void test7() {
string smi = "c1ccccc1C";
#if 1
Mol *m = SmilesToMol(smi);
Mol::AromaticAtomIterator atomIt;
Mol::AromaticAtomIterator beginP(m->beginAromaticAtoms());
Mol::AromaticAtomIterator endP(m->endAromaticAtoms());
unsigned int idx = 0;
for (atomIt = beginP; atomIt != endP; atomIt++) {
TEST_ASSERT((*atomIt)->getIdx() == idx);
idx++;
}
TEST_ASSERT(idx == 6);
atomIt = beginP;
atomIt++;
atomIt--;
TEST_ASSERT((*atomIt)->getIdx() == 0);
delete m;
smi = "Cc1ccccc1";
m = SmilesToMol(smi);
beginP = m->beginAromaticAtoms();
endP = m->endAromaticAtoms();
idx = 0;
for (atomIt = beginP; atomIt != endP; atomIt++) {
TEST_ASSERT((*atomIt)->getIdx() == idx + 1);
idx++;
}
TEST_ASSERT(idx == 6);
#endif
BOOST_LOG(rdInfoLog) << "test7 done" << endl;
}
void MyFrame::OnReadFile (wxString filename)
{
if (mol.ReadPdb((const char*)filename.mb_str(wxConvUTF8) )) {
if ((mol.natm==0) && (mol.nhetatm!=0)) geoSettings.showHetatm=true;
MyTab::EnableGeom();
UpdateShadowmap();
wxString name( mol.GetMolName(), wxConvUTF8 );
SetTitle( name.BeforeLast('.')+ _T(" - QuteMol") );
m_tb->SetTitleText(name);
geoSettings.Apply();
// redo shaders, as texture size could have changed
cgSettings.UpdateShaders();
} else {
wxMessageBox(wxString::FromAscii(QAtom::lastReadError), _T(":-("), wxOK | wxICON_EXCLAMATION, this);
m_tb->SetTitleText();
}
// remake shaders cos texture size could have changed...
//theText->LoadFile(openFileDialog->GetFilename());
//SetStatusText(GetCurrentFilename(), 0);
}
Mol *read_atomic_coordinates(const char *file)
{
long fpos;
float x, y, z;
int ord, natoms;
free_dyna();
if(find_string("Standard orientation")) {
do {
fpos = ftell(fp);
natoms = addTrajectoryStep();
} while(find_string("Standard orientation"));
}
else {
rewind(fp);
if(find_string("Z-Matrix orientation")) {
do {
fpos = ftell(fp);
natoms = addTrajectoryStep();
} while(find_string("Z-Matrix orientation"));
}
else {
rewind(fp);
if(find_string("Input orientation")) {
do {
fpos = ftell(fp);
natoms = addTrajectoryStep();
} while(find_string("Input orientation"));
}
}
}
Mol *mol = add_mol(file);
dynamics.molecule = mol;
dynamics.current = dynamics.ntotalsteps - 1;
fseek(fp, fpos, SEEK_SET);
if(!find_string("Coordinates (Angstroms)")) return 0;
if(!find_string("-----")) return 0;
fgets(line, 255, fp);
do {
if(flagG9803) {
if(sscanf(line, "%*d %d %*d %f %f %f", &ord, &x, &y, &z) != 4) return 0;
}
else {
if(sscanf(line, "%*d %d %f %f %f", &ord, &x, &y, &z) != 4) return 0;
}
if(ord >= 0) mol->AddNewAtom(ord, x, y, z);
fgets(line, 255, fp);
} while(!strstr(line, "------"));
return mol;
}
AOgpu2::AOgpu2( Point3f dir, Mol &m, int ndir){
shadowmap.computeAsTexture(dir, true, shadowAOCanvas );
glFinish();
moltextureCanvas.SetAsOutput();
glDisable(GL_VERTEX_PROGRAM_ARB);
glEnable(GL_FRAGMENT_PROGRAM_ARB);
aogpu_settings.BindDrawAOShader();
for (int i=0; i<3; i++) {
glProgramEnvParameter4fARB(GL_FRAGMENT_PROGRAM_ARB, i,
matSM[0][i],matSM[1][i],matSM[2][i],matSM[3][i]
);
//printf("Sending %d (%f %f %f %f)\n", i, mat[0][i],mat[1][i],mat[2][i],mat[3][i]);
}
glProgramEnvParameter4fARB(GL_FRAGMENT_PROGRAM_ARB, 3, dir[0],dir[1],dir[2], 4.0/ndir );
glProgramEnvParameter4fARB(GL_FRAGMENT_PROGRAM_ARB, 4,
0,stick_radius,0,0
);
m.DrawOnTexture();
glDisable(GL_BLEND);
glEnable(GL_VERTEX_PROGRAM_ARB);
};
void test5() {
string smi = "CCCC";
Mol *m = SmilesToMol(smi);
Mol::BondIterator bondIt;
unsigned int idx = 0;
for (bondIt = m->beginBonds(); bondIt != m->endBonds(); bondIt++) {
