// compare to another molecule instance; null is equivalent to empty; return values:
// -1 if Mol < Other
// 0 if Mol == Other
// 1 if Mol > Other
// can be used to sort molecules, albeit crudely; does not do any kind of canonical preprocessing
public virtual int CompareTo(Molecule Other)
{
if (Other == null)
return NumAtoms() == 0?0:1; // null is equivalent to empty
if (NumAtoms() < Other.NumAtoms())
return - 1;
if (NumAtoms() > Other.NumAtoms())
return 1;
if (NumBonds() < Other.NumBonds())
return - 1;
if (NumBonds() > Other.NumBonds())
return 1;
for (int n = 1; n <= NumAtoms(); n++)
{
int c = String.CompareOrdinal(AtomElement(n), Other.AtomElement(n));
if (c != 0)
return c;
if (AtomX(n) < Other.AtomX(n))
return - 1;
if (AtomX(n) > Other.AtomX(n))
return 1;
if (AtomY(n) < Other.AtomY(n))
return - 1;
if (AtomY(n) > Other.AtomY(n))
return 1;
if (AtomCharge(n) < Other.AtomCharge(n))
return - 1;
if (AtomCharge(n) > Other.AtomCharge(n))
return 1;
if (AtomUnpaired(n) < Other.AtomUnpaired(n))
return - 1;
if (AtomUnpaired(n) > Other.AtomUnpaired(n))
return 1;
if (AtomHExplicit(n) < Other.AtomHExplicit(n))
return - 1;
if (AtomHExplicit(n) > Other.AtomHExplicit(n))
return 1;
}
for (int n = 1; n <= NumBonds(); n++)
{
if (BondFrom(n) < Other.BondFrom(n))
return - 1;
if (BondFrom(n) > Other.BondFrom(n))
return 1;
if (BondTo(n) < Other.BondTo(n))
return - 1;
if (BondTo(n) > Other.BondTo(n))
return 1;
if (BondOrder(n) < Other.BondOrder(n))
return - 1;
if (BondOrder(n) > Other.BondOrder(n))
return 1;
if (BondType(n) < Other.BondType(n))
return - 1;
if (BondType(n) > Other.BondType(n))
return 1;
}
return 0;
}
public static void WriteMDLMOL(System.IO.StreamWriter output, Molecule mol)
{
//UPGRADE_ISSUE: Class 'java.text.DecimalFormat' was not converted. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1000_javatextDecimalFormat'"
//UPGRADE_ISSUE: Constructor 'java.text.DecimalFormat.DecimalFormat' was not converted. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1000_javatextDecimalFormat'"
// DecimalFormat fmt = new DecimalFormat("0.0000");
string fmtStr = "N4";
output.Write("\nNuGenChem MOLfile\n\n");
output.Write(intrpad(mol.NumAtoms(), 3) + intrpad(mol.NumBonds(), 3) + " 0 0 0 0 0 0 0 0999 V2000\n");
System.String line;
for (int n = 1; n <= mol.NumAtoms(); n++)
{
string str = mol.AtomX(n).ToString(fmtStr);
line = rep(" ", 10 - str.Length) + str;
str = mol.AtomY(n).ToString(fmtStr);
line += (rep(" ", 10 - str.Length) + str);
line += " 0.0000 ";
str = mol.AtomElement(n);
line += (str + rep(" ", 4 - str.Length) + "0");
int chg = mol.AtomCharge(n), spin = mol.AtomUnpaired(n);
if (chg >= - 3 && chg <= - 1)
chg = 4 - chg;
else if (chg == 0 && spin == 2)
chg = 4;
else if (chg < 1 || chg > 3)
chg = 0;
line += (intrpad(chg, 3) + " 0 0 0 0 0 0 0 0 0 0");
output.Write(line + "\n");
}
for (int n = 1; n <= mol.NumBonds(); n++)
{
int type = mol.BondOrder(n);
if (type < 1 || type > 3)
type = 1;
int stereo = mol.BondType(n);
if (stereo == Molecule.BONDTYPE_NORMAL)
{
