/// <summary>
/// 读取SDF文件中的内容，并赋值给List<SDFSection>对象。该功能通过Openbabel开源项目实现
/// </summary>
/// <param name="fileName">SDF文件名</param>
/// <returns></returns>
public static List <SDFSection> ReadSDF(string fileName)
{
List <SDFSection> result = new List <SDFSection>();
OBConversion conv = new OBConversion();
OBMol mol = new OBMol();
conv.SetInFormat("sdf");
conv.ReadFile(mol, fileName);
do //遍历SDF文件并赋值
{
SDFSection section = new SDFSection();
conv.SetOutFormat("mol");
section.MolFile = conv.WriteString(mol);
var data = mol.GetAllData(1);
foreach (var d in data)
{
if (d.GetOrigin().ToString() == "fileformatInput")
{
section.Properties.Add(new SDFProperty
{
Name = d.GetAttribute(),
Value = d.GetValue(),
});
}
}
result.Add(section);
} while (conv.Read(mol));
return(result);
}
/// <summary>
/// Calculates Hall-Kier alpha value for a molecule
/// </summary>
/// <param name="mol"></param>
/// <returns></returns>
public static double HallKierAlpha(this OBMol mol)
{
var accum = 0.0;
foreach (var atom in mol.Atoms())
{
uint atomicNumber;
try
{
atomicNumber = atom.GetAtomicNum();
}
catch (Exception)
{
continue;
}
double alpha;
var hkAlphas = AtomicConstants.GetHallKierAlphas(atomicNumber);
if (hkAlphas != null)
{
var hyb = atom.Hybridization() - 2;
var length = hkAlphas.Length;
alpha = hyb < length ? (hkAlphas[hyb].HasValue ? hkAlphas[hyb].Value : hkAlphas[length - 1].Value) : hkAlphas[length - 1].Value;
}
else
{
alpha = AtomicConstants.GetrVdW(atomicNumber) / AtomicConstants.GetrVdW(6) - 1;
}
accum += alpha;
}
return(accum);
}
public static bool pairwiseangle(OBMol mol, ref double pangle)
{
VectorVecInt mapping = new VectorVecInt();
if (findcarboxylates(mol, ref mapping))
{
double sum = 0;
List <double> angles = new List <double>();
if (mapping.Count > 1)
{
OBAtom c1 = mol.GetAtom(mapping[0][1]);
OBAtom a1 = mol.GetAtom(mapping[0][3]);
OBAtom c2 = mol.GetAtom(mapping[1][1]);
OBAtom a2 = mol.GetAtom(mapping[1][3]);
pangle = pairwiseangle(c1, a1, c2, a2);
return(true);
}
else
{
return(false);
}
}
else
{
return(false);
}
}
public MolDescriptor(OBMol mol)
{
var newMol = new OBMol(mol);
newMol.DeleteHydrogens();
this._mol = new OBMolExtended(newMol);
}
public static void moltoCML(OBMol mol, string file)
{
OBConversion obconv = new OBConversion();
obconv.SetOutFormat("cml");
obconv.WriteFile(mol, file);
}
/// <summary>
/// 从2D生成3D坐标，支持SMILES和Mol文件格式
/// </summary>
/// <param name="molString">Mol文件或者SMILES</param>
/// <returns>含有3D坐标的Mol文件</returns>
public static string Generate3D(string molString)
{
OBConversion conversion = new OBConversion();
OBMol mol = new OBMol();
if (molString.TrimEnd().EndsWith("M END"))
{
conversion.SetInFormat("mol");
}
else if (!molString.Trim().Contains(" "))
{
conversion.SetInFormat("smi");
}
else
{
throw new Exception("Wrong chemical file format !!");
}
conversion.SetOutFormat("mol");
conversion.ReadString(mol, molString);
OBBuilder builder = new OBBuilder();
builder.Build(mol);
return(conversion.WriteString(mol));
}
private void OpenStructure(string StName)
{
// Создаём OpenBabel объекты
OBConversion obconv = new OBConversion();
OBMol mol = Functions.ReadMoleculeFromFile(StName);
obconv.SetOutFormat("_png2");
obconv.AddOption("w", OBConversion.Option_type.OUTOPTIONS, panel1.Width.ToString());
obconv.AddOption("h", OBConversion.Option_type.OUTOPTIONS, panel1.Height.ToString());
string TempPic = Functions.TempFile();
obconv.WriteFile(mol, TempPic); // Пишем картинку в temp // Это такое колдунство // Мне стыдно, но по-другому не выходит
obconv.CloseOutFile();
Bitmap bmp = new Bitmap(panel1.Width, panel1.Height);
// Рисуем на панели
panel1.BackgroundImage = bmp;
Image IM = Image.FromFile(TempPic);
Graphics g = Graphics.FromImage(panel1.BackgroundImage);