CHECK_INVARIANT((*bondIt)->getIdx() == idx, "bad idx");
idx++;
}
CHECK_INVARIANT(idx == 3, "bad idx");
idx = 0;
for (bondIt = m->beginBonds(); bondIt != m->endBonds(); bondIt++) {
CHECK_INVARIANT((*bondIt)->getIdx() == idx, "bad idx");
idx++;
}
CHECK_INVARIANT(idx == 3, "bad idx");
idx = 0;
Mol::BondIterator beginP(m->beginBonds());
Mol::BondIterator endP(m->endBonds());
for (bondIt = beginP; bondIt != endP; bondIt++) {
CHECK_INVARIANT((*bondIt)->getIdx() == idx, "bad idx");
idx++;
}
CHECK_INVARIANT(idx == 3, "bad idx");
BOOST_LOG(rdInfoLog) << "test5 done" << endl;
}
void GeoSettings::Apply(){
if (mol.IsReady()) {
if (mode==BALL_N_STICKS) {
mol.SetBallAndSticks(stickRadius);
}
if (mode==LICORICE) {
mol.SetLicorice(licoRadius);
}
if (mode==SPACE_FILL) mol.SetSpaceFill();
}
cgSettings.setGeoSettings(*this);
cgSettings.UpdateShaders();
UpdateShadowmap();
mol.ResetAO();
}
void test8() {
{
string smi = "CC1CC2CC1C2";
Mol *m = SmilesToMol(smi);
QueryAtom *q = new QueryAtom();
q->setQuery(makeAtomExplicitDegreeQuery(3));
q->expandQuery(makeAtomRingBondCountQuery(2));
unsigned int nSeen = 0;
for (Mol::QueryAtomIterator queryIt = m->beginQueryAtoms(q);
queryIt != m->endQueryAtoms(); ++queryIt) {
TEST_ASSERT((*queryIt)->getIdx() == 1);
nSeen++;
}
TEST_ASSERT(nSeen == 1);
delete m;
delete q;
}
BOOST_LOG(rdInfoLog) << "test8 done" << endl;
};
void MyFrame::OnIdle(wxIdleEvent& event){
if (mol.DoingAO()) {
m_tb->UpdateGearsIcon(true);
if (mol.PrepareAOstep()) {
m_canvas->SceneChanged();
event.RequestMore(false);
m_tb->UpdateGearsIcon(false);
return;
}
else event.RequestMore(true);
} else {
event.RequestMore(false);
if (hardSettings.STILL_QUALITY!=hardSettings.MOVING_QUALITY)
if (!m_canvas->shownHQ) {
m_canvas->shownHQ=true;
mustDoHQ=true;
m_canvas->Refresh(false);
}
m_tb->UpdateGearsIcon(false);
}
}
void test3() {
string smi = "C1COCCNCOCNSCC1";
unsigned char heteros[] = {2, 5, 7, 9, 10};
Mol *m = SmilesToMol(smi);
{
unsigned int nSeen = 0;
for (Mol::HeteroatomIterator heteroIt = m->beginHeteros();
heteroIt != m->endHeteros(); heteroIt++) {
CHECK_INVARIANT((*heteroIt)->getIdx() == heteros[nSeen], "bad hetero");
nSeen++;
}
}
{
unsigned int nSeen = 0;
for (Mol::HeteroatomIterator heteroIt = m->beginHeteros();
heteroIt != m->endHeteros(); ++heteroIt) {
CHECK_INVARIANT((*heteroIt)->getIdx() == heteros[nSeen], "bad hetero");
nSeen++;
}
}
{
Mol::HeteroatomIterator heteroIt = m->beginHeteros();
heteroIt++;
heteroIt++;
heteroIt--;
CHECK_INVARIANT((*heteroIt)->getIdx() == heteros[1], "bad hetero");
CHECK_INVARIANT((*--heteroIt)->getIdx() == heteros[0], "bad hetero");
CHECK_INVARIANT((*heteroIt)->getIdx() == heteros[0], "bad hetero");
}
BOOST_LOG(rdInfoLog) << "test3 done" << endl;
};
void testIssue263() {
string smi = "c1ccccc1C";
#if 1
Mol *m = SmilesToMol(smi);
Mol::AtomIterator atomIt;
unsigned int idx = 0;
for (atomIt = m->beginAtoms(); atomIt != m->endAtoms(); ++atomIt) {
TEST_ASSERT((*atomIt)->getIdx() == idx);
idx++;
}
TEST_ASSERT(idx == 7);
Mol::BondIterator bondIt;
idx = 0;
for (bondIt = m->beginBonds(); bondIt != m->endBonds(); ++bondIt) {
CHECK_INVARIANT((*bondIt)->getIdx() == idx, "bad idx");
idx++;
}
CHECK_INVARIANT(idx == 7, "bad idx");
#endif
BOOST_LOG(rdInfoLog) << "testIssue263 done" << endl;
}
AO::AO( Point3f _dir, Mol &m) {
dir=_dir.Normalize();
// orthonormal basis
Point3f ax,ay,az=dir;
ax=az^Point3f(1,0,0);
if (ax.SquaredNorm()<0.1) ax=az^Point3f(0,1,0);
ax=ax.Normalize();
ay=(az^ax).Normalize();
// project...
