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 MolStat GetMolStat()
{
/* 统计原子 */
uint _numAtoms = mol.NumAtoms(); //所有原子总数
uint _numHvyAtoms = mol.NumHvyAtoms(); //所有除去氢原子的原子总数
int _totalCharge = mol.GetTotalCharge(); //总电荷数
int n_C = 0; // number of carbon atoms 碳原子总数
int n_C1 = 0; // number of carbon atoms with sp1 hybridization sp1杂化的碳原子数
int n_C2 = 0; // number of carbon atoms with sp1 hybridization sp2杂化的碳原子数
int n_CHB1p = 0; // number of carbon atoms with at least 1 bond to a hetero atom 至少连接一个杂原子的碳原子数
int n_CHB2p = 0; // number of carbon atoms with at least 2 bonds to a hetero atom 至少连接两个个杂原子的碳原子数
int n_CHB3p = 0; // number of carbon atoms with at least 3 bonds to a hetero atom 至少连接三个杂原子的碳原子数
int n_CHB4 = 0; // number of carbon atoms with 4 bonds to a hetero atom 连接了4个杂原子的碳原子数
int n_O = 0; // number of oxygen atoms 氧原子数
int n_O2 = 0; // number of sp2-hybridized oxygen atoms sp2杂化的氧原子数
int n_O3 = 0; // number of sp3-hybridized oxygen atoms sp3杂化的氧原子数
int n_N = 0; // number of nitrogen atoms 氮原子数
int n_N1 = 0; // number of sp-hybridized nitrogen atoms sp杂化的氮原子数
int n_N2 = 0; // number of sp2-hybridized nitrogen atoms sp2杂化的氮原子数
int n_N3 = 0; // number of sp3-hybridized nitrogen atoms sp3杂化的氮原子数
int n_S = 0; // number of sulfur atoms 硫原子数
int n_SeTe = 0; // total number of selenium and tellurium atoms 硒和碲原子的数目
int n_F = 0; // number of fluorine atoms 氟原子的数目
int n_Cl = 0; // number of chlorine atoms 氯原子的数目
int n_Br = 0; // number of bromine atoms 溴原子的数目
int n_I = 0; // number of iodine atoms 碘原子的数目
int n_P = 0; // number of phosphorus atoms 磷原子的数目
int n_B = 0; // number of boron atoms 硼原子的数目
int n_Met = 0; // total number of metal atoms 金属原子的数目
int n_X = 0; // total number of "other" atoms (not listed above) and halogens 其他原子的数目，除了以上列出的之外。
for (int i = 1; i <= _numAtoms; i++)
{
OBAtom _atom = mol.GetAtom(i);
uint _AtomicNum = _atom.GetAtomicNum(); //原子种类，周期表序号
uint _hyb = _atom.GetHyb(); //原子的杂化形态，1 for sp1, 2 for sp2, 3 for sp3
uint _HeteroValence = _atom.GetHeteroValence(); //连接在这个原子上杂（非氢，碳）原子的数目
//uint _HeteroValence = _atom.GetHeteroDegree(); //For openbabel 3.0
if (_AtomicNum == 6) //碳原子
{
n_C++;
switch (_hyb)
{
case 1:
n_C1++;
break;
case 2:
n_C2++;
break;
default:
break;
}
if (_HeteroValence >= 4)
{
n_CHB4++;
}
if (_HeteroValence >= 3)
{
n_CHB3p++;
}
if (_HeteroValence >= 2)
{
n_CHB2p++;
}
if (_HeteroValence >= 1)
{
n_CHB1p++;
}
}
else if (_AtomicNum == 8)
{
n_O++;
switch (_hyb)
{
case 2:
n_O2++;
break;
case 3:
n_O3++;
break;
default:
break;
}
}
else if (_AtomicNum == 7)
{
n_N++;
switch (_hyb)
{
case 1:
n_N1++;
break;
case 2:
n_N2++;
break;
case 3:
n_N3++;
break;
default:
break;
}
}
else if (_AtomicNum == 16)
{
n_S++;
}
else if (_AtomicNum == 34 || _AtomicNum == 52)
{
n_SeTe++;
}
else if (_AtomicNum == 9)
{
n_F++;
}
else if (_AtomicNum == 17)
{
n_Cl++;
}
else if (_AtomicNum == 35)
