// Action_DihedralScan::IntervalAngles()
void Action_DihedralScan::IntervalAngles(Frame& currentFrame) {
Matrix_3x3 rotationMatrix;
double theta_in_radians = interval_ * Constants::DEGRAD;
// Write original frame
if (!outfilename_.empty())
outtraj_.WriteSingle(outframe_++, currentFrame);
for (std::vector<DihedralScanType>::iterator dih = BB_dihedrals_.begin();
dih != BB_dihedrals_.end();
dih++)
{
// Set axis of rotation
Vec3 axisOfRotation = currentFrame.SetAxisOfRotation((*dih).atom1, (*dih).atom2);
// Calculate rotation matrix for interval
rotationMatrix.CalcRotationMatrix(axisOfRotation, theta_in_radians);
if (debug_ > 0) {
mprintf("\tRotating Dih %s-%s by %.2f deg %i times.\n",
CurrentParm_->TruncResAtomName( (*dih).atom1 ).c_str(),
CurrentParm_->TruncResAtomName( (*dih).atom2 ).c_str(), interval_, maxVal_);
}
for (int rot = 0; rot < maxVal_; ++rot) {
// Rotate around axis
currentFrame.Rotate(rotationMatrix, (*dih).Rmask);
// Write output trajectory
if (!outfilename_.empty())
outtraj_.WriteSingle(outframe_++, currentFrame);
}
}
}
// Action_MakeStructure::DoAction()
Action::RetType Action_MakeStructure::DoAction(int frameNum, Frame* currentFrame,
Frame** frameAddress)
{
Matrix_3x3 rotationMatrix;
for (std::vector<SecStructHolder>::iterator ss = secstruct_.begin();
ss != secstruct_.end(); ++ss)
{
std::vector<float>::iterator theta = ss->thetas_.begin();
std::vector<AtomMask>::iterator Rmask = ss->Rmasks_.begin();
for (DihedralSearch::mask_it dih = ss->dihSearch_.begin();
dih != ss->dihSearch_.end(); ++dih, ++theta, ++Rmask)
{
double theta_in_radians = (double)*theta;
// Calculate current value of dihedral
double torsion = Torsion( currentFrame->XYZ( (*dih).A0() ),
currentFrame->XYZ( (*dih).A1() ),
currentFrame->XYZ( (*dih).A2() ),
currentFrame->XYZ( (*dih).A3() ) );
// Calculate delta needed to get to theta
double delta = theta_in_radians - torsion;
// Set axis of rotation
Vec3 axisOfRotation = currentFrame->SetAxisOfRotation((*dih).A1(), (*dih).A2());
// Calculate rotation matrix for delta
rotationMatrix.CalcRotationMatrix(axisOfRotation, delta);
if (debug_ > 0) {
std::string a0name = CurrentParm_->TruncResAtomName( (*dih).A0() );
std::string a1name = CurrentParm_->TruncResAtomName( (*dih).A1() );
std::string a2name = CurrentParm_->TruncResAtomName( (*dih).A2() );
std::string a3name = CurrentParm_->TruncResAtomName( (*dih).A3() );
mprintf("\tRotating Dih %i:%s (%i-%i-%i-%i) (@%.2f) by %.2f deg to get to %.2f.\n",
(*dih).ResNum()+1, (*dih).Name().c_str(),
(*dih).A0() + 1, (*dih).A1() + 1, (*dih).A2() + 1, (*dih).A3() + 1,
torsion*Constants::RADDEG, delta*Constants::RADDEG, theta_in_radians*Constants::RADDEG);
}
// Rotate around axis
currentFrame->Rotate(rotationMatrix, *Rmask);
}
}
return Action::OK;
}
// -----------------------------------------------------------------------------
// Exec_PermuteDihedrals::IntervalAngles()
void Exec_PermuteDihedrals::IntervalAngles(Frame const& frameIn, Topology const& topIn,
double interval_in_deg)
{
Matrix_3x3 rotationMatrix;
double theta_in_radians = interval_in_deg * Constants::DEGRAD;
int maxVal = (int) (360.0 / interval_in_deg);
if (maxVal < 0) maxVal = -maxVal;
// Write original frame
if (outtraj_.IsInitialized())
outtraj_.WriteSingle(outframe_++, frameIn);
if (crdout_ != 0)
crdout_->AddFrame( frameIn );
Frame currentFrame = frameIn;
for (std::vector<PermuteDihedralsType>::const_iterator dih = BB_dihedrals_.begin();
dih != BB_dihedrals_.end();
++dih)
{
// Set axis of rotation
Vec3 axisOfRotation = currentFrame.SetAxisOfRotation(dih->atom1, dih->atom2);
// Calculate rotation matrix for interval
rotationMatrix.CalcRotationMatrix(axisOfRotation, theta_in_radians);
