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 static Molecule ReadGRO(TextReader sr)
{
lastresID =-1;
lastchainID = "NONE";
nowresidue = -1;
nowchain = 0;
nbatom=0;
nbresidue=0;
Molecule mol = new Molecule ();
Residue r =new Residue();
chainID = "None";
mol.Chains.Add(new Chain("ATOM",chainID));
mol.Chains.Add(new Chain("HETATM",chainID));
//We skip the first two lines
sr.ReadLine ();
sr.ReadLine ();
while ((s=sr.ReadLine())!=null) {
if(s.Length>50) {
resID = int.Parse(s.Substring(0,5));
if((lastresID != resID)){
resname = s.Substring(5,5).Trim();
if(resname != "SOL" &&resname != "DLC" &&resname != "WAT" && resname != "HOH"){
r =new Residue(resname,nbresidue,resID,mol.Chains[0]);
/*everything after dlc is a hetatm
if(nowchain != 0){
nowresidue = -1;
}
nowchain =0;
*/
mol.Chains[nowchain].Residues.Add(r);
mol.Residues.Add(r);
nbresidue++;
}
else{
r =new Residue(resname,nbresidue,resID,mol.Chains[1]);
if(nowchain != 1){
nowresidue = -1;
}
nowchain =1;
mol.Chains[nowchain].Residues.Add(r);
mol.Residues.Add(r);
nbresidue++;
}
nowresidue++;
lastresID = resID;
}
atomname = s.Substring(10,5).Trim ();
if(resname != "SOL" &&resname != "DLC" &&resname != "WAT" ){
Atom at =new Atom(atomname,0.0f,nbatom,r,mol.Chains[0]);
mol.Chains[nowchain].Residues[nowresidue].Atoms.Add(at);
mol.Chains[nowchain].Atoms.Add(at);
mol.Atoms.Add(at);
}
else{
Atom at =new Atom(atomname,0.0f,nbatom,r,mol.Chains[1]);
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
x = -float.Parse (s.Substring(20,8),System.Globalization.CultureInfo.InvariantCulture);
y = float.Parse (s.Substring(28,8),System.Globalization.CultureInfo.InvariantCulture);
z = float.Parse (s.Substring(36,8),System.Globalization.CultureInfo.InvariantCulture);
//convert nanometers to Angstorms
x*=10;
y*=10;
z*=10;
vect = new Vector3(x,y,z);
mol.Atoms[nbatom].Location[0] = vect;
nbatom++;
}
}
sr.Close ();
Debug.Log ("atoms:" + mol.Atoms.Count);
return mol;
}
public Residue(Residue r,Chain c)
: base(r)
{
number = r.number;
atoms = new List<Atom>();
resName =r.resName;
resID = r.resID;
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 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;
}
public void SetClosestElements(Molecule m,GameObject d)
{
int index;
for (index =0; index < m.Atoms.Count; index++) {
if (m.Atoms [index].Active)
break;
}
minDistChain = m.Atoms [index].AtomChain;
minDistResidue = m.Atoms[index].AtomResidue;
minDistAtom = m.Atoms [index];
float minDist = Vector3.Distance(minDistAtom.Location[Main.current_frame],d.transform.position);
float dist;
//Future implementation ?
/*
Ray ray = new Ray (o.transform.position, o.transform.forward);
RaycastHit rHit;
if (Physics.Raycast(ray, out rHit)) {
minDistAtom.atom = rHit.collider.gameObject;
}
*/
for (int i =index+1; i < m.Atoms.Count; i++) {
if(m.Atoms[i].Active){
dist = Vector3.Distance(m.Atoms[i].Location[Main.current_frame],d.transform.position);
if(dist < minDist){
minDist = dist;
minDistAtom = m.Atoms[i];
minDistResidue = m.Atoms[i].AtomResidue;
minDistChain =m.Atoms[i].AtomChain;
}
}
}
}