private void RemoveSameAlignData(List <AlignData> alignDatas)
{
IList <UILineInfo> lines = cachedTextGenerator.lines;
List <AlignData> removeAlignDatas = new List <AlignData>();
for (int i = 0; i < alignDatas.Count; i++)
{
AlignData alignData = alignDatas[i];
for (int j = 0; j < lines.Count; j++)
{
UILineInfo lInfo = lines[j];
if (lInfo.startCharIdx <= alignData.startCharIndex)
{
alignData.lineIndex = j;
alignData.lineStartCharIndex = lInfo.startCharIdx;
if (j == lines.Count - 1)
{
if (alignData.startCharIndex > cachedTextGenerator.characterCountVisible)
{
removeAlignDatas.Add(alignData);
}
else
{
alignData.lineEndCharIndex = cachedTextGenerator.characterCountVisible;
}
}
}
else
{
alignData.lineEndCharIndex = lInfo.startCharIdx - 1;
break;
}
}
alignDatas[i] = alignData;
}
List <int> lineList = new List <int>();
for (int i = 0; i < alignDatas.Count; i++)
{
AlignData alignData = alignDatas[i];
//Debug.Log("alignData.lineIndex :" + alignData.lineIndex);
if (lineList.Contains(alignData.lineIndex))
{
removeAlignDatas.Add(alignData);
continue;
}
else
{
lineList.Add(alignData.lineIndex);
}
}
for (int i = 0; i < removeAlignDatas.Count; i++)
{
alignDatas.Remove(removeAlignDatas[i]);
}
}
public static void GetEnergies(AlignData data1, IList <Vector> coords2
, out double pot_rmsd, out double pot_enrg, out double pot_enrg_full, out double pot_enrg_anisou
, Pdb pdb2 = null
, string pdb2outpath = null
)
{
Anisou[] anisous1;// = data1.GetAnisous();
double[] bfactor1;
{
List <Mode> modes = new List <Mode>(data1.GetModes());
for (int i = 0; i < 6; i++)
{
modes.RemoveAt(0);
}
bfactor1 = HBioinfo.GetBFactor(modes.ToArray(), data1.masses);
HDebug.Assert(data1.size == bfactor1.Length);
anisous1 = Anisou.FromBFactor(bfactor1, scale: 10000 * 1000);
}
//Trans3 trans = MinAnisou.GetTrans(data1.coords, anisous1, coords2);
Trans3 trans = GetTrans(data1.coords, bfactor1, coords2);
List <Vector> coords2trans = new List <Vector>(trans.GetTransformed(coords2));
if (pdb2 != null && pdb2outpath != null)
{
data1.pdb.ToFile(pdb2outpath, coords2trans, anisous: anisous1.GetUs());
}
pot_rmsd = data1.GetRmsdFrom(coords2trans);
pot_enrg = data1.GetEnergyFromDiag(coords2trans);
pot_enrg_full = data1.GetEnergyFromFull(coords2trans);
pot_enrg_anisou = data1.GetEnergyFromAnisou(coords2trans);
}
// This updates the dragging
private void Update()
{
snaptocardinaldirection = (General.Interface.ShiftState && General.Interface.AltState); //mxd
snaptogrid = (snaptocardinaldirection || General.Interface.ShiftState ^ General.Interface.SnapToGrid);
snaptonearest = General.Interface.CtrlState;
snaptogridincrement = (!snaptocardinaldirection && General.Interface.AltState); //mxd
//mxd. Snap to nearest linedef
if (selectedthings.Count == 1 && snaptonearest && !snaptocardinaldirection &&
Thing.AlignableRenderModes.Contains(dragitem.RenderMode) &&
MoveThingsRelative(mousemappos - dragstartmappos, snaptogrid, snaptogridincrement, false, false))
{
Linedef l = General.Map.Map.NearestLinedefRange(oldpositions[0] + mousemappos - dragstartmappos, BuilderPlug.Me.StitchRange / renderer.Scale);
bool restoresettings = false;
if (aligndata == null)
{
aligndata = new AlignData(dragitem);
}
if (l != null)
{
if (Tools.TryAlignThingToLine(dragitem, l))
{
aligndata.Position = new PointF(dragitem.Position.x, dragitem.Position.y);
aligndata.Active = true;
}
else if (dragitem.AngleDoom != aligndata.InitialAngle) //restore initial angle?
