// Action_Distance::action()
Action::RetType Action_Distance::DoAction(int frameNum, Frame* currentFrame, Frame** frameAddress) {
double Dist;
Matrix_3x3 ucell, recip;
Vec3 a1, a2;
if (useMass_) {
a1 = currentFrame->VCenterOfMass( Mask1_ );
a2 = currentFrame->VCenterOfMass( Mask2_ );
} else {
a1 = currentFrame->VGeometricCenter( Mask1_ );
a2 = currentFrame->VGeometricCenter( Mask2_ );
}
switch ( ImageType() ) {
case NONORTHO:
currentFrame->BoxCrd().ToRecip(ucell, recip);
Dist = DIST2_ImageNonOrtho(a1, a2, ucell, recip);
break;
case ORTHO:
Dist = DIST2_ImageOrtho(a1, a2, currentFrame->BoxCrd());
break;
case NOIMAGE:
Dist = DIST2_NoImage(a1, a2);
break;
}
Dist = sqrt(Dist);
dist_->Add(frameNum, &Dist);
//fprintf(outfile,"%10i %10.4lf\n",frameNum,D);
return Action::OK;
}
double Action_LIE::Calculate_LJ(Frame const& frameIn, Topology const& parmIn) const {
double result = 0;
// Loop over ligand atoms
AtomMask::const_iterator mask1_end = Mask1_.end();
AtomMask::const_iterator mask2_end = Mask2_.end();
for (AtomMask::const_iterator maskatom1 = Mask1_.begin();
maskatom1 != mask1_end; maskatom1++) {
int crdidx1 = (*maskatom1) * 3; // index into coordinate array
Vec3 atm1 = Vec3(frameIn.CRD(crdidx1));
for (AtomMask::const_iterator maskatom2 = Mask2_.begin();
maskatom2 != mask2_end; maskatom2++) {
int crdidx2 = (*maskatom2) * 3; // index into coordinate array
Vec3 atm2 = Vec3(frameIn.CRD(crdidx2));
double dist2;
// Get imaged distance
Matrix_3x3 ucell, recip;
switch( ImageType() ) {
case NONORTHO:
frameIn.BoxCrd().ToRecip(ucell, recip);
dist2 = DIST2_ImageNonOrtho(atm1, atm2, ucell, recip);
break;
case ORTHO:
dist2 = DIST2_ImageOrtho(atm1, atm2, frameIn.BoxCrd());
break;
default:
dist2 = DIST2_NoImage(atm1, atm2);
}
if (dist2 > cut2vdw_) continue;
// Here we add to our nonbonded (VDW) energy
NonbondType const& LJ = parmIn.GetLJparam(*maskatom1, *maskatom2);
double r2 = 1 / dist2;
double r6 = r2 * r2 * r2;
result += LJ.A() * r6 * r6 - LJ.B() * r6;
}
}
return result;
}
double Action_LIE::Calculate_Elec(Frame const& frameIn) const {
double result = 0;
// Loop over ligand atoms
AtomMask::const_iterator mask1_end = Mask1_.end();
AtomMask::const_iterator mask2_end = Mask2_.end();
for (AtomMask::const_iterator maskatom1 = Mask1_.begin();
maskatom1 != mask1_end; maskatom1++) {
int crdidx1 = (*maskatom1) * 3; // index into coordinate array
Vec3 atm1 = Vec3(frameIn.CRD(crdidx1));
for (AtomMask::const_iterator maskatom2 = Mask2_.begin();
maskatom2 != mask2_end; maskatom2++) {
int crdidx2 = (*maskatom2) * 3; // index into coordinate array
Vec3 atm2 = Vec3(frameIn.CRD(crdidx2));
double dist2;
// Get imaged distance
Matrix_3x3 ucell, recip;
switch( ImageType() ) {
case NONORTHO:
frameIn.BoxCrd().ToRecip(ucell, recip);
dist2 = DIST2_ImageNonOrtho(atm1, atm2, ucell, recip);
break;
case ORTHO:
dist2 = DIST2_ImageOrtho(atm1, atm2, frameIn.BoxCrd());
break;
default:
dist2 = DIST2_NoImage(atm1, atm2);
}
if (dist2 > cut2elec_) continue;
// Here we add to our electrostatic energy
double qiqj = atom_charge_[*maskatom1] * atom_charge_[*maskatom2];
double shift = (1 - dist2 * onecut2_);