m.Transform(ax,ay,az);
int target=32; //
bufx=bufy=target;
float bufscalex=target/(m.tx1-m.tx0);
float bufscaley=target/(m.ty1-m.ty0);
bufscale=(bufscalex<bufscaley)?bufscalex:bufscaley;
m.ScaleTransl(bufscale);
CubeMapSamp::Transform(ax,ay,az);
printf("Scale=%f\n",bufscale);
buf.resize(target*target,infty);
for (int i=0; i<m.atom.size()-1; i++) {
QAtom &a=m.atom[i];
CheckAtom(a);
RenderSphere( a.trp[0], a.trp[1], a.trp[2], a.trr );
PrintBuffer();
}
}
void test4() {
string smi = "C1COCCNCOCNSCC1";
unsigned int heteros1[] = {2, 7};
Mol *m = SmilesToMol(smi);
QueryAtom *q = new QueryAtom();
q->setQuery(makeAtomNumQuery(8));
{
unsigned int nSeen = 0;
for (Mol::QueryAtomIterator queryIt = m->beginQueryAtoms(q);
queryIt != m->endQueryAtoms(); queryIt++) {
CHECK_INVARIANT((*queryIt)->getIdx() == heteros1[nSeen], "bad query");
nSeen++;
}
}
{
Mol::QueryAtomIterator queryIt = m->beginQueryAtoms(q);
queryIt++;
queryIt--;
CHECK_INVARIANT((*queryIt)->getIdx() == heteros1[0], "bad query");
CHECK_INVARIANT((*++queryIt)->getIdx() == heteros1[1], "bad query");
CHECK_INVARIANT((*queryIt)->getIdx() == heteros1[1], "bad query");
}
{
Mol::QueryAtomIterator queryIt = m->beginQueryAtoms(q);
queryIt++;
queryIt--;
Mol::QueryAtomIterator queryIt2 = queryIt;
CHECK_INVARIANT((*queryIt2)->getIdx() == heteros1[0], "bad query");
CHECK_INVARIANT((*++queryIt2)->getIdx() == heteros1[1], "bad query");
CHECK_INVARIANT((*queryIt2)->getIdx() == heteros1[1], "bad query");
}
smi = "CC(C)CC(C)CC(C)CC(C)C";
unsigned int heteros2[] = {1, 4, 7, 10};
m = SmilesToMol(smi);
// m->debugMol(cout);
q->setQuery(makeAtomImplicitValenceQuery(1));
{
unsigned int nSeen = 0;
for (Mol::QueryAtomIterator queryIt = m->beginQueryAtoms(q);
queryIt != m->endQueryAtoms(); ++queryIt) {
CHECK_INVARIANT((*queryIt)->getIdx() == heteros2[nSeen], "bad query");
nSeen++;
}
}
BOOST_LOG(rdInfoLog) << "test4 done" << endl;
};
void TestGLCanvas::OnPaint( wxPaintEvent& event )
{
/* must always be here */
wxPaintDC dc(this);
#ifndef __WXMOTIF__
if (!GetContext()) return;
#endif
SetCurrent();
if (!initdone) {
static bool once=false;
if (!once) {
once=true;
int errcode=initGl();
if (errcode!=ERRGL_OK){
wxMessageBox(errorMSG(errcode), _T("Unrecoverable error: Problems initializing graphics"), wxOK | wxICON_EXCLAMATION, this);
exit(0);
}
else initdone=true;
}
}
if (!initdone) wxGLCanvas::OnPaint(event); else
if (mol.IsReady()) {
if (mustDoHQ) {
drawFrame( hardSettings.STILL_QUALITY );
shownHQ=true;
mustDoHQ=false;
} else {
drawFrame( hardSettings.MOVING_QUALITY );
shownHQ=false;
}
SwapBuffers();
}
else {
clearFrame();
SwapBuffers();
}
}
void test2() {
string smi = "C1COC1";
Mol *m = SmilesToMol(smi);
Mol::BondIterator bondIt;
unsigned int idx = 0;
for (bondIt = m->beginBonds(); bondIt != m->endBonds(); bondIt++) {
CHECK_INVARIANT((*bondIt)->getIdx() == idx, "bad idx");
idx++;
}
bondIt = m->beginBonds();
Mol::BondIterator bondIt2 = m->beginBonds();
CHECK_INVARIANT(bondIt == bondIt2, "iterators don't compare equal");
bondIt++;
CHECK_INVARIANT((*bondIt)->getIdx() == 1, "bad idx");
bondIt++;
bondIt++;
bondIt--;
CHECK_INVARIANT((*bondIt)->getIdx() == 2, "bad idx");
CHECK_INVARIANT(bondIt != bondIt2, "iterators don't compare different");
bondIt--;
--bondIt;
CHECK_INVARIANT((*bondIt)->getIdx() == 0, "bad idx");
CHECK_INVARIANT(bondIt == bondIt2, "iterator inequality failed");
bondIt++;
++bondIt;
CHECK_INVARIANT((*bondIt)->getIdx() == 2, "bad idx");
// past the end stuff
bondIt2 = m->endBonds();
bondIt = m->beginBonds();
bondIt--;
BOOST_LOG(rdInfoLog) << "test2 done" << endl;
};
int InitQuteMol(const char * filename)
{
CubeMapSamp::SetSize(CSIZE);
OctaMapSamp::SetSize(CSIZE);
if (filename==NULL) filename="porin.pdb";
mol.ReadPdb(filename);
cgSettings.SetDefaults();
// initGl gets called from the GL canvas on startup. It's not
// legal to call it before that time because the OpenGL context
// does not exist yet.
