public static void WriteBlank(string pmlpath
, bool append
)
{
StreamWriter file;
if (append)
{
file = HFile.AppendText(pmlpath);
}
else
{
file = HFile.CreateText(pmlpath);
}
file.Close();
}
public static void WriteImport(string pypath, bool append = false)
{
StreamWriter file;
if (append)
{
file = HFile.AppendText(pypath);
}
else
{
file = HFile.CreateText(pypath);
}
file.WriteLine("from pymol.cgo import *");
file.WriteLine("from pymol import cmd");
file.Close();
}
public static void WriteLineStrips(string pmlpath
, string objname
, IList <LineStrip> linestrips
, bool append = false
)
{
StreamWriter file;
if (append)
{
file = HFile.AppendText(pmlpath);
}
else
{
file = HFile.CreateText(pmlpath);
}
{
//StreamWriter file = File.AppendText(pypath);
file.WriteLine("from pymol.cgo import *");
file.WriteLine("from pymol import cmd");
file.WriteLine("obj = [");
foreach (var linestrip in linestrips)
{
file.WriteLine("BEGIN, LINE_STRIP,");
if (linestrip.linewidth != null)
{
file.WriteLine(" LINEWIDTH, {0:0.000},", linestrip.linewidth);
}
file.WriteLine(" ALPHA, {0:0.000}, COLOR, {1:0.000}, {2:0.000}, {3:0.000}, ", linestrip.alpha, linestrip.red, linestrip.green, linestrip.blue);
for (int i = 0; i < linestrip.coords.Count; i++)
{
Vector vert = linestrip.coords[i];
file.Write(" VERTEX, {0:0.000}, {1:0.000}, {2:0.000}, ", vert[0], vert[1], vert[2]);
}
file.WriteLine();
file.WriteLine(" END,");
}
file.WriteLine("]");
// file.WriteLine("cmd.load_cgo(obj,\"channel_path\")");
file.WriteLine("cmd.load_cgo(obj,\"" + objname + "\")");
file.WriteLine();
}
file.Close();
}
public static void WriteLineStrip(string pmlpath
, string objname
, IList <Vector> pathcoords
, double?linewidth = null
, double alpha = 1.0, double red = 1.0, double green = 1.0, double blue = 1.0
, bool append = false
)
{
StreamWriter file;
if (append)
{
file = HFile.AppendText(pmlpath);
}
else
{
file = HFile.CreateText(pmlpath);
}
{
//StreamWriter file = File.AppendText(pypath);
file.WriteLine("from pymol.cgo import *");
file.WriteLine("from pymol import cmd");
file.WriteLine("obj = [");
file.WriteLine("BEGIN, LINE_STRIP,");
if (linewidth != null)
{
file.WriteLine("LINEWIDTH, {0:0.000},", linewidth);
}
file.WriteLine("ALPHA, {0:0.000}, COLOR, {1:0.000}, {2:0.000}, {3:0.000}, ", alpha, red, green, blue);
for (int i = 0; i < pathcoords.Count; i++)
{
Vector vert = pathcoords[i];
file.Write("VERTEX, {0:0.000}, {1:0.000}, {2:0.000}, ", vert[0], vert[1], vert[2]);
}
file.WriteLine();
file.WriteLine("END");
file.WriteLine("]");
// file.WriteLine("cmd.load_cgo(obj,\"channel_path\")");
file.WriteLine("cmd.load_cgo(obj,\"" + objname + "\")");
file.WriteLine();
}
file.Close();
}
public static void WriteSphere(string pmlpath
, string objname
, IList <Tuple <Vector, double, Tuple <double, double, double, double> > > lst_centercoord_radii_color
, double?linewidth = null
, bool append = true
)
{
#region python source
//def writeChannelPathAndForcedAtoms(pypath, pathcoords, atomcoords, constfrc):
// writeChannelPath(pypath, pathcoords);
// file = open(pypath, 'a');
// file.write('\n');
