public void Hydrate()
{
var tokens = new List <string>();
AbbreviationLabel.Parse("•H2O", tokens);
Assert.IsTrue(tokens.SequenceEqual(new string[] { "•", "H2", "O" }));
}
public void NonAbbreviationLabel()
{
var tokens = new List <string>();
Assert.IsFalse(AbbreviationLabel.Parse("A Random Label - Don't Reverse", tokens));
Assert.AreEqual(1, tokens.Count);
}
public void ReversingBracketsWithNumbers()
{
List <string> tokens = new List <string>();
Assert.IsTrue(AbbreviationLabel.Parse("B(OH)2", tokens));
AbbreviationLabel.Reverse(tokens);
Assert.AreEqual("(HO)2B", string.Join("", tokens));
}
public void ReversingBrackets()
{
var tokens = new List <string>();
Assert.IsTrue(AbbreviationLabel.Parse("N(CH2CH2O)CH2", tokens));
AbbreviationLabel.Reverse(tokens);
Assert.AreEqual("H2C(OH2CH2C)N", string.Join("", tokens));
}
public void ParseBrackets()
{
var tokens = new List <string>();
Assert.IsTrue(AbbreviationLabel.Parse("N(CH2CH2O)CH2", tokens));
Assert.AreEqual(10, tokens.Count);
Assert.IsTrue(Compares.AreOrderLessDeepEqual(new[] { "N", "(", "C", "H2", "C", "H2", "O", ")", "C", "H2" }, tokens));
}
public void CO2Et()
{
var tokens = new List <string>();
Assert.IsTrue(AbbreviationLabel.Parse("CO2Et", tokens));
Assert.AreEqual(3, tokens.Count);
Assert.IsTrue(Compares.AreOrderLessDeepEqual(new[] { "C", "O2", "Et" }, tokens));
}
public void Triphenylmethyl()
{
var tokens = new List <string>();
Assert.IsTrue(AbbreviationLabel.Parse("CPh3", tokens));
Assert.AreEqual(2, tokens.Count);
Assert.IsTrue(Compares.AreOrderLessDeepEqual(new[] { "C", "Ph3" }, tokens));
}
public void Peglinker()
{
var tokens = new List <string>();
Assert.IsTrue(AbbreviationLabel.Parse("CH2CH2OCH2CH2O", tokens));
Assert.AreEqual(10, tokens.Count);
Assert.IsTrue(Compares.AreOrderLessDeepEqual(new[] { "C", "H2", "C", "H2", "O", "C", "H2", "C", "H2", "O" }, tokens));
}
public void Carboxylate()
{
var tokens = new List <string>();
Assert.IsTrue(AbbreviationLabel.Parse("COO-", tokens));
Assert.AreEqual(4, tokens.Count);
Assert.IsTrue(Compares.AreOrderLessDeepEqual(new[] { "C", "O", "O", "-" }, tokens));
}
public void ParseFeacac3()
{
var tokens = new List <string>();
Assert.IsTrue(AbbreviationLabel.Parse("Fe(acac)3", tokens));
Assert.AreEqual(5, tokens.Count);
Assert.IsTrue(Compares.AreOrderLessDeepEqual(new[] { "Fe", "(", "acac", ")", "3" }, tokens));
}
public void ReversingFormatPOOHOEt()
{
List <string> tokens = new List <string>();
Assert.IsTrue(AbbreviationLabel.Parse("PO(OH)OEt", tokens));
AbbreviationLabel.Reverse(tokens);
AbbreviationLabel.Format(tokens);
Assert.AreEqual("EtO(HO)OP", string.Join("", tokens));
}
public void FormatTBu()
{
var tokens = new[] { "tBu" };
List <AbbreviationLabel.FormattedText> texts = AbbreviationLabel.Format(tokens);
Assert.AreEqual(2, texts.Count);
Assert.AreEqual("t", texts[0].Text);
Assert.AreEqual(AbbreviationLabel.STYLE_ITALIC, texts[0].Style);
Assert.AreEqual("Bu", texts[1].Text);
Assert.AreEqual(AbbreviationLabel.STYLE_NORMAL, texts[1].Style);