}
else if (stereo == Molecule.BONDTYPE_INCLINED)
{
stereo = 1; type = 1;
}
else if (stereo == Molecule.BONDTYPE_DECLINED)
{
stereo = 6; type = 1;
}
else if (stereo == Molecule.BONDTYPE_UNKNOWN)
{
stereo = 4; type = 1;
}
else
stereo = 0;
output.Write(intrpad(mol.BondFrom(n), 3) + intrpad(mol.BondTo(n), 3) + intrpad(type, 3) + intrpad(stereo, 3) + " 0 0 0\n");
}
int count = 0;
line = "";
for (int n = 1; n <= mol.NumAtoms(); n++)
if (mol.AtomCharge(n) != 0)
{
line += (intrpad(n, 4) + intrpad(mol.AtomCharge(n), 4));
count++;
if (count == 8)
{
output.Write("M CHG" + intrpad(count, 3) + line + "\n");
count = 0; line = "";
}
}
if (count > 0)
output.Write("M CHG" + intrpad(count, 3) + line + "\n");
count = 0;
line = "";
for (int n = 1; n <= mol.NumAtoms(); n++)
if (mol.AtomUnpaired(n) != 0)
{
line += (intrpad(n, 4) + intrpad(mol.AtomUnpaired(n), 4));
count++;
if (count == 8)
{
output.Write("M RAD" + intrpad(count, 3) + line + "\n");
count = 0; line = "";
}
}
if (count > 0)
output.Write("M RAD" + intrpad(count, 3) + line + "\n");
output.Write("M END\n");
output.Flush();
}
public static void WriteCMLXML(System.IO.StreamWriter output, Molecule mol)
{
output.Write("<cml>\n");
output.Write(" <molecule xmlns=\"http://www.xml-cml.org/schema/cml2/core\">\n");
output.Write(" <atomArray>\n");
for (int n = 1; n <= mol.NumAtoms(); n++)
{
output.Write(" <atom id=\"a" + n + "\" elementType=\"" + mol.AtomElement(n) + "\"" + " x2=\"" + mol.AtomX(n) + "\" y2=\"" + mol.AtomY(n) + "\" hydrogenCount=\"" + mol.AtomHydrogens(n) + "\"/>\n");
}
output.Write(" </atomArray>\n");
output.Write(" <bondArray>\n");
for (int n = 1; n <= mol.NumBonds(); n++)
{
output.Write(" <bond id=\"b" + n + "\" atomRefs2=\"a" + mol.BondFrom(n) + " a" + mol.BondTo(n) + "\" order=\"" + mol.BondOrder(n) + "\"/>\n");
}
output.Write(" </bondArray>\n");
output.Write(" </molecule>\n");
output.Write("</cml>\n");
output.Flush();
}
public static void WriteNative(System.IO.StreamWriter output, Molecule mol)
{
//UPGRADE_ISSUE: Class 'java.text.DecimalFormat' was not converted. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1000_javatextDecimalFormat'"
//UPGRADE_ISSUE: Constructor 'java.text.DecimalFormat.DecimalFormat' was not converted. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1000_javatextDecimalFormat'"
// DecimalFormat fmt = new DecimalFormat("0.0000");
string fmtStr = "N4";
output.Write("SketchEl!(" + mol.NumAtoms() + "," + mol.NumBonds() + ")\n");
for (int n = 1; n <= mol.NumAtoms(); n++)
{
System.String hy = mol.AtomHExplicit(n) != Molecule.HEXPLICIT_UNKNOWN?("e" + mol.AtomHExplicit(n)):("i" + mol.AtomHydrogens(n));
output.Write(mol.AtomElement(n) + "=" + mol.AtomX(n).ToString(fmtStr) + "," + mol.AtomY(n).ToString(fmtStr) + ";" + mol.AtomCharge(n) + "," + mol.AtomUnpaired(n) + "," + hy + "\n");
}
for (int n = 1; n <= mol.NumBonds(); n++)
{
output.Write(mol.BondFrom(n) + "-" + mol.BondTo(n) + "=" + mol.BondOrder(n) + "," + mol.BondType(n) + "\n");
}
output.Write("!End\n");
output.Flush();
}