Ejemplo n.º 1
0
            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);
            }
Ejemplo n.º 2
0
            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;
            }
Ejemplo n.º 3
0
            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));
            }