/// <summary>
/// Checks and canonicalises options.
/// </summary>
/// <param name="ops">Space delimited string of options to pass to InChI library.
/// Each option may optionally be preceded by a command line
/// switch (/ or -).</param>
protected internal static string CheckOptions(string ops)
{
if (ops == null)
{
throw new ArgumentNullException(nameof(ops), "Null options");
}
var tok = Strings.Tokenize(ops);
var sbOptions = string.Join(" ", tok.Select(n =>
{
string op = n;
if (op.StartsWithChar('-') || op.StartsWithChar('/'))
{
op = op.Substring(1);
}
var option = InChIOption.ValueOfIgnoreCase(op);
if (option != null)
{
return(FlagChar + option.Name);
}
throw new NInchiException("Unrecognised InChI option");
}));
return(sbOptions);
}
private static string CheckOptions(string ops)
{
if (ops == null)
{
throw new ArgumentNullException(nameof(ops));
}
var sbOptions = new StringBuilder();
bool hasUserSpecifiedTimeout = false;
var tok = Strings.Tokenize(ops);
string options = string.Join(" ", tok.Select(n =>
{
string op = n;
if (op.StartsWithChar('-') || op.StartsWithChar('/'))
{
op = op.Substring(1);
}
InChIOption option = InChIOption.ValueOfIgnoreCase(op);
if (option != null)
{
return(FLAG_CHAR + option.Name);
}
else if (IsTimeoutOptions(op))
{
hasUserSpecifiedTimeout = true;
return(FLAG_CHAR + op);
}
// 1,5 tautomer option
else if (string.Equals("15T", op, StringComparison.Ordinal))
{
return(FLAG_CHAR + "15T");
}
// keto-enol tautomer option
else if (string.Equals("KET", op, StringComparison.Ordinal))
{
return(FLAG_CHAR + "KET");
}
else
{
throw new NInchiException("Unrecognised InChI option");
}
}));
if (!hasUserSpecifiedTimeout)
{
if (options.Length > 0)
{
options += " ";
}
options += FIVE_SECOND_TIMEOUT;
}
return(options);
}
/// <summary>
/// Constructor. Generates CMLMolecule from InChI.
/// </summary>
/// <param name="inchi"></param>
/// <param name="builder"></param>
/// <param name="options"></param>
internal InChIToStructure(string inchi, IChemObjectBuilder builder, IEnumerable <string> options)
{
if (options == null)
{
throw new ArgumentNullException(nameof(options));
}
try
{
input = new NInchiInputInchi(inchi, options.Select(n => InChIOption.ValueOfIgnoreCase(n)));
}
catch (NInchiException jie)
{
throw new CDKException("Failed to convert InChI to molecule: " + jie.Message);
}
GenerateAtomContainerFromInChI(builder);
}
private static string CheckOptions(string ops)
{
if (ops == null)
{
throw new ArgumentNullException(nameof(ops));
}
var sbOptions = new StringBuilder();
bool hasUserSpecifiedTimeout = false;
var tok = Strings.Tokenize(ops);
string options = string.Join(" ", tok.Select(n =>
{
string op = n;
if (op.StartsWithChar('-') || op.StartsWithChar('/'))
{
op = op.Substring(1);
}
var option = InChIOption.ValueOfIgnoreCase(op);
if (option != null)
{
return(FLAG_CHAR + option.Name);
}
else if (IsTimeoutOptions(op))
{
hasUserSpecifiedTimeout = true;
// only reformat if we actually have a decimal
if (IsSubSecondTimeout(op))
{
// because the JNI-InChI library is expecting an platform number, format it as such
var time = double.Parse(op.Substring(1));
return($"{FLAG_CHAR}W{time.ToString("F2")}");
}
else
{
return($"{FLAG_CHAR}{op}");
}
}
// 1,5 tautomer option
else if (string.Equals("15T", op, StringComparison.Ordinal))
{
return(FLAG_CHAR + "15T");
}
// keto-enol tautomer option
else if (string.Equals("KET", op, StringComparison.Ordinal))
{
return(FLAG_CHAR + "KET");
}
else
{
throw new NInchiException("Unrecognised InChI option");
}
}));
if (!hasUserSpecifiedTimeout)
{
if (options.Length > 0)
{
options += " ";
}
options += FIVE_SECOND_TIMEOUT;
}
return(options);
}