}
public void Tertbutyls()
{
var tokens = new List <string>(1);
foreach (var str in new[] { "tBu", "tertBu", "t-Bu", "t-Butyl", "tertButyl" })
{
tokens.Clear();
Assert.IsTrue(AbbreviationLabel.Parse(str, tokens), str);
Assert.AreEqual(1, tokens.Count);
}
}
public void FormatFeacac3()
{
var tokens = new List <string>();
Assert.IsTrue(AbbreviationLabel.Parse("Fe(acac)3", tokens));
List <AbbreviationLabel.FormattedText> formatted = AbbreviationLabel.Format(tokens);
Assert.AreEqual("Fe(acac)", formatted[0].Text);
Assert.AreEqual(0, formatted[0].Style);
Assert.AreEqual("3", formatted[1].Text);
Assert.AreEqual(-1, formatted[1].Style);
}
public AtomSymbol GenerateAbbreviatedSymbol(string label, HydrogenPosition position)
{
var tokens = new List <string>();
if (AbbreviationLabel.Parse(label, tokens))
{
return(GenerateAbbreviationSymbol(tokens, position));
}
else
{
return(new AtomSymbol(new TextOutline(label, font, emSize), Array.Empty <TextOutline>()));
}
}
public void FormatOPO3()
{
var tokens = new[] { "O", "P", "O3", "-2" };
var texts = AbbreviationLabel.Format(tokens);
Assert.AreEqual(3, texts.Count);
Assert.AreEqual("OPO", texts[0].Text);
Assert.AreEqual(AbbreviationLabel.STYLE_NORMAL, texts[0].Style);
Assert.AreEqual("3", texts[1].Text);
Assert.AreEqual(AbbreviationLabel.STYLE_SUBSCRIPT, texts[1].Style);
Assert.AreEqual("2−", texts[2].Text);
Assert.AreEqual(AbbreviationLabel.STYLE_SUPSCRIPT, texts[2].Style);
}
public void FormatOPO3H2()
{
var tokens = new[] { "O", "P", "O3", "H2" };
List <AbbreviationLabel.FormattedText> texts = AbbreviationLabel.Format(tokens);
Assert.AreEqual(4, texts.Count);
Assert.AreEqual("OPO", texts[0].Text);
Assert.AreEqual(0, texts[0].Style);
Assert.AreEqual("3", texts[1].Text);
Assert.AreEqual(-1, texts[1].Style);
Assert.AreEqual("H", texts[2].Text);
Assert.AreEqual(0, texts[2].Style);
Assert.AreEqual("2", texts[3].Text);
Assert.AreEqual(-1, texts[3].Style);
}
public void FormatRubpy3Cl2()
{
var tokens = new List <string>();
Assert.IsTrue(AbbreviationLabel.Parse("Ru(bpy)3Cl2", tokens));
var formatted = AbbreviationLabel.Format(tokens);
AbbreviationLabel.Reduce(formatted, 0, formatted.Count);
Assert.AreEqual("Ru(bpy)", formatted[0].Text);
Assert.AreEqual(0, formatted[0].Style);
Assert.AreEqual("3", formatted[1].Text);
Assert.AreEqual(-1, formatted[1].Style);
Assert.AreEqual("Cl", formatted[2].Text);
Assert.AreEqual(0, formatted[2].Style);
Assert.AreEqual("2", formatted[3].Text);
Assert.AreEqual(-1, formatted[3].Style);
}
public void NEt3DotHCl()
{
List <string> tokens = new List <string>();
Assert.IsTrue(AbbreviationLabel.Parse("NEt3·HCl", tokens));
Assert.AreEqual(5, tokens.Count);
Assert.AreEqual("N", tokens[0]);
Assert.AreEqual("Et3", tokens[1]);
Assert.AreEqual("·", tokens[2]);
Assert.AreEqual("H", tokens[3]);
Assert.AreEqual("Cl", tokens[4]);
List <AbbreviationLabel.FormattedText> formatted = AbbreviationLabel.Format(tokens);
AbbreviationLabel.Reduce(formatted, 0, formatted.Count);