/*if (!initGl()) {
printf("failed to initialize! :(\n");
return 0;
}*/
//FillRandomTexture();
//mol.DuplicateTexels(texture, TSIZE);
//ReloadTexture(texture, bilinear);
return 1;
}
// FOR HALOS
void prepareDepthTextureForCurrentViewpoint(){
// Draw depth texture from current viewpoint
haloCanvas.SetSameRes( mainCanvas );
haloCanvas.SetAsOutput();
if (use_accurate_halo)
shadowSettingsAcc.BindShaders();
else
shadowSettings.BindShaders();
glClear( GL_DEPTH_BUFFER_BIT ) ;
mol.Draw();
mainCanvas.SetAsOutput();
glActiveTextureARB(GL_TEXTURE1_ARB);
haloCanvas.SetAsTexture();
glEnable(GL_TEXTURE_2D);
}
void test1() {
string smi = "CCOC";
Mol *m = SmilesToMol(smi);
Mol::AtomIterator atIt;
unsigned int idx = 0;
for (atIt = m->beginAtoms(); atIt != m->endAtoms(); atIt++) {
CHECK_INVARIANT((*atIt)->getIdx() == idx, "bad idx");
idx++;
}
atIt = m->beginAtoms();
CHECK_INVARIANT((*(atIt + 2))->getIdx() == 2, "bad idx");
atIt = m->beginAtoms();
Mol::AtomIterator atIt2 = m->beginAtoms();
CHECK_INVARIANT(atIt == atIt2, "iterators don't compare equal");
atIt++;
CHECK_INVARIANT((*atIt)->getIdx() == 1, "bad idx");
atIt += 2;
CHECK_INVARIANT((*atIt)->getIdx() == 3, "bad idx");
atIt -= 1;
CHECK_INVARIANT((*atIt)->getIdx() == 2, "bad idx");
CHECK_INVARIANT(atIt != atIt2, "iterators don't compare different");
CHECK_INVARIANT(atIt2 < atIt, "iterator inequality failed");
CHECK_INVARIANT(atIt2 <= atIt, "iterator inequality failed");
CHECK_INVARIANT(atIt > atIt2, "iterator inequality failed");
CHECK_INVARIANT(atIt >= atIt2, "iterator inequality failed");
atIt--;
--atIt;
CHECK_INVARIANT((*atIt)->getIdx() == 0, "bad idx");
CHECK_INVARIANT(atIt == atIt2, "iterator inequality failed");
atIt++;
++atIt;
CHECK_INVARIANT((*atIt)->getIdx() == 2, "bad idx");
atIt = m->beginAtoms();
atIt = atIt + 2;
atIt = atIt - 2;
CHECK_INVARIANT((*atIt)->getIdx() == 0, "bad idx");
atIt2 = m->beginAtoms();
atIt2 += 2;
CHECK_INVARIANT(atIt2 - atIt == 2, "subtraction failed");
CHECK_INVARIANT(atIt - atIt2 == -2, "subtraction failed");
// past the end stuff
atIt2 = m->endAtoms();
atIt = m->beginAtoms() + 10;
CHECK_INVARIANT(atIt >= atIt2, "past-the-end failed");
// this is whack
atIt = m->beginAtoms();
atIt -= 10;
CHECK_INVARIANT(atIt >= atIt2, "past-the-end failed");
BOOST_LOG(rdInfoLog) << "test1 done" << endl;
};
void TestGLCanvas::OnKeyDown( wxKeyEvent& event ){
wxConsumeTrackBallEvent(event,true,track);
#ifdef __DARWIN__
wxString path = wxStandardPaths::Get().GetResourcesDir() + "/presets/new.preset";
#else
wxString path = "presets\\new.preset";
#endif
if (event.GetKeyCode() == WXK_F7 ) {
cgSettings.Save(path.c_str());
}
if (event.GetKeyCode() == WXK_F6 ) {
if (cgSettings.Load(path.c_str())) {
MyTab::UpdateAll();
cgSettings.ResetHalo();
cgSettings.UpdateShaders();
SceneChanged();
}
}
if (event.GetKeyCode() == WXK_F5 ) {
mol.PrepareAOSingleView();
SceneChanged();
}
if (event.GetKeyCode() == WXK_F2 ) {
static int status=0;
status=(status+1) % 5;
draw_balls = (status==0) || (status==1) || (status==2) ;
draw_sticks = (status==0) || (status==1) || (status==3) || (status==4) ;
draw_wireframe_balls= (status==1) ;
draw_wireframe_sticks= (status==1) || (status==3) ;
SceneChanged();
}
if (event.GetKeyCode() == WXK_F1 ) {
wxString text;
if (!mol.IsReady() ) text=wxT("(no molecule)");
else {
text=wxString( mol.GetMolName(), wxConvUTF8 ).BeforeLast('.') +
wxT("\n (file: \"")+wxString( mol.filename, wxConvUTF8 ) +wxT("\")\n\n");
text=text+wxString::Format(wxT("%d atoms\n"),mol.atom.size());
if (mol.sticks) {
text=text+wxString::Format(wxT("%d bonds\n"),mol.bond.size());
}
text=text+wxString::Format(
_T("\nUsing:\n Texture size = %dx%d\n Patch size=%dx%d"),
moltextureCanvas.GetHardRes(),
moltextureCanvas.GetHardRes(),
CSIZE,CSIZE
);
}
wxMessageBox(text, _T("QuteMol - file info"), wxOK | wxICON_INFORMATION, this);
}
if (event.GetKeyCode() == WXK_F6 ) {
use_accurate_halo=!use_accurate_halo;
SceneChanged();
}
// temp, should e set auto depending on dist
if (event.GetKeyCode() == WXK_F2 ) {
cgSettings.P_capping=!cgSettings.P_capping;
cgSettings.UpdateShaders();
SceneChanged();
}
}
void MyFrame::OnSaveSnap (wxCommandEvent & event)
{
int sx,sy;
static const wxString FILETYPES = _T(
"PNG (lossless)|*.png|"
"JPEG (lossy)|*.jpg|"
"GIF animation|*.gif"
);
wxFileDialog * saveSnapDialog =
new wxFileDialog ( this,
wxString (_T("Save a snapshot")),
wxString(), // def path
wxString(),
FILETYPES,
wxSAVE | /*wxCHANGE_DIR |*/ wxOVERWRITE_PROMPT
);
static int lastFilterIndex=-1;
if (lastFilterIndex==-1) lastFilterIndex=saveSnapDialog->GetFilterIndex();
saveSnapDialog->SetFilterIndex( lastFilterIndex );
wxString ext;
if (lastFilterIndex==1) ext=_T(".jpg");
else if (lastFilterIndex==2) ext=_T(".gif");
else ext=_T(".png");
saveSnapDialog->SetFilename( wxString( mol.GetFilenameSnap(), wxConvUTF8 )+ ext );
static wxString CANNOT_SAVE = _T("Could not save snap!\n\nYou might try setting\na lower resolution\nor removing AntiAliasing...");
if (saveSnapDialog->ShowModal() == wxID_OK)
if ((new savesnapDialog(this,saveSnapDialog->GetFilterIndex()))->ShowModal() == wxID_OK )