result += qiqj / sqrt(dist2) * shift * shift;
}
}
return result;
}
double Action_Spam::Calculate_Energy(Frame *frameIn, Residue const& res) {
// The first atom of the solvent residue we want the energy from
double result = 0;
/* Now loop through all atoms in the residue and loop through the pairlist to
* get the energies
*/
for (int i = res.FirstAtom(); i < res.LastAtom(); i++) {
Vec3 atm1 = Vec3(frameIn->XYZ(i));
for (int j = 0; j < CurrentParm_.Natom(); j++) {
if (j >= res.FirstAtom() && j < res.LastAtom()) continue;
Vec3 atm2 = Vec3(frameIn->XYZ(j));
double dist2;
// Get imaged distance
Matrix_3x3 ucell, recip;
switch( ImageType() ) {
case NONORTHO:
frameIn->BoxCrd().ToRecip(ucell, recip);
dist2 = DIST2_ImageNonOrtho(atm1, atm2, ucell, recip);
break;
case ORTHO:
dist2 = DIST2_ImageOrtho(atm1, atm2, frameIn->BoxCrd());
break;
default:
dist2 = DIST2_NoImage(atm1, atm2);
}
if (dist2 < cut2_) {
double qiqj = atom_charge_[i] * atom_charge_[j];
NonbondType const& LJ = CurrentParm_.GetLJparam(i, j);
double r2 = 1 / dist2;
double r6 = r2 * r2 * r2;
// Shifted electrostatics: qiqj/r * (1-r/rcut)^2 + VDW
double shift = (1 - dist2 * onecut2_);
result += qiqj / sqrt(dist2) * shift * shift + LJ.A() * r6 * r6 - LJ.B() * r6;
}
}
}
return result;
}
Action::RetType Action_DNAionTracker::DoAction(int frameNum, Frame* currentFrame, Frame** frameAddress) {
Matrix_3x3 ucell, recip;
double d_tmp, dval;
Vec3 P1, P2, BASE;
// Setup imaging info if necessary
if (ImageType()==NONORTHO)
currentFrame->BoxCrd().ToRecip(ucell,recip);
// Get center for P1, P2, and Base
if (useMass_) {
P1 = currentFrame->VCenterOfMass( p1_ );
P2 = currentFrame->VCenterOfMass( p2_ );
BASE = currentFrame->VCenterOfMass( base_ );
} else {
P1 = currentFrame->VGeometricCenter( p1_ );
P2 = currentFrame->VGeometricCenter( p2_ );
BASE = currentFrame->VGeometricCenter( base_ );
}
// Calculate P -- P distance and centroid
double d_pp = DIST2(P1.Dptr(), P2.Dptr(), ImageType(), currentFrame->BoxCrd(), ucell, recip);
Vec3 pp_centroid = (P1 + P2) / 2.0;
// Cutoff^2
double d_cut = d_pp*0.25 + (poffset_*poffset_); // TODO: precalc offset^2
// Calculate P -- base centroid to median point
double d_pbase = DIST2(pp_centroid.Dptr(), BASE.Dptr(), ImageType(), currentFrame->BoxCrd(),
ucell, recip);
//double d_min = DBL_MAX;
if (bintype_ == SHORTEST)
dval = DBL_MAX; //d_min;
else
dval = 0;
// Loop over ion positions
for (AtomMask::const_iterator ion = ions_.begin(); ion != ions_.end(); ++ion)
{
const double* ionxyz = currentFrame->XYZ(*ion);
double d_p1ion = DIST2(P1.Dptr(), ionxyz, ImageType(), currentFrame->BoxCrd(),
ucell, recip);
double d_p2ion = DIST2(P2.Dptr(), ionxyz, ImageType(), currentFrame->BoxCrd(),
ucell, recip);
double d_baseion = DIST2(BASE.Dptr(), ionxyz, ImageType(), currentFrame->BoxCrd(),
ucell, recip);
//mprintf("DEBUG: ion atom %i to P1 is %f\n", *ion+1, sqrt(d_p1ion));
//mprintf("DEBUG: ion atom %i to P2 is %f\n", *ion+1, sqrt(d_p2ion));
//mprintf("DEBUG: ion atom %i to base is %f\n", *ion+1, sqrt(d_baseion));
//mprintf("DEBUG: d_pp is %f, poffset is %f, d_cut is %f\n", sqrt(d_pp), poffset_, sqrt(d_cut));