Assert.AreEqual(3, formatted.Count);
Assert.AreEqual("NEt", formatted[0].Text);
Assert.AreEqual(AbbreviationLabel.STYLE_NORMAL, formatted[0].Style);
Assert.AreEqual("3", formatted[1].Text);
Assert.AreEqual(AbbreviationLabel.STYLE_SUBSCRIPT, formatted[1].Style);
Assert.AreEqual("·HCl", formatted[2].Text);
Assert.AreEqual(AbbreviationLabel.STYLE_NORMAL, formatted[2].Style);
}
public void NonAsciiLabel()
{
// phenyl
Assert.IsFalse(AbbreviationLabel.Parse("苯基", new List <string>()));
}
public void ParseNumberOnly()
{
Assert.IsFalse(AbbreviationLabel.Parse("1", new List <string>()));
}
public void ParseChargeOnly()
{
Assert.IsFalse(AbbreviationLabel.Parse("+", new List <string>()));
}
public void Het()
{
// 'Het' not 'He'lium and 't'erts
Assert.IsFalse(AbbreviationLabel.Parse("Het", new List <string>()));
}
/// <summary>
/// Generate a formatted abbreviation AtomSymbol for the given Hydrogen position.
/// </summary>
/// <param name="tokens">the parsed tokens</param>
/// <param name="position">hydrogen position - determines if we reverse the label</param>
/// <returns>the generated symbol</returns>
public AtomSymbol GenerateAbbreviationSymbol(List <string> tokens, HydrogenPosition position)
{
if (position == HydrogenPosition.Left)
{
AbbreviationLabel.Reverse(tokens);
}
var tmpRefPoint = new TextOutline("H", font, emSize);
var fTexts = AbbreviationLabel.Format(tokens);
var italicFont = new Typeface(font.FontFamily, FontStyles.Italic, font.Weight, font.Stretch);
var outlines = new List <TextOutline>(fTexts.Count);
foreach (var fText in fTexts)
{
var outline = fText.Style == AbbreviationLabel.STYLE_ITALIC
? new TextOutline(fText.Text, italicFont, emSize)
: new TextOutline(fText.Text, font, emSize);
// resize and position scripts
if (fText.Style == AbbreviationLabel.STYLE_SUBSCRIPT)
{
outline = outline.Resize(scriptSize, scriptSize);
outline = PositionSubscript(tmpRefPoint, outline);
}
else if (fText.Style == AbbreviationLabel.STYLE_SUPSCRIPT)
{
outline = outline.Resize(scriptSize, scriptSize);
outline = PositionSuperscript(tmpRefPoint, outline);
}
outlines.Add(outline);
}
// position the outlines relative to each other
for (int i = 1; i < outlines.Count; i++)
{
var ref_ = outlines[i - 1];
var curr = outlines[i];
// charge aligns to symbol not a subscript part
if (fTexts[i].Style == AbbreviationLabel.STYLE_SUPSCRIPT &&
fTexts[i - 1].Style == AbbreviationLabel.STYLE_SUBSCRIPT && i > 1)
{
ref_ = outlines[i - 2];
}
outlines[i] = PositionAfter(ref_, curr);
}
// find symbol where we want to attach the bond
// this becomes the primary outline
int index;
if (position == HydrogenPosition.Left)
{
for (index = outlines.Count - 1; index >= 0; index--)
{
if ((fTexts[index].Style & 0x1) == 0)
{
break;
}
}
}
else
{
for (index = 0; index < outlines.Count; index++)
{
if ((fTexts[index].Style & 0x1) == 0)
{
break;
}
}
}
var primary = outlines[index];
outlines.RemoveAt(index);
return(new AtomSymbol(primary, outlines));
}