public void LoadMolecule()
{
string filestring = Manager.GetComponent <OpenFileButton>().filestring;
// TODO: display an error if filestring is null
// First we will get the frames using Regex.Split
GetFrames(filestring);
// Then we get information about each individual atom with each frame. Most important: Atom#, Element, X, Y, Z
GetAtoms(filestring);
GetAtomInfo();
// fill out top.NATOM with the total number of atoms and pass it to Load
Manager.GetComponent <Load>().top.NATOM = top.NATOM;
// Fill our molecule struct and pass to Load
Manager.GetComponent <Load>().molecule = molecule;
// Fill out number of frames and pass to Load
Manager.GetComponent <Load>().framenum = framenum;
// Delete everything here
molecule = null;
filestring = null;
framenum = 0;
Models.Clear();
}
/*
*
* Group 1: Element
* Group 2: X
* Group 3: Y
* Group 4: Z
* Group 5:
*
*/
void GetAtomInfo()
{
framenum = Models.Count();
Manager.GetComponent <Load>().molecule = new atominfo[framenum, top.NATOM];
molecule = new atominfo[framenum, top.NATOM];
foreach (string model in Models)
{
// This is to get the Atom#, Element, and X,Y,Z coord
string reg = @"\r?\n?([A-Z]+)\s+(\S+)\s+(\S+)\s+(\S+)\r?\n?";
Regex r = new Regex(reg);
Match m = r.Match(model);
for (int a = 0; a < top.NATOM; a++)
{
Vector3 original = new Vector3(float.Parse(m.Groups[2].ToString()) / 25, float.Parse(m.Groups[3].ToString()) / 25, float.Parse(m.Groups[4].ToString()) / 25);
//original = Fitbox.GetComponent<Fitbox>().toQuat*original;
// Need this line because the HologramCollection is moved by the Fitbox when loading the app so we are correcting the X,Y,Z for that
original = original + HologramCollection.transform.position;
molecule[Models.IndexOf(model), a].x = original.x;
molecule[Models.IndexOf(model), a].y = original.y;
molecule[Models.IndexOf(model), a].z = original.z;
molecule[0, a].element = m.Groups[1].ToString();
m = m.NextMatch();
}
}
}
public void CreateLines(atominfo[,] molecule)
{
foreach (Bonds k in GetComponent <ThisFileInfo>().Bonds[0])
{
GameObject myLine = new GameObject();
myLine.tag = "Sticks";
myLine.AddComponent <LineRenderer>();
myLine.name = string.Format("Line{0}.{1}", k.a1, k.a2);
lr = myLine.GetComponent <LineRenderer>();
lr.SetWidth(0.003f, 0.003f);
lr.material = mat;
lr.useWorldSpace = false;
lr.startColor = Colors(molecule[0, k.a1].element);
lr.endColor = Colors(molecule[0, k.a2].element);
float x1, y1, z1, x2, y2, z2;
x1 = molecule[0, k.a1].x;
y1 = molecule[0, k.a1].y;
z1 = molecule[0, k.a1].z;
x2 = molecule[0, k.a2].x;
y2 = molecule[0, k.a2].y;
z2 = molecule[0, k.a2].z;
Vector3 firstatom = new Vector3(x1, y1, z1) * 0.5f;
Vector3 secondatom = new Vector3(x2, y2, z2) * 0.5f;
offset = new Vector3(0, 0, 0f + MoleculeCollection.transform.position.z);
lr.SetPosition(0, firstatom + offset);
lr.SetPosition(1, secondatom + offset);
lr.transform.parent = transform.GetChild(1).gameObject.transform;
}
}
/*
*
* Group 1: Element
* Group 2: Atomic number
* Group 3: X
* Group 4: Y
* Group 5: Z
*
*/
void GetAtomInfo()
{
top.NATOM = Regex.Matches(Models[0], @"\r?\n?\s*([A-Z][A-Z]?)\s*([0-9]+)\s*(\S*)\s*(\S*)\s*(\S*)").Count;
framenum = Models.Count();
Manager.GetComponent <Load>().molecule = new atominfo[framenum, top.NATOM];
molecule = new atominfo[framenum, top.NATOM];
foreach (string model in Models)
{
string reg = @"\r?\n?\s*([A-Z][A-Z]?)\s*([0-9]+)\s*(\S*)\s*(\S*)\s*(\S*)";
Regex r = new Regex(reg);
Match m = r.Match(model);
for (int a = 0; a < top.NATOM; a++)
{
