public static string WriteMolString(Molecule mol)
{
//First we write to a temp file, we then open the file, read all of the text and return it as a string
WriteMolFile("writertemp.mol", mol);
string molString = File.ReadAllText("writertemp.mol");
//Now we delete the temp file
File.Delete("writertemp.mol");
return molString;
}
public static void ReadMolFile(string filePath, ref Molecule mol)
{
using (StreamReader reader = File.OpenText(filePath))
{
ParseHeaderBlock(reader, ref mol);
ParseCountsLine(reader, ref mol);
ParseAtomBlock(reader, ref mol);
ParseBondBlock(reader, ref mol);
ParsePropertiesBlock(reader, ref mol);
}
}
public static void WriteMolFile(string filePath, Molecule mol)
{
using (StreamWriter writer = File.CreateText(filePath))
{
WriteHeaderBlock(writer, mol);
WriteCountsLine(writer, mol);
WriteAtomBlock(writer, mol);
WriteBondBlock(writer, mol);
writer.WriteLine("M END");
}
}
public static void ReadMolData(string text, ref Molecule mol)
{
StringBuilder builder = new StringBuilder(text);
System.Text.ASCIIEncoding encode = new ASCIIEncoding();
byte[] byteArray = encode.GetBytes(text);
using (Stream s = new MemoryStream(byteArray))
{
using (StreamReader reader = new StreamReader(s))
{
ParseHeaderBlock(reader, ref mol);
ParseCountsLine(reader, ref mol);
ParseAtomBlock(reader, ref mol);
ParseBondBlock(reader, ref mol);
ParsePropertiesBlock(reader, ref mol);
}
}
}
private static void WriteAtomBlock(StreamWriter writer, Molecule mol)
{
//It goes xxxxx.xxxxyyyyy.yyyyzzzzz.zzzz aaaddcccssshhhbbbvvvHHHrrriiimmmnnneee for each atom
foreach (Node atom in mol.Atoms.Values)
{
string line = string.Empty;
string x = atom.Position.X.ToString();
if (atom.Position.X == Math.Round(atom.Position.X)) //is it an intergral #
x += ".0000";
x = x.PadLeft(10, ' '); //pad left so we get 10 chars
line += x;
string y = atom.Position.Y.ToString();
if (atom.Position.Y == Math.Round(atom.Position.Y))
y += ".0000";
y = y.PadLeft(10, ' ');
line += y;
string z = string.Empty;
if (atom.Position.Z == 0 || Math.Round(atom.Position.Z) == atom.Position.Z)
z = atom.Position.Z.ToString() + ".0000";
else
z = atom.Position.Z.ToString();
z = z.PadLeft(10);
line += z + " "; //one extra space after coords
//next is atom sybmol
string symbol = atom.Symbol;
symbol = symbol.PadRight(4);
line += symbol;
line += "0 "; //mass difference is skipped
//Next part is the charge
line += atom.Charge + " ";
//next parity which is skipped
line += "0 ";
//next is hydrogen count
line += atom.RequiredHydrogens + " ";
//skip next
line += "0 ";
//finally valence
line += atom.Valence + " 0 0 0 0 0 0";
writer.WriteLine(line);
}
}
private static void WriteBondBlock(StreamWriter writer, Molecule mol)
{
// 111222tttsssxxxrrrccc first atom # second atom # bond type bond stereo
foreach (Bond bond in mol.Bonds)
{
Console.WriteLine("MolFileWriter.WriteBondBlock: atom {0} connected to atom {1}", bond.Node1.ID, bond.Node2.ID);
string line = string.Empty;
string atom1 = bond.Node1.ID.ToString();
atom1 = atom1.PadLeft(3, ' ');
line += atom1;
string atom2 = bond.Node2.ID.ToString();
