static public Atom[] FindBromide(Molecule m)
{
return(FindElement(m, "Br"));
}
static public Atom[] FindHalides(Molecule m)
{
string[] halogens = { "F", "Cl", "Br", "I" };
return(FindElements(m, halogens));
}
static public string[] PhosphorousFunctionality(Molecule m)
{
List <string> retVal = new List <string>();
// Get the P atons.
Atom[] p = FindElement(m, "P");
// If there aren't any, returnn an array with zero elements.
if (p.Length == 0)
{
return(retVal.ToArray <string>());
}
// Look for a heterocyclic containing P
Atom[][] pHeteorRings = HeteroCyclic(m, "P");
if (pHeteorRings.Length != 0)
{
// If there is one, add the 'phosphorine' functionality.
retVal.Add("phosphorine");
}
// Now lets look what is attached to each Phosphorous atom...
foreach (Atom a in p)
{
List <Atom> O = new List <Atom>();
List <Atom> N = new List <Atom>();
List <Atom> S = new List <Atom>();
List <Atom> C = new List <Atom>();
List <Atom> P = new List <Atom>();
//Atom a = m.GetAtoms()[p[i]];
//Atom[] bonded = a.BondedAtoms;
//for (int j = 0; j < bonded.Length; j++)
// If it connected to two other atoms...
foreach (Atom bonded in a.BondedAtoms)
{
switch (bonded.Element)
{
case ELEMENTS.C:
C.Add(bonded);
break;
case ELEMENTS.N:
N.Add(bonded);
break;
case ELEMENTS.O:
O.Add(bonded);
break;
case ELEMENTS.P:
P.Add(bonded);
break;
case ELEMENTS.S:
S.Add(bonded);
break;
}
}
if (a.BondedAtoms.Length == 2)
{
}
if (a.BondedAtoms.Length == 3)
{
if (C.Count == 3)
{
retVal.Add("phosphine");
}
if (O.Count == 3)
{
retVal.Add("phosphite");
}
if ((O.Count == 2) && (C.Count == 1))
{
retVal.Add("phosphonite");
}
if ((O.Count == 1) && (C.Count == 2))
{
retVal.Add("phosphinite");
}
if ((O.Count == 2) && (N.Count == 1))
{
retVal.Add("phosphoramidite");
}
if ((O.Count == 1) && (N.Count == 2))
{
retVal.Add("phosphorodiamidite");
}
if ((O.Count == 1) && (N.Count == 1) && (C.Count == 1))
{
retVal.Add("phosphonamidite");
}
if ((O.Count == 2) && (S.Count == 1))
{
retVal.Add("phosphorothioite");
}
if ((O.Count == 1) && (S.Count == 2))
{
retVal.Add("phosphorodithioite");
}
}
if (a.BondedAtoms.Length == 4)
{
if (O.Count == 4)
{
retVal.Add("phosphate");
}
if ((O.Count == 3) && (C.Count == 1))
{
retVal.Add("phosphonate");
}
if ((O.Count == 2) && (C.Count == 2))
{
retVal.Add("phosphinate");
}
if ((O.Count == 1) && (C.Count == 3))
{
retVal.Add("phospine oxide");
}
if ((O.Count == 3) && (N.Count == 1))
{
retVal.Add("phosphoramidate");
}
if ((O.Count == 2) && (N.Count == 2))
{
retVal.Add("phosphorodiamidate");
}
if ((O.Count == 1) && (N.Count == 3))
{
retVal.Add("phosphoramide");
}
if ((O.Count == 2) && (N.Count == 1) && (C.Count == 1))
{
retVal.Add("phosphonamidate");
}
if ((O.Count == 1) && (N.Count == 2) && (C.Count == 1))
{
retVal.Add("phosphonamide");
}
if ((O.Count == 1) && (N.Count == 1) && (C.Count == 2))
{
retVal.Add("phosphinamide");
}
if ((O.Count == 3) && (S.Count == 1))
{
retVal.Add("phosphorothioate");
}
if ((O.Count == 2) && (S.Count == 2))
{
retVal.Add("phosphorodithioate");
}
}
}
return(retVal.ToArray <string>());
}
static public Atom[] FindChloride(Molecule m)
{
return(FindElement(m, "Cl"));
}
void ImportMolFile(string filename)
{
atomTable.Clear();
bondTable.Clear();
molecule = new Molecule();
int numAtoms = 0;
int numBonds = 0;
// This information is contained in the header (first 3 lines) of the mol file. It is currently not being used, but code has been created for
// future use.
string name = string.Empty;
string program = string.Empty;
string user = string.Empty;
//// used to test Line 2 reading below.
//string MM = string.Empty;
//string DD = string.Empty;
//string YY = string.Empty;
//string HH = string.Empty;
//string mm = string.Empty;
int MM = 1;
int DD = 1;
int YY = 0;
int HH = 0;
int mm = 0;
string dimensionalCodes = string.Empty;
//// used to test Line 2 reading below.
