public void NonNumber()
{
CharBuffer buffer = CharBuffer.FromString("H3");
Assert.AreEqual(buffer.GetNumber(), -1);
Assert.AreEqual(buffer.NextChar, 'H');
}
public void NoHCount()
{
CharBuffer buffer = CharBuffer.FromString("-1");
Assert.AreEqual(Parser.ReadHydrogens(buffer), 0);
Assert.IsTrue(buffer.NextIs('-'));
}
public void Length()
{
Assert.AreEqual(CharBuffer.FromString("").Length, 0);
Assert.AreEqual(CharBuffer.FromString(".").Length, 1);
Assert.AreEqual(CharBuffer.FromString("..").Length, 2);
Assert.AreEqual(CharBuffer.FromString("...").Length, 3);
}
public void NoCharge()
{
CharBuffer buffer = CharBuffer.FromString(":");
Assert.AreEqual(Parser.ReadCharge(buffer), 0);
Assert.IsTrue(buffer.NextIs(':'));
}
public void Read()
{
foreach (var config in Configuration.Values)
{
Assert.AreEqual(config,
Configuration.Read(CharBuffer.FromString(config.Symbol)));
}
}
public void GetSingleDigitNumber()
{
Assert.AreEqual(CharBuffer.FromString("1").GetNumber(), 1);
CharBuffer buffer = CharBuffer.FromString("2C");
Assert.AreEqual(buffer.GetNumber(), 2);
Assert.AreEqual(buffer.NextChar, 'C');
}
public void EndOfBufferHasNoneRemaining()
{
CharBuffer buffer = CharBuffer.FromString("-");
Assert.IsTrue(buffer.HasRemaining());
buffer.Get();
Assert.IsFalse(buffer.HasRemaining());
}
public void GetNumberWithLeadingZeros()
{
Assert.AreEqual(CharBuffer.FromString("0002").GetNumber(), 2);
CharBuffer buffer = CharBuffer.FromString("002H");
Assert.AreEqual(buffer.GetNumber(), 2);
Assert.AreEqual(buffer.NextChar, 'H');
}
public void GetTwoDigitNumber()
{
Assert.AreEqual(CharBuffer.FromString("12").GetNumber(), 12);
CharBuffer buffer = CharBuffer.FromString("20C");
Assert.AreEqual(buffer.GetNumber(), 20);
Assert.AreEqual(buffer.NextChar, 'C');
}
public void GetThreeDigitNumber()
{
Assert.AreEqual(CharBuffer.FromString("123").GetNumber(), 123);
CharBuffer buffer = CharBuffer.FromString("212C");
Assert.AreEqual(buffer.GetNumber(), 212);
Assert.AreEqual(buffer.NextChar, 'C');
}
public void GetProgressesPosition()
{
CharBuffer buffer = CharBuffer.FromString("abcd");
Assert.AreEqual(buffer.Get(), 'a');
Assert.AreEqual(buffer.Get(), 'b');
Assert.AreEqual(buffer.Get(), 'c');
Assert.AreEqual(buffer.Get(), 'd');
}
public void GetAsDigit()
{
CharBuffer buffer = CharBuffer.FromString("c1");
Assert.IsFalse(buffer.NextIsDigit());
Assert.AreEqual(buffer.Get(), 'c');
Assert.IsTrue(buffer.NextIsDigit());
Assert.AreEqual(buffer.GetAsDigit(), 1);
Assert.IsFalse(buffer.NextIsDigit());
}
public void Position()
{
Assert.AreEqual(CharBuffer.FromString("").Position, 0);
CharBuffer buffer = CharBuffer.FromString("...");
Assert.AreEqual(buffer.Position, 0);
Assert.AreEqual(buffer.Get(), '.');
Assert.AreEqual(buffer.Position, 1);
Assert.AreEqual(buffer.Get(), '.');
Assert.AreEqual(buffer.Position, 2);
Assert.AreEqual(buffer.Get(), '.');
Assert.AreEqual(buffer.Position, 3);
}
public static Graph Parse(string smi, bool strict, ISet <string> warnings)
{
if (smi == null)
{
throw new ArgumentNullException("no SMILES provided");
}
var parser = new Parser(CharBuffer.FromString(smi), strict);
foreach (var warning in parser.Warnings())
{
warnings.Add(warning);
}
return(parser.Molecule());
}
/// <summary>
/// Convenience method to create a graph from a provided SMILES string.
/// </summary>
/// <param name="smi">string containing SMILES line notation</param>.
