static public Atom[] findPhosphate(Molecule m)
{
List <Atom> retVal = new List <Atom>();
Atom[] atoms = m.GetAtoms();
foreach (Atom a1 in atoms)
{
if (a1.Element == ELEMENTS.P)
{
if (a1.BondedAtoms.Length == 4)
{
bool allOxygen = true;
foreach (Atom a2 in a1.BondedAtoms)
{
if (a2.Element != ELEMENTS.O)
{
allOxygen = false;
}
}
if (allOxygen)
{
retVal.Add(a1);
}
}
}
}
return(retVal.ToArray <Atom>());
}
static public Atom[] BranchAtoms(Molecule m)
{
List <Atom> retVal = new List <Atom>();
foreach (Atom a in m.GetAtoms())
{
if (a.BondedAtoms.Length > 2)
{
retVal.Add(a);
}
}
return(retVal.ToArray());
}
static public Atom[] FindElements(Molecule m, string[] elements)
{
List <Atom> retVal = new List <Atom>();
Atom[] atoms = m.GetAtoms();
foreach (Atom a in atoms)
{
if (elements.Contains(a.Element.ToString()))
{
retVal.Add(a);
}
}
return(retVal.ToArray <Atom>());
}
static public Atom[] FindElement(Molecule m, String element)
{
List <Atom> retVal = new List <Atom>();
Atom[] atoms = m.GetAtoms();
foreach (Atom a in atoms)
{
if (a.Element.ToString() == element)
{
retVal.Add(a);
}
}
return(retVal.ToArray <Atom>());
}
static public String[] Elements(Molecule m)
{
List <string> retVal = new List <string>();
Atom[] atoms = m.GetAtoms();
foreach (Atom a in atoms)
{
if (!retVal.Contains(a.Element.ToString()))
{
retVal.Add(a.Element.ToString());
}
}
return(retVal.ToArray());
}