/// <summary>
/// A variant which returns an OBMol based on host.
/// </summary>
/// <param name="host"></param>
/// <returns></returns>
public static OBMol designgraphtomol(designGraph host)
{
OBElementTable periodictable = new OBElementTable();
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);
int anum = 0;
n.localLabels.Sort();
foreach (string label in n.localLabels)
{
if (label.Length < 4)
{
if (label != "sp2" && label != "sp3") ///so openbabel gets less crap
{
anum = periodictable.GetAtomicNum(label);
if (anum > 0)
{
break;
}
}
}
}
i++;
atom.SetAtomicNum(anum); //set atomic number
nodeatomlookup.Add(n.name, i); //add the atom to dictionary and mol
mol.AddAtom(atom);
}
foreach (arc a in host.arcs)
{
OBBond bond = new OBBond();
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);
}
public void parsePDB()
{
// for determining hydrogen bonds
List <Vector3> hBondAcceptors = new List <Vector3> ();
List <Vector3> hBondDonors = new List <Vector3> ();
parseMol: // iteration start if multiple input files are used
BezierSpline[] ribbonSplineList = new BezierSpline[30]; //for drawing protein lines (30 is max number of chains)
int numAtoms = (int)mol.NumAtoms() + 1;
atoms = new GameObject[numAtoms];
int maxHelix = 500;
radius = new float[maxHelix, numAtoms];
int ribbonChainIndex = 0;
OBElementTable table = new OBElementTable();
int currentChain = -1;
OBAtom[] alphaCarbons = new OBAtom[numAtoms / 4];
int alphaCarbonCount = 0;
List <Vector3> atomPositions = new List <Vector3> ();
List <string> atomElements = new List <string> ();
for (int i = 1; i < numAtoms; i++)
{
OBAtom atom = mol.GetAtom(i);
string tag;
OBResidue res = atom.GetResidue();
Vector3 position = new Vector3((float)atom.GetX(), (float)atom.GetY(), (float)atom.GetZ());
string elem = table.GetSymbol((int)atom.GetAtomicNum()).ToUpper();
//checks for pharmacophore labels
if (res.GetName() == "ACC" || res.GetName() == "FOB" || res.GetName() == "POS" || res.GetName() == "NEG" || res.GetName() == "RNG" || res.GetName() == "DON")
{
if (atom.IsHydrogen()) //added hydrogens gets the same resName and has to be ignored
{
continue;
}
renderPharmacophore = true;
}
else
{
renderPharmacophore = false;
}
// pharmacophores
if (res.GetName() == "EXC")
{
if (atom.IsHydrogen()) //added hydrogens gets the same resName and has to be ignored
{
continue;
}
renderEXC = true;
renderPharmacophore = true;
}
else
{
renderEXC = false;
}
//creates the atom object
atoms[i] = createAtomType(elem, position);
int n;
if (int.TryParse(res.GetName(), out n))
{
if (CollectionOfLigands == null)
{
CollectionOfLigands = new List <List <GameObject> >();
CollectionOfLigands.Add(new List <GameObject>());
}
while (n + 1 > CollectionOfLigands.Count)
{
CollectionOfLigands.Add(new List <GameObject>());
}
CollectionOfLigands[n].Add(atoms[i]);
}
if (res.GetResidueProperty(9)) //water
{
tag = "water";
}
else if (res.GetAtomProperty(atom, 4) || (atom.IsHydrogen() && !res.GetResidueProperty(5))) //ligand
{
if (res.GetResidueProperty(5)) //ion (should be 3 but a bug in openbabel labels ions as protein, thats why the check has to be done inside the ligand check)
{
tag = "ion";
}
else
{
TextMesh lText = atoms [i].transform.Find("Text").GetComponent <TextMesh> ();
lText.color = textColor;
if (renderPharmacophore)
{
tag = "hetatms"; //make sure pharmacophores always show
lText.text = res.GetName() + ":" + res.GetIdx();
lText.fontSize = labelFontSize;
}
else
{
tag = "hetatmbs";
if (ligandText)
{
lText.text = elem + ":" + i.ToString();
lText.fontSize = labelFontSize;
}
}
if (sphere)
{
atoms [i].transform.localScale *= 4;
}
if (atom.IsHbondAcceptor())
{
foreach (Vector3 candidatePos in hBondDonors)
{
checkHBond(candidatePos, position);
}
}
if (atom.IsHbondDonor())
{
foreach (Vector3 candidatePos in hBondAcceptors)
{
checkHBond(candidatePos, position);
}
}
}
}
else //protein
{
tag = "balls";
atomPositions.Add(position);
atomElements.Add(elem);
if (atom.IsHbondAcceptor())
{
hBondAcceptors.Add(position);
}
else
{
hBondDonors.Add(position);
}
if (res.GetAtomProperty(atom, 0)) //alpha carbon
{
alphaCarbons[alphaCarbonCount] = atom;
if (alphaCarbonCount > 6) //check if the ribbon is alpha helix using torsion angles
{
double torsion = mol.GetTorsion(atom, alphaCarbons[alphaCarbonCount - 1], alphaCarbons[alphaCarbonCount - 2], alphaCarbons[alphaCarbonCount - 3]);
