public Residue(Residue r,Chain c)
: base(r)
{
number = r.number;
atoms = new List<Atom>();
resName =r.resName;
resID = r.resID;
resChain = c;
}
public static Molecule ReadPDB(TextReader sr)
{
Molecule mol = new Molecule ();
bool mul_pos =false;
Chain c = new Chain();
Residue r = new Residue();
lastresID =-1;
lastchainID = "NONE";
nowresidue = -1;
nowchain = -1;
nbatom = 0;
nbresidue=0;
while((s=sr.ReadLine())!=null) {
if(s.StartsWith("ENDMDL") && !mul_pos){
break;
}
if(s.StartsWith("MODEL")){
mul_pos =true;
nbatom =0;
int frame = int.Parse(s.Substring(10,4));
if(frame > 1)
{
Main.total_frames++;
}
}
if(s.Length>4) {
if(s.StartsWith("ATOM") || s.StartsWith("HETATM")) {
if(Main.total_frames < 2){
chainID = s.Substring(21,1).Trim();
if(String.Compare(lastchainID,chainID) !=0){
if(s.StartsWith("ATOM"))
c=new Chain("ATOM",chainID);
else
c=new Chain("HETATM",chainID);
mol.Chains.Add(c);
nowchain++;
nowresidue =-1;
lastchainID = chainID;
}
resID = int.Parse(s.Substring(22,4));
if((lastresID != resID)){
resname=s.Substring(17,3).Trim();
r = new Residue(resname,nbresidue,resID,c);
mol.Chains[nowchain].Residues.Add(r);
mol.Residues.Add(r);
nowresidue++;
nbresidue++;
lastresID = resID;
}
atomname=s.Substring(12,4).Trim();
Atom at = new Atom(atomname,0.0f,nbatom,r,c);
mol.Chains[nowchain].Residues[nowresidue].Atoms.Add(at);
mol.Chains[nowchain].Atoms.Add(at);
mol.Atoms.Add(at);
}
//Unity has a left-handed coordinates system while PDBs are right-handed
//So we have to reverse the X coordinates
//InvariantCulture necessary form cross-platform
x=-float.Parse(s.Substring(30,8),System.Globalization.CultureInfo.InvariantCulture);
y=float.Parse(s.Substring(38,8),System.Globalization.CultureInfo.InvariantCulture);
z=float.Parse(s.Substring(46,8),System.Globalization.CultureInfo.InvariantCulture);
vect = new Vector3(x,y,z);
mol.Atoms[nbatom].Location[Main.total_frames-1] = vect;
nbatom++;
}
}
}
sr.Close ();
Debug.Log ("atoms:" + mol.Atoms.Count);
return mol;
}
public Residue(string resname,int num,int resid,Chain c)
: base()
{
number = num;
resName = resname;
resID = resid;
atoms = new List<Atom> ();
resChain = c;
}
public Molecule(Molecule m)
: base(m)
{
chains = new List<Chain> ();
residues = new List<Residue> ();
atoms = new List<Atom> ();
for (int i = 0; i<m.Chains.Count; i++) {
Chain c= new Chain(m.Chains[i]);
this.Chains.Add(c);
for (int j = 0; j<m.Chains[i].Residues.Count; j++) {
Residue r = new Residue(m.Chains[i].Residues[j],c);
this.Chains[i].Residues.Add(r);
this.Residues.Add(r);
for (int k =0; k<m.Chains[i].Residues[j].Atoms.Count; k++) {
Atom a = new Atom(m.Chains[i].Residues[j].Atoms[k],r,c);
this.Chains[i].Residues[j].Atoms.Add(a);
this.Chains[i].Atoms.Add(a);
this.Atoms.Add(a);
}
}
}
bonds = new List<int[]> (m.Bonds);
chainsBonds = new List<List<int>> (m.chainsBonds);
color = m.color;
type = m.type;
render = m.render;
select = m.select;
energies = m.energies;
}
public Chain(Chain c)
: base(c)
{
chainID = c.chainID;
type = c.type;
residues = new List<Residue> ();
atoms = new List<Atom> ();
}
public Atom(Atom a,Residue r,Chain c)
: base(a)
{
number = a.number;
atomFullName = a.atomFullName;
atomName = a.atomName;
atomCharge = a.atomCharge;
bonds = new List<int>(a.bonds);
atomMass = a.atomMass;
atomRadius = a.atomRadius;
atomResidue = r;
atomChain = c;
}
public Atom(string name,float charge,int num,Residue r,Chain c)
: base()
{
number = num;
atomFullName = name;
atomName = name [0].ToString();
atomCharge = charge;
bonds = new List<int> ();
int i =0;
while((atomName != tableName[i]) && (i < tableName.Length)){
i++;
}
atomMass = tableMass [i];
atomRadius = tableRadius [i];
atomResidue = r;
atomChain = c;
}