public static void GetBFactor(string topolpath, string eigenvecpath, out string[] name, out int[] resSeq, out double[] BFactor
, bool ignoreNegativeEigval = true
)
{
Top topol = Top.FromFile(topolpath);
Eigenvec eigenvec = Eigenvec.FromFile(eigenvecpath);
GetBFactor(topol, eigenvec, out name, out resSeq, out BFactor, ignoreNegativeEigval);
}
public static void SelfTest(string rootpath, string[] args)
{
if (selftest == false)
{
return;
}
selftest = false;
string filepath = rootpath + @"\Bioinfo\External.Gromacs\Selftest\eigenvec.txt";
Eigenvec eigvec = FromFile(filepath);
}
public static Eigenvec FromFile(string filepath)
{
List <List <string> > frameliness;
{
string[] lines = HFile.ReadAllLines(filepath);
frameliness = GroupByFrames(lines);
}
Eigenvec eigvec = new Eigenvec();
eigvec.frames = new List <Frame>();
foreach (List <string> framelines in frameliness)
{
Frame frame = Frame.FromLines(framelines.ToArray());
eigvec.frames.Add(frame);
}
return(eigvec);
}
public static void GetBFactor(Top topol, Eigenvec eigenvec, out string[] name, out int[] resSeq, out double[] BFactor
, bool ignoreNegativeEigval = true
)
{
List <Gromacs.Top.Atom> atoms = topol.GetAtoms();
name = new string[atoms.Count];
resSeq = new int[atoms.Count];
BFactor = new double[atoms.Count];
for (int i = 0; i < atoms.Count; i++)
{
name[i] = atoms[i].atom;
resSeq[i] = atoms[i].resnr;
int count_lambda_0 = 0;
foreach (var frame in eigenvec.frames)
{
if (frame.lambda != 0)
{
continue;
}
if (frame.step <= 6)
{
HDebug.Assert(frame.step == frame.frameidx);
continue;
}
count_lambda_0++;
Vector[] eigvec = frame.x;
double eigval = frame.time;
HDebug.AssertIf(eigval < 0, Math.Abs(eigval) < 0.00001);
if (ignoreNegativeEigval)
{
if (eigval < 0)
{
continue;
}
}
HDebug.Assert(BFactor.Length == eigvec.Length);
BFactor[i] += LinAlg.VtV(eigvec[i], eigvec[i]) / eigval;
}
}
}