{
int jj=saveSnapDialog->GetFilterIndex();
lastFilterIndex=jj;
Byte* snap;
int AAMult=(hardSettings.SNAP_ANTIALIAS)?2:1;
bool useTransp=(hardSettings.PNG_TRANSPARENT==1) && (jj==0);
if (jj!=2) {
sx=sy=hardSettings.SNAP_SIZE*AAMult;
if ((useTransp) && (cgSettings.UseHalo()>0)) {
cgSettings.doingAlphaSnapshot=true;
cgSettings.ResetHalo();
cgSettings.UpdateShaders();
}
snap= GetSnapshot(sx,sy, useTransp );
if (cgSettings.doingAlphaSnapshot) {
cgSettings.doingAlphaSnapshot=false;
cgSettings.ResetHalo();
cgSettings.UpdateShaders();
}
if (!snap) {
wxMessageBox(CANNOT_SAVE, _T("OpenGL problems?"), wxOK | wxICON_EXCLAMATION, this);
return;
}
} else sx=sy=hardSettings.GIF_SNAP_SIZE*AAMult;
{
wxString fn=saveSnapDialog->GetPath();
// fix filename Extension
//////////////////////////
//wxString ext[3]={ _T("png"), _T("jpg") , _T("png") };
//wxString cext=fn.AfterLast('.');
//if (cext.CmpNoCase(ext[0])||cext.CmpNoCase(ext[1])) fn=fn.BeforeLast('.');
//fn=fn+_T('.')+ext[ jj ];
switch (jj) {
case 0:
case 1:
if (!useTransp) {
StartProgress("Saving snap!", 2);
wxImage snapi(sx,sy,snap);
if (AAMult!=1) snapi=snapi.Scale(sx/AAMult,sy/AAMult);
UpdateProgress(1);
wxBitmap(snapi.Mirror(false)).SaveFile(
fn,
(jj==0)?wxBITMAP_TYPE_PNG:wxBITMAP_TYPE_JPEG
);
UpdateProgress(2);
EndProgress();
}
else {
if (AAMult!=1) downsample2x2(snap, sx, sy);
PNGSaveWithAlpha((const char*)fn.mb_str(wxConvUTF8),snap,sx/AAMult,sy/AAMult,1);
};
break;
case 2: {
GifWrapper gifw;
int N;
double totalTime;
double subStepTime=0;
double startTime;startTime=hardSettings.GIF_INITIAL_PAUSE/1000.0;
if (hardSettings.GIF_ANIMATION_MODE==0) {
N=hardSettings.GIF_ROT_N_FRAMES;
totalTime=hardSettings.GIF_ROT_MSEC/1000.0;
}
if (hardSettings.GIF_ANIMATION_MODE==1) {
N=hardSettings.GIF_INSP_N_FRAMES;
totalTime=hardSettings.GIF_INSP_MSEC/1000.0;
}
if (hardSettings.GIF_ANIMATION_MODE==2) {
N=hardSettings.GIF_6SIDES_N_FRAMES*6;
totalTime=hardSettings.GIF_6SIDES_MSEC*6.0/1000.0;
subStepTime=hardSettings.GIF_6SIDES_PAUSE/1000.0;
}
StartProgress("Saving GIF", N);
for (int i=0; i<N; i++) {
if (!UpdateProgress(i)) break;
setAniStep(double(i)/N);
snap = GetSnapshot(sx,sy, false);
if (!snap) {
wxMessageBox(CANNOT_SAVE, _T("OpenGL problems?"), wxOK | wxICON_EXCLAMATION, this);
EndProgress();
return;
}
if (AAMult!=1) downsample2x2NoAlpha(snap, sx, sy);
gifw.AddFrame(snap, sx/AAMult, sy/AAMult,
totalTime/N
+ ( (i==0)?startTime:0)
+ ( (i%(N/6)==0)?subStepTime:0)
);
}
stopAni();
gifw.Save( (const char*)fn.mb_str(wxConvUTF8) );
EndProgress();
} break;
}
}
}
}
void test4() {
BOOST_LOG(rdErrorLog) << "---------------------- Test4" << std::endl;
Mol m;
Atom *a = new Atom(6);
// we copy in addAtom, so this is safe
m.addAtom(a);
m.addAtom(a);
m.addAtom(a);
m.addAtom(a);
m.addAtom(a);
m.addAtom(a);
m.addAtom(a);
delete a;
m.addBond(0, 1, Bond::SINGLE);
m.addBond(1, 2, Bond::DOUBLE);
m.addBond(2, 3, Bond::SINGLE);
m.addBond(3, 4, Bond::DOUBLE);
m.addBond(4, 5, Bond::SINGLE);
m.addBond(5, 0, Bond::DOUBLE);
m.addBond(5, 6, Bond::SINGLE);
MolOps::sanitizeMol(m);
ATOM_NULL_QUERY *aeq = makeAtomNullQuery();
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(0)), "");
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(1)), "");
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(5)), "");
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(6)), "");
delete aeq;
BOOST_LOG(rdErrorLog) << "Done!" << std::endl;
}
void test1() {
BOOST_LOG(rdErrorLog) << "---------------------- Test1" << std::endl;
Mol qM;
Mol m;
Atom *a = new Atom(6);
// we copy in addAtom, so this is safe
m.addAtom(a);
m.addAtom(a);
delete a;
m.addBond(0, 1, Bond::SINGLE);
a = new Atom(8);
m.addAtom(a);
delete a;
m.addBond(1, 2, Bond::DOUBLE);
MolOps::sanitizeMol(m);
QueryAtom *qA = new QueryAtom(6);
CHECK_INVARIANT(qA->Match(m.getAtomWithIdx(0)), "");
CHECK_INVARIANT(qA->Match(m.getAtomWithIdx(1)), "");
CHECK_INVARIANT(!qA->Match(m.getAtomWithIdx(2)), "");
qA->expandQuery(makeAtomImplicitValenceQuery(3));
CHECK_INVARIANT(qA->Match(m.getAtomWithIdx(0)), "");
CHECK_INVARIANT(!qA->Match(m.getAtomWithIdx(1)), "");
CHECK_INVARIANT(!qA->Match(m.getAtomWithIdx(2)), "");
qM.addAtom(qA);
delete qA;
qA = new QueryAtom(6);
qA->expandQuery(makeAtomNumQuery(8), Queries::COMPOSITE_OR);
qM.addAtom(qA);
delete qA;
qM.addAtom(new QueryAtom(8), true, true);
// Atom::ATOM_SPTR qA(new QueryAtom(6));
QueryBond *qB;
qB = new QueryBond(Bond::UNSPECIFIED);
qB->setOwningMol(qM);
qB->setBeginAtomIdx(0);
qB->setEndAtomIdx(1);
CHECK_INVARIANT(qB->Match(m.getBondWithIdx(0)), "");
CHECK_INVARIANT(qB->Match(m.getBondWithIdx(1)), "");
qM.addBond(qB, true);
qB = new QueryBond(Bond::DOUBLE);
qB->setOwningMol(qM);
qB->setBeginAtomIdx(1);
qB->setEndAtomIdx(2);
qM.addBond(qB, true);
CHECK_INVARIANT(qM.getAtomWithIdx(0)->Match(m.getAtomWithIdx(0)), "");
CHECK_INVARIANT(!qM.getAtomWithIdx(0)->Match(m.getAtomWithIdx(1)), "");
CHECK_INVARIANT(!qM.getAtomWithIdx(0)->Match(m.getAtomWithIdx(2)), "");
CHECK_INVARIANT(qM.getAtomWithIdx(1)->Match(m.getAtomWithIdx(0)), "");