{
restoresettings = true;
}
}
else if (dragitem.AngleDoom != aligndata.InitialAngle) //restore initial angle?
{
restoresettings = true;
}
if (restoresettings)
{
aligndata.Position = PointF.Empty;
aligndata.Active = false;
dragitem.Rotate(aligndata.InitialAngle);
}
UpdateRedraw(); // Redraw
renderer.Present();
return;
}
// Move selected geometry
if (MoveThingsRelative(mousemappos - dragstartmappos, snaptogrid, snaptogridincrement, snaptonearest, snaptocardinaldirection))
{
// Redraw
UpdateRedraw();
renderer.Present();
}
}
public static AlignData FromFiles(string path_pdb, string path_hess, IList <double> masses, string cachebase = null)
{
AlignData data = new AlignData();
data.pdb = Pdb.FromFile(path_pdb);
data.coords = data.pdb.atoms.ListCoord();
data.cachebase = cachebase;
int n = data.coords.Count;
{ // data.hess
List <string> lines = HFile.ReadLines(path_hess).ToList();
int row, col;
{
string[] tokens = lines[1].Split(new char[] { ' ', ',', '\t' }, StringSplitOptions.RemoveEmptyEntries);
HDebug.Assert(tokens.Length == 2);
row = int.Parse(tokens[0]);
col = int.Parse(tokens[1]);
HDebug.Assert(row == col);
}
HDebug.Assert(row == n * 3, col == n * 3);
MatrixByArr[,] hess = new MatrixByArr[n, n];
for (int c = 0; c < n; c++)
{
for (int r = 0; r < n; r++)
{
hess[c, r] = new double[3, 3];
}
}
for (int c = 0; c < col; c++)
{
string line = lines[c + 2];
string[] tokens = line.Split(new char[] { ' ', ',', '\t' }, StringSplitOptions.RemoveEmptyEntries);
HDebug.Assert(tokens.Length == row);
for (int r = 0; r < row; r++)
{
double val = double.Parse(tokens[r]);
hess[c / 3, r / 3][c % 3, r % 3] += val;
hess[r / 3, c / 3][r % 3, c % 3] += val;
}
}
for (int c = 0; c < n; c++)
{
for (int r = 0; r < n; r++)
{
hess[c, r] /= 2;
}
}
data.hess = hess;
}
data.masses = masses.ToArray();
return(data);
}
public static void GetEnergies(AlignData data1, IList <Vector> coords2
, out double geo_rmsd, out double geo_enrg, out double geo_enrg_full, out double geo_enrg_anisou
, Pdb pdb2, string pdb2outpath
)
{
Trans3 trans = GetTrans(data1.coords, coords2);
List <Vector> coords2trans = new List <Vector>(trans.GetTransformed(coords2).ToArray());
if (pdb2 != null && pdb2outpath != null)
{
pdb2.ToFile(pdb2outpath, coords2);
}
geo_rmsd = data1.GetRmsdFrom(coords2trans);
geo_enrg = data1.GetEnergyFromDiag(coords2trans);
geo_enrg_full = data1.GetEnergyFromFull(coords2trans);
geo_enrg_anisou = data1.GetEnergyFromAnisou(coords2trans);
}
//public static Trans3 GetTrans(IList<Vector> C1, Matrix[] anisou1, IList<Vector> C2)
//{
// int size = C1.Count;
// Tuple<Vector[], double[]>[] eigs1 = new Tuple<Vector[], double[]>[size];
// {
// for(int i=0; i<size; i++)
// {
// Vector[] eigvec;
// double[] eigval;
// Debug.Verify(NumericSolver.Eig(anisou1[i], out eigvec, out eigval));
// { // normalize eigval and eigvec
// double l;
// l = eigvec[0].Dist; eigvec[0] /= l; eigval[0] *= (l*l); eigval[0] = Math.Pow(eigval[0], 2); Debug.Assert(eigval[0] >= 0);