if (debug_ > 0) {
mprintf("\tRotating Dih %s-%s by %.2f deg %i times.\n",
topIn.TruncResAtomName( dih->atom1 ).c_str(),
topIn.TruncResAtomName( dih->atom2 ).c_str(), interval_in_deg, maxVal);
}
for (int rot = 0; rot != maxVal; ++rot) {
// Rotate around axis
currentFrame.Rotate(rotationMatrix, dih->Rmask);
// Write output trajectory
if (outtraj_.IsInitialized())
outtraj_.WriteSingle(outframe_++, currentFrame);
if (crdout_ != 0)
crdout_->AddFrame( currentFrame );
}
}
}
// Exec_PermuteDihedrals::RandomizeAngles()
void Exec_PermuteDihedrals::RandomizeAngles(Frame& currentFrame, Topology const& topIn) {
Matrix_3x3 rotationMatrix;
# ifdef DEBUG_PERMUTEDIHEDRALS
// DEBUG
int debugframenum=0;
Trajout_Single DebugTraj;
DebugTraj.PrepareTrajWrite("debugtraj.nc",ArgList(),(Topology*)&topIn,
CoordinateInfo(), BB_dihedrals_.size()*max_factor_,
TrajectoryFile::AMBERNETCDF);
DebugTraj.WriteSingle(debugframenum++,currentFrame);
# endif
int next_resnum;
int bestLoop = 0;
int number_of_rotations = 0;
// Set max number of rotations to try.
int max_rotations = (int)BB_dihedrals_.size();
max_rotations *= max_factor_;
// Loop over all dihedrals
std::vector<PermuteDihedralsType>::const_iterator next_dih = BB_dihedrals_.begin();
next_dih++;
for (std::vector<PermuteDihedralsType>::const_iterator dih = BB_dihedrals_.begin();
dih != BB_dihedrals_.end();
++dih, ++next_dih)
{
++number_of_rotations;
// Get the residue atom of the next dihedral. Residues up to and
// including this residue will be checked for bad clashes
if (next_dih != BB_dihedrals_.end())
next_resnum = next_dih->resnum;
else
next_resnum = dih->resnum - 1;
// Set axis of rotation
Vec3 axisOfRotation = currentFrame.SetAxisOfRotation(dih->atom1, dih->atom2);
// Generate random value to rotate by in radians
// Guaranteed to rotate by at least 1 degree.
// NOTE: could potentially rotate 360 - prevent?
// FIXME: Just use 2PI and rn_gen, get everything in radians
double theta_in_degrees = ((int)(RN_.rn_gen()*100000) % 360) + 1;
double theta_in_radians = theta_in_degrees * Constants::DEGRAD;
// Calculate rotation matrix for random theta
rotationMatrix.CalcRotationMatrix(axisOfRotation, theta_in_radians);
int loop_count = 0;
double clash = 0;
double bestClash = 0;
if (debug_>0) mprintf("DEBUG: Rotating dihedral %zu res %8i:\n", dih - BB_dihedrals_.begin(),
dih->resnum+1);
bool rotate_dihedral = true;
while (rotate_dihedral) {
if (debug_>0) {
mprintf("\t%8i %12s %12s, +%.2lf degrees (%i).\n",dih->resnum+1,
topIn.AtomMaskName(dih->atom1).c_str(),
topIn.AtomMaskName(dih->atom2).c_str(),
theta_in_degrees,loop_count);
}
// Rotate around axis
currentFrame.Rotate(rotationMatrix, dih->Rmask);
# ifdef DEBUG_PERMUTEDIHEDRALS
// DEBUG
DebugTraj.WriteSingle(debugframenum++,currentFrame);
# endif
// If we dont care about sterics exit here
if (!check_for_clashes_) break;
// Check resulting structure for issues
int checkresidue;
if (!checkAllResidues_)
checkresidue = CheckResidue(currentFrame, topIn, *dih, next_resnum, clash);
else
checkresidue = CheckResidue(currentFrame, topIn, *dih, topIn.Nres(), clash);
if (checkresidue==0)
rotate_dihedral = false;
else if (checkresidue==-1) {
if (dih - BB_dihedrals_.begin() < 2) {
mprinterr("Error: Cannot backtrack; initial structure already has clashes.\n");
number_of_rotations = max_rotations + 1;
} else {
dih--; // 0
dih--; // -1
next_dih = dih;
next_dih++;
if (debug_>0)
mprintf("\tCannot resolve clash with further rotations, trying previous again.\n");
}
break;
}
if (clash > bestClash) {bestClash = clash; bestLoop = loop_count;}
//n_problems = CheckResidues( currentFrame, second_atom );