CHECK_INVARIANT(qM.getAtomWithIdx(1)->Match(m.getAtomWithIdx(1)), "");
CHECK_INVARIANT(qM.getAtomWithIdx(1)->Match(m.getAtomWithIdx(2)), "");
CHECK_INVARIANT(!qM.getAtomWithIdx(2)->Match(m.getAtomWithIdx(0)), "");
CHECK_INVARIANT(!qM.getAtomWithIdx(2)->Match(m.getAtomWithIdx(1)), "");
CHECK_INVARIANT(qM.getAtomWithIdx(2)->Match(m.getAtomWithIdx(2)), "");
CHECK_INVARIANT(qM.getBondWithIdx(0)->Match(m.getBondWithIdx(0)), "");
CHECK_INVARIANT(qM.getBondWithIdx(0)->Match(m.getBondWithIdx(1)), "");
CHECK_INVARIANT(!qM.getBondWithIdx(1)->Match(m.getBondWithIdx(0)), "");
CHECK_INVARIANT(qM.getBondWithIdx(1)->Match(m.getBondWithIdx(1)), "");
BOOST_LOG(rdErrorLog) << "Done!" << std::endl;
}
void test3() {
BOOST_LOG(rdErrorLog) << "---------------------- Test3" << std::endl;
Mol m;
Atom *a = new Atom(6);
// we copy in addAtom, so this is safe
m.addAtom(a);
m.addAtom(a);
m.addAtom(a);
m.addAtom(a);
m.addAtom(a);
m.addAtom(a);
m.addAtom(a);
delete a;
m.addBond(0, 1, Bond::SINGLE);
m.addBond(1, 2, Bond::DOUBLE);
m.addBond(2, 3, Bond::SINGLE);
m.addBond(3, 4, Bond::DOUBLE);
m.addBond(4, 5, Bond::SINGLE);
m.addBond(5, 0, Bond::DOUBLE);
m.addBond(5, 6, Bond::SINGLE);
MolOps::sanitizeMol(m);
ATOM_EQUALS_QUERY *aeq = makeAtomExplicitDegreeQuery(3);
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(0)), "");
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(1)), "");
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(5)), "");
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(6)), "");
delete aeq;
aeq = makeAtomExplicitDegreeQuery(2);
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(0)), "");
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(1)), "");
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(5)), "");
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(6)), "");
delete aeq;
aeq = makeAtomHCountQuery(1);
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(0)), "");
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(1)), "");
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(5)), "");
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(6)), "");
delete aeq;
aeq = makeAtomInNRingsQuery(1);
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(0)), "");
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(1)), "");
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(5)), "");
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(6)), "");
delete aeq;
aeq = makeAtomInNRingsQuery(0);
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(0)), "");
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(1)), "");
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(5)), "");
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(6)), "");
delete aeq;
aeq = makeAtomAromaticQuery();
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(0)), "");
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(1)), "");
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(5)), "");
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(6)), "");
delete aeq;
aeq = makeAtomAliphaticQuery();
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(0)), "");
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(1)), "");
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(5)), "");
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(6)), "");
delete aeq;
aeq = makeAtomInRingQuery();
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(0)), "");
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(1)), "");
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(5)), "");
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(6)), "");
aeq->setNegation(true);
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(0)), "");
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(1)), "");
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(5)), "");
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(6)), "");
delete aeq;
aeq = makeAtomInRingOfSizeQuery(6);
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(0)), "");
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(1)), "");
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(5)), "");
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(6)), "");
aeq->setNegation(true);
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(0)), "");
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(1)), "");
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(5)), "");
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(6)), "");
delete aeq;
aeq = makeAtomInRingOfSizeQuery(5);
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(0)), "");
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(1)), "");
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(5)), "");
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(6)), "");
aeq->setNegation(true);
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(0)), "");
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(1)), "");
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(5)), "");
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(6)), "");
delete aeq;
