/// <summary>
/// Internal - load the SMARTS patterns for each atom type from MMFFSYMB.sma.
/// </summary>
/// <param name="smaIn">input stream of MMFFSYMB.sma</param>
/// <returns>array of patterns</returns>
/// <exception cref="IOException"></exception>
internal static AtomTypePattern[] LoadPatterns(Stream smaIn)
{
var matchers = new List <AtomTypePattern>();
using (var br = new StreamReader(smaIn))
{
string line = null;
while ((line = br.ReadLine()) != null)
{
if (SkipLine(line))
{
continue;
}
var cols = Strings.Tokenize(line, ' ');
var sma = cols[0];
var symb = cols[1];
try
{
matchers.Add(new AtomTypePattern(SmartsPattern.Create(sma).SetPrepare(false), symb));
}
catch (ArgumentException ex)
{
throw new IOException(ex.Message);
}
}
return(matchers.ToArray());
}
}
/// <summary>
/// Create a pattern for the provided SMARTS - if the SMARTS is '?' a pattern
/// is not created.
/// </summary>
/// <param name="smarts">a smarts pattern</param>
/// <param name="builder">chem object builder</param>
/// <returns>the pattern to match</returns>
private static Pattern CreatePattern(string smarts, IChemObjectBuilder builder)
{
var ptrn = SmartsPattern.Create(smarts, builder);
ptrn.SetPrepare(false); // avoid redoing aromaticity etc
return(ptrn);
}
/// <summary>
/// Create a pattern for the provided SMARTS - if the SMARTS is '?' a pattern
/// is not created.
/// </summary>
/// <param name="smarts">a smarts pattern</param>
/// <returns>the pattern to match</returns>
private static Pattern CreatePattern(string smarts)
{
var ptrn = SmartsPattern.Create(smarts);
ptrn.SetPrepare(false); // avoid redoing aromaticity etc
return(ptrn);
}
/// <summary>
/// Set the SMARTS patterns.
/// </summary>
/// <param name="smarts">the SMARTS</param>
private void SetSmarts(IEnumerable <string> smarts)
{
keys.Clear();
foreach (var key in smarts)
{
var qmol = new QueryAtomContainer();
var ptrn = SmartsPattern.Create(key);
ptrn.SetPrepare(false); // prepare is done once
keys.Add(new Key(key, ptrn));
}
}
/// <summary>
/// Creat a new query pharmacophore group
/// </summary>
/// <param name="symbol">The symbol for the group</param>
/// <param name="smarts">The SMARTS pattern to be used for matching</param>
public PharmacophoreQueryAtom(string symbol, string smarts)
{
this.Symbol = symbol;
this.Smarts = smarts;
// Note that we allow a special form of SMARTS where the | operator
// represents logical or of multi-atom groups (as opposed to ','
// which is for single atom matches)
var subSmarts = Strings.Tokenize(smarts, '|');
CompiledSmarts = new SmartsPattern[subSmarts.Count];
for (int i = 0; i < CompiledSmarts.Length; i++)
{
CompiledSmarts[i] = SmartsPattern.Create(subSmarts[i]).SetPrepare(false);
}
}