Vector3 original = new Vector3(float.Parse(m.Groups[3].Value) / 25, float.Parse(m.Groups[4].Value) / 25, float.Parse(m.Groups[5].Value) / 25);
//original = Fitbox.GetComponent<Fitbox>().toQuat*original;
original = original + HologramCollection.transform.position;
molecule[Models.IndexOf(model), a].x = original.x;
molecule[Models.IndexOf(model), a].y = original.y;
molecule[Models.IndexOf(model), a].z = original.z;
molecule[0, a].element = m.Groups[1].ToString();
m = m.NextMatch();
}
}
}
public void LoadMolecule()
{
if (Manager.GetComponent <Dropdowns>().filetypeSelected == "AMBER Parm")
{
topfilestring = Manager.GetComponent <OpenFileButton>().filestring;
LoadTopology();
}
if (Manager.GetComponent <Dropdowns>().filetypeSelected == "AMBER Coord")
{
xfilestring = Manager.GetComponent <OpenFileButton>().filestring;
GetFrameNum();
GetCrds();
GetAtomInfo();
Manager.GetComponent <Load>().molecule = molecule;
Manager.GetComponent <Load>().top = top;
Manager.GetComponent <Load>().framenum = framenum;
molecule = null;
topfilestring = null;
xfilestring = null;
framenum = 0;
Models.Clear();
}
}
/*
*
* Group 1: Element
* Group 2: X
* Group 3: Y
* Group 4: Z
*
*
*/
void GetAtomInfo()
{
framenum = Models.Count();
GetComponent <Load>().molecule = new atominfo[framenum, top.NATOM];
molecule = new atominfo[framenum, top.NATOM];
int thisframe = 0;
foreach (string model in Models)
{
// This is to get the Atom#, Element, and X,Y,Z coord
string reg = @"([A-Z][A-Z]?)\s*(\S*)\s*(\S*)\s*(\S*)";
Regex r = new Regex(reg);
Match m = r.Match(model);
for (int a = 0; a < top.NATOM; a++)
{
Vector3 original = new Vector3(float.Parse(m.Groups[2].ToString()), float.Parse(m.Groups[3].ToString()), float.Parse(m.Groups[4].ToString()));
molecule[Models.IndexOf(model), a].x = original.x;
molecule[Models.IndexOf(model), a].y = original.y;
molecule[Models.IndexOf(model), a].z = original.z;
molecule[Models.IndexOf(model), a].element = m.Groups[1].ToString();
m = m.NextMatch();
}
thisframe += 1;
}
}
public void LoadMolecule()
{
#if !UNITY_EDITOR
filestring = Manager.GetComponent<OpenFileButton>().filestring;
#endif
// First we will get all info from the frames using ANTLR4
// We start this on new threads and then join them at the end for a small processing speedup
istream = new AntlrInputStream(filestring);
lexer = new XYZLexer(istream);
tokens = new CommonTokenStream(lexer);
parser = new XYZParser(tokens);
// takes 0.5 seconds to parse
fileContext = parser.file();
//
firstFrame = fileContext.frame()[0];
top.NATOM = Convert.ToInt32(firstFrame.header().GetText());
framenum = fileContext.frame().Length;
molecule = new atominfo[framenum, top.NATOM];
//double st = Time.realtimeSinceStartup;
atomX = 0; frameX = 0;
atomY = 0; frameY = 0;
atomZ = 0; frameZ = 0;
atomE = 0; frameE = 0;
var X = new Task(() => GetX());
var Y = new Task(() => GetY());
var Z = new Task(() => GetZ());
var E = new Task(() => GetE());
X.Start();
Y.Start();
Z.Start();
E.Start();
X.Wait();
Y.Wait();
Z.Wait();
E.Wait();
// Debug.Log($"0:{Time.realtimeSinceStartup - st}");
// fill out top.NATOM with the total number of atoms and pass it to Load
Manager.GetComponent<Load>().top.NATOM = top.NATOM;
// Fill our molecule struct and pass to Load
Manager.GetComponent<Load>().molecule = molecule;
// Fill out number of frames and pass to Load
Manager.GetComponent<Load>().framenum = framenum;
// Delete everything here
molecule = null;
filestring = null;
framenum = 0;
}
/*
*
* Group 1: Element
* Group 2: Atomic number
* Group 3: X
* Group 4: Y
* Group 5: Z
*
*/
void GetAtomInfo()
{