BOND_EQUALS_QUERY *beq = makeBondIsInRingQuery();
CHECK_INVARIANT(beq->Match(m.getBondWithIdx(0)), "");
CHECK_INVARIANT(!beq->Match(m.getBondWithIdx(6)), "");
CHECK_INVARIANT(beq->Match(m.getBondBetweenAtoms(0, 1)), "");
CHECK_INVARIANT(beq->Match(m.getBondBetweenAtoms(1, 0)), "");
CHECK_INVARIANT(!beq->Match(m.getBondBetweenAtoms(5, 6)), "");
CHECK_INVARIANT(!beq->Match(m.getBondBetweenAtoms(6, 5)), "");
BOOST_LOG(rdErrorLog) << "Done!" << std::endl;
}
void ResetColMode(){
float tmp=mol.colMode;
mol.colMode=-1;
mol.SetColMode(tmp);
}
void SetColMode(float mode){
mol.SetColMode(mode);
}
void MyFrame::ResetAO(){
mol.ResetAO();
}
void test5() {
BOOST_LOG(rdErrorLog) << "---------------------- Test5" << std::endl;
Mol m;
Atom *a = new Atom(6);
// we copy in addAtom, so this is safe
m.addAtom(a);
m.addAtom(a);
m.addAtom(a);
m.addAtom(a);
m.addAtom(a);
m.addAtom(a);
m.addAtom(a);
delete a;
m.addBond(0, 1, Bond::SINGLE);
m.addBond(1, 2, Bond::DOUBLE);
m.addBond(2, 3, Bond::SINGLE);
m.addBond(3, 4, Bond::DOUBLE);
m.addBond(4, 5, Bond::SINGLE);
m.addBond(5, 0, Bond::DOUBLE);
m.addBond(5, 6, Bond::SINGLE);
MolOps::sanitizeMol(m);
unsigned int valenceProd;
valenceProd = queryAtomBondProduct(m.getAtomWithIdx(0));
TEST_ASSERT(valenceProd == 1681); // aromatic*aromatic = 41 * 41 = 1681
valenceProd = queryAtomBondProduct(m.getAtomWithIdx(1));
TEST_ASSERT(valenceProd == 1681);
valenceProd = queryAtomBondProduct(m.getAtomWithIdx(5));
TEST_ASSERT(valenceProd == 5043);
valenceProd = queryAtomBondProduct(m.getAtomWithIdx(6));
TEST_ASSERT(valenceProd == 3);
valenceProd = queryAtomAllBondProduct(m.getAtomWithIdx(6));
TEST_ASSERT(valenceProd == 81);
BOOST_LOG(rdErrorLog) << "Done!" << std::endl;
}
void MyToolbar::UpdateGearsIcon(){
UpdateGearsIcon( mol.DoingAO() );
}
void test2() {
BOOST_LOG(rdErrorLog) << "---------------------- Test2" << std::endl;
Mol qM;
Mol m;
Atom *a = new Atom(6);
// we copy in addAtom, so this is safe
m.addAtom(a);
m.addAtom(a);
m.addAtom(a);
delete a;
m.addBond(0, 1, Bond::TRIPLE);
m.addBond(1, 2, Bond::SINGLE);
a = new Atom(8);
m.addAtom(a);
delete a;
m.addBond(2, 3, Bond::DOUBLE);
MolOps::sanitizeMol(m);
QueryBond *qB;
qB = new QueryBond(Bond::SINGLE);
CHECK_INVARIANT(!qB->Match(m.getBondWithIdx(0)), "");
CHECK_INVARIANT(qB->Match(m.getBondWithIdx(1)), "");
CHECK_INVARIANT(!qB->Match(m.getBondWithIdx(2)), "");
BOND_EQUALS_QUERY *newQ = makeBondOrderEqualsQuery(Bond::DOUBLE);
qB->expandQuery(newQ, Queries::COMPOSITE_OR);
CHECK_INVARIANT(!qB->Match(m.getBondWithIdx(0)), "");
CHECK_INVARIANT(qB->Match(m.getBondWithIdx(1)), "");
CHECK_INVARIANT(qB->Match(m.getBondWithIdx(2)), "");
BOOST_LOG(rdErrorLog) << "Done!" << std::endl;
}
void drawFrame() {
cgSettings.MakeShaders();
if (mol.DoingAO()) {
// do at least one more step per rendering
mol.PrepareAOstep(1);
// continue until decent
while (!mol.DecentAO()) mol.PrepareAOstep(1);
}
/*if (cgSettings.UseHalo()>0) {
// write depth in HaloTexture
glBindFramebufferEXT(GL_FRAMEBUFFER_EXT, haloFrame);
} else {
// write depth in depthbuffer
glBindFramebufferEXT(GL_FRAMEBUFFER_EXT, 0);
}*/
mainCanvas.SetAsOutput();
if (cgSettings.doingAlphaSnapshot)
glClearColor( cgSettings.P_halo_col, cgSettings.P_halo_col, cgSettings.P_halo_col, 0.0f);
else
glClearColor( cgSettings.P_bg_color_R, cgSettings.P_bg_color_G, cgSettings.P_bg_color_B, 0.0f);
glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT);
glMatrixMode(GL_MODELVIEW);
glLoadIdentity();
Point3f lightDir;
if ( cgSettings.P_sem_effect // fixed light dir sem effect
// || mol.sticks // quick Hack: fixed light dir when bonds
)
lightDir= Point3f(0,0,1);
else
lightDir=getDirFromTrackball(lightTrack);
setLightDir( lightDir );
// gluLookAt(0,0,-3, 0,0,0, 0,1,0); original
// gluLookAt(0,0,-3, 0,0,0, 0,1,0); ok for tra
if (mol.hasDefaultView())
gluLookAt(0,0, 40, 0,0,0, 0,1,0);
else
gluLookAt(0,0,-40, 0,0,0, 0,1,0);
if(MovingLightMode)
drawLightDir();
glColor3f(1,1,1);
if (mol.hasDefaultView()) {
float angle, axisX, axisY, axisZ;
mol.getDefaultViewRotation(&angle, &axisX, &axisY, &axisZ);
glRotatef(angle, axisX, axisY, axisZ);
}
if (1) {
//track.center=Point3f(0, 0, 0);
//track.radius= 1;
//setProjection();
if (aniStep>=0) // BH: Doesn't normally seem to be aniStep>=0
{
double extraRot=360.0*aniStep;
// set extra rotation for GIF animation:
switch (hardSettings.GIF_ANIMATION_MODE) {
default:
case 0:
glRotated(-hardSettings.GIF_ROT_SIDEVIEW_ANGLE,1,0,0);
glRotated(extraRot,0,1,0);
break;
case 1:
glRotated(-extraRot,0,0,1);
glRotated(hardSettings.GIF_INSP_ANGLE,0,1,0);
glRotated(extraRot,0,0,1);
break;
case 2:{
double substep[6];
for (int i=0; i<6; i++) {
substep[i]=(aniStep*6-i)*90.0;
if (substep[i]<0) substep[i]=0;
if (substep[i]>90.0) substep[i]=90.0;
}
glRotated(-substep[5], 1,0,0);
glRotated(-substep[4], 0,1,0);
glRotated(-substep[3], 0,1,0);
glRotated(-substep[2], 1,0,0);
glRotated(-substep[1], 0,1,0);
glRotated(-substep[0], 0,1,0);
}break;
}
}
setProjection( mainCanvas.GetVideoSize() );
track.GetView();
track.Apply(false); // Set to true to see the trackball itself.