int bound = 0;
int boundLower = 0;
int boundUpper = 0;
if (d_p1ion < d_cut && d_p2ion < d_cut)
bound = 1;
if (d_baseion < d_pbase)
boundLower = 1;
if (bound && boundLower == 0)
boundUpper = 1;
//if (d_tmp > d_min)
// d_min = d_tmp;
switch (bintype_) {
case COUNT:
dval += (double)bound; break;
case SHORTEST:
if (d_p1ion < d_p2ion)
d_tmp = d_p1ion;
else
d_tmp = d_p2ion;
if (d_tmp > d_baseion)
d_tmp = d_baseion;
if (d_tmp < dval)
dval = d_tmp;
break;
case TOPCONE:
dval += (double)boundUpper; break;
case BOTTOMCONE:
dval += (double)boundLower; break;
}
}
if (bintype_ == SHORTEST)
dval = sqrt(dval);
distance_->Add(frameNum, &dval);
return Action::OK;
}
void CImageEx::RotateCimage( CImage *Imgn, int nAngle )
{
double alpha = nAngle*3.141592654/180;
IMAGEPARAMENT P;
RGBQUAD ColorTab[256];
int i, j, ww, Xd, Yd, Dx, Dy,nSize;
double centerx, centery, sintheta, costheta;
double X1, Y1, X2, Y2, theta, xx, yy, rr;
BYTE **list, *sc;
int x1, y1, x2, y2, flag;
double p, q, a, b, c, d, t1, t2, t3;
if (ImageType() == 2) flag = 1; //flag为标志位，当取值为1时，表示双线性内插法 ,此时图像类型为灰阶图像
else flag = 0; //0表示最近邻点法
GetImageParament(this,&P);
Dx = P.nWidth;
Dy = P.nHeight;
nSize = 0;
if (Dx < Dy)
{
nSize = Dy;
}
else
{
nSize = Dx;
}
int nLineBytes = (nSize * P.nBitCount + 31) / 32 * 4;
//还有一点要修改，不然当图像高度远大于宽度时会崩溃
sc = (BYTE*) malloc(2 * nLineBytes); // * P.nBytesPerLine); //申请工作单元
//
list = (BYTE**) malloc(Dy * sizeof(BYTE*)); //对原位图建立二维数组
for (i = 0; i < Dy; i++)
list[i] = (BYTE*) GetPixelAddress(0, i);
centerx = Dx / 2; //计算位图中心位置
centery = Dy / 2;
rr = sqrt(centerx * centerx + centery *centery); //计算对角线长度
theta = atan((double) centery / (double) centerx);
X1 = fabs(rr * cos(alpha + theta)) + 0.5;
Y1 = fabs(rr * sin(alpha + theta)) + 0.5;
X2 = fabs(rr * cos(alpha - theta)) + 0.5;
Y2 = fabs(rr * sin(alpha - theta)) + 0.5;
if (X2 > X1) X1 = X2; //得外接矩形宽度
if (Y2 > Y1) Y1 = Y2; //外接矩形高度
ww = (int) (2 * X1);
Imgn ->Destroy();
//建立结果位图
Imgn ->Create(ww, (int) (2 * Y1), P.nBitCount,CImage::createAlphaChannel );
if (P.nBitCount == 8)
{
GetAllPalette(this,ColorTab);
//修改一，设置目标调色板
SetAllPalette(Imgn, ColorTab); //复制调色板
}
sintheta = sin(alpha);
costheta = cos(alpha);
for (j = (int) (centery - Y1), Yd = 0; j <= (centery + Y1); j++, Yd++)
{
if (P.nBitCount == 8)
memset (sc, 0, ww); //256色位图像素行置背景值
else memset(sc, 0, ww * P.nBytesPerPixel); //真彩色位图像素行置背景值
for (i = (int) (centerx - X1), Xd = 0; i <= centerx + X1; i++, Xd += P.nBytesPerPixel)
{
xx = centerx + costheta * (i - centerx) + sintheta * (j - centery);
yy = centery - sintheta * (i - centerx) + costheta * (j - centery);
x1 = (int) xx;
x2 = x1 + 1;
p = xx - x1;
y1 = (int) yy;
y2 = y1 + 1;
q = yy - y1;
if (((x1 < 0)||(x2 >= P.nWidth )||(y1 < 0)||(y2 >= P.nHeight )))
continue;
if (flag == 0)
{
if (q > 0.5) y1 = y2;
if (p > 0.5) x1 = x2;
//修改二, sc[Xd]
memcpy(&sc[Xd], &list[y1][x1 * P.nBytesPerPixel], P.nBytesPerPixel); //从源位图复制像素数据
}
else
{ // flag等于1，双线性内插法
a = (double) list[y1][x1]; //从源位图取数据
b = (double) list[y1][x2];
c = (double) list[y2][x1];
d = (double) list[y2][x2];
