// Exec_PermuteDihedrals::Execute()
Exec::RetType Exec_PermuteDihedrals::Execute(CpptrajState& State, ArgList& argIn) {
debug_ = State.Debug();
mode_ = INTERVAL;
// Get Keywords - first determine mode
if (argIn.hasKey("random"))
mode_ = RANDOM;
else if (argIn.hasKey("interval"))
mode_ = INTERVAL;
// 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;
}
mprintf(" PERMUTEDIHEDRALS: Using COORDS '%s'\n", CRD->legend());
// Get residue range
Range resRange;
resRange.SetRange(argIn.GetStringKey("resrange"));
if (!resRange.Empty())
resRange.ShiftBy(-1); // User res args start from 1
mprintf("\tPermutating dihedrals in");
if (resRange.Empty())
mprintf(" all solute residues.\n");
else
mprintf(" residue range [%s]\n", resRange.RangeArg());
// Determine which angles to search for
DihedralSearch dihSearch;
dihSearch.SearchForArgs(argIn);
// If nothing is enabled, enable all
dihSearch.SearchForAll();
mprintf("\tSearching for types:");
dihSearch.PrintTypes();
mprintf("\n");
// Setup output trajectory
outframe_ = 0;
std::string outfilename = argIn.GetStringKey("outtraj");
if (!outfilename.empty()) {
mprintf("\tCoordinates output to '%s'\n", outfilename.c_str());
Topology* outtop = State.DSL().GetTopology( argIn );
if (outtop == 0) {
mprinterr("Error: No topology for output traj.\n");
return CpptrajState::ERR;
}
// Setup output trajectory FIXME: Correct frames for # of rotations
if (outtraj_.PrepareTrajWrite(outfilename, argIn, CRD->TopPtr(), CRD->CoordsInfo(),
CRD->Size(), TrajectoryFile::UNKNOWN_TRAJ))
return CpptrajState::ERR;
}
// Setup output coords
outfilename = argIn.GetStringKey("crdout");
if (!outfilename.empty()) {
mprintf("\tCoordinates saved to set '%s'\n", outfilename.c_str());
crdout_ = (DataSet_Coords_CRD*)State.DSL().AddSet(DataSet::COORDS, outfilename);
if (crdout_ == 0) return CpptrajState::ERR;
crdout_->CoordsSetup( CRD->Top(), CRD->CoordsInfo() );
}
// Get specific mode options.
double interval_in_deg = 60.0;
if ( mode_ == INTERVAL ) {
interval_in_deg = argIn.getNextDouble(60.0);
mprintf("\tDihedrals will be rotated at intervals of %.2f degrees.\n", interval_in_deg);
} else if (mode_ == RANDOM) {
check_for_clashes_ = argIn.hasKey("check");
checkAllResidues_ = argIn.hasKey("checkallresidues");
cutoff_ = argIn.getKeyDouble("cutoff",0.8);
rescutoff_ = argIn.getKeyDouble("rescutoff",10.0);
backtrack_ = argIn