setProjection( mainCanvas.GetSoftRes() );
if (cgSettings.P_use_shadowmap()) {
shadowmap.computeAsTexture( getGlLightPos() , cgSettings.do_use_doubleshadow(), shadowmapCanvas);
//shadowmap.computeAsTexture( Point3f(0,1,0) );
}
cgSettings.BindShaders();
glEnable(GL_TEXTURE_2D);
//glBindTexture(GL_TEXTURE_2D, molTexture);
glActiveTextureARB(GL_TEXTURE1_ARB);
shadowmapCanvas.SetAsTexture();
mol.Draw();
// shadowmap.m.DrawShadowmap(false);
glDisable(GL_VERTEX_PROGRAM_ARB);
glDisable(GL_FRAGMENT_PROGRAM_ARB);
glDisable(GL_BLEND);
if (cgSettings.UseHalo()>0) mol.DrawHalos();
}
}
void Mol::Draw(){
glPushMatrix();
glScalef(1/r,1/r,1/r);
glTranslatef(-px,-py,-pz);
float x[4][4], scalef;
glGetFloatv(GL_MODELVIEW_MATRIX, &(x[0][0]));
glProgramEnvParameter4fARB(GL_VERTEX_PROGRAM_ARB, 0,
scalef=extractCurrentScaleFactor(x),0,0,0
);
/*
glProgramEnvParameter4fARB(GL_FRAGMENT_PROGRAM_ARB, 6,
1.0 / ( scalef*scalef) , 0,0,0
);*/
/* printf("ScaleFactor= %f, ShadowScaleFactor= %f\n",
scalef, shadowScaleFactor );*/
glEnable(GL_VERTEX_PROGRAM_ARB);
glEnable(GL_TEXTURE_2D);
glActiveTextureARB(GL_TEXTURE0_ARB);
moltextureCanvas.SetAsTexture();
if (cgSettings.P_shadowstrenght>0) {
ShadowMap::GetCurrentPVMatrix();
ShadowMap::FeedParameters();
}
for (int i=0; i<3; i++)
glProgramEnvParameter4fARB(GL_FRAGMENT_PROGRAM_ARB, i,
x[i][0],x[i][1],x[i][2],0
);
glProgramEnvParameter4fARB(GL_FRAGMENT_PROGRAM_ARB, 6,
mol.PredictAO(),0,0,0
);
if (draw_balls) {
if (draw_wireframe_balls) {
glDisable(GL_FRAGMENT_PROGRAM_ARB);
for (int i=0; i<atom.size(); i++) {
glColor3f(0,0,1);
glBegin(GL_LINE_LOOP);
atom[i].Draw();
glEnd();
}
} else {
glEnable(GL_VERTEX_PROGRAM_ARB);
glEnable(GL_FRAGMENT_PROGRAM_ARB);
//if (DL_atoms==666) glGenD
glBegin(GL_QUADS);
for (int i=0; i<atom.size(); i++) atom[i].Draw();
glEnd();
glDisable(GL_VERTEX_PROGRAM_ARB);
glDisable(GL_FRAGMENT_PROGRAM_ARB);
}
}
if (draw_sticks)
if (sticks) {
glEnable(GL_VERTEX_PROGRAM_ARB);
glEnable(GL_FRAGMENT_PROGRAM_ARB);
cgSettings.BindStickShaders();
ShadowMap::FeedParameters();
for (int i=0; i<3; i++)
glProgramEnvParameter4fARB(GL_FRAGMENT_PROGRAM_ARB, i,
x[i][0],x[i][1],x[i][2],0
);
/*
glProgramEnvParameter4fARB(GL_FRAGMENT_PROGRAM_ARB, 6,
1.0 / ( scalef*scalef) , stick_radius,1.0 / ( scalef) ,0
);*/
glEnable(GL_TEXTURE_2D);
glProgramEnvParameter4fARB(GL_VERTEX_PROGRAM_ARB, 0,
scalef, stick_radius,stick_radius*2,0 );
glColor3f(1,1,1);
if (draw_wireframe_sticks) {
glDisable(GL_FRAGMENT_PROGRAM_ARB);
for (int i=0; i<bond.size(); i++) {
glColor3f(0,0.6,0.3);
glBegin(GL_LINE_LOOP);
bond[i].Draw();
glEnd();
}
}
else {
glBegin(GL_QUADS);
for (int i=0; i<bond.size(); i++) bond[i].Draw();
glEnd();
}
cgSettings.BindShaders();
}
glPopMatrix();
}