/// <returns>graph instance from the SMILES</returns>
/// <exception cref="InvalidSmilesException">if there was a syntax error while parsing the SMILES.</exception>
public static Graph FromSmiles(string smi)
{
if (smi == null)
{
throw new ArgumentNullException(nameof(smi), "no SMILES provided");
}
var parser = new Parser(CharBuffer.FromString(smi), false);
foreach (var warn in parser.Warnings())
{
foreach (var line in warn.Split('\n'))
{
Console.Error.WriteLine($"SMILES Warning: {line}");
}
}
return(parser.Molecule());
}
public void NextDoesNotProgressPosition()
{
CharBuffer buffer = CharBuffer.FromString("abcd");
Assert.AreEqual(buffer.NextChar, 'a');
Assert.AreEqual(buffer.Position, 0);
Assert.AreEqual(buffer.NextChar, 'a');
Assert.AreEqual(buffer.Position, 0);
Assert.AreEqual(buffer.NextChar, 'a');
Assert.AreEqual(buffer.Position, 0);
Assert.AreEqual(buffer.NextChar, 'a');
Assert.AreEqual(buffer.Position, 0);
buffer.Get();
Assert.AreEqual(buffer.Position, 1);
Assert.AreEqual(buffer.NextChar, 'b');
Assert.AreEqual(buffer.Position, 1);
Assert.AreEqual(buffer.NextChar, 'b');
}
public void NextIs()
{
CharBuffer buffer = CharBuffer.FromString("[C@H]");
Assert.IsFalse(buffer.NextIs('C'));
Assert.IsFalse(buffer.NextIs('@'));
Assert.IsFalse(buffer.NextIs('H'));
Assert.IsFalse(buffer.NextIs(']'));
Assert.IsTrue(buffer.NextIs('['));
Assert.AreEqual(buffer.Get(), '[');
Assert.IsFalse(buffer.NextIs('['));
Assert.IsFalse(buffer.NextIs('@'));
Assert.IsFalse(buffer.NextIs('H'));
Assert.IsFalse(buffer.NextIs(']'));
Assert.IsTrue(buffer.NextIs('C'));
Assert.AreEqual(buffer.Get(), 'C');
Assert.IsFalse(buffer.NextIs('['));
Assert.IsFalse(buffer.NextIs('C'));
Assert.IsFalse(buffer.NextIs('H'));
Assert.IsFalse(buffer.NextIs(']'));
Assert.IsTrue(buffer.NextIs('@'));
Assert.AreEqual(buffer.Get(), '@');
Assert.IsFalse(buffer.NextIs('['));
Assert.IsFalse(buffer.NextIs('C'));
Assert.IsFalse(buffer.NextIs('@'));
Assert.IsFalse(buffer.NextIs(']'));
Assert.IsTrue(buffer.NextIs('H'));
Assert.AreEqual(buffer.Get(), 'H');
Assert.IsFalse(buffer.NextIs('['));
Assert.IsFalse(buffer.NextIs('C'));
Assert.IsFalse(buffer.NextIs('@'));
Assert.IsFalse(buffer.NextIs('H'));
Assert.IsTrue(buffer.NextIs(']'));
Assert.AreEqual(buffer.Get(), ']');
}
public void GetThreeDigitNumber_2DigitsOnly()
{
Assert.AreEqual(CharBuffer.FromString("123").GetNumber(2), 12);
}
/// <summary>
/// Create a new (loose) parser for the specified string.
/// </summary>
/// <param name="str">SMILES string</param>
/// <exception cref="InvalidSmilesException">thrown if the SMILES could not be parsed</exception>
public Parser(string str)
: this(CharBuffer.FromString(str), false)
{
}
/// <summary>
/// Strict parsing of the provided SMILES string. The strict parser will
/// throw more exceptions for unusual input.
/// </summary>
/// <param name="str">the SMILES string to process</param>
/// <returns>a graph created with the strict parser</returns>
public static Graph GetStrict(string str)
{
return(new Parser(CharBuffer.FromString(str), true).Molecule());
}
/// <summary>
/// Loose parsing of the provided SMILES string. The loose parser is more
/// relaxed and will allow abnormal aromatic elements (e.g. 'te') as well as
/// bare 'H', 'D' and 'T' for hydrogen and it's isotopes. Note the hydrogen
/// and isotopes are replaced with their correct bracket equivalent.
/// </summary>
/// <param name="str">the SMILES string to process</param>
/// <returns>a graph created with the loose parser</returns>
public static Graph Losse(string str)
{
return(new Parser(CharBuffer.FromString(str), false).Molecule());
}
private void Verify(string str, int atomClass)
{
Assert.AreEqual(Parser.ReadClass(CharBuffer.FromString(str)), atomClass);
}
public void NonEmptyBufferHasRemaining()
{
CharBuffer buffer = CharBuffer.FromString("-");
Assert.IsTrue(buffer.HasRemaining());
}
public void EmptyBufferHasNoneRemaining()
{
CharBuffer buffer = CharBuffer.FromString("");
Assert.IsFalse(buffer.HasRemaining());
}
public void NextIsEmpty()
{
Assert.IsFalse(CharBuffer.FromString("").NextIs('?'));
}
public void InvalidSPNumber()
{
Configuration.Read(CharBuffer.FromString("@SP4"));
}
public void RingBondMismatch()
{
Parser.DecideBond(Bond.Single, Bond.Double, CharBuffer.FromString(""));
}
public void InvalidTHNumber()
{
Configuration.Read(CharBuffer.FromString("@TH5"));
}
public void RingBondDecision()
{
Assert.AreEqual(Parser.DecideBond(Bond.Double, Bond.Double, CharBuffer.FromString("")), Bond.Double);
Assert.AreEqual(Parser.DecideBond(Bond.Double, Bond.Implicit, CharBuffer.FromString("")), Bond.Double);
Assert.AreEqual(Parser.DecideBond(Bond.Implicit, Bond.Double, CharBuffer.FromString("")), Bond.Double);
}
public void NoSPNumber()
{
Configuration.Read(CharBuffer.FromString("@SP"));
}