top.NATOM = Regex.Matches(Models[0], @"\r?\n?\s*([0-9]+)\s*([0-9])\s*([0-9])\s*(\S*)\s*(\S*)\s*(\S*)\r?\n?").Count;
framenum = Models.Count();
Manager.GetComponent <Load>().molecule = new atominfo[framenum, top.NATOM];
molecule = new atominfo[framenum, top.NATOM];
foreach (string model in Models)
{
string reg = @"\r?\n?\s*([0-9]+)\s*([0-9])\s*([0-9])\s*(\S*)\s*(\S*)\s*(\S*)\r?\n?";
Regex r = new Regex(reg);
Match m = r.Match(model);
for (int a = 0; a < top.NATOM; a++)
{
Vector3 original = new Vector3(float.Parse(m.Groups[4].Value) / 25f, float.Parse(m.Groups[5].Value) / 25f, float.Parse(m.Groups[6].Value) / 25f);
original = original + HologramCollection.transform.position;
molecule[Models.IndexOf(model), a].x = original.x;
molecule[Models.IndexOf(model), a].y = original.y;
molecule[Models.IndexOf(model), a].z = original.z;
switch (m.Groups[2].ToString())
{
case "1":
molecule[0, a].element = "H";
break;
case "6":
molecule[0, a].element = "C";
break;
case "7":
molecule[0, a].element = "N";
break;
case "8":
molecule[0, a].element = "O";
break;
default:
molecule[0, a].element = "S";
break;
// TODO: Add more elements here
// There is a switch case like this in LoadAMBER as well so copy paste there
}
m = m.NextMatch();
}
//Debug.Log(molecule[Models.IndexOf(model), 1].x);
}
}
public void LoadMolecule()
{
// display an error if filestring is null
GetFrames(Manager.GetComponent <OpenFileButton>().filestring);
GetAtomInfo();
Manager.GetComponent <Load>().top.NATOM = top.NATOM;
Manager.GetComponent <Load>().molecule = molecule;
Manager.GetComponent <Load>().framenum = framenum;
molecule = null;
//filestring = null;
framenum = 0;
Models.Clear();
}
public async Task LoadMoleculeAsync()
{
// Check if any file was loaded in
if (GetComponent <OpenFileButton>().filestring == null)
{
GameObject sphere = GameObject.CreatePrimitive(PrimitiveType.Cube);
sphere.transform.localScale = new Vector3(0.1f, 0.1f, 0.1f);
sphere.transform.position = new Vector3(0, 0, 1);
goto NoFile; // Skips to the end of this function
}
// delete anything else in molecule collection (just one file at a time)
// Create a new FileObject
ThisFile = (GameObject)Instantiate(FilePrefab);
ThisFile.transform.localScale = Vector3.one;
ThisFile.SetActive(true);
ThisFile.transform.parent = MoleculeCollection.transform;
ThisFile.transform.name = String.Format("File {0}", FileNumber);
// Get the AtomCollection object
NewLineCollection = ThisFile.transform.GetChild(1).gameObject;
//await loadDel[Manager.GetComponent<Dropdowns>().filetypes.IndexOf(Manager.GetComponent<Dropdowns>().filetypeSelected) - 1](ThisFile);
await LoadXYZ(ThisFile);
// maybe do this w moleculecolleciton instead
ThisFile.transform.localScale = new Vector3(0.3f, 0.3f, 0.3f);
// Can we put this data directly in the right place instead of moving it around and then deleting it?
GetComponent <OpenFileButton>().filestring = null;
molecule = null;
AtomNumber = 0;
FileNumber++;
NoFile:
Resources.UnloadUnusedAssets();
GC.Collect();
}
public void LoadMolecule()
{
filestring = Manager.GetComponent <OpenFileButton>().filestring;
// display an error if filestring is null
GetFrames();
//GetTotalAtoms();
GetAtomInfo();
Manager.GetComponent <Load>().top.NATOM = top.NATOM;
Manager.GetComponent <Load>().molecule = molecule;
Manager.GetComponent <Load>().framenum = framenum - 1;
//txt.GetComponent<ChangeText>().totalFrames = framenum - 1;
molecule = null;
filestring = null;
framenum = 0;
Models.Clear();
}
// (......)(.....)(.....)(.)(...).(.)(....)(.)...(........)(........)(........)(......)(......)......(....)(..)
