public static bool carboxylatesBlocked(OBMol mol, OBAtom aA, OBAtom carbA, OBAtom aB, OBAtom carbB)
{
bool inCone = OBFunctions.atomsInCarboxylateCone(aA, carbA, mol);
inCone = inCone || OBFunctions.atomsInCarboxylateCone(aB, carbB, mol);
return(inCone);
}
public static void trajectoryFrameToCIF(string frame, string outFile, List <int> esequence,
OBConversion obconv)
{
//converts a frame from the above function into a CIF file
//lammps trajectory files have unit cell dimension data for every frame
//requires an element sequence for identifying element type from lammps atom types
OBUnitCell uc = new OBUnitCell();
OBMol mol = new OBMol();
OBMatrix3x3 mat = new OBMatrix3x3();
using (StringReader reader = new StringReader(frame)) {
string line = "";
bool foundMatrix = false;
do
{
line = reader.ReadLine();
if (line.Contains("BOX BOUNDS"))
{
//data from lammps is in this format
//ITEM: BOX BOUNDS xy xz yz
//xlo_bound xhi_bound xy
//ylo_bound yhi_bound xz
//zlo_bound zhi_bound yz
string row0 = reader.ReadLine();
double[] row0d = OBFunctions.spacedStringToDoubleArray(row0);
double xlo = row0d[0];
double xhi = row0d[1];
double xy = row0d[2];
string row1 = reader.ReadLine();
double[] row1d = OBFunctions.spacedStringToDoubleArray(row1);
double ylo = row1d[0];
double yhi = row1d[1];
double xz = row1d[2];
string row2 = reader.ReadLine();
double[] row2d = OBFunctions.spacedStringToDoubleArray(row2);
double zlo = row2d[0];
double zhi = row2d[1];
double yz = row2d[2];
//adjust box bounds, taken from VMD's source for reading lammps files
double xdelta = Math.Min(0, xy);
xdelta = Math.Min(xdelta, xz);
xdelta = Math.Min(xdelta, xy + xz);
xlo = xlo - xdelta;
xdelta = Math.Max(0, xy);
xdelta = Math.Max(xdelta, xz);
xdelta = Math.Max(xdelta, xy + xz);
xhi = xhi - xdelta;
ylo = ylo - Math.Min(0, yz);
yhi = yhi - Math.Max(0, yz);
OBVector3 A = new OBVector3(xhi - xlo, 0, 0);
OBVector3 B = new OBVector3(xy, yhi - ylo, 0);
OBVector3 C = new OBVector3(xz, yz, zhi - zlo);
//OBVector3 A = new OBVector3 (xhi-xlo, xy, xz);
//OBVector3 B = new OBVector3 (0, yhi-ylo, yz);
//OBVector3 C= new OBVector3 (0, 0, zhi-zlo);
mat = new OBMatrix3x3(A, B, C);
uc.SetData(A, B, C);
foundMatrix = true;
}
} while (!foundMatrix);
//uc.SetData (mat);
bool foundAtoms = false;
do
{
line = reader.ReadLine();
if (line.Contains("ITEM: ATOMS"))
{
foundAtoms = true;
}
} while (!foundAtoms);
while ((line = reader.ReadLine()) != null)
{
string[] splitline = line.Split((char[])null, StringSplitOptions.RemoveEmptyEntries);
int lammpstype = Convert.ToInt32(splitline[1]) - 1;
int atype = esequence[lammpstype];
OBAtom a = new OBAtom();
a.SetAtomicNum(atype);
//position in fraction coordinates
OBVector3 fvec = new OBVector3(Convert.ToDouble(splitline[3]), Convert.ToDouble(splitline[4]),
Convert.ToDouble(splitline[5]));
//OBVector3 fvec = new OBVector3 (Convert.ToDouble (splitline [2]), Convert.ToDouble (splitline [3]), Convert.ToDouble (splitline [4]));
//convert to cartesian.
OBVector3 cvec = uc.FractionalToCartesian(fvec);
a.SetVector(cvec);
mol.AddAtom(a);
}
mol.CloneData(uc);
obconv.SetOutFormat("cif");
obconv.AddOption("b");
obconv.WriteFile(mol, outFile);
}
}
public static double trajectoryFrameVolume(string frame)
{
using (StringReader reader = new StringReader(frame)) {
string line = "";
bool foundMatrix = false;
double volume = 0;
do
{
line = reader.ReadLine();
if (line.Contains("BOX BOUNDS"))
{
//data from lammps is in this format
//ITEM: BOX BOUNDS xy xz yz
//xlo_bound xhi_bound xy
//ylo_bound yhi_bound xz
//zlo_bound zhi_bound yz
string row0 = reader.ReadLine();
double[] row0d = OBFunctions.spacedStringToDoubleArray(row0);
double xlo = row0d[0];
double xhi = row0d[1];
double xy = row0d[2];
string row1 = reader.ReadLine();
double[] row1d = OBFunctions.spacedStringToDoubleArray(row1);
double ylo = row1d[0];
double yhi = row1d[1];
double xz = row1d[2];
string row2 = reader.ReadLine();
double[] row2d = OBFunctions.spacedStringToDoubleArray(row2);
double zlo = row2d[0];
double zhi = row2d[1];
double yz = row2d[2];
//adjust box bounds, taken from VMD's source for reading lammps files
double xdelta = Math.Min(0, xy);
xdelta = Math.Min(xdelta, xz);
xdelta = Math.Min(xdelta, xy + xz);
xlo = xlo - xdelta;
xdelta = Math.Max(0, xy);
xdelta = Math.Max(xdelta, xz);
xdelta = Math.Max(xdelta, xy + xz);
xhi = xhi - xdelta;
ylo = ylo - Math.Min(0, yz);
yhi = yhi - Math.Max(0, yz);
double[] A = new double[] { xhi - xlo, 0, 0 };
double[] B = new double[] { xy, yhi - ylo, 0 };
double[] C = new double[] { xz, yz, zhi - zlo };
volume = StarMath.dotProduct(A, StarMath.crossProduct(B, C));
foundMatrix = true;
}
} while (!foundMatrix);
return(volume);
}
}