//if (n_problems > -1) {
// mprintf("%i\tCheckResidues: %i problems.\n",frameNum,n_problems);
// rotate_dihedral = false;
//} else if (loop_count==0) {
if (loop_count==0 && rotate_dihedral) {
if (debug_>0)
mprintf("\tTrying dihedral increments of +%i\n",increment_);
// Instead of a new random dihedral, try increments
theta_in_degrees = (double)increment_;
theta_in_radians = theta_in_degrees * Constants::DEGRAD;
// Calculate rotation matrix for new theta
rotationMatrix.CalcRotationMatrix(axisOfRotation, theta_in_radians);
}
++loop_count;
if (loop_count == max_increment_) {
if (debug_>0)
mprintf("%i iterations! Best clash= %.3lf at %i\n",max_increment_,
sqrt(bestClash),bestLoop);
if (dih - BB_dihedrals_.begin() < backtrack_) {
mprinterr("Error: Cannot backtrack; initial structure already has clashes.\n");
number_of_rotations = max_rotations + 1;
} else {
for (int bt = 0; bt < backtrack_; bt++)
dih--;
next_dih = dih;
next_dih++;
if (debug_>0)
mprintf("\tCannot resolve clash with further rotations, trying previous %i again.\n",
backtrack_ - 1);
}
break;
// Calculate how much to rotate back in order to get to best clash
/*int num_back = bestLoop - 359;
theta_in_degrees = (double) num_back;
theta_in_radians = theta_in_degrees * Constants::DEGRAD;
// Calculate rotation matrix for theta
calcRotationMatrix(rotationMatrix, axisOfRotation, theta_in_radians);
// Rotate back to best clash
frm.Frm().RotateAroundAxis(rotationMatrix, theta_in_radians, dih->Rmask);
// DEBUG
DebugTraj.WriteFrame(debugframenum++,currentParm,*currentFrame);
// Sanity check
CheckResidue(currentFrame, *dih, second_atom, &clash);
rotate_dihedral=false;*/
//DebugTraj.EndTraj();
//return 1;
}
} // End dihedral rotation loop
// Safety valve - number of defined dihedrals times * maxfactor
if (number_of_rotations > max_rotations) {
mprinterr("Error: # of rotations (%i) exceeds max rotations (%i), exiting.\n",
number_of_rotations, max_rotations);
//# ifdef DEBUG_PERMUTEDIHEDRALS
// DebugTraj.EndTraj();
//# endif
// Return gracefully for now
break;
//return 1;
}
} // End loop over dihedrals
# ifdef DEBUG_PERMUTEDIHEDRALS
DebugTraj.EndTraj();
mprintf("\tNumber of rotations %i, expected %u\n",number_of_rotations,BB_dihedrals_.size());
# endif
}
// Exec_RotateDihedral::Execute()
Exec::RetType Exec_RotateDihedral::Execute(CpptrajState& State, ArgList& argIn) {
// Get input COORDS set
std::string setname = argIn.GetStringKey("crdset");
if (setname.empty()) {
mprinterr("Error: Specify COORDS dataset name with 'crdset'.\n");
return CpptrajState::ERR;
}
DataSet_Coords* CRD = (DataSet_Coords*)State.DSL().FindCoordsSet( setname );
if (CRD == 0) {
mprinterr("Error: Could not find COORDS set '%s'\n", setname.c_str());
return CpptrajState::ERR;
}
if (CRD->Size() < 1) {
mprinterr("Error: COORDS set is empty.\n");
return CpptrajState::ERR;
}
int frame = argIn.getKeyInt("frame", 0);
if (frame < 0 || frame >= (int)CRD->Size()) {
mprinterr("Error: Specified frame %i is out of range.\n", frame+1);
return CpptrajState::ERR;
}
mprintf(" ROTATEDIHEDRAL: Using COORDS '%s', frame %i\n", CRD->legend(), frame+1);
// Get target frame
Frame FRM = CRD->AllocateFrame();
CRD->GetFrame(frame, FRM);
// Save as reference
Frame refFrame = FRM;
// Create output COORDS set if necessary
DataSet_Coords* OUT = 0;
int outframe = 0;
std::string outname = argIn.GetStringKey("name");
if (outname.empty()) {
// This will not work for TRAJ data sets
if (CRD->Type() == DataSet::TRAJ) {
mprinterr("Error: Using TRAJ as input set requires use of 'name' keyword for output.\n");
return CpptrajState::ERR;
}
OUT = CRD;
outframe = frame;
} else {
// Create new output set with 1 empty frame.