/// <summary>
/// (1-6) : "ATOM"/"HETATM"/"TER" : CHAR : Group 1
/// (7-11) : Atom serial number : INT : Group 2
/// 12 : BLANK
/// (13-16) : Atom name : CHAR : Group 3
/// (17) : Alternate location indicator : CHAR : Group 4
/// (18-20) : Residue name : CHAR : Group 5
/// 21 : BLANK
/// (22) : Chain identifier : CHAR : Group 6
/// (23-26) : Residue sequence number : INT : Group 7
/// (27) : Code for insertions of residues: CHAR : Group 8
/// 28-30 : BLANK
/// (31-38) : X orthogonal A coordinate : FLOAT : Group 9
/// (39-46) : Y orthogonal A coordinate : FLOAT : Group 10
/// (47-54) : Z orthogonal A coordinate : FLOAT : Group 11
/// (55-60) : Occupancy : FLOAT : Group 12
/// (61-66) : Temperature factor : FLOAT : Group 13
/// (73-76) : Segment identifier : CHAR : Group 14
/// (77-78) : Element symbol : CHAR : Group 15
/// </summary>
///
void GetAtomInfo()
{
Manager.GetComponent <Load>().molecule = new atominfo[framenum, top.NATOM];
molecule = new atominfo[framenum, top.NATOM];
Vector3 hc = HologramCollection.transform.position;
double starttime = Time.realtimeSinceStartup;
foreach (string model in Models)
{
string reg = "(......)(.....)(.....)(.)(...).(.)(....)(.)...(........)(........)(........)(......)(......)......(....)(..)";
Regex r = new Regex(reg);
Match m = r.Match(model);
for (int a = 0; a < top.NATOM; a++)
{
// original should be unmodified, not divided by 25 here. this is not the place for rescaling. localposition is used in movespheres() already
Vector3 original = new Vector3(float.Parse(m.Groups[9].ToString().Trim()), float.Parse(m.Groups[10].ToString().Trim()), float.Parse(m.Groups[11].ToString().Trim()));
//original = Fitbox.GetComponent<Fitbox>().toQuat*original;
// Need this line because the HologramCollection is moved by the Fitbox when loading the app so we are correcting the X,Y,Z for that
original = original + hc;
molecule[Models.IndexOf(model), a].x = original.x;
molecule[Models.IndexOf(model), a].y = original.y;
molecule[Models.IndexOf(model), a].z = original.z;
molecule[0, a].atomsym = m.Groups[3].ToString().Trim();
molecule[0, a].element = m.Groups[15].ToString().Trim();
molecule[0, a].resnum = Convert.ToInt32(m.Groups[7].ToString().Trim());
molecule[0, a].resid = m.Groups[5].ToString().Trim();
m = m.NextMatch();
}
}
Debug.Log($"time to load: {Time.realtimeSinceStartup - starttime}");
}
atominfo[,] GetCrds()
{
molecule = new atominfo[framenum, top.NATOM];
//Models = new string[framenum];
GetFrames();
rescale = 25;
for (int i = 0; i < framenum; i++)
{
temp = Models[i];
string pattern = @"\s+(\S+)"; /// (x) (y) (z) {top.NATOM}
Regex r = new Regex(pattern);
m = r.Match(temp);
for (int a = 0; a < top.NATOM; a++)
{
// molecule[i, a].atomnum = a+1;// Convert.ToInt32(m.Groups[1].ToString());
//molecule[i, a].atomsym = m.Groups[2].ToString();
//molecule[i, a].resid = m.Groups[3].ToString();
//molecule[i, a].resnum = Convert.ToInt32(m.Groups[5].ToString());
//var fmt = new NumberFormatInfo();
//fmt.NegativeSign = "-";
molecule[i, a].x = float.Parse(m.Groups[1].ToString()) / rescale;
m = m.NextMatch();
molecule[i, a].y = float.Parse(m.Groups[1].ToString()) / rescale;
m = m.NextMatch();
molecule[i, a].z = float.Parse(m.Groups[1].ToString()) / rescale;
//molecule[i, a].element = m.Groups[11].ToString();
m = m.NextMatch();
}
}
return(molecule);
}
public void LoadMolecule()
{
filestring = Manager.GetComponent <OpenFileButton>().filestring;
// TODO: display an error if filestring is null
if (filestring == null)
{
// Console text += " filetring is null"
// `goto` somewhere at end of this LoadMolecule() function
}
// First we will get the frames using Regex.Split
double starttime = Time.realtimeSinceStartup;
GetFrames();
txt.text += $"\n GetFrames time : {Time.realtimeSinceStartup - starttime}"; starttime = Time.realtimeSinceStartup;