// l = eigvec[1].Dist; eigvec[1] /= l; eigval[1] *= (l*l); eigval[1] = Math.Pow(eigval[1], 2); Debug.Assert(eigval[1] >= 0);
// l = eigvec[2].Dist; eigvec[2] /= l; eigval[2] *= (l*l); eigval[2] = Math.Pow(eigval[2], 2); Debug.Assert(eigval[2] >= 0);
// }
// {
// eigval[0] = 1 / eigval[0];
// eigval[1] = 1 / eigval[1];
// eigval[2] = 1 / eigval[2];
// }
// eigs1[i] = new Tuple<Vector[], double[]>(eigvec, eigval);
// }
// }
// return GetTrans(C1, eigs1, C2);
//}
public static void GetEnergies(AlignData data1, IList <Vector> coords2
, out double pot_rmsd, out double pot_enrg, out double pot_enrg_full, out double pot_enrg_anisou
, Pdb pdb2 = null
, string pdb2outpath = null
)
{
Anisou[] anisous1 = data1.GetAnisous();
Trans3 trans = GetTrans(data1.coords, anisous1, coords2);
List <Vector> coords2trans = new List <Vector>(trans.GetTransformed(coords2));
if (pdb2 != null && pdb2outpath != null)
{
pdb2.ToFile(pdb2outpath, coords2trans);
}
//data1.pdb.ToFile(pdb2outpath, coords2trans, anisous: anisous1.GetUs());
pot_rmsd = data1.GetRmsdFrom(coords2trans);
pot_enrg = data1.GetEnergyFromDiag(coords2trans);
pot_enrg_full = data1.GetEnergyFromFull(coords2trans);
pot_enrg_anisou = data1.GetEnergyFromAnisou(coords2trans);
}
private void RichTextAlignDataSupport(VertexHelper toFill)
{
if (!supportRichText)
{
base.OnPopulateMesh(toFill);
return;
}
string changedText = "";
var orignText = m_Text;
m_Text = DealWithTextContent(m_Text);
changedText = m_Text;
base.OnPopulateMesh(toFill);
m_Text = orignText;
IList <UILineInfo> lines = cachedTextGenerator.lines;
IList <UICharInfo> characters = cachedTextGenerator.characters;
Rect rectExtents = cachedTextGenerator.rectExtents;
//Debug.Log("cachedTextGenerator.characterCountVisible :"+cachedTextGenerator.characterCountVisible);
List <UIVertex> stream = new List <UIVertex>();
toFill.GetUIVertexStream(stream);
List <AlignData> removeAlignDatas = new List <AlignData>();
for (int i = 0; i < alignDatas.Count; i++)
{
AlignData alignData = alignDatas[i];
for (int j = 0; j < lines.Count; j++)
{
UILineInfo lInfo = lines[j];
if (lInfo.startCharIdx <= alignData.startCharIndex)
{
alignData.lineIndex = j;
alignData.lineStartCharIndex = lInfo.startCharIdx;
if (j == lines.Count - 1)
{
if (alignData.startCharIndex > cachedTextGenerator.characterCountVisible)
{
removeAlignDatas.Add(alignData);
}
else
{
alignData.lineEndCharIndex = cachedTextGenerator.characterCountVisible;
}
}
}
else
{
alignData.lineEndCharIndex = lInfo.startCharIdx - 1;
break;
}
}
alignDatas[i] = alignData;
}
List <int> lineList = new List <int>();
for (int i = 0; i < alignDatas.Count; i++)
{
AlignData alignData = alignDatas[i];
//Debug.Log("alignData.lineIndex :" + alignData.lineIndex);
if (lineList.Contains(alignData.lineIndex))
{
removeAlignDatas.Add(alignData);
continue;
}
else
{
lineList.Add(alignData.lineIndex);
}
}
for (int i = 0; i < removeAlignDatas.Count; i++)
{
alignDatas.Remove(removeAlignDatas[i]);
}
//Debug.Log("alignDatas :" + alignDatas.Count);
