internal virtual void TestMol()
{
Molecule mol = new Molecule();
mol.AddAtom("N", 0, 0);
mol.AddAtom("C", 1.2, 0);
mol.AddAtom("O", 2, 0.8);
mol.AddAtom("H", 3, - 0.8);
mol.AddAtom("H", 4, 0);
mol.AddBond(1, 2, 1);
mol.AddBond(2, 3, 2);
mol.AddBond(3, 4, 1);
mol.AddBond(4, 5, 0);
editor.Replace(mol);
}
// returns an equivalent replica of the molecule
public virtual Molecule Clone()
{
Molecule mol = new Molecule();
for (int n = 1; n <= NumAtoms(); n++)
{
Atom a = atoms[n - 1];
int num = mol.AddAtom(a.Element, a.X, a.Y, a.Charge, a.Unpaired);
mol.SetAtomHExplicit(num, AtomHExplicit(n));
}
for (int n = 1; n <= NumBonds(); n++)
{
Bond b = bonds[n - 1];
mol.AddBond(b.From, b.To, b.Order, b.Type);
}
return mol;
}
internal static Molecule ReadXML(FileStream istr)
{
Molecule mol = new Molecule();
const string NAMESPACE = "http://www.xml-cml.org/schema/cml2/core";
const string ATTRIBUTENS = "";
XmlDocument xmlDoc = new XmlDocument();
xmlDoc.Load(istr);
XPathNavigator navigator = xmlDoc.CreateNavigator();
if (navigator.MoveToFirstChild())
{
navigator.MoveToChild("molecule", NAMESPACE);
//navigator.MoveToFirstChild();
if (navigator.MoveToChild("atomArray", NAMESPACE))
{
if (navigator.MoveToChild("atom", NAMESPACE))
{
do
{
string elementType= navigator.GetAttribute("elementType", ATTRIBUTENS);
string x2String = navigator.GetAttribute("x2", ATTRIBUTENS);
if (!string.IsNullOrEmpty(x2String))
{
double x2 = Utility.SafeDouble(x2String);
double y2 = Utility.SafeDouble(navigator.GetAttribute("y2", ATTRIBUTENS));
int hydrogenCount = Utility.SafeInt(navigator.GetAttribute("hydrogenCount", ATTRIBUTENS));
// TODO: How do we handle hydrogen count?
mol.AddAtom(elementType, x2, y2);
}
else
{
double x3 = Utility.SafeDouble(navigator.GetAttribute("x3", ATTRIBUTENS));
double y3 = Utility.SafeDouble(navigator.GetAttribute("y3", ATTRIBUTENS));
int hydrogenCount = Utility.SafeInt(navigator.GetAttribute("hydrogenCount", ATTRIBUTENS));
// TODO: How do we handle hydrogen count?
mol.AddAtom(elementType, x3, y3);
}
} while (navigator.MoveToNext("atom", NAMESPACE));
navigator.MoveToParent();
}
navigator.MoveToParent();
}
if (navigator.MoveToChild("bondArray", NAMESPACE))
{
if (navigator.MoveToChild("bond", NAMESPACE))
{
do
{
string atomRefs = navigator.GetAttribute("atomRefs2", ATTRIBUTENS);
string[] parts = atomRefs.Split(' ');
if (parts.Length == 2)
{
int from = Utility.SafeInt(parts[0].Substring(1));
int to = Utility.SafeInt(parts[1].Substring(1));
int order = Utility.SafeInt(navigator.GetAttribute("order", ATTRIBUTENS));
int type = 0; // Where or is type stored?
// TODO: How do we handle hydrogen count?
mol.AddBond(from, to, order, type);
}
} while (navigator.MoveToNext("bond", NAMESPACE));
navigator.MoveToParent();
}
navigator.MoveToParent();
}
}
return mol;
}
public static Molecule ReadNative(System.IO.StreamReader in_Renamed)
{
Molecule mol = new Molecule();
//UPGRADE_NOTE: Final was removed from the declaration of 'GENERIC_ERROR '. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1003'"
System.String GENERIC_ERROR = "Invalid SketchEl file.";
try
{
System.String line = in_Renamed.ReadLine();
if (!line.StartsWith("SketchEl!"))