atom2 = atom2.PadLeft(3, ' ');
line += atom2;
string order = bond.BondOrder.ToString();
order = order.PadLeft(3, ' ');
line += order;
string stereo = bond.BondStereo.ToString();
stereo = stereo.PadLeft(3, ' ');
line += stereo;
//For now we skip topology and reaction center status
line += " 0 0 0";
writer.WriteLine(line);
}
}
private static void ParseAtomBlock(StreamReader reader, ref Molecule mol)
{
//It goes xxxxx.xxxxyyyyy.yyyyzzzzz.zzzz aaaddcccssshhhbbbvvvHHHrrriiimmmnnneee for each atom
//From the counts line we know how many atoms to expect
for (int i = 1; i <= mol.NumberOfAtoms; i++)
{
string line = reader.ReadLine();
//First the coords
Node atomToAdd = new Node();
double x, y, z;
bool result = double.TryParse(line.Substring(0, 10), out x);
if (!result)
Console.WriteLine("Could not parse x coords");
result = double.TryParse(line.Substring(10, 10), out y);
if (!result)
Console.WriteLine("Could not parse y coords");
result = double.TryParse(line.Substring(20,10), out z);
if (!result)
Console.WriteLine("Could not parse z coords");
if (z == 0) z = 0.0000;
Vector3 coords = new Vector3(x, y, z);
atomToAdd.Position = coords;
//Next we split the string into parts and the 3rd entry is the atomic symbol
string[] delim = { " " };
string[] parts = line.Split(delim, StringSplitOptions.RemoveEmptyEntries);
atomToAdd.Symbol = parts[3];
//The fourth is mass difference ?!?!? NOT added
int massDifference;
result = int.TryParse(parts[4], out massDifference);
if (!result)
Console.WriteLine("Could not parse mass difference");
else
atomToAdd.MassDiff = massDifference;
//The fifth is charge
int charge;
result = int.TryParse(parts[5], out charge);
if (!result)
Console.WriteLine("Could not parse atomic charge");
else
{
atomToAdd.Charge = charge;
Console.WriteLine("ATOM " + atomToAdd.Symbol + " CHARGE " + charge);
}
//The sixth is atom stereo parity which is ignored
//The seventh is hydrogen count
int hCount;
result = int.TryParse(parts[7], out hCount);
if (!result)
Console.WriteLine("Could not parse hydrogen count");
else
{
if (hCount > 0)
Console.WriteLine("hcount above 0");
Console.WriteLine("ATOM " + atomToAdd.Symbol + " HS " + hCount);
atomToAdd.RequiredHydrogens = hCount;
}
//Stereo care box is skipped
//The ninth is valence 0 = no marking default, includes number of bonds on this atom including implied
//hydrogens
int valence;
result = int.TryParse(parts[9], out valence);
if (!result)
Console.WriteLine("Could not parse valence");
else
atomToAdd.Valence = valence;
atomToAdd.ID = i;
//finally we add the atom to the list
mol.Atoms.Add(i, atomToAdd);
}
}
private static void WriteHeaderBlock(StreamWriter writer, Molecule mol)
{
//Line 1 : molecule name, can be blank, no longer than 80 letters
writer.WriteLine(mol.Name);
/*Line 2: IIPPPPPPPPMMDDYYHHmmddSSssssssssssEEEEEEEEEEEERRRRRR
*User's first and last initials (l), program name (P),
*date/time (M/D/Y,H:m), dimensional codes (d), scaling factors (S, s),
* energy (E) if modeling program input,
* internal registry number (R) if input through MDL form.