for (int i = 0; i < alignDatas.Count; i++)
{
AlignData alignData = alignDatas[i];
//Debug.Log("characters.Count :" + characters.Count + " stream.Count:" + stream.Count + " alignData.lineEndCharIndex:" + alignData.lineEndCharIndex);
if (alignData.lineEndCharIndex >= characters.Count)
{
continue;
}
if (alignData.lineStartCharIndex >= characters.Count)
{
continue;
}
if ((alignData.lineEndCharIndex * 6) > stream.Count)
{
continue;
}
if (alignData.lineStartCharIndex * 6 >= stream.Count)
{
continue;
}
if (alignData.alignType == AlignType.Right)
{
UICharInfo uiChar = characters[alignData.lineEndCharIndex];
float detaMove = rectExtents.width / 2 - uiChar.cursorPos.x - uiChar.charWidth;
for (int v = alignData.lineStartCharIndex * 6; v < alignData.lineEndCharIndex * 6; v++)
{
UIVertex ver = stream[v];
ver.position += new Vector3(detaMove, 0, 0);
//ver.color = Color.red;
stream[v] = ver;
}
}
else if (alignData.alignType == AlignType.Left)
{
UICharInfo uiChar = characters[alignData.lineStartCharIndex];
float detaMove = (-rectExtents.width / 2) - uiChar.cursorPos.x;
//Debug.Log("LLeft alignData.lineStartCharIndex：" + alignData.lineStartCharIndex + " alignData.lineEndCharIndex:" + alignData.lineEndCharIndex);
for (int v = alignData.lineStartCharIndex * 6; v < alignData.lineEndCharIndex * 6; v++)
{
UIVertex ver = stream[v];
ver.position += new Vector3(detaMove, 0, 0);
//ver.color = Color.green;
stream[v] = ver;
}
}
else if (alignData.alignType == AlignType.Center)
{
float lineCharLenth = 0;
for (int j = alignData.lineStartCharIndex; j < alignData.lineEndCharIndex; j++)
{
lineCharLenth += characters[j].charWidth;
}
float detaMove = -lineCharLenth / 2 - characters[alignData.lineStartCharIndex].cursorPos.x;
for (int v = alignData.lineStartCharIndex * 6; v < alignData.lineEndCharIndex * 6; v++)
{
UIVertex ver = stream[v];
ver.position += new Vector3(detaMove, 0, 0);
//ver.color = Color.blue;
stream[v] = ver;
}
}
}
toFill.AddUIVertexTriangleStream(stream);
}
private string DealWithTextContent(string content)
{
alignDatas.Clear();
var temp = content;
while (true)
{
for (int i = 0; i < temp.Length; i++)
{
if (temp[i] == '<')
{
int surplusLenth = temp.Length - i - 1;
string testStr = "";
bool isResult = false;
if (surplusLenth >= alignRightString.Length)
{
testStr = temp.Substring(i, alignRightString.Length);
if (testStr == alignRightString)
{
isResult = true;
AlignData align = new AlignData();
align.alignType = AlignType.Right;
align.startCharIndex = i;
alignDatas.Add(align);
}
}
if (!isResult)
{
if (surplusLenth >= alignLeftString.Length)
{
testStr = temp.Substring(i, alignLeftString.Length);
if (testStr == alignLeftString)
{
isResult = true;
AlignData align = new AlignData();
align.alignType = AlignType.Left;
align.startCharIndex = i;
alignDatas.Add(align);
}
}
}
if (!isResult)
{
if (surplusLenth >= alignCenterString.Length)
{
testStr = temp.Substring(i, alignCenterString.Length);
if (testStr == alignCenterString)
{
isResult = true;
AlignData align = new AlignData();