g.DrawImage(IM, 0, 0);
IM.Dispose();
g.Dispose();
panel1.Invalidate();
// Высчитываем параметры
label3.Text = "Молярная масса: " + Math.Round(mol.GetExactMass(), 4);
label4.Text = "Брутто-формула: " + mol.GetFormula();
}
/// <summary>
/// Chi1v atomic valence connectivity index (order 0)
/// </summary>
/// <param name="mol"></param>
/// <returns></returns>
public static double Chi1v(this OBMol mol)
{
var deltas = mol.HkDeltas(false);
return(mol.Bonds().Where(b => deltas[b.GetBeginAtomIdx() - 1] * deltas[b.GetEndAtomIdx() - 1] > 0)
.Select(b => Math.Sqrt(1 / (double)(deltas[b.GetBeginAtomIdx() - 1] * deltas[b.GetEndAtomIdx() - 1]))).Sum());
}
public static double EstimateProperty(OBMol mol, string propName)
{
if (!obDesc.Keys.Contains(propName))
obDesc[propName] = OBDescriptor.FindType(propName);
return obDesc[propName].Predict(mol);
}
public static OBMol obminimizeUFF(OBMol mol, double crit, int steps)
{
bool sd = false;
bool cut = false;
bool newton = false;
bool hydrogens = true;
double rvdw = 6.0;
double rele = 10.0;
int freq = 10;
//var watch = Stopwatch.StartNew();
OBForceField ff = OBForceField.FindForceField("UFF");
//watch.Stop();
//watch.Start();
ff.Setup(mol);
ff.SetVDWCutOff(rvdw);
ff.SetElectrostaticCutOff(rele);
ff.SetUpdateFrequency(freq);
ff.EnableCutOff(cut);
ff.ConjugateGradientsInitialize(steps, crit);
bool done = true;
while (done)
{
done = ff.ConjugateGradientsTakeNSteps(1);
//ff.GetCoordinates(mol);
}
ff.GetCoordinates(mol);
//watch.Stop();//doesn't look like there is much I can do to optimize this, energy minimization just takes time
return(mol);
}
public void DistanceMatrixTest()
{
var converter = new OBConversion();
converter.SetInFormat("smi");
var mol = new OBMol();
converter.ReadString(mol, "CC=C");
var dMat = new FloydWarshall(mol, false, false).DistanceMatrix;
Assert.AreEqual(0d, dMat.Get(0, 0));
Assert.AreEqual(1d, dMat.Get(0, 1));
Assert.AreEqual(2d, dMat.Get(0, 2));
Assert.AreEqual(1d, dMat.Get(1, 0));
Assert.AreEqual(0d, dMat.Get(1, 1));
Assert.AreEqual(1d, dMat.Get(1, 2));
Assert.AreEqual(2d, dMat.Get(2, 0));
Assert.AreEqual(1d, dMat.Get(2, 1));
Assert.AreEqual(0d, dMat.Get(2, 2));
dMat = new FloydWarshall(mol, true, false).DistanceMatrix;
Assert.AreEqual(0d, dMat.Get(0, 0));
Assert.AreEqual(1d, dMat.Get(0, 1));
Assert.AreEqual(1.5, dMat.Get(0, 2));
Assert.AreEqual(1d, dMat.Get(1, 0));
Assert.AreEqual(0d, dMat.Get(1, 1));
Assert.AreEqual(0.5, dMat.Get(1, 2));
Assert.AreEqual(1.5, dMat.Get(2, 0));
Assert.AreEqual(0.5, dMat.Get(2, 1));
Assert.AreEqual(0d, dMat.Get(2, 2));
}
public OBMol quickMinimization(OBMol mol, string coeff, string lmpdat, bool periodic)
{
double etol = 0.0;
double ftol = 1.0e-6;
int maxiter = 40000;
int maxeval = 20000;
double padding = 50;
lammps.LAMMPSsettings minSettings = new lammps.LAMMPSsettings();
if (periodic)
{
minSettings.boundary = "p p p";
padding = 0;
}
moltoUFF(mol, coeff, lmpdat, false, padding);
///graphconverter.designgraphtoUFF(child, iodir + coeff, iodir + lmpdat, false);
//LAMMPSinstance lammps = new LAMMPSinstance(iodir + data, lmpSettings);//, &lmpptr);
lammps lmps = new lammps(minSettings);
lmps.runCommand("read_data " + lmpdat);
lmps.openFile(coeff);
lmps.minimize(etol, ftol, maxiter, maxeval, "cg");
double[,] pos = lmps.getAtomPos();
OBFunctions.updatexyz(mol, pos);
return(mol);
}
// public static bool isInCone(OBVector3 x, OBVector3 apex, OBVector3 axis, double aperture )
// {
// //got it from here:http://stackoverflow.com/questions/10768142/verify-if-point-is-inside-a-cone-in-3d-space
// //test if point x is inside an infinite cone defined by apex point with normal vector axis and aperture angle(in radians)
// double halfAperture=aperture/2;
// OBVector3 apexToXVect = OBVector3(apex,x);
// OBVector3.