OUT = (DataSet_Coords*)State.DSL().AddSet( DataSet::COORDS, outname );
if (OUT == 0) return CpptrajState::ERR;
OUT->Allocate( DataSet::SizeArray(1, 1) );
OUT->CoordsSetup( CRD->Top(), CRD->CoordsInfo() );
OUT->AddFrame( CRD->AllocateFrame() );
mprintf("\tOutput to set '%s'\n", OUT->legend());
}
// Determine whether we are setting or incrementing.
enum ModeType { SET = 0, INCREMENT };
ModeType mode = SET;
if (argIn.Contains("value"))
mode = SET;
else if (argIn.Contains("increment"))
mode = INCREMENT;
else {
mprinterr("Error: Specify 'value <value>' or 'increment <increment>'\n");
return CpptrajState::ERR;
}
double value = argIn.getKeyDouble(ModeStr[mode], 0.0);
switch (mode) {
case SET: mprintf("\tDihedral will be set to %g degrees.\n", value); break;
case INCREMENT: mprintf("\tDihedral will be incremented by %g degrees.\n", value); break;
}
// Convert to radians
value *= Constants::DEGRAD;
// Select dihedral atoms
int A1, A2, A3, A4;
if (argIn.Contains("type")) {
// By type
ArgList typeArg = argIn.GetStringKey("type");
if (typeArg.empty()) {
mprinterr("Error: No dihedral type specified after 'type'\n");
return CpptrajState::ERR;
}
DihedralSearch dihSearch;
dihSearch.SearchForArgs( typeArg );
if (dihSearch.NoDihedralTokens()) {
mprinterr("Error: Specified dihedral type not recognized.\n");
return CpptrajState::ERR;
}
// Get residue
int res = argIn.getKeyInt("res", -1);
if (res <= 0) {
mprinterr("Error: If 'type' specified 'res' must be specified and > 0.\n");
return CpptrajState::ERR;
}
// Search for dihedrals. User residue #s start from 1.
if (dihSearch.FindDihedrals(CRD->Top(), Range(res-1)))
return CpptrajState::ERR;
DihedralSearch::mask_it dih = dihSearch.begin();
A1 = dih->A0();
A2 = dih->A1();
A3 = dih->A2();
A4 = dih->A3();
} else {
// By masks
AtomMask m1( argIn.GetMaskNext() );
AtomMask m2( argIn.GetMaskNext() );
AtomMask m3( argIn.GetMaskNext() );
AtomMask m4( argIn.GetMaskNext() );
if (CRD->Top().SetupIntegerMask( m1 )) return CpptrajState::ERR;
if (CRD->Top().SetupIntegerMask( m2 )) return CpptrajState::ERR;
if (CRD->Top().SetupIntegerMask( m3 )) return CpptrajState::ERR;
if (CRD->Top().SetupIntegerMask( m4 )) return CpptrajState::ERR;
if (m1.Nselected() != 1) return MaskError( m1 );
if (m2.Nselected() != 1) return MaskError( m2 );
if (m3.Nselected() != 1) return MaskError( m3 );
if (m4.Nselected() != 1) return MaskError( m4 );
A1 = m1[0];
A2 = m2[0];
A3 = m3[0];
A4 = m4[0];
}
mprintf("\tRotating dihedral defined by atoms '%s'-'%s'-'%s'-'%s'\n",
CRD->Top().AtomMaskName(A1).c_str(),
CRD->Top().AtomMaskName(A2).c_str(),
CRD->Top().AtomMaskName(A3).c_str(),
CRD->Top().AtomMaskName(A4).c_str());
// Set mask of atoms that will move during dihedral rotation
AtomMask Rmask = DihedralSearch::MovingAtoms(CRD->Top(), A2, A3);
// Calculate current value of dihedral
double torsion = Torsion( FRM.XYZ(A1), FRM.XYZ(A2), FRM.XYZ(A3), FRM.XYZ(A4) );
// Calculate delta needed to get to target value.
double delta;
switch (mode) {
case SET: delta = value - torsion; break;
case INCREMENT: delta = value; break;
}
mprintf("\tOriginal torsion is %g, rotating by %g degrees.\n",
torsion*Constants::RADDEG, delta*Constants::RADDEG);
// Set axis of rotation
Vec3 axisOfRotation = FRM.SetAxisOfRotation( A2, A3 );
// Calculate rotation matrix for delta.
Matrix_3x3 rotationMatrix;
rotationMatrix.CalcRotationMatrix(axisOfRotation, delta);
// Rotate around axis
FRM.Rotate(rotationMatrix, Rmask);
// RMS-fit the non-moving part of the coords back on original
AtomMask refMask = Rmask;
refMask.InvertMask();
FRM.Align( refFrame, refMask );
// Update coords
OUT->SetCRD( outframe, FRM );
return CpptrajState::OK;
}