public static Universe Build(Pdb pdb, Gromacs.Top top)
{
return(BuilderGromacs.Build(pdb, top, new TextLogger()));
}
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);
}
public static Universe Build(Pdb pdb, Gromacs.Top top, ITextLogger logger)
{
return(BuilderGromacs.Build(pdb, top, logger));
}