* can be blank */
string line2 = string.Empty;
if (mol.CreatedBy.Length == 2)
line2 += mol.CreatedBy;
else
line2 += " "; //no initials means two spaces added
//The program is eight chars so we check our program name (generally SynType or ChemDraw)
string buildSoft = mol.BuildSoftware;
buildSoft = buildSoft.PadRight(8, ' ');
line2 += buildSoft;
//The next is the date
string month; //month is not always 2 digits so we make sure it is
if (mol.CreationTime.Month < 10)
{
month = mol.CreationTime.Month.ToString();
month = month.PadLeft(2, '0');
}
else
month = mol.CreationTime.Month.ToString();
string day; //day is also not always 2 digits so we pad as well
if (mol.CreationTime.Day < 10)
{
day = mol.CreationTime.Day.ToString();
day = day.PadLeft(2, '0');
}
else
day = mol.CreationTime.Day.ToString();
int year = mol.CreationTime.Year;
int hour = mol.CreationTime.Hour;
int min = mol.CreationTime.Minute;
Console.WriteLine("MolFileWriter: DT {0}/{1}/{2} {3}:{4}", day, month, year, hour, min);
line2 += month + day + year.ToString().Substring(2) +hour.ToString() + min.ToString();
//add in 2D at the end and write the line
line2 += "2D";
writer.WriteLine(line2);
//Finally we add the 3rd line which is comments
writer.WriteLine(mol.Comments);
}
private void CheckFormulaKeys(object sender, System.Windows.Forms.KeyPressEventArgs e)
{
if (e.KeyChar == (char)13) //if enter has been pressed we try and build a molecule from the formula
{
molecule = new Molecule(this);
molecule.Formula = formulaTextBox.Text;
molecule.OnlyHasFormula = true;
molWeightLabel.Text = molecule.MolecularWeight.ToString();
}
}
public object Clone()
{
//First we make a copy of the atoms
Dictionary<int, Node> atomCopy = new Dictionary<int, Node>();
foreach (int id in atoms.Keys)
{
atomCopy.Add(id, (Node) atoms[id].Clone());
}
//Then a copy of the bonds
List<Bond> bondCopy = new List<Bond>();
foreach (Bond bond in bonds)
{
bondCopy.Add((Bond)bond.Clone());
}
Molecule copy = new Molecule(atomCopy, this.name, this.numberOfAtoms, this.numberOfBonds, this.createdBy, this.buildSoftware, this.comments, bondCopy, this.form);
return copy;
}
private static void WriteCountsLine(StreamWriter writer, Molecule mol)
{
string line = string.Empty;
string atomCount = mol.Atoms.Count.ToString();
atomCount = atomCount.PadLeft(3, ' ');
line += atomCount;
//Next are the bonds
string bondCount = mol.Bonds.Count.ToString();
bondCount = bondCount.PadLeft(3, ' ');
line += bondCount;
//next we skip to the chiral spot
line += " 0 ";
if (mol.IsChiral)
line += "1";
else
line += "0";
//Then we write the rest of the line 0 0 0 0 0 0999 V2000
line += " 0 0 0 0 0 0999 V2000";
writer.WriteLine(line);
}
private void AddCompoundForm_Load(object sender, EventArgs e)
{
//Build the type selection drop down box
typeSelection.Items.Add("Reactant");
typeSelection.Items.Add("Reagent");
typeSelection.Items.Add("Product");
typeSelection.SelectedIndex = 0;
//Build the state selection drop down
stateSelection.Items.Add("Solid");
stateSelection.Items.Add("Liquid");
stateSelection.Items.Add("Gas");
stateSelection.Items.Add("Solution");
stateSelection.SelectedIndex = 0;
//The following unit selection boxes have to follow the UNIT_POWERS Enum, that is none = 0, u = 1, m = 2, k = 3
//Build the mols unit selection drop down
molUnitSelection.Items.Add("mol");
molUnitSelection.Items.Add("umol");
molUnitSelection.Items.Add("mmol");
molUnitSelection.SelectedIndex = 0;
//Build the mass unit selection drop down
massUnitSelection.Items.Add("g");
massUnitSelection.Items.Add("ug");
massUnitSelection.Items.Add("mg");
massUnitSelection.Items.Add("kg");
massUnitSelection.SelectedIndex = 0;
//Build the volume unit selection drop down
volumeUnitSelection.Items.Add("l");
volumeUnitSelection.Items.Add("ul");
volumeUnitSelection.Items.Add("ml");
volumeUnitSelection.SelectedIndex = 2;
molecule = new Molecule();
//setup event handler for the formula textbox
this.formulaTextBox.KeyPress += new System.Windows.Forms.KeyPressEventHandler(CheckFormulaKeys);
this.molsTextBox.KeyPress += new KeyPressEventHandler(molsTextBox_KeyPress);
//Next we need to create the molViewer
molViewer.Paint +=new PaintEventHandler(molViewer.paint);
//If the synthesis already has a limiting reactant we remove the islimitingcheckbox