//string scalingFactor1 = string.Empty;
int scalingFactor1 = 0;
//// used to test Line 2 reading below.
//string scalingFactor2 = string.Empty;
double scalingFactor2 = 0;
// used to test Line 2 reading below.
string energy = string.Empty;
string registryNumber = string.Empty;
string comments = string.Empty;
using (var reader = new System.IO.StreamReader(filename))
{
string s = reader.ReadToEnd();
string[] lines = s.Split('\n');
// Line 1 contains the compound name. It can not be longer than 80 characters, and is allowed to be empty.
// The length of the line is not relevant in how this is read, so it is not checked.
name = lines[0];
//// used to test Line 2 reading below.
//lines[1] = "IIPPPPPPPPMMDDYYHHmmddSSssssssssssEEEEEEEEEEEERRRRRR";
// Line 2 is optional. Skip this if it is not there.
if (lines[1] != string.Empty)
{
// Line format: IIPPPPPPPPMMDDYYHHmmddSSssssssssssEEEEEEEEEEEERRRRRR
// A2<--A8--><---A10-->A2I2<--F10.5-><---F12.5--><-I6->
//User's first and last initials (l), program name (P), date/time (M/D/Y,H:m),
//dimensional codes (d), scaling factors (S, s), energy (E) if modeling program input,
//internal registry number (R) if input through MDL form.
if (lines[1].Length > 2)
{
user = lines[1].Substring(0, 2); // II
}
if (lines[1].Length > 10)
{
program = lines[1].Substring(2, 8); // PPPPPPPP
}
if (lines[1].Length > 20)
{
//// used to test Line 2 reading below.
//MM = lines[1].Substring(10, 2); // MMDDYYHHmm
//DD = lines[1].Substring(12, 2); // MMDDYYHHmm
//YY = lines[1].Substring(14, 2); // MMDDYYHHmm
//HH = lines[1].Substring(16, 2); // MMDDYYHHmm
//mm = lines[1].Substring(18, 2); // MMDDYYHHmm
MM = Convert.ToInt32(lines[1].Substring(10, 2)); // MMDDYYHHmm
DD = Convert.ToInt32(lines[1].Substring(12, 2)); // MMDDYYHHmm
YY = Convert.ToInt32(lines[1].Substring(14, 2)); // MMDDYYHHmm
HH = Convert.ToInt32(lines[1].Substring(16, 2)); // MMDDYYHHmm
mm = Convert.ToInt32(lines[1].Substring(18, 2)); // MMDDYYHHmm
}
if (lines[1].Length > 22)
{
dimensionalCodes = lines[1].Substring(20, 2); // dd
}
//// used to test Line 2 reading below.
// if (lines[1].Length > 24) scalingFactor1 = lines[1].Substring(22, 2); //SS
if (lines[1].Length > 24)
{
scalingFactor1 = Convert.ToInt32(lines[1].Substring(22, 2)); //SS
}
//// used to test Line 2 reading below.
// if (lines[1].Length > 34) scalingFactor2 = lines[1].Substring(24, 10); //ss
if (lines[1].Length > 34)
{
scalingFactor2 = Convert.ToDouble(lines[1].Substring(24, 10)); //ss
}
if (lines[1].Length > 46)
{
energy = lines[1].Substring(34, 12); //EEEEEEEEEEEE
}
if (lines[1].Length == 52)
{
registryNumber = lines[1].Substring(46, 6); //RRRRRR
}
}
comments = lines[2];
// Counts Line
// aaabbblllfffcccsssxxxrrrpppiiimmmvvvvvv
numAtoms = Convert.ToInt32(lines[3].Substring(0, 3));
numBonds = Convert.ToInt32(lines[3].Substring(3, 3));
int atomLists = Convert.ToInt32(lines[3].Substring(6, 3));
//int fObsolete = Convert.ToInt32(lines[3].Substring(9, 3));
bool chiral = false;
if (Convert.ToInt32(lines[3].Substring(12, 3)) == 1)
{
chiral = true;
}
int sText = Convert.ToInt32(lines[3].Substring(15, 3));
//int xObsolete = Convert.ToInt32(lines[3].Substring(18, 3));
//int rObsolete = Convert.ToInt32(lines[3].Substring(21, 3));
//int pObsolete = Convert.ToInt32(lines[3].Substring(24, 3));
//int iObsolete = Convert.ToInt32(lines[3].Substring(27, 3));
int properties = Convert.ToInt32(lines[3].Substring(30, 3));
string version = lines[3].Substring(33, 6);
molecule = new Molecule();