// Then we get information about each individual atom with each frame. Most important: Atom#, Element, X, Y, Z
GetAtomInfo();
txt.text += $"\n GetAtomInfo time : {Time.realtimeSinceStartup - starttime}"; starttime = Time.realtimeSinceStartup;
// fill out top.NATOM with the total number of atoms and pass it to Load
Manager.GetComponent <Load>().top.NATOM = top.NATOM;
// Fill our molecule struct and pass to Load
Manager.GetComponent <Load>().molecule = molecule;
// Fill out number of frames and pass to Load
Manager.GetComponent <Load>().framenum = framenum;
// Delete everything here
molecule = null;
filestring = null;
framenum = 0;
Models.Clear();
}
public void MoveLine(int frame, atominfo[,] molecule)
{
int atom1, atom2;
GameObject sphereone, spheretwo;
if (GetComponent <ThisFileInfo>().dynamicBonds == true)
{
// Check for bonds which exist for the frame but were not constructed in a previous frame
foreach (Bonds k in GetComponent <ThisFileInfo>().Bonds[frame])
{
Transform[] children = transform.GetChild(1).transform.GetComponentsInChildren <Transform>();
string[] childrenNames = new string[children.Length];
foreach (Transform c in children)
{
childrenNames[Array.IndexOf(children, c)] = c.name;
}
if (!childrenNames.Contains($"Line{k.a1}.{k.a2}"))
{
GameObject myLine = new GameObject();
myLine.tag = "Sticks";
myLine.AddComponent <LineRenderer>();
myLine.name = string.Format("Line{0}.{1}", k.a1, k.a2);
lr = myLine.GetComponent <LineRenderer>();
lr.SetWidth(0.003f, 0.003f);
lr.material = mat;
lr.useWorldSpace = false;
lr.startColor = Colors(molecule[frame, k.a1].element);
lr.endColor = Colors(molecule[frame, k.a2].element);
float x1, y1, z1, x2, y2, z2;
x1 = molecule[frame, k.a1].x;
y1 = molecule[frame, k.a1].y;
z1 = molecule[frame, k.a1].z;
x2 = molecule[frame, k.a2].x;
y2 = molecule[frame, k.a2].y;
z2 = molecule[frame, k.a2].z;
Vector3 firstatom = new Vector3(x1, y1, z1) * 0.5f;
Vector3 secondatom = new Vector3(x2, y2, z2) * 0.5f;
offset = new Vector3(0, 0, 0f + MoleculeCollection.transform.position.z);
lr.transform.parent = transform.GetChild(1).gameObject.transform;
lr.SetPosition(0, firstatom + offset);
lr.SetPosition(1, secondatom + offset);
myLine.transform.localPosition = new Vector3(0, 0, 0);
myLine.transform.localRotation = new Quaternion(0, 0, 0, 1);
myLine.transform.localScale = Vector3.one;
}
}
}
// Check for bonds which are extra for this frame and delete them, then update the lines' positions for the frame
foreach (Transform k in transform.GetChild(1).GetComponentInChildren <Transform>())
{
atom1 = Convert.ToInt32(Regex.Match(k.name, $"Line([0-9]+).([0-9]+)").Groups[1].ToString());
atom2 = Convert.ToInt32(Regex.Match(k.name, $"Line([0-9]+).([0-9]+)").Groups[2].ToString());
if (GetComponent <ThisFileInfo>().dynamicBonds == true)
{
string[] bondNames = new string[GetComponent <ThisFileInfo>().Bonds[frame].Count];
foreach (Bonds m in GetComponent <ThisFileInfo>().Bonds[frame])
{
bondNames[GetComponent <ThisFileInfo>().Bonds[frame].IndexOf(m)] = $"Line{m.a1}.{m.a2}";
}
if (!bondNames.Contains(k.name))
{
Destroy(k.gameObject);
goto SkipMove; // line 167
}
}
sphereone = AtomCollection.transform.GetChild(atom1).gameObject;
spheretwo = AtomCollection.transform.GetChild(atom2).gameObject;
float x1, y1, z1, x2, y2, z2;
x1 = sphereone.transform.localPosition.x;
y1 = sphereone.transform.localPosition.y;
z1 = sphereone.transform.localPosition.z + 1;
x2 = spheretwo.transform.localPosition.x;
y2 = spheretwo.transform.localPosition.y;
z2 = spheretwo.transform.localPosition.z + 1;
Vector3 firstatom = new Vector3(x1, y1, z1);
Vector3 secondatom = new Vector3(x2, y2, z2);
GameObject myLine = k.gameObject;
lr = myLine.GetComponent <LineRenderer>();
lr.SetPosition(0, firstatom);
lr.SetPosition(1, secondatom);
SkipMove:
lr.useWorldSpace = false;
}
//Debug.Log($"Move Time: {Time.realtimeSinceStartup - sttime}");
}