if (currentSynthesis.LimitingReactant != null)
{
isLimitingCheckBox.Hide();
}
}
public Compound(Molecule mol, string fileName, string directory, int compoundType, string formula,
int compoundState, bool isTarget, double weight, double density, Unit mols,
Unit mass, Unit volume)
{
molFileName = fileName;
this.directory = directory;
this.type = compoundType;
this.molecule = mol;
this.state = compoundState;
this.isTarget = isTarget;
this.density = density;
this.mols = mols;
this.mass = mass;
this.volume = volume;
DisplayRefNameWhenDrawn = false;
}
public CompoundRegion(Compound comp, Molecule visualComp, RectangleF rect)
{
this.compound = comp;
this.rect = rect;
this.visualMol = visualComp;
}
private BoundingBox GetBoundingBox(Molecule molecule, RectangleF region)
{
//First we find the min/max in x and y for all the points
double minX = 0; double maxX = 0;
double minY = 0; double maxY = 0;
foreach (Node atom in molecule.Atoms.Values)
{
if (minX == 0) minX = atom.Position.X;
if (maxX == 0) maxX = atom.Position.X;
if (minY == 0) minY = atom.Position.Y;
if (maxY == 0) maxY = atom.Position.Y;
double currentX = atom.Position.X; double currentY = atom.Position.Y;
if (currentX < minX) minX = currentX;
if (currentX > maxX) maxX = currentX;
if (currentY < minY) minY = currentY;
if (currentY > maxY) maxY = currentY;
}
//So now we get the distance between min and max
double distX = maxX - minX + region.X;
double distY = maxY - minY + region.Y;
//The center of this box is the dist/2
double midX = distX / 2 + region.X;
double midY = distY / 2 + region.Y;
return new BoundingBox((float)distX, (float)distY, new PointF((float)midX, (float)midY), new PointF((float)minX, (float)minY), 0);
}
private void pasteMDL_Click(object sender, EventArgs e)
{
molecule = new Molecule();
GetMolFromClipboard();
//Now fill in the data fields, first is formula
formulaTextBox.Text = molecule.Formula.ToString();
//Next is mol weight
molWeightLabel.Text = molecule.MolecularWeight.ToString();
structurePasted = true;
//and finally we set the molviewer's molecule
molViewer.Mol = (Molecule) molecule.Clone();
molViewer.Invalidate(); //redraw the viewer
}
private static void ParseBondBlock(StreamReader reader, ref Molecule mol)
{
//One bond per line in format
// 111222tttsssxxxrrrccc first atom # second atom # bond type bond stereo
//Generally there will be spaces otherwise this f***s up
string line = string.Empty;
for (int i = 0; i < mol.NumberOfBonds; i++)
{
string[] delim = { " " };
string[] parts = reader.ReadLine().Split(delim, StringSplitOptions.RemoveEmptyEntries);
//The first two pars are atoms 1 and 2
int atom1Key, atom2Key;
bool result = int.TryParse(parts[0], out atom1Key);
if (!result)
Console.WriteLine("Could not get the first atom number");
result = int.TryParse(parts[1], out atom2Key);
if (!result)
Console.WriteLine("Could not get the second atom number");
int bondOrder;
result = int.TryParse(parts[2], out bondOrder);
if (!result)
Console.WriteLine("Could not get the bond order for "+atom1Key+"'s connection to"+atom2Key);
//Now we build the bond
try
{
Bond bondToAdd = new Bond(mol.Atoms[atom1Key], mol.Atoms[atom2Key], bondOrder);
mol.Bonds.Add(bondToAdd);
}
catch (ArgumentOutOfRangeException)
{
Console.WriteLine("The keys found were out of range 1:" + atom1Key + " 2:" + atom2Key + " atom count" +
mol.Atoms.Count);
}
}
}
private static void ParsePropertiesBlock(StreamReader reader, ref Molecule mol)
{
//properties block is mmm lines (999) and ends with M END
//We check real fast to see if there is even any props
string line = reader.ReadLine();
if (line == "M END")
{
Console.WriteLine("Mol file has been completely parsed \n");
return; //we're done jump out
}
}
private static void ParseHeaderBlock(StreamReader reader, ref Molecule mol)
{
//Line 1 : molecule name, can be blank, no longer than 80 letters
mol.Name = reader.ReadLine();
if (mol.Name.Length > 80)
Console.WriteLine("Name in mol file was too long");
/*Line 2: IIPPPPPPPPMMDDYYHHmmddSSssssssssssEEEEEEEEEEEERRRRRR
*User's first and last initials (l), program name (P),
*date/time (M/D/Y,H:m), dimensional codes (d), scaling factors (S, s),
* energy (E) if modeling program input,
* internal registry number (R) if input through MDL form.