// bool insideCone = StarMath.dotProduct(apex,axis)/StarMath.norm2(apexToXVect)/StarMath.norm2(axis) > Math.Cos(aperture);
// return insideCone;
// }
public static bool atomsInCarboxylateCone(OBAtom a, OBAtom carba, OBMol mol)
{
//angle should probably not be hardcoded
double aperture = 120 * Math.PI / 180;
double[] axis = obvec2dubs(OBVector3.Sub(carba.GetVector(), a.GetVector()));
//axis = StarMath.divide (axis, StarMath.norm2 (axis));
double[] apex = obvec2dubs(carba.GetVector());
List <uint> exclude = new List <uint>();
exclude.Add(carba.GetIdx());
foreach (OBBond b in carba.Bonds())
{
OBAtom other = b.GetNbrAtom(carba);
if (other != a)
{
exclude.Add(other.GetIdx());
}
}
foreach (OBAtom n in mol.Atoms())
{
if (!exclude.Contains(n.GetIdx()))
{
double[] x = obvec2dubs(n.GetVector());
//if any point is found to be in the carboxylate's cone, return true
if (isInCone(x, apex, axis, aperture))
{
return(true);
}
}
}
return(false);
}
public static bool carboxylatesBlocked(OBMol mol, OBAtom aA, OBAtom carbA, OBAtom aB, OBAtom carbB)
{
bool inCone = OBFunctions.atomsInCarboxylateCone(aA, carbA, mol);
inCone = inCone || OBFunctions.atomsInCarboxylateCone(aB, carbB, mol);
return(inCone);
}
/// <summary>
/// Computes the number of fragments in molecule given a SMARTS pattern
/// </summary>
/// <param name="mol"></param>
/// <param name="pattern">SMARTS pattern (string)</param>
/// <returns></returns>
public static int SmartPatternCount(this OBMol mol, string pattern)
{
var sp = new OBSmartsPattern();
sp.Init(pattern);
sp.Match(mol);
return(sp.GetUMapList().Count);
}
public static double radial_weight(OBMol mol, OBAtom carbon1, OBAtom a1)
{
OBVector3 compos = mol_com(mol);
OBVector3 v2 = carbon1.GetVector();
OBVector3 v3 = a1.GetVector();
return(openbabel_csharp.Point2Line(compos, v2, v3));
}
/// <summary>
/// 从MolFile格式生成Openbabel的OBMol对象
/// </summary>
/// <param name="molfile">Mol文件格式的字符串</param>
/// <returns>OBMol对象</returns>
public static OBMol LoadMolFromMolfile(string molfile)
{
OBConversion conversion = new OBConversion();
OBMol mol = new OBMol();
conversion.SetInFormat("mol");
conversion.ReadString(mol, molfile);
return(mol);
}
static void Main(string[] args)
{
OBConversion obconv = new OBConversion();
obconv.SetInFormat("smi");
OBMol mol = new OBMol();
obconv.ReadString(mol, "CCC");
System.Console.WriteLine(mol.GetMolWt());
//System.Console.ReadKey();
}
/// <summary>
/// 从SMILES格式生成Openbabel的OBMol对象
/// </summary>
/// <param name="smiles">SMILES格式的字符串</param>
/// <returns>OBMol对象</returns>
public static OBMol LoadMolFromSmiles(string smiles)
{
OBConversion conversion = new OBConversion();
OBMol mol = new OBMol();
conversion.SetInFormat("smi");
conversion.ReadString(mol, smiles);
return(mol);
}
/// <summary>
/// A variant which returns an OBMol based on host.
