Assert(false);
logger.Log(string.Format
("try to add non-existing angle (({0}, prm {1})-({2}, prm {3})-({4}, prm {5})) in prm"
, atom0, type0, atom1, type1, atom2, type2
));
continue;
}
Angle angle = new Angle(atom0, atom1, atom2, prm_angle);
angles.Add(angle);
atom0.Angles.Add(angle); atom0.Inter123.Add(atom1); atom0.Inter123.Add(atom2);
atom1.Angles.Add(angle); atom1.Inter123.Add(atom2); atom1.Inter123.Add(atom0);
atom2.Angles.Add(angle); atom2.Inter123.Add(atom0); atom2.Inter123.Add(atom1);
}
// dihedrals
Dihedrals dihedrals = new Dihedrals();
for (int i = 0; i < psf.dihedrals.GetLength(0); i++)
{
int id0 = psf.dihedrals[i, 0]; if (id_atom.ContainsKey(id0) == false)
{
continue;
}
Atom atom0 = id_atom[id0]; string type0 = atom0.AtomType;
int id1 = psf.dihedrals[i, 1]; if (id_atom.ContainsKey(id1) == false)
{
continue;
}
Atom atom1 = id_atom[id1]; string type1 = atom1.AtomType;
int id2 = psf.dihedrals[i, 2]; if (id_atom.ContainsKey(id2) == false)
{
continue;
}
Atom atom2 = id_atom[id2]; string type2 = atom2.AtomType;
int id3 = psf.dihedrals[i, 3]; if (id_atom.ContainsKey(id3) == false)
{
continue;
}
Atom atom3 = id_atom[id3]; string type3 = atom3.AtomType;
var prm_dihedrals = prm.FindDihedral(type0, type1, type2, type3, logger);
if (prm_dihedrals.Length == 0)
{
HDebug.Assert(false);
logger.Log(string.Format
("try to add non-existing dihedral (({0}, prm {1})-({2}, prm {3})-({4}, prm {5})-({6}, prm {7})) in prm"
, atom0, type0, atom1, type1, atom2, type2, atom3, type3
));
continue;
}
foreach (var prm_dihedral in prm_dihedrals)
{
Dihedral dihedral;
if (atom0.ID < atom3.ID)
{
dihedral = new Dihedral(atom0, atom1, atom2, atom3, prm_dihedral);
}
else
{
dihedral = new Dihedral(atom3, atom2, atom1, atom0, prm_dihedral);
}
dihedrals.Add(dihedral);
atom0.Dihedrals.Add(dihedral); //atom0.Inter123.Add(atom1); atom0.Inter123.Add(atom2); atom0.Inter123.Add(atom3);
atom1.Dihedrals.Add(dihedral); //atom1.Inter123.Add(atom2); atom1.Inter123.Add(atom3); atom1.Inter123.Add(atom0);
atom2.Dihedrals.Add(dihedral); //atom2.Inter123.Add(atom3); atom2.Inter123.Add(atom0); atom2.Inter123.Add(atom1);
atom3.Dihedrals.Add(dihedral); //atom3.Inter123.Add(atom0); atom3.Inter123.Add(atom1); atom3.Inter123.Add(atom2);
}
}
// impropers
Impropers impropers = new Impropers();
for (int i = 0; i < psf.impropers.GetLength(0); i++)
{
int id0 = psf.impropers[i, 0]; if (id_atom.ContainsKey(id0) == false)
{
continue;
}
Atom atom0 = id_atom[id0]; string type0 = atom0.AtomType;
int id1 = psf.impropers[i, 1]; if (id_atom.ContainsKey(id1) == false)
{
continue;
}
Atom atom1 = id_atom[id1]; string type1 = atom1.AtomType;
int id2 = psf.impropers[i, 2]; if (id_atom.ContainsKey(id2) == false)
{
continue;
}
Atom atom2 = id_atom[id2]; string type2 = atom2.AtomType;
int id3 = psf.impropers[i, 3]; if (id_atom.ContainsKey(id3) == false)
{
continue;
}
Atom atom3 = id_atom[id3]; string type3 = atom3.AtomType;
Improper improper = new Improper(atom0, atom1, atom2, atom3, prm.FindImproper(type0, type1, type2, type3, logger));
impropers.Add(improper);
atom0.Impropers.Add(improper); //atom0.Inter123.Add(atom1); atom0.Inter123.Add(atom2); atom0.Inter123.Add(atom3);
atom1.Impropers.Add(improper); //atom1.Inter123.Add(atom2); atom1.Inter123.Add(atom3); atom1.Inter123.Add(atom0);
atom2.Impropers.Add(improper); //atom2.Inter123.Add(atom3); atom2.Inter123.Add(atom0); atom2.Inter123.Add(atom1);
atom3.Impropers.Add(improper); //atom3.Inter123.Add(atom0); atom3.Inter123.Add(atom1); atom3.Inter123.Add(atom2);
}
// 1-4 interactions
for (int i = 0; i < atoms.Count; i++)
{
HashSet <Atom> Inter14 = new HashSet <Atom>();
BuildInter1toN(atoms[i], 4, Inter14); // find all atoms for 1-4 interaction
Inter14.Remove(atoms[i]); // remove self
foreach (Atom atom in atoms[i].Inter123)
{
Inter14.Remove(atom); // remove all 1-2, 1-3 interactions
}
atoms[i].Inter14 = Inter14;
}
Nonbonded14s nonbonded14s = new Nonbonded14s();
nonbonded14s.Build(atoms);
//// nonbondeds
//// do not make this list in advance, because it depends on the atom positions
//Nonbondeds nonbondeds = new Nonbondeds();
//nonbondeds.Build(atoms);
//Universe univ = new Universe();
univ.pdb = pdb;
univ.refs.Add("psf", psf);
univ.refs.Add("prm", prm);
univ.atoms = atoms;
univ.bonds = bonds;
univ.angles = angles;
univ.dihedrals = dihedrals;
univ.impropers = impropers;
//univ.nonbondeds = nonbondeds ; // do not make this list in advance, because it depends on the atom positions
univ.nonbonded14s = nonbonded14s;
HDebug.Assert(univ.Verify());
return(univ);
}
