public static List <Top.Atom> SelectMatchToPdb(this IList <Top.Atom> atoms, IList <Pdb.Atom> pdbatoms)
{
Dictionary <int, Pdb.Atom> dict = new Dictionary <int, Pdb.Atom>(pdbatoms.Count);
foreach (Pdb.Atom pdbatom in pdbatoms)
{
dict.Add(pdbatom.serial, pdbatom);
}
List <Top.Atom> select = new List <Top.Atom>();
foreach (Top.Atom atom in atoms)
{
if (dict.ContainsKey(atom.cgnr))
{
Pdb.Atom pdbatom = dict[atom.cgnr];
if ((atom.residu == pdbatom.resName) && (atom.resnr == pdbatom.resSeq))
{
HDebug.AssertOr(atom.atom.Trim() == pdbatom.name.Trim()
, atom.atom.Trim() == (pdbatom.name.Substring(1) + pdbatom.name[0]).Trim() // (top) HG21 <=> 1HG2 (pdb)
);
select.Add(atom);
}
}
}
HDebug.Assert(pdbatoms.Count == select.Count);
return(select);
}
public TextLogger(object writter)
{
HDebug.AssertOr
(writter == null
, writter is TextWriter
, writter is StringBuilder
, writter is List <string>
);
this.writter = writter;
}
public static MixHessInfo GetHessMixEAnm(Universe univ, IList <Vector> coords, ILinAlg la, IList <ResInfo> lstResAllAtom
, bool bAllowAllToCoarse, bool bOnlyCoarseConnBackbone
, Tuple <double, double> anmSprcstCutoffAll // all-all
, Tuple <double, double> anmSprcstCutoffMix // all/buffer-coarse
, Tuple <double, double> anmSprcstCutoffCoarse // coarse-coarse
, out string errmsg
, bool bGetIntmInfo, string strBkbnReso
)
{
double anmSprcstAll = anmSprcstCutoffAll.Item1;
double anmSprcstMix = anmSprcstCutoffMix.Item1;
double anmSprcstCoarse = anmSprcstCutoffCoarse.Item1;
double anmCutoffAll = anmSprcstCutoffAll.Item2;
double anmCutoffMix = anmSprcstCutoffMix.Item2;
double anmCutoffCoarse = anmSprcstCutoffCoarse.Item2;
HDebug.Assert(anmCutoffAll >= 0);
HDebug.Assert(anmCutoffCoarse >= 0);
MixModel.FnGetHess GetHess = delegate(Universe luniv, IList <Vector> lcoords, int[] idxAll, int[] idxBuffer, int[] idxCoarse, int[] idxBackbone)
{
int size = coords.Count;
HashSet <int> setIdxAll = idxAll.HToHashSet();
HashSet <int> setIdxBuffer = idxBuffer.HToHashSet();
HashSet <int> setIdxCoarse = idxCoarse.HToHashSet();
HashSet <int> setIdxBackbone = idxBackbone.HToHashSet();
Matrix anmKij = Matrix.Zeros(size, size);
for (int c = 0; c < size; c++)
{
if (lcoords[c] == null)
{
continue;
}
int typec = 0;
if (setIdxAll.Contains(c))
{
HDebug.Assert(typec == 0); typec = 1;
}
if (setIdxBuffer.Contains(c))
{
HDebug.Assert(typec == 0); typec = 2;
}
if (setIdxCoarse.Contains(c))
{
HDebug.Assert(typec == 0); typec = 3;
}
HDebug.Assert(typec != 0);
for (int r = c + 1; r < size; r++)
{
if (lcoords[r] == null)
{
continue;
}
int typer = 0;
if (setIdxAll.Contains(r))
{
HDebug.Assert(typer == 0); typer = 1;
}
if (setIdxBuffer.Contains(r))
{
HDebug.Assert(typer == 0); typer = 2;
}
if (setIdxCoarse.Contains(r))
{
HDebug.Assert(typer == 0); typer = 3;
}
HDebug.Assert(typer != 0);
double sprcst;
double cutoff;
int type0 = Math.Min(typec, typer);
int type1 = Math.Max(typec, typer);
int type01 = type0 * 10 + type1;
switch (type01)
{
case 11: sprcst = anmSprcstAll; cutoff = anmCutoffAll; break; // All - All
case 12: sprcst = anmSprcstAll; cutoff = anmCutoffAll; break; // All - Buffer
case 22: sprcst = anmSprcstAll; cutoff = anmCutoffAll; break; // Buffer - Buffer
case 33: sprcst = anmSprcstCoarse; cutoff = anmCutoffCoarse; break; // Coarse - Coarse
case 23: sprcst = anmSprcstMix; cutoff = anmCutoffMix; break; // Buffer - Coarse
case 13: // All - Buffer
if (bAllowAllToCoarse == false)
{
continue;
}
sprcst = anmSprcstMix;
cutoff = anmCutoffMix;
break;
default: throw new Exception();
}
HDebug.Assert(bOnlyCoarseConnBackbone == false); // "true" makes the result bad
if (bOnlyCoarseConnBackbone)
{
bool c_bkbn = setIdxBackbone.Contains(c);
bool r_bkbn = setIdxBackbone.Contains(r);
if (c_bkbn && r_bkbn)
{
// special treatment that in-between backbones use only coarse grained onnections.
sprcst = anmSprcstCoarse;
cutoff = anmCutoffCoarse;
}
else if ((type01 == 11) || (type01 == 12) || (type01 == 22))
{
// do nothing. use the above setting.
}
else
{
// all-to-coarse
HDebug.AssertOr(type01 == 13, type01 == 23);
if (type01 == 33)
{
HDebug.Assert(type01 != 33); // should be treated by (c_bkbn && r_bkbn)
throw new Exception("HDebug.Assert(type01 != 33)");
}
continue;
}
}
double cutoff2 = cutoff * cutoff;
double dist2 = (coords[c] - coords[r]).Dist2;
if (dist2 <= cutoff2)
{
anmKij[c, r] = sprcst;
anmKij[r, c] = sprcst;
}
}
}
var hessinfo = Hess.GetHessEAnm(luniv, lcoords, anmKij);
return(hessinfo);
};
return(MixModel.GetHessMixModel(univ, coords, la, lstResAllAtom, GetHess, out errmsg, bGetIntmInfo, strBkbnReso));
}