/// </summary>
/// <param name="host"></param>
/// <returns></returns>
public static OBMol designgraphtomol(designGraph host)
{
var mol = new OBMol();
Dictionary <string, int> nodeatomlookup = new Dictionary <string, int>(); //dictionary for looking up which nodes go to which atoms by their names
int i = 0;
foreach (node n in host.nodes)
{
OBAtom atom = new OBAtom();
double x = scale * n.X;
double y = scale * n.Y;
double z = scale * n.Z; //set coordinates of atom
atom.SetVector(x, y, z);
n.localLabels.Sort();
foreach (string label in n.localLabels)
{
if (label.Length < 4)
{
if (label != "sp2" && label != "sp3") ///so openbabel gets less crap
{
atom.SetAtomicNum(elementTabel[label]); //set atomic number
break;
}
}
}
i++;
nodeatomlookup.Add(n.name, i); //add the atom to dictionary and mol
mol.AddAtom(atom);
}
foreach (arc a in host.arcs)
{
int bondorder = 0;
bool hassingle = a.localLabels.Contains("s");
bool hasdouble = a.localLabels.Contains("d");
bool hastriple = a.localLabels.Contains("t"); //bonds will probably not be anything other than single, double, or triple
//although we could have dative bonds
if (hassingle ^ hasdouble ^ hastriple) //we do not want more than one bond type
{
if (hassingle)
{
bondorder = 1;
}
if (hasdouble)
{
bondorder = 2;
}
if (hastriple)
{
bondorder = 3;
}
}
mol.AddBond(nodeatomlookup[a.To.name], nodeatomlookup[a.From.name], bondorder);
}
return(mol);
}
/// <summary>
/// Проверка соответствия молекулы паттерну.
/// </summary>
/// <param name="Mol"></param>
/// <param name="DB_Mol"></param>
/// <returns></returns>
private bool CheckMol(string Mol, string DB_Mol)
{
DataBase.Log($"Получены молекула {DB_Mol} и паттерн {Mol}");
DataBase.Log($"Формирование объектов для сравнения");
// Создаём объекты OpenBabel
OBSmartsPattern SP = null;
OBConversion obconv = null;
OBMol mol = null;
try
{
SP = new OBSmartsPattern();
obconv = new OBConversion();
obconv.SetInFormat("smi");
mol = new OBMol();
obconv.ReadString(mol, Mol);
obconv.SetOutFormat("smi");
DataBase.Log($"Объекты сформированы");
}
catch (Exception e)
{
DataBase.Log($"Объекты не сформированы: причина {e.Message}");
}
string Temp = obconv.WriteString(mol);
DataBase.Log($"Обработанный паттерн {Temp}");
if (!mol.DeleteHydrogens())
{
Console.WriteLine("DeleteHidrogens() failed!");
}
; //Убираем все водороды
DataBase.Log($"Водороды убраны");
string SubMol = System.Text.RegularExpressions.Regex.Replace(obconv.WriteString(mol), "[Hh ]", ""); //Убираем все водороды
SP.Init(SubMol); //Задаём структуру поиска в SMARTS
DataBase.Log($"Инициализация поиска по паттерну {SubMol}");
obconv.SetInFormat("smi");
obconv.ReadString(mol, DB_Mol); //Добавляем структуру из БД
SP.Match(mol); //Сравниваем
DataBase.Log($"Сравнение прошло");
VectorVecInt Vec = SP.GetUMapList();
DataBase.Log($"Число совпадений {Vec.Count}");
if (Vec.Count > 0)
{
return(true);
}
else
{
return(false);
}; //Возвращаем результат
}
public List <int> moltoUFFPeriodic(OBMol mol, string coefficientfilename, string datafilename, int x_rep, int y_rep, int z_rep)
{
LAMMPSNow lammpssetup = new LAMMPSNow(parameters, atomtypes, periodictable);
lammpssetup.setupUFFPeriodic(mol, coefficientfilename, datafilename, x_rep, y_rep, z_rep);
List <int> esequence = lammpssetup.getesequence();
return(esequence);
}
public List <int> moltoUFF_azo(OBMol mol, string coefficientfilename, string datafilename, double padding)
{
LAMMPSNow lammpssetup = new LAMMPSNow(parameters, atomtypes, periodictable);
