public virtual void Visit(ArraySource arraySource, State state)
{
foreach (var item in arraySource.Items)
{
if (_exitFast)
{
return;
}
VisitCore(item, state);
}
}
public Aa(int residueNumber, bool nTerminus, bool cTerminus)
{
_atoms = new ArraySource <IAtom>(this);
//AtomDefinition[] atomDefinitions = AaTable.GetAtomDefinitions(residueNumber, nTerminus, cTerminus);
//Atom[] atoms = new Atom[atomDefinitions.Length];
//for(int i = 0; i < atomDefinitions.Length; i++)
//{
// Vector3 position = new Vector3(atomDefinitions[i].X, atomDefinitions[i].Y, atomDefinitions[i].Z);
// atoms[i] = new Atom(atomDefinitions[i], position);
//}
//AddRange(atoms);
IsNTerminus = nTerminus;
IsCTerminus = cTerminus;
ResidueNumber = residueNumber;
}
public Aa(IAa other, bool nTerminus, bool cTerminus)
{
_atoms = new ArraySource <IAtom>(this, other);
ResidueNumber = other.ResidueNumber;
IsNTerminus = nTerminus;
IsCTerminus = cTerminus;
AtomDefinition[] definitions = AaTable.GetAtomDefinitions(ResidueNumber, IsNTerminus, IsCTerminus);
Matrix unidentifiedAtomTransform = Matrix.Identity;
//if (TransformSetting == TransformSettings.Transform)
{
Vector3[] vLocal = new Vector3[] { definitions[N_].Xyz, definitions[CA_].Xyz, definitions[C_].Xyz };
Vector3[] vOther = new Vector3[] { other[N_].Xyz, other[CA_].Xyz, other[C_].Xyz };
unidentifiedAtomTransform = VectorMath.GetRmsdAlignmentMatrix(vLocal, false, vOther, false);
}
// Create atoms at final positions
for (int i = 0; i < definitions.Length; i++)
{
Vector3 position = Vector3.Transform(definitions[i].Xyz, unidentifiedAtomTransform);
Atom atom = new Atom(definitions[i], position);
Add(atom);
}
this[N_].Xyz = other[N_].Xyz;
this[CA_].Xyz = other[CA_].Xyz;
this[C_].Xyz = other[C_].Xyz;
this[O_].Xyz = other[O_].Xyz;
for (int i = Aa.SidechainStart_; i < other.Count; i++)
{
IAtom otherAtom = other[i];
IAtom thisAtom = this[otherAtom.Name];
if (thisAtom != null)
{
thisAtom.Xyz = otherAtom.Xyz;
}
}
// Remove parent context - this will result in atoms NOT BEING IN THE ORIGINAL LOCATION
this.Parent = null;
}
/// <summary>
/// Scans for all the grammar rules that are considered for the token at the specified text position.
/// </summary>
private Parser <LexicalToken> GetBestGrammarAtPosition(int position)
{
var offset = GetTokenIndex(position);
var source = new ArraySource <LexicalToken>(_code.LexerTokens);
Parser <LexicalToken> bestGrammar = null;
int bestLength = -1;
_code.Grammar.Search(source, (_parser, _source, _start, _prevWasMissing) =>
{
// capture the best grammar
if (_start == offset && _parser.Tag != null)
{
var scanLength = _parser.Scan(source, _start);
if (scanLength > bestLength)
{
bestGrammar = _parser;
bestLength = scanLength;
}
}
});
return(bestGrammar);
}
public ArrayEnumerator(ArraySource <T> source)
{
Source = source;
}
private TArray(ArraySource <T> arrayData)
{
ArrayData = arrayData;
}
public SequentialModel(IReadOnlyList <ILayer> layers, ArraySource?arraySource = null)
{
Layers = layers;
ArraySource = arraySource ?? (size => new double[size]);
}
public SequentialModel(ArraySource arraySource, params ILayer[] layers) : this(layers, arraySource)
{
}
