private void OpenStructure(string StName)
{
// Создаём OpenBabel объекты
OBConversion obconv = new OBConversion();
OBMol mol = Functions.ReadMoleculeFromFile(StName);
obconv.SetOutFormat("_png2");
obconv.AddOption("w", OBConversion.Option_type.OUTOPTIONS, panel1.Width.ToString());
obconv.AddOption("h", OBConversion.Option_type.OUTOPTIONS, panel1.Height.ToString());
string TempPic = Functions.TempFile();
obconv.WriteFile(mol, TempPic); // Пишем картинку в temp // Это такое колдунство // Мне стыдно, но по-другому не выходит
obconv.CloseOutFile();
Bitmap bmp = new Bitmap(panel1.Width, panel1.Height);
// Рисуем на панели
panel1.BackgroundImage = bmp;
Image IM = Image.FromFile(TempPic);
Graphics g = Graphics.FromImage(panel1.BackgroundImage);
g.DrawImage(IM, 0, 0);
IM.Dispose();
g.Dispose();
panel1.Invalidate();
// Высчитываем параметры
label3.Text = "Молярная масса: " + Math.Round(mol.GetExactMass(), 4);
label4.Text = "Брутто-формула: " + mol.GetFormula();
}
private PicElement DrawMoleculeElement(Molecule Mol)
{
// Настраиваем конвертер
OBConversion obconv = new OBConversion();
obconv.SetOutFormat("_png2");
Mol.Structure.SetTitle("");
obconv.AddOption("w", OBConversion.Option_type.OUTOPTIONS, BMP_Width.ToString());
obconv.AddOption("h", OBConversion.Option_type.OUTOPTIONS, (BMP_Height - TextPanel).ToString());
// Получаем файл с картинкой
string TempPic = Functions.TempFile();
obconv.WriteFile(Mol.Structure, TempPic);
obconv.CloseOutFile();
// Рисуем структуру
Image IM = Image.FromFile(TempPic);
//Img
Bitmap bmp = new Bitmap(BMP_Width, BMP_Height);
Graphics g = Graphics.FromImage(bmp);
g.Clear(Color.White);
g.DrawImage(IM, 0, 0);
g.DrawString(Mol.name,
new Font("Arial", 14, FontStyle.Bold),
new SolidBrush(Color.Black),
new PointF(5, BMP_Height - TextPanel + 5));
g.DrawString(Mol.Status,
new Font("Arial", 12, FontStyle.Regular),
new SolidBrush(Color.Black),
new PointF(5, BMP_Height - TextPanel + 5 + new Font("Arial", 14, FontStyle.Bold).GetHeight()));
g.Dispose();
Mol.Structure.SetTitle(Mol.name);
PicElement El = new PicElement();
El.Image = bmp;
El.ID = Mol.ID;
return(El);
//Всё подчищаем
// bmp.Dispose();
// IM.Dispose();
}
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 void Get_Passport(Molecule Mol, string Filename)
{
// Настраиваем конвертер
OBConversion obconv = new OBConversion();
obconv.SetOutFormat("_png2");
Mol.Structure.SetTitle("");
obconv.AddOption("w", OBConversion.Option_type.OUTOPTIONS, "1182");
obconv.AddOption("h", OBConversion.Option_type.OUTOPTIONS, "1182");
// Получаем файл с картинкой
string TempPic = Functions.TempFile();
obconv.WriteFile(Mol.Structure, TempPic);
obconv.CloseOutFile();
Mol.Structure.SetTitle(Mol.name);
var doc = new Document(PageSize.A4);
PdfWriter.GetInstance(doc, new FileStream(Filename, FileMode.Create));
doc.Open();
BaseFont Times = BaseFont.CreateFont(Application.StartupPath + @"\Fonts\times.ttf",
BaseFont.IDENTITY_H, BaseFont.NOT_EMBEDDED);
BaseFont TimesBold = BaseFont.CreateFont(Application.StartupPath + @"\Fonts\timesb.ttf",
BaseFont.IDENTITY_H, BaseFont.NOT_EMBEDDED);
BaseFont TimesItalic = BaseFont.CreateFont(Application.StartupPath + @"\Fonts\timesi.ttf",
BaseFont.IDENTITY_H, BaseFont.NOT_EMBEDDED);
BaseFont TimesBoldItalic = BaseFont.CreateFont(Application.StartupPath + @"\Fonts\timesbi.ttf",
BaseFont.IDENTITY_H, BaseFont.NOT_EMBEDDED);
Font Regular = new Font(Times, 14);
Font Bold = new Font(TimesBold, 14);
Font LargeBold = new Font(TimesBold, 18);
Font SubScribe = new Font(Times, 10);
doc.Add(AddText("Институт органического синтеза им. И.Я. Постовского УрО РАН", Bold,
Element.ALIGN_CENTER));
doc.Add(AddText(" ", Bold));
doc.Add(AddText("620041, г. Екатеринбург, ул. С. Ковалевской/Академическая, 20/22,\n" +
"Телефоны (343) 374-11-89, (343) 369-30-58", Regular, Element.ALIGN_CENTER));
doc.Add(AddLine());
doc.Add(AddText("ПАСПОРТ НА ОБРАЗЕЦ № " + Mol.name, LargeBold, Element.ALIGN_CENTER));
doc.Add(AddImage(TempPic, 250));
doc.Add(AddText("Молярная масса: ",
new[] { new Phrase(Math.Round(Mol.Structure.GetMolWt(), 2).ToString(), Regular) }, Bold));
doc.Add(AddText("Брутто формула: ",
new[] { SetSuperSubScript(Mol.Structure.GetFormula(), Regular, SubScribe, SUBSCRIPT) }, Bold));
doc.Add(AddText("Физическое состояние: ",
new[] { new Phrase(Mol.State, Regular) }, Bold));
doc.Add(AddText("Температура плавления: ",
new[] { new Phrase(Mol.MeltingPoint, Regular) }, Bold));
doc.Add(AddText("Охарактеризовано: ",
new[] { SetSuperSubScript(Mol.GetAnalys_Whom(), Regular, SubScribe, SUPERSCRIPT) }, Bold));
doc.Add(AddText("Растворимость: ",
new[] { new Phrase(Mol.Solution, Regular) }, Bold));
doc.Add(AddText("Условия хранения: ",
new[] { new Phrase(Mol.Conditions, Regular) }, Bold));
doc.Add(AddText("Масса образца: ",
new[] { new Phrase(Mol.Mass + " мг", Regular) }, Bold));
doc.Add(AddText("Синтезировал: ",
new[] { new Phrase(Mol.MadeBy.Job + ", " + Mol.MadeBy.GetInitNameFirst() +
" (" + Mol.LaboratoryName + ")", Regular) }, Bold));
doc.Add(AddText("НАУЧНЫЙ РУКОВОДИТЕЛЬ", Bold));
PdfPTable table = new PdfPTable(2);
table.WidthPercentage = 100;
table.AddCell(new PdfPCell(new Phrase("академик", Bold))
{
HorizontalAlignment = Element.ALIGN_LEFT,
BorderWidth = 0
});
table.AddCell(new PdfPCell(new Phrase("В.Н. Чарушин", Bold))
{
HorizontalAlignment = Element.ALIGN_RIGHT,
BorderWidth = 0
});
doc.Add(table);
doc.Close();
}