* can be blank */
string line2 = reader.ReadLine();
if (!string.IsNullOrEmpty(line2))
{
mol.CreatedBy = line2.Substring(0, 2);
mol.BuildSoftware = line2.Substring(2, 8);
//To get the date time we need to shove in some characters so it parses correctly
string originalDT = line2.Substring(10, 10);
int month;
int.TryParse(originalDT.Substring(0, 2), out month);
int day;
int.TryParse(originalDT.Substring(2, 2), out day);
int year;
int.TryParse(originalDT.Substring(4, 2), out year);
year += 2000; //add 2000 to the year so we get the correct year, at least for the next 90 years
int hour;
int.TryParse(originalDT.Substring(6, 2), out hour);
int min;
int.TryParse(originalDT.Substring(8, 2), out min);
DateTime dt = new DateTime(year, month, day, hour, min, 0);
//To be added if needed
Console.WriteLine("MOL creation time was changed to " + dt.ToString());
mol.CreationTime = dt;
}
//Line 3 is for comments
mol.Comments = reader.ReadLine();
}
private static void ParseCountsLine(StreamReader reader, ref Molecule mol)
{
//it goes
//aaabbblllfffcccsssxxxrrrpppiiimmm
string countsLine = reader.ReadLine();
//We split by spaces
string[] delim = {" "};
string[] parts = countsLine.Split(delim, StringSplitOptions.RemoveEmptyEntries);
//Only three of the parts are useful, number of atoms, number of bonds
//and whether or not the molecule is chiral, so spots 0, 1, 4
int nAtoms;
int nBonds;
int isChiral;
bool result = int.TryParse(parts[0], out nAtoms);
if (!result)
{
Console.WriteLine("Could not get the number of atoms");
}
else
mol.NumberOfAtoms = nAtoms;
result = int.TryParse(parts[1], out nBonds);
if (!result)
{
Console.WriteLine("Could not get the númber of bonds");
}
else
mol.NumberOfBonds = nBonds;
result = int.TryParse(parts[4], out isChiral);
if (!result)
{
Console.WriteLine("Could not get whether molecule is chiral.");
}
else
{
if (isChiral == 0) mol.IsChiral = false;
else mol.IsChiral = true;
}
}
public Compound(Molecule mol, string refname, int compoundType, int compoundState, bool isLimiting, bool isTarget,
double density, Unit mols, Unit mass, Unit volume, Solution solution)
{
this.type = compoundType;
this.refName = refname;
this.molecule = mol;
this.state = compoundState;
this.isLimiting = isLimiting;
this.isTarget = isTarget;
this.density = density;
this.mols = mols;
this.mass = mass;
this.volume = volume;
this.solution = solution;
DisplayRefNameWhenDrawn = false;
}
public Compound(string name, string refid, string localid, int fileid, int compoundType, int compoundState, bool isLimiting, bool isTarget, string formula,
double density, Unit mols, Unit mass, Unit volume, Solution solution)
{
this.type = compoundType;
this.molecule = new Molecule();
this.molecule.Name = name;
this.refName = refid;
this.localid = localid;
this.fileid = fileid;
this.state = compoundState;
this.isLimiting = isLimiting;
this.isTarget = isTarget;
this.molecule.Formula = formula;
this.density = density;
this.mols = mols;
this.mass = mass;
this.volume = volume;
this.solution = solution;
DisplayRefNameWhenDrawn = false;
}
private void DrawMolecule(Molecule mol, Graphics g)
{
//First we draw bonds
foreach (Bond bond in mol.Bonds)
{
PointF p1 = new PointF((float)bond.Node1.Position.X, (float)bond.Node1.Position.Y);
PointF p2 = new PointF((float)bond.Node2.Position.X, (float)bond.Node2.Position.Y);
DrawBonds(g, p1, p2, bond.BondOrder, bond.WhichSide);
}
//Then we draw symbols
foreach (Node atom in mol.Atoms.Values)
{
if (atom.Symbol != "C")
{
//First we draw a white circle with radius 10 at the atom location