lammpssetup.setupUFF(mol, padding);
lammpssetup.setupcalculationsUFF_azobenzene(mol, coefficientfilename, datafilename);
List <int> esequence = lammpssetup.getesequence();
return(esequence);
}
public void designgraphtoCML(designGraph host, string filename)
{
OBConversion obconv = new OBConversion();
obconv.SetOutFormat("cml");
OBMol mol = new OBMol();
OBFunctions.designgraphtomol(host, ref mol);
obconv.WriteFile(mol, filename);
}
public static OBMol contingencyminimization(OBMol mol)
{
OBForceField uff = OBForceField.FindForceField("UFF");
//uff.ParseParamFile();
uff.SetLogLevel(1);
uff.Setup(mol);
uff.ConjugateGradients(10);
return(mol);
}
/// <summary>
/// Performs a mol copy and adds explicit hydrogens to each heavy atom to the copy
/// </summary>
/// <param name="mol"></param>
/// <returns>Copy of original mol with explicit hydrogens</returns>
public static OBMol AddExplicitHydrogens(this OBMol mol)
{
var newMol = new OBMol(mol);
foreach (var atom in newMol.Atoms())
{
newMol.AddHydrogens(atom);
}
return(newMol);
}
/// <summary>
/// Mol文件格式转换成SMILES格式
/// </summary>
/// <param name="molFile">Mol</param>
/// <returns>SMILES</returns>
public static string ConvertMolFileToSmiles(string molFile)
{
OBConversion conversion = new OBConversion();
OBMol mol = new OBMol();
conversion.SetInFormat("mol");
conversion.ReadString(mol, molFile);
conversion.SetOutFormat("smi");
return(conversion.WriteString(mol));
}
/// <summary>
/// Calculate the angle between 2 carboxylates
/// </summary>
public static double CalAngle(OBMol mol)
{
var mapping = OBFunctions.findcarboxylates(mol);
var carbA = mol.GetAtom(mapping[0][1]); // carbon in carboxylate
var aA = mol.GetAtom(mapping[0][3]); // atom that the carbon connects to
var carbB = mol.GetAtom(mapping[1][1]);
var aB = mol.GetAtom(mapping[1][3]);
var pAngle = OBFunctions.pairwiseangle(carbA, aA, carbB, aB); // angle between carboxylates
return(pAngle);
}
public static string moltoSMILES(OBMol mol)
{
OBConversion obconv = new OBConversion();
obconv.SetOutFormat("can");
string smi = obconv.WriteString(mol);
smi = smi.Replace("\t", "");
smi = smi.Replace("\n", "");
return(smi);
}
/// <summary>
/// Assigns Gasteiger partial charges to molecule
/// </summary>
/// <returns>OBMol with Gasteiger partial charges assigned</returns>
public static OBMol AssignGasteigerCharges(this OBMol mol)
{
var newMol = mol.AddExplicitHydrogens();
newMol.UnsetPartialChargesPerceived();
foreach (var atom in newMol.Atoms())
{
atom.GetPartialCharge();
}
return(newMol);
}
public static VectorVecInt findcarboxylates(OBMol mol)
{
//finds carboxylates and returns a mapping, mapping must be initialized
OBSmartsPattern findcbxl = new OBSmartsPattern();
findcbxl.Init("[#8]=[#6](-[#8])-*"); //find the carboxylate
var mapping = new VectorVecInt();
findcbxl.Match(mol, mapping, OBSmartsPattern.MatchType.AllUnique);
return(mapping);
}
//functions for evaluating
public static bool findcarboxylates(OBMol mol, ref VectorVecInt mapping)
{
//finds carboxylates and returns a mapping, mapping must be initialized
OBSmartsPattern
findcbxl =
new OBSmartsPattern(); //initialization is sufficiently fast that we do not need to worry about initializing an obsmartspattern and keeping it around
findcbxl.Init("[#8]=[#6](-[#8])-*"); //find the carboxylate
return(findcbxl.Match(mol, mapping, OBSmartsPattern.MatchType.AllUnique));
}
public static string Estimate(OBMol mol, params string[] propNames)
{
return OBDescriptor.GetValues(mol, "");
}