throw new System.IO.IOException("Not a SketchEl file.");
int p1 = line.IndexOf('('), p2 = line.IndexOf(','), p3 = line.IndexOf(')');
if (p1 == 0 || p2 == 0 || p3 == 0)
throw new System.IO.IOException(GENERIC_ERROR);
int numAtoms = System.Int32.Parse(line.Substring(p1 + 1, (p2) - (p1 + 1)).Trim());
int numBonds = System.Int32.Parse(line.Substring(p2 + 1, (p3) - (p2 + 1)).Trim());
for (int n = 0; n < numAtoms; n++)
{
line = in_Renamed.ReadLine();
// TODO: verify java's split method syntax: "[\\=\\,\\;]"
System.String[] bits = line.Split('=', ',', ';');
if (bits.Length < 5)
throw new System.IO.IOException(GENERIC_ERROR);
int num = mol.AddAtom(bits[0], System.Double.Parse(bits[1].Trim()), System.Double.Parse(bits[2].Trim()), System.Int32.Parse(bits[3].Trim()), System.Int32.Parse(bits[4].Trim()));
if (bits.Length >= 6 && bits[5].Length > 0 && bits[5][0] == 'e')
mol.SetAtomHExplicit(num, System.Int32.Parse(bits[5].Substring(1)));
}
for (int n = 0; n < numBonds; n++)
{
line = in_Renamed.ReadLine();
System.String[] bits = line.Split('-', '=', ','); // "[\\-\\=\\,]");
if (bits.Length < 4)
throw new System.IO.IOException(GENERIC_ERROR);
mol.AddBond(System.Int32.Parse(bits[0].Trim()), System.Int32.Parse(bits[1].Trim()), System.Int32.Parse(bits[2].Trim()), System.Int32.Parse(bits[3].Trim()));
}
line = in_Renamed.ReadLine();
if (String.CompareOrdinal(line, "!End") != 0)
throw new System.IO.IOException(GENERIC_ERROR);
}
catch (System.Exception)
{
throw new System.IO.IOException(GENERIC_ERROR);
}
return mol;
}
public static Molecule ReadMDLMOL(StreamReader in_Renamed)
{
Molecule mol = new Molecule();
//UPGRADE_NOTE: Final was removed from the declaration of 'GENERIC_ERROR '. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1003'"
System.String GENERIC_ERROR = "Invalid MDL MOL file.";
try
{
System.String line = null;
for (int n = 0; n < 4; n++)
line = in_Renamed.ReadLine();
if (line == null || !line.Substring(34, (39) - (34)).Equals("V2000"))
throw new System.IO.IOException(GENERIC_ERROR);
int numAtoms = System.Int32.Parse(line.Substring(0, (3) - (0)).Trim());
int numBonds = System.Int32.Parse(line.Substring(3, (6) - (3)).Trim());
for (int n = 0; n < numAtoms; n++)
{
line = in_Renamed.ReadLine();
double x = System.Double.Parse(line.Substring(0, (10) - (0)).Trim());
double y = System.Double.Parse(line.Substring(10, (20) - (10)).Trim());
System.String el = line.Substring(31, (33) - (31)).Trim();
int chg = System.Int32.Parse(line.Substring(36, (39) - (36)).Trim()), rad = 0;
if (chg <= 3)
{
}
else if (chg == 4)
{
chg = 0; rad = 2;
}
else
chg = 4 - chg;
mol.AddAtom(el, x, y, chg, rad);
}
for (int n = 0; n < numBonds; n++)
{
line = in_Renamed.ReadLine();
int from = System.Int32.Parse(line.Substring(0, (3) - (0)).Trim()), to = System.Int32.Parse(line.Substring(3, (6) - (3)).Trim());
int type = System.Int32.Parse(line.Substring(6, (9) - (6)).Trim()), stereo = System.Int32.Parse(line.Substring(9, (12) - (9)).Trim());
if (from == to || from < 1 || from > numAtoms || to < 1 || to > numAtoms)
throw new System.IO.IOException(GENERIC_ERROR);
int order = type >= 1 && type <= 3?type:1;
int style = Molecule.BONDTYPE_NORMAL;
if (stereo == 1)
style = Molecule.BONDTYPE_INCLINED;
else if (stereo == 6)
style = Molecule.BONDTYPE_DECLINED;
else if (stereo == 3 || stereo == 4)
style = Molecule.BONDTYPE_UNKNOWN;
mol.AddBond(from, to, order, style);
}
while (true)
{
line = in_Renamed.ReadLine();
if (line.StartsWith("M END"))
break;
int type = 0;
if (line.StartsWith("M CHG"))
type = 1;
else if (line.StartsWith("M RAD"))
type = 2;
if (type > 0)
{
int len = System.Int32.Parse(line.Substring(6, (9) - (6)).Trim());
for (int n = 0; n < len; n++)
{
int apos = System.Int32.Parse(line.Substring(9 + 8 * n, (13 + 8 * n) - (9 + 8 * n)).Trim());
int aval = System.Int32.Parse(line.Substring(13 + 8 * n, (17 + 8 * n) - (13 + 8 * n)).Trim());
if (type == 1)
mol.SetAtomCharge(apos, aval);
else
mol.SetAtomUnpaired(apos, aval);
}
}
}
}
catch (System.Exception)
{
throw new System.IO.IOException(GENERIC_ERROR);
}
return mol;
}