g.FillEllipse(Brushes.White, (float)atom.Position.X - 10, (float)atom.Position.Y - 10, 20, 20);
//Then we draw the symbol
string symbol = atom.Symbol;
if (symbol == "S" || symbol == "O" || symbol == "N")
{
if (atom.ImplicitHydrogens == 0)
{
g.DrawString(symbol, font, Brushes.Black, (float)atom.Position.X - 9, (float)atom.Position.Y - 12);
continue;
}
else if (atom.ImplicitHydrogens == 1)
{
symbol += "H";
g.DrawString(symbol, font, Brushes.Black, (float)atom.Position.X - 9, (float)atom.Position.Y - 12);
continue;
}
else
{
//If there are more than one hydrogen we have to make a sub script
Font normalFont = font;
Font subscriptFont = new Font("Times New Roman", 10);
symbol += "H";
g.DrawString(symbol, normalFont, Brushes.Black, (float)atom.Position.X - 9, (float)atom.Position.Y - 12);
g.DrawString(atom.ImplicitHydrogens.ToString(), subscriptFont, Brushes.Black, (float)atom.Position.X + 20, (float)(atom.Position.Y + 5));
continue;
}
}
g.DrawString(symbol, font, Brushes.Black, (float)atom.Position.X - 9, (float)atom.Position.Y - 12);
}
}
}
public Compound(Molecule mol)
{
this.molecule = mol;
this.mols = new Unit(0, "mol", (int)UNIT_POWERS.none);
this.mass = new Unit(0, "g", (int)UNIT_POWERS.none);
this.Volume = new Unit(0, "l", (int)UNIT_POWERS.m);
DisplayRefNameWhenDrawn = false;
}
private void NormalizeCoords(Molecule mol, COMPOUND_TYPES type, int id)
{
if (mol == null) return;
//First we get the region we are working in
RectangleF region;
if (type == COMPOUND_TYPES.Reactant) region = reactantRegions[id];
else if (type == COMPOUND_TYPES.Reagent) region = reagentRegions[0]; //we only ever have one reagent region
else region = productRegions[id];
//we get the bounds of the raw copy for initial sizing for the given region
mol.Bounds = GetBoundingBox(mol, region);
PointF center = new PointF(region.X + region.Width / 2, region.Y + region.Height / 2);
//The scale values for x and y are then calculated
//We want to keep the same ratio so we get the ratio, find the max sx can be and then calculte sy from that
float ratio = mol.Bounds.Width/mol.Bounds.Height;
double sx = 40; //region.Width / mol.Bounds.Width-30;
double sy = 30; //ratio / sx;
foreach (Node atom in mol.Atoms.Values)
{
double ox = atom.Position.X;
double oy = atom.Position.Y;
double x = (ox * sx + center.X);
double y = (oy * sy + center.Y);
atom.Position = new Vector3(x, y, 0);
//Finally we go through the bonds and update their nodes, due to some error in copying
foreach (Bond bond in mol.Bonds)
{
if (bond.Node1.ID == atom.ID)
bond.Node1 = atom;
else if (bond.Node2.ID == atom.ID)
bond.Node2 = atom;
}
//and again go through one more time to calculate the paths
foreach (Bond bond in mol.Bonds)
{
bond.CalculateBoundPath();
}
}
//We also need to get the new size of the bounding box and get the bounds for each bond
mol.Bounds = GetBoundingBox(mol, region);
}
private static void ReadMolData(XmlDocument doc, List<Compound> compounds)
{
//We read in the mol data, with the compound file id and then fill the molecule out with information
//First we find the correct xml node
XmlNodeList molDataNodes = doc.GetElementsByTagName("moldata");
//now we run through the nodes
foreach (XmlNode node in molDataNodes)
{
foreach (Compound c in compounds)
{
if (c.FileID == int.Parse(node.Attributes["fileid"].Value))
{
Molecule m = new Molecule();
if (node.InnerText == string.Empty)
{
//sometimes we have no mol data, just a formula
m.Formula = node.Attributes["formula"].Value;
m.OnlyHasFormula = true;
}
else
{
MolFileReader.ReadMolData(node.InnerText, ref m);
}
Console.WriteLine(m.ToString());
c.MoleculeData = m;
}
}
}
}