align.alignType = AlignType.Center;
align.startCharIndex = i;
alignDatas.Add(align);
}
}
}
if (isResult)
{
temp = temp.Remove(i, testStr.Length);
i = 0;
}
}
}
break;
}
//Debug.Log("alignDatas :" + alignDatas.Count);
return(temp);
}
private void RichTextAlignDataSupport(VertexHelper toFill)
{
if (!supportRichText)
{
base.OnPopulateMesh(toFill);
return;
}
List <AlignData> alignDatas = new List <AlignData>();
//string changedText = "";
var orignText = m_Text;
m_Text = DealWithTextContent(m_Text, ref alignDatas);
//changedText = m_Text;
base.OnPopulateMesh(toFill);
m_Text = orignText;
RectTransform rectTransform = GetComponent <RectTransform>();
float rangeWith = rectTransform.sizeDelta.x;
IList <UICharInfo> characters = cachedTextGenerator.characters;
Rect rectExtents = cachedTextGenerator.rectExtents;
List <UIVertex> stream = new List <UIVertex>();
toFill.GetUIVertexStream(stream);
toFill.Clear();
RemoveSameAlignData(alignDatas);
for (int i = 0; i < alignDatas.Count; i++)
{
AlignData alignData = alignDatas[i];
//Debug.Log("characters.Count :" + characters.Count + " stream.Count:" + stream.Count + " alignData.lineEndCharIndex:" + alignData.lineEndCharIndex);
if (alignData.lineEndCharIndex >= characters.Count)
{
continue;
}
if (alignData.lineStartCharIndex >= characters.Count)
{
continue;
}
if ((alignData.lineEndCharIndex * 6) > stream.Count)
{
continue;
}
if (alignData.lineStartCharIndex * 6 >= stream.Count)
{
continue;
}
int indexEnd = alignData.lineEndCharIndex * 6 - 3;
int indexStart = alignData.lineStartCharIndex * 6;
if (alignData.alignType == AlignType.Right)
{
float detaMove = rangeWith / 2 - stream[indexEnd].position.x;
for (int v = alignData.lineStartCharIndex * 6; v < alignData.lineEndCharIndex * 6; v++)
{
UIVertex ver = stream[v];
//if (v >= ((alignData.lineEndCharIndex - 1) * 6) && v <= (alignData.lineEndCharIndex * 6))
//Debug.Log("Pos :" + ver.position);
ver.position += new Vector3(detaMove, 0, 0);
// ver.color = Color.red;
stream[v] = ver;
}
}
else if (alignData.alignType == AlignType.Left)
{
float detaMove = (-rangeWith / 2) - stream[indexStart].position.x;
//Debug.Log("LLeft alignData.lineStartCharIndex：" + alignData.lineStartCharIndex + " alignData.lineEndCharIndex:" + alignData.lineEndCharIndex);
for (int v = alignData.lineStartCharIndex * 6; v < alignData.lineEndCharIndex * 6; v++)
{
UIVertex ver = stream[v];
ver.position += new Vector3(detaMove, 0, 0);
//if(v== (alignData.lineEndCharIndex * 6-1))
//ver.color = Color.green;
stream[v] = ver;
}
}
else if (alignData.alignType == AlignType.Center)
{
float lineCharLenth = Mathf.Abs(stream[indexEnd].position.x) + Mathf.Abs(stream[indexStart].position.x);
float detaMove = (lineCharLenth) / 2 - stream[indexEnd].position.x;
for (int v = alignData.lineStartCharIndex * 6; v < alignData.lineEndCharIndex * 6; v++)
{
UIVertex ver = stream[v];
ver.position += new Vector3(detaMove, 0, 0);
//ver.color = Color.blue;
stream[v] = ver;
}
}
}
toFill.AddUIVertexTriangleStream(stream);
}