{
n_Br++;
}
else if (_AtomicNum == 53)
{
n_I++;
}
else if (_AtomicNum == 15)
{
n_P++;
}
else if (_AtomicNum == 5)
{
n_B++;
}
else if ((_AtomicNum >= 3 && _AtomicNum <= 4) || (_AtomicNum >= 11 && _AtomicNum <= 13) || (_AtomicNum >= 19 && _AtomicNum <= 32) || (_AtomicNum >= 37 && _AtomicNum <= 51) || (_AtomicNum >= 55 && _AtomicNum <= 84) || (_AtomicNum >= 87))
{
n_Met++;
}
}
n_X = (int)_numHvyAtoms - n_B - n_C - n_Met - n_N - n_O - n_P - n_S - n_SeTe;
/* 统计化学键 */
uint _numBonds = mol.NumBonds(); //所有化学键的总数
int n_b1 = 0; // number of single bonds 单键的个数
int n_b1_NoH = 0; // number of none C-H single bonds 不含氢的单键个数
int n_b2 = 0; // number of double bonds 双键的个数
int n_b3 = 0; // number of triple bonds 三键的个数
int n_bar = 0; // number of aromatic bonds 芳香键的个数
int n_C1O = 0; // number of C-O single bonds 碳-氧单键的个数
int n_C2O = 0; // number of C=O double bonds 碳=氧双键的个数
int n_CN = 0; // number of C/N bonds (any type) 任何类型的碳氮键的个数
int n_XY = 0; // number of heteroatom/heteroatom bonds (any type) 任何类型的杂原子之间化学健的个数
for (int i = 0; i < _numBonds; i++)
{
OBBond _bond = mol.GetBond(i);
OBAtom _beginAtom = _bond.GetBeginAtom();
OBAtom _endAtom = _bond.GetEndAtom();
uint _beginAtomAtomicNum = _beginAtom.GetAtomicNum();
uint _endAtomAtomicNum = _endAtom.GetAtomicNum();
if (_bond.IsSingle()) //Replace IsSingle() method in Openbabel 3.0
{
n_b1++;
if (_beginAtomAtomicNum != 1 && _endAtomAtomicNum != 1)
{
n_b1_NoH++;
}
}
else if (_bond.IsDouble()) // Replace IsDouble() method in Openbabel 3.0
{
n_b2++;
}
else if (_bond.IsTriple()) // Replace IsTriple() method in Openbabel 3.0
{
n_b3++;
}
else if (_bond.IsAromatic())
{
n_bar++;
}
if ((_beginAtomAtomicNum == 6 && _endAtomAtomicNum == 8) || (_beginAtomAtomicNum == 8 && _endAtomAtomicNum == 6))
{
uint _bondOrder = _bond.GetBondOrder();
if (_bondOrder == 1)
{
n_C1O++;
}
else if (_bondOrder == 2)
{
n_C2O++;
}
}
else if ((_beginAtomAtomicNum == 6 && _endAtomAtomicNum == 7) || (_beginAtomAtomicNum == 7 && _endAtomAtomicNum == 6))
{
n_CN++;
}
else if (_beginAtomAtomicNum != 6 && _endAtomAtomicNum != 6)
{
n_XY++;
}
}
/* 统计环 */
#region 统计环
VectorpRing _SSSR = mol.GetSSSR();
int n_r3 = 0; // number of 3-membered rings 3元环个数
int n_r4 = 0; // number of 4-membered rings 4元环个数
int n_r5 = 0; // number of 5-membered rings 5元环个数
int n_r6 = 0; // number of 6-membered rings 6元环个数
int n_r7 = 0; // number of 7-membered rings 7元环个数
int n_r8 = 0; // number of 8-membered rings 8元环个数
int n_r9 = 0; // number of 9-membered rings 9元环个数
int n_r10 = 0; // number of 10-membered rings 10元环个数
int n_r11 = 0; // number of 11-membered rings 11元环个数
int n_r12 = 0; // number of 12-membered rings 12元环个数
int n_r13p = 0; // number of 13-membered or larger rings 13元环或者更大的环的个数
int n_rN = 0; // number of rings containing nitrogen (any number) 含氮环的个数
int n_rN1 = 0; // number of rings containing 1 nitrogen atom 含一个氮原子的环的个数
