public static List <Pdb.Element> UpdateElement(this List <Pdb.Element> elements)
{
elements = elements.HClone();
int?iatom_lastserial = 0;
for (int i = 0; i < elements.Count; i++)
{
elements[i] = elements[i].UpdateElement();
if (elements[i] is Pdb.IAtom)
{
Pdb.IAtom iatom = elements[i] as Pdb.IAtom;
bool hexserial = false;
if (iatom_lastserial >= 99999)
{
if (iatom.Serial(true) >= 99999)
{
hexserial = true;
}
}
iatom.hexserial = hexserial;
iatom_lastserial = iatom.Serial();
}
}
return(elements);
}
public static PdbStatic.ResInfo GetResInfo(this Pdb.IAtom atom)
{
return(new PdbStatic.ResInfo
{
resName = atom.resName,
chainID = atom.chainID,
resSeq = atom.resSeq,
iCode = atom.iCode,
});
}
public static IEnumerable <IList <Pdb.IAtom> > SoakMoleculeISolventBox(IList <Pdb.IAtom> mole, IList <IList <Pdb.IAtom> > solv_atoms, Namd.Prm prm)
{
yield return(mole);
KDTree.KDTree <Pdb.IAtom> kdtree_mole = new KDTree.KDTree <Pdb.IAtom>(3);
foreach (var atom in mole)
{
kdtree_mole.insert(atom.coord, atom);
}
//List<Pdb.IAtom> socked = new List<Pdb.IAtom>();
//socked.AddRange(mole);
Dictionary <string, double> elem_radius = new Dictionary <string, double>
{
#region {"C", 1.90}, ...
// public static NbndInfo[] nbndinfo_set_SSTeMcs6c = new NbndInfo[]
// {
{ "C", 1.90 }, // new NbndInfo{ nbndtype=NbndType.nbnd , atomelem="C", rmin2=1.90, charge=0.0, epsilon=-0.1},
{ "H", 1.20 }, // new NbndInfo{ nbndtype=NbndType.nbnd , atomelem="H", rmin2=1.20, charge=0.0, epsilon=-0.1},
{ "O", 1.70 }, // new NbndInfo{ nbndtype=NbndType.nbnd , atomelem="O", rmin2=1.70, charge=0.0, epsilon=-0.1},
{ "N", 1.85 }, // new NbndInfo{ nbndtype=NbndType.nbnd , atomelem="N", rmin2=1.85, charge=0.0, epsilon=-0.1},
{ "S", 2.00 }, // new NbndInfo{ nbndtype=NbndType.nbnd , atomelem="S", rmin2=2.00, charge=0.0, epsilon=-0.1},
{ "F", 1.47 }, // new NbndInfo{ nbndtype=NbndType.nbnd , atomelem="F", rmin2=1.47, charge=0.0, epsilon=-0.1}, /// same to unif0
{ "P", 1.80 }, // new NbndInfo{ nbndtype=NbndType.nbnd , atomelem="P", rmin2=1.80, charge=0.0, epsilon=-0.1}, /// same to unif0
// new NbndInfo{ nbndtype=NbndType.nbnd14, atomelem="C", rmin2=1.90, charge=0.0, epsilon=-0.1},
// new NbndInfo{ nbndtype=NbndType.nbnd14, atomelem="H", rmin2=1.20, charge=0.0, epsilon=-0.1},
// new NbndInfo{ nbndtype=NbndType.nbnd14, atomelem="O", rmin2=1.40, charge=0.0, epsilon=-0.1}, /// special treatment: 1.70 -> 1.40
// new NbndInfo{ nbndtype=NbndType.nbnd14, atomelem="N", rmin2=1.55, charge=0.0, epsilon=-0.1}, /// special treatment: 1.85 -> 1.55
// new NbndInfo{ nbndtype=NbndType.nbnd14, atomelem="S", rmin2=2.00, charge=0.0, epsilon=-0.1},
// new NbndInfo{ nbndtype=NbndType.nbnd14, atomelem="F", rmin2=1.47, charge=0.0, epsilon=-0.1}, /// same to unif0
// new NbndInfo{ nbndtype=NbndType.nbnd14, atomelem="P", rmin2=1.80, charge=0.0, epsilon=-0.1}, /// same to unif0
// ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
// //new NbndInfo{ nbndtype=NbndType.nbnd, atomelem="", rmin2=0.00, charge=0.0, epsilon=-0.1},
// // http://en.wikipedia.org/wiki/Van_der_Waals_radius
{ "CL", 1.75 }, // new NbndInfo{ nbndtype=NbndType.nbnd, atomelem="CL", rmin2=1.75, charge=0.0, epsilon=-0.1},
{ "CU", 1.40 }, // new NbndInfo{ nbndtype=NbndType.nbnd, atomelem="CU", rmin2=1.40, charge=0.0, epsilon=-0.1},
// // http://en.wikipedia.org/wiki/Atomic_radii_of_the_elements_(data_page)
{ "MG", 1.73 }, // new NbndInfo{ nbndtype=NbndType.nbnd, atomelem="MG", rmin2=1.73, charge=0.0, epsilon=-0.1}, // magnesium
{ "K", 2.75 }, // new NbndInfo{ nbndtype=NbndType.nbnd, atomelem="K" , rmin2=2.75, charge=0.0, epsilon=-0.1}, // potassium
{ "POT", 2.75 }, // new NbndInfo{ nbndtype=NbndType.nbnd, atomelem="POT",rmin2=2.75, charge=0.0, epsilon=-0.1}, // potassium
// ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
// // par_all27_prot_na.prm
// // FE 0.010000 0.000000 0.650000 ! ALLOW HEM
// new NbndInfo{ nbndtype=NbndType.nbnd , atomelem="FE" ,rmin2=0.65, charge=0.0, epsilon=-0.1},
// new NbndInfo{ nbndtype=NbndType.nbnd14, atomelem="FE" ,rmin2=0.65, charge=0.0, epsilon=-0.1},
// };
#endregion
};
bool noclash_with_mole = false;
foreach (var atoms in solv_atoms)
{
List <Pdb.IAtom> noclash_atoms = new List <Pdb.IAtom>();
foreach (var atom in atoms)
{
Vector atom_coord = atom.coord;
double atom_rmin = elem_radius[atom.element.Trim()];
Pdb.IAtom near = kdtree_mole.nearest(atom_coord);
double near_rmin = elem_radius[near.element.Trim()];
double dist = (atom_coord - near.coord).Dist;
if (atom.name == "OH2 ")
{
if ((atom_rmin + near_rmin) < dist)
{
noclash_with_mole = true;
}
else
{
noclash_with_mole = false;
}
}
if (noclash_with_mole)
{
noclash_atoms.Add(atom);
//yield return atom;
//socked.Add(atom);
}
}
if (noclash_atoms.Count != 0)
{
yield return(noclash_atoms);
}
}
}
public static double[] GetCoord(this Pdb.IAtom iatom)
{
return(new double[] { iatom.x, iatom.y, iatom.z });
}
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,
});
}