for (int i = 0; i < numAtoms; i++)
{
Atom a = molecule.AddAtom(lines[4 + i].Substring(31, 3).Replace(" ", string.Empty));
// xxxxx.xxxxyyyyy.yyyyzzzzz.zzzz aaaddcccssshhhbbbvvvHHHrrriiimmmnnneee
a.x = Convert.ToDouble(lines[4 + i].Substring(0, 10));
a.y = Convert.ToDouble(lines[4 + i].Substring(10, 10));
a.z = Convert.ToDouble(lines[4 + i].Substring(20, 10));
string text = lines[4 + i].Substring(34, 2);
a.massDiff = Convert.ToInt32(lines[4 + i].Substring(34, 2));
a.charge = Convert.ToInt32(lines[4 + i].Substring(36, 3));
a.stereoParity = Convert.ToInt32(lines[4 + i].Substring(39, 3));
a.hydrogenCount = Convert.ToInt32(lines[4 + i].Substring(42, 3));
a.stereoCareBox = Convert.ToInt32(lines[4 + i].Substring(45, 3));
a.valence = Convert.ToInt32(lines[4 + i].Substring(48, 3));
// string H0 = lines[4 + i].Substring(51, 3);
// a.HO = Convert.ToInt32(lines[4 + i].Substring(51, 3));
a.rNotUsed = lines[4 + i].Substring(54, 3);
a.iNotUsed = lines[4 + i].Substring(57, 3);
a.atomMapping = Convert.ToInt32(lines[4 + i].Substring(60, 3));
a.inversionRetension = Convert.ToInt32(lines[4 + i].Substring(63, 3));
a.exactChange = Convert.ToInt32(lines[4 + i].Substring(66, 3));
//DataRow atomRow = atomTable.NewRow();
//atomTable.Rows.Add(atomRow);
//atomRow["X"] = a.x;
//atomRow["Y"] = a.y;
//atomRow["Z"] = a.z;
//atomRow["element"] = a.Element.ToString();
//atomRow["MassDiff"] = a.massDiff;
//atomRow["Charge"] = a.charge;
//atomRow["StereoParity"] = a.stereoParity;
//atomRow["HydrogenCount"] = a.hydrogenCount;
//atomRow["StereoBoxCare"] = a.stereoCareBox;
//atomRow["Valence"] = a.valence;
////atomRow["H0"] = a.HO;
//atomRow["rNotUsed"] = a.rNotUsed;
//atomRow["iNotUsed"] = a.iNotUsed;
//atomRow["AtomMapping"] = a.atomMapping;
//atomRow["InversionRetention"] = a.inversionRetension;
//atomRow["ExactChange"] = a.exactChange;
}
for (int i = 0; i < numBonds; i++)
{
Bond b = new Bond();
// 111222tttsssxxxrrrccc
string line = lines[4 + numAtoms + i];
b.firstAtom = Convert.ToInt32(lines[4 + numAtoms + i].Substring(0, 3));
b.secondAtom = Convert.ToInt32(lines[4 + numAtoms + i].Substring(3, 3));
b.bondType = (BondType)Convert.ToInt32(lines[4 + numAtoms + i].Substring(6, 3));
b.bondStereo = (BondStereo)Convert.ToInt32(lines[4 + numAtoms + i].Substring(9, 3));
b.xNotUsed = lines[4 + numAtoms + i].Substring(12, 3);
b.bondTopology = (BondTopology)Convert.ToInt32(lines[4 + numAtoms + i].Substring(15, 3));
int reactingCenter = Convert.ToInt32(lines[4 + numAtoms + i].Substring(18, 3));
if (reactingCenter == 13)
{
b.reactingCenter = BondReactingCenterStatus.bondMadeOrBroken | BondReactingCenterStatus.bondOrderChanges | BondReactingCenterStatus.aCenter;
}
else if (reactingCenter == 12)
{
b.reactingCenter = BondReactingCenterStatus.bondMadeOrBroken | BondReactingCenterStatus.bondOrderChanges;
}
else if (reactingCenter == 9)
{
b.reactingCenter = BondReactingCenterStatus.bondOrderChanges | BondReactingCenterStatus.aCenter;
}
else if (reactingCenter == 5)
{
b.reactingCenter = BondReactingCenterStatus.bondMadeOrBroken | BondReactingCenterStatus.aCenter;
}
else
{
b.reactingCenter = (BondReactingCenterStatus)reactingCenter;
}
DataRow bondRow = bondTable.NewRow();
bondRow["firstAtom"] = b.firstAtom;
bondRow["secondAtom"] = b.secondAtom;
bondRow["bondType"] = b.bondType;
bondRow["bondStereo"] = b.bondStereo;
bondRow["xNotUsed"] = b.xNotUsed;
bondRow["bondTopology"] = b.bondTopology;
bondRow["reactingCenter"] = b.reactingCenter;
molecule.AddBond(b.firstAtom - 1, b.secondAtom - 1);
}
}
}