double prevTorsion = mol.GetTorsion(alphaCarbons[alphaCarbonCount - 4], alphaCarbons[alphaCarbonCount - 5], alphaCarbons[alphaCarbonCount - 6], alphaCarbons[alphaCarbonCount - 7]);
double torsionSum = torsion + prevTorsion;
if (torsionSum > 99 && torsionSum < 111)
{
for (int j = ribbonChainIndex - 7; j <= ribbonChainIndex; j++)
{
radius [currentChain, j] = 1.5f; //alpha helix
}
}
else
{
radius [currentChain, ribbonChainIndex] = 0.5f;
}
}
alphaCarbonCount++;
if (proteinText) //only displays text on alpha carbons
{
TextMesh pText = atoms [i].transform.Find("Text").GetComponent <TextMesh> ();
pText.color = textColor;
pText.text = res.GetName() + " -" + res.GetNumString();
pText.fontSize = labelFontSize;
}
int tempChain = (int)res.GetChainNum();
if (tempChain != currentChain)
{
currentChain = tempChain;
ribbonChainIndex = 0;
}
//add points for ribbon rendering
addBezierPoint(ribbonSplineList, currentChain, ribbonChainIndex, position);
ribbonChainIndex++;
}
}
atoms[i].transform.tag = tag;
centerPos += position;
centerCount++;
}
//createSurface (atomPositions,atomElements);
Debug.Log(hBondAcceptors.Count + " " + hBondDonors.Count);
//evaluate bonds
for (int i = 0; i < mol.NumBonds(); i++)
{
OBBond bond = mol.GetBond(i);
OBAtom atom = mol.GetAtom((int)bond.GetBeginAtomIdx());
OBResidue res = atom.GetResidue();
bool ligand = res.GetAtomProperty(atom, 4) || (atom.IsHydrogen() && !res.GetResidueProperty(5));
if (ligand && sphere) //no ligand bonds if display mode is CPK sphere
{
continue;
}
try {
connect(atoms[bond.GetBeginAtomIdx()], atoms[bond.GetEndAtomIdx()], bond);
} catch (System.Exception e) {
Debug.Log(e);
}
}
//handle pharmacophore vectors
if (mol.HasData("VECTOR"))
{
string[] vectors = mol.GetData("VECTOR").GetValue().Split(new string[] { "\n" }, StringSplitOptions.None);
foreach (string vector in vectors)
{
string[] idx = vector.Split((char[])null, StringSplitOptions.RemoveEmptyEntries);
try {
Vector3 pos = new Vector3(float.Parse(idx[1]), float.Parse(idx[2]), float.Parse(idx[3]));
int id = int.Parse(idx[0]);
drawVector(atoms[id], pos, mol.GetAtom(id).GetResidue().GetName());
} catch (System.Exception e) {
Debug.Log(e);
}
}
}
//render protein ribbons
drawRibbons(ribbonSplineList, "ribbons"); //must be before alpha due to indexing
drawRibbons(ribbonSplineList, "alpha");
// check for separate ligand file
if (file.Contains("protein"))
{
file = file.Replace("protein", "ligand");
string file1 = file.Replace("." + extension, ".sdf"); // .+extension incase the format would also appear in the file name
string file2 = file.Replace("." + extension, ".mol2");
if (File.Exists(file1))
{
readMol(file);
goto parseMol;
}
else if (File.Exists(file2))
{
readMol(file);
goto parseMol;
}
}
center = createObject(new GameObject(), centerPos / centerCount); //the center of the pdb
show();
}
public designGraph moltoDesignGraph(OBMol mol)
{
//OBConversion obconv = new OBConversion ();
designGraph host = new designGraph();
OBConversion obconv = new OBConversion();
Dictionary <uint, int> atomid2nodeid = new Dictionary <uint, int>();
//obconv.SetInFormat("smi");
//var format =obconv.GetInFormat();
//uint d=mol.NumAtoms();
OBElementTable ptable = new OBElementTable();
//mol.FindTorsions ();
int nodecount = 0;
//loop through all atoms in the file and make them into nodes in the graph
foreach (OBAtom a in mol.Atoms())
{
node n = new node();
n.name = "n" + nodecount;
var atype = a.GetAtomType();
n.X = a.GetX() * (1 / scale);
n.Y = a.GetY() * (1 / scale);
n.Z = a.GetZ() * (1 / scale);
uint anum = a.GetAtomicNum();
string sym = ptable.GetSymbol((int)anum);
//double test =ptable.GetIonization ((int)anum);
int maxbonds = ptable.GetMaxBonds((int)anum);
uint val = a.GetImplicitValence();
n.localLabels.Add(sym);
n.localLabels.Add(atype);
n.localVariables.Add((double)maxbonds);
n.localVariables.Add((double)val);
host.addNode(n);
atomid2nodeid.Add(a.GetId(), nodecount);
//Console.WriteLine (x);
nodecount++;
}
int arccount = 0;
foreach (OBBond b in mol.Bonds())
{
arc ac = new arc();
ac.directed = false;
ac.name = "a" + arccount;
//uint bondorder = b.GetBondOrder ();
if (b.IsSingle())
{
ac.localLabels.Add("s");
}
if (b.IsTriple())
{
ac.localLabels.Add("t");
}
if (b.IsDouble())
{
ac.localLabels.Add("d");
}
uint toid = b.GetEndAtomIdx();
uint fromid = b.GetBeginAtomIdx();
ac.To = host.nodes[atomid2nodeid[toid - 1]];
ac.From = host.nodes[atomid2nodeid[fromid - 1]];
host.arcs.Add(ac);
arccount++;
}
return(host);
}