// file.write('sphobj = ['+'\n');
// for idx in range(constfrc['count']):
// atm0 = constfrc['key0' ][idx]; atm0 = atomcoords[atm0, :];
// atm1 = constfrc['key1' ][idx]; atm1 = atomcoords[atm1, :];
// frc = constfrc['value'][idx];
// file.write('ALPHA, 0.500, COLOR, 1.000, 0.000, 0.000, ');
// file.write('SPHERE, %6.3f, %6.3f, %6.3f, %6.3f, ' % (atm0[0]*10, atm0[1]*10, atm0[2]*10, 0.3));
// file.write('SPHERE, %6.3f, %6.3f, %6.3f, %6.3f, ' % (atm1[0]*10, atm1[1]*10, atm1[2]*10, 0.3));
// file.write('\n');
// pass
// file.write(']'+'\n');
// file.write('cmd.load_cgo(sphobj,"forced_atoms")'+'\n');
// file.close();
// return
#endregion
StreamWriter file;
if (append)
{
file = HFile.AppendText(pmlpath);
}
else
{
file = HFile.CreateText(pmlpath);
}
{
file.WriteLine("from pymol.cgo import *");
file.WriteLine("from pymol import cmd");
file.WriteLine("obj = [");
file.Write("BEGIN, ");
if (linewidth != null)
{
file.WriteLine("LINEWIDTH, {0:0.000},", linewidth);
}
{
foreach (var centercoord_radii_color in lst_centercoord_radii_color)
{
Vector coord = centercoord_radii_color.Item1;
double radii = centercoord_radii_color.Item2;
double alpha = centercoord_radii_color.Item3.Item1;
double red = centercoord_radii_color.Item3.Item2;
double green = centercoord_radii_color.Item3.Item3;
double blue = centercoord_radii_color.Item3.Item4;
file.Write("ALPHA, {0:0.000}, COLOR, {1:0.000}, {2:0.000}, {3:0.000}, ", alpha, red, green, blue);
file.Write("SPHERE, {0:0.000}, {1:0.000}, {2:0.000}, {3:0.000}, ", coord[0], coord[1], coord[2], radii);
file.WriteLine();
}
}
file.Write("END, ");
file.WriteLine("]");
// file.WriteLine("cmd.load_cgo(sphobj,\"forced_atoms\")");
file.WriteLine("cmd.load_cgo(obj,\"" + objname + "\")");
file.WriteLine();
}
file.Close();
}
public static void WriteLines(string pmlpath
, string objname
, IList <Vector> pathcoords
, double?linewidth = null
, double alpha = 1.0, double red = 1.0, double green = 1.0, double blue = 1.0
, bool append = false
)
{
#region python source
//def writeChannelPath(pypath, pathcoords):
// file = open(pypath, 'w');
// file.write('from pymol.cgo import *'+'\n');
// file.write('from pymol import cmd'+'\n');
// file.write('obj = ['+'\n');
// file.write('BEGIN, LINES,'+'\n');
// for idx in range(pathcoords.shape[0]-1):
// vert1 = pathcoords[idx,:];
// vert2 = pathcoords[idx+1,:];
// file.write('ALPHA, 1.000, COLOR, 1.000, 0.000, 0.000, ');
// file.write('VERTEX, %6.3f, %6.3f, %6.3f, ' % (vert1[0], vert1[1], vert1[2]));
// file.write('VERTEX, %6.3f, %6.3f, %6.3f, ' % (vert2[0], vert2[1], vert2[2]));
// file.write('\n');
// pass
// file.write('END'+'\n');
// file.write(']'+'\n');
// file.write('cmd.load_cgo(obj,"channel_path")'+'\n');
// file.close();
// return
#endregion
StreamWriter file;
if (append)
{
file = HFile.AppendText(pmlpath);
}
else
{
file = HFile.CreateText(pmlpath);
}
{
//StreamWriter file = File.AppendText(pypath);
file.WriteLine("from pymol.cgo import *");
file.WriteLine("from pymol import cmd");
file.WriteLine("obj = [");
file.WriteLine("BEGIN, LINES,");
if (linewidth != null)
{