int n_rN2 = 0; // number of rings containing 2 nitrogen atoms 含两个个氮原子的环的个数
int n_rN3p = 0; // number of rings containing 3 or more nitrogen atoms 含三个或以上个氮原子的环的个数
int n_rO = 0; // number of rings containing oxygen (any number) 含氧环的个数
int n_rO1 = 0; // number of rings containing 1 oxygen atom 含一个氧原子的环的个数
int n_rO2p = 0; // number of rings containing 2 or more oxygen atoms 含三个或以上个氧原子的环的个数
int n_rS = 0; // number of rings containing sulfur (any number) 含硫环的个数
int n_rX = 0; // number of heterocycles (any type) 杂环的个数
int n_rar = 0; // number of aromatic rings (any type) 芳香环的个数
if (_SSSR.Count != 0 || _SSSR != null)
{
foreach (OBRing _ring in _SSSR)
{
uint _ringSize = _ring.Size();
if (_ringSize == 3)
{
n_r3++;
}
else if (_ringSize == 4)
{
n_r4++;
}
else if (_ringSize == 5)
{
n_r5++;
}
else if (_ringSize == 6)
{
n_r6++;
}
else if (_ringSize == 7)
{
n_r7++;
}
else if (_ringSize == 8)
{
n_r8++;
}
else if (_ringSize == 9)
{
n_r9++;
}
else if (_ringSize == 10)
{
n_r10++;
}
else if (_ringSize == 11)
{
n_r11++;
}
else if (_ringSize == 12)
{
n_r12++;
}
else if (_ringSize >= 13)
{
n_r13p++;
}
if (_ring.IsAromatic())
{
n_rar++;
}
VectorInt _pathes = _ring._path;
int _ct_N = 0;
int _ct_O = 0;
int _ct_S = 0;
bool _isRingX = false;
foreach (int _p in _pathes)
{
OBAtom _atom = mol.GetAtom(_p);
uint _AtomicNum = _atom.GetAtomicNum();
if (_AtomicNum == 7) //N原子
{
_ct_N++;
}
else if (_AtomicNum == 8) //O原子
{
_ct_O++;
}
else if (_AtomicNum == 16) //S原子
{
_ct_S++;
}
if (_AtomicNum != 6)
{
_isRingX = true;
}
}
if (_ct_N == 1)
{
n_rN1++;
}
else if (_ct_N == 2)
{
n_rN2++;
}
else if (_ct_N >= 3)
{
n_rN3p++;
}
n_rN = n_rN1 + n_rN2 + n_rN3p;
if (_ct_O == 1)
{
n_rO1++;
}
else if (_ct_O >= 2)
{
n_rO2p++;
}
n_rO = n_rO1 + n_rO2p;
if (_ct_S >= 1)
{
n_rS++;
}
if (_isRingX)
{
n_rX++;
}
}
}
#endregion
// 统计数字映射成MolStat对象
MolStat stat = new MolStat
{
// General info
AtomsCount = (int)_numAtoms,
HeavyAtomsCount = (int)_numHvyAtoms,
TotalCharge = _totalCharge,
// Atoms info
N_B = n_B,
N_Br = n_Br,
N_C = n_C,
N_C1 = n_C1,
N_C2 = n_C2,
N_CHB1p = n_CHB1p,
N_CHB2p = n_CHB2p,
N_CHB3p = n_CHB3p,
N_CHB4 = n_CHB4,
N_Cl = n_Cl,
N_F = n_F,
N_I = n_I,
N_Met = n_Met,
N_N = n_N,
N_N1 = n_N1,
N_N2 = n_N2,
N_N3 = n_N3,
N_O = n_O,
N_O2 = n_O2,
N_O3 = n_O3,
N_P = n_P,
N_S = n_S,
N_SeTe = n_SeTe,
N_X = n_X,
// Bonds info
BondsCount = (int)_numBonds,
N_b1 = n_b1,
N_b1_NoH = n_b1_NoH,
N_b2 = n_b2,
N_b3 = n_b3,
N_bar = n_bar,
N_C1O = n_C1O,
N_C2O = n_C2O,
N_CN = n_CN,
N_XY = n_XY,
// Rings info
RingsCount = _SSSR.Count,
N_r10 = n_r10,
N_r11 = n_r11,
N_r12 = n_r12,
N_r13p = n_r13p,
N_r3 = n_r3,
N_r4 = n_r4,
N_r5 = n_r5,
N_r6 = n_r6,
N_r7 = n_r7,
N_r8 = n_r8,
N_r9 = n_r9,
N_rar = n_rar,
N_rN = n_rN,
N_rN1 = n_rN1,
N_rN2 = n_rN2,
N_rN3p = n_rN3p,
N_rO = n_rO,
N_rO1 = n_rO1,
N_rO2p = n_rO2p,
N_rS = n_rS,
N_rX = n_rX
};
return(stat);
}
