public Bond(Atom parent, Atom connectedAtom, BondType type, BondStereo stereo, BondTopology topology, BondReactingCenterStatus rcStatus)
{
ParentAtom = parent;
ConnectedAtom = connectedAtom;
BondType = type;
DrawType = type;
Stereo = stereo;
Topology = topology;
ReactingCenter = rcStatus;
BondLength = 0; // parent.CovalentRadius + connectedAtom.CovalentRadius;
}
public Bond AddBond(Atom atom, BondType type, BondStereo stereo, BondTopology topology, BondReactingCenterStatus rcStatus)
{
Bond b = new Bond(this, atom, type, BondStereo.NotStereoOrUseXYZ, BondTopology.Either, BondReactingCenterStatus.notACenter);
this.BondedAtoms.Add(b);
return(b);
}
//static Molecule ReadMoleFile(string filename)
//{
// using (var reader = new System.IO.StreamReader(filename))
// {
// string s = reader.ReadToEnd();
// if (s.Contains("V2000")) return MoleFileReader.ParseMoleFile2(s);
// if (s.Contains("V3000")) throw new Exception("Version 3000 Mol file is currently not supported.");
// throw new Exception("Mol file type not recognized. It is does not contain a version number.");
// }
//}
static Molecule ParseMoleFile2(string moleFile)
{
Molecule molecule = new Molecule();
//atoms.Clear();
//cycles.Clear();
//fusedRings.Clear();
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;
string[] lines = moleFile.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);
for (int i = 0; i < numAtoms; i++)
{
Atom a = new ChemInfo.Atom(lines[4 + i].Substring(31, 3).Trim());
molecule.AddAtom(a);
// 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));
}
for (int i = 0; i < numBonds; i++)
{
//Bond b = new Bond();
// 111222tttsssxxxrrrccc
string line = lines[4 + numAtoms + i];
int firstAtom = Convert.ToInt32(lines[4 + numAtoms + i].Substring(0, 3));
int secondAtom = Convert.ToInt32(lines[4 + numAtoms + i].Substring(3, 3));
BondType bondType = (BondType)Convert.ToInt32(lines[4 + numAtoms + i].Substring(6, 3));
BondStereo bondStereo = (BondStereo)Convert.ToInt32(lines[4 + numAtoms + i].Substring(9, 3));
string xNotUsed = lines[4 + numAtoms + i].Substring(12, 3);
BondTopology bondTopology = (BondTopology)Convert.ToInt32(lines[4 + numAtoms + i].Substring(15, 3));
int rc = Convert.ToInt32(lines[4 + numAtoms + i].Substring(18, 3));
BondReactingCenterStatus reactingCenter = BondReactingCenterStatus.Unmarked;
if (rc == 13)
{
reactingCenter = BondReactingCenterStatus.bondMadeOrBroken | BondReactingCenterStatus.bondOrderChanges | BondReactingCenterStatus.aCenter;
}
else if (rc == 12)
{
reactingCenter = BondReactingCenterStatus.bondMadeOrBroken | BondReactingCenterStatus.bondOrderChanges;
}
else if (rc == 9)
{
reactingCenter = BondReactingCenterStatus.bondOrderChanges | BondReactingCenterStatus.aCenter;
}
else if (rc == 5)
{
reactingCenter = BondReactingCenterStatus.bondMadeOrBroken | BondReactingCenterStatus.aCenter;
}
else
{
reactingCenter = (BondReactingCenterStatus)rc;
}
molecule.AddBond(molecule.Atoms[firstAtom - 1], molecule.Atoms[secondAtom - 1], bondType, bondStereo, bondTopology, reactingCenter);
}
molecule.FindRings();
return(molecule);
}