file.WriteLine("LINEWIDTH, {0:0.000},", linewidth);
}
for (int i = 0; i < pathcoords.Count / 2; i++)
{
Vector vert1 = pathcoords[i * 2 + 0];
Vector vert2 = pathcoords[i * 2 + 1];
file.Write("ALPHA, {0:0.000}, COLOR, {1:0.000}, {2:0.000}, {3:0.000}, ", alpha, red, green, blue);
file.Write("VERTEX, {0:0.000}, {1:0.000}, {2:0.000}, ", vert1[0], vert1[1], vert1[2]);
file.Write("VERTEX, {0:0.000}, {1:0.000}, {2:0.000}, ", vert2[0], vert2[1], vert2[2]);
file.WriteLine();
}
file.WriteLine("END");
file.WriteLine("]");
// file.WriteLine("cmd.load_cgo(obj,\"channel_path\")");
file.WriteLine("cmd.load_cgo(obj,\"" + objname + "\")");
file.WriteLine();
}
file.Close();
}
public static void WriteCircles(string pmlpath
, string objname
, IList <Circle> lst_circle
//, int numLinesInCircle = 50
//, double? linewidth = null
//, double alpha=1.0, double red=1.0, double green=1.0, double blue=1.0
, bool append = false
)
{
StreamWriter file;
if (append)
{
file = HFile.AppendText(pmlpath);
}
else
{
file = HFile.CreateText(pmlpath);
}
{
//StreamWriter file = File.AppendText(pypath);
file.WriteLine("from pymol.cgo import *");
file.WriteLine("from pymol import cmd");
file.WriteLine("obj = [");
foreach (var circle in lst_circle)
{
//Vector center = center_normal_radii_numseg_color_width.Item1;
//Vector normal = center_normal_radii_numseg_color_width.Item2;
//double radii = center_normal_radii_numseg_color_width.Item3;
//int numLinesInCircle = center_normal_radii_numseg_color_width.Item4;
//double? alpha = center_normal_radii_numseg_color_width.Item5.Item1;
//double? red = center_normal_radii_numseg_color_width.Item5.Item2;
//double? green = center_normal_radii_numseg_color_width.Item5.Item3;
//double? blue = center_normal_radii_numseg_color_width.Item5.Item4;
//double? linewidth = center_normal_radii_numseg_color_width.Item6;
Trans3 trans = Trans3.GetTransformNoScale(new double[3] {
0, 0, 0
}
, new double[3] {
0, 0, 1
}
, circle.center
, circle.center + circle.normal.UnitVector()
);
Vector[] pts = new Vector[circle.numLinesInCircle + 1];
double di = (2 * Math.PI) / circle.numLinesInCircle;
for (int i = 0; i < circle.numLinesInCircle; i++)
{
Vector lpt = new double[3] {
circle.radii *Math.Cos(di * i), circle.radii *Math.Sin(di * i), 0
};
pts[i] = trans.DoTransform(lpt);
}
pts[circle.numLinesInCircle] = pts[0];
file.Write("BEGIN, LINE_STRIP, ");
if (circle.linewidth != null)
{
file.Write("LINEWIDTH, {0:0.000}, ", circle.linewidth);
}
if (circle.alpha != null)
{
file.Write("ALPHA, {0:0.000},", circle.alpha);
}
if (circle.color != null)
{
file.Write("COLOR, {0:0.000}, {1:0.000}, {2:0.000}, ", circle.color.Item1, circle.color.Item2, circle.color.Item3);
}
for (int i = 0; i < pts.Length; i++)
{
if (i % 10 == 0)
{
file.WriteLine();
file.Write(" ");
}
file.Write("VERTEX, {0:0.000}, {1:0.000}, {2:0.000}, ", pts[i][0] + 0.000001, pts[i][1] + 0.000001, pts[i][2] + 0.000001);
}
file.WriteLine();
file.WriteLine(" END, ");
}
file.WriteLine("]");
// file.WriteLine("cmd.load_cgo(obj,\"channel_path\")");
file.WriteLine("cmd.load_cgo(obj,\"" + objname + "\")");
file.WriteLine();
}
file.Close();
}