t1 = (1 - p) * a + p * b; //双线性内插计算
t2 = (1 - p) * c + p * d;
t3 = (1 - q) * t1 + q * t2;
//修改三
sc[Xd] = (BYTE) t3;
}
}
SetRectValue(Imgn, 0, Yd, ww, 1, sc);
}
//png图像
if ( P.nBitCount == 32 )
{
LPVOID pBitsSrc = NULL;
BYTE * psrc = NULL;
BITMAP stBmpInfo;
HBITMAP hBmp = (HBITMAP)m_ImageClone;
::GetObject(hBmp, sizeof(BITMAP), &stBmpInfo);
if (32 != stBmpInfo.bmBitsPixel || NULL == stBmpInfo.bmBits)
return;
psrc = (BYTE *) stBmpInfo.bmBits;
for (int nPosY = 0; nPosY < abs(stBmpInfo.bmHeight); nPosY++)
{
for (int nPosX = stBmpInfo.bmWidth; nPosX > 0; nPosX--)
{
BYTE alpha = psrc[3];
psrc[0] = (BYTE)((psrc[0] * alpha) / 255);
psrc[1] = (BYTE)((psrc[1] * alpha) / 255);
psrc[2] = (BYTE)((psrc[2] * alpha) / 255);
psrc += 4;
}
}
}
free(list); //释放工作单元
free(sc);
}
// Action_Watershell::action()
Action::RetType Action_Watershell::DoAction(int frameNum, ActionFrame& frm) {
Matrix_3x3 ucell, recip;
int nlower = 0;
int nupper = 0;
if (ImageType()==NONORTHO) frm.Frm().BoxCrd().ToRecip(ucell,recip);
int Vidx, Uidx, Vat, currentRes;
int NU = soluteMask_.Nselected();
int NV = solventMask_.Nselected();
double dist;
# ifdef _OPENMP
int mythread;
#pragma omp parallel private(dist,Vidx,Vat,currentRes,Uidx,mythread)
{
mythread = omp_get_thread_num();
#pragma omp for
# endif
// Assume solvent mask is the larger one.
// Loop over solvent atoms
for (Vidx = 0; Vidx < NV; Vidx++) {
// Figure out which solvent residue this is
Vat = solventMask_[Vidx];
currentRes = (*CurrentParm_)[ Vat ].ResNum();
// Loop over solute atoms
for (Uidx = 0; Uidx < NU; Uidx++) {
// If residue is not yet marked as 1st shell, calc distance
# ifdef _OPENMP
if ( activeResidues_thread_[mythread][currentRes] < 2 )
# else
if ( activeResidues_[currentRes] < 2 )
# endif
{
dist = DIST2(frm.Frm().XYZ(soluteMask_[Uidx]), frm.Frm().XYZ(Vat),
ImageType(), frm.Frm().BoxCrd(), ucell, recip );
// Less than upper, 2nd shell
if (dist < upperCutoff_)
{
# ifdef _OPENMP
activeResidues_thread_[mythread][currentRes] = 1;
# else
activeResidues_[currentRes] = 1;
# endif
// Less than lower, 1st shell
if (dist < lowerCutoff_)
# ifdef _OPENMP
activeResidues_thread_[mythread][currentRes] = 2;
# else
activeResidues_[currentRes] = 2;
# endif
}
}
} // End loop over solute atoms
} // End loop over solvent atoms
# ifdef _OPENMP
} // END parallel
// Combine results from each thread.
for (int res = 0; res < NactiveResidues_; res++) {
int shell = 0;
for (int thread = 0; thread < numthreads_; thread++) {
if (activeResidues_thread_[thread][res] > shell)
shell = activeResidues_thread_[thread][res];
// Dont break here so we can reset counts. Could also do with a fill
activeResidues_thread_[thread][res] = 0;
}
if (shell > 0) {
++nupper;
if (shell > 1) ++nlower;
}
}
# else
// Now each residue is marked 0 (no shell), 1 (second shell), 2 (first shell)
for (std::vector<int>::iterator shell = activeResidues_.begin();
shell != activeResidues_.end(); ++shell)
{
if ( *shell > 0 ) {
++nupper;
if ( *shell > 1 ) ++nlower;
}
// Reset for next pass
*shell = 0;
}
# endif
lower_->Add(frameNum, &nlower);
upper_->Add(frameNum, &nupper);
return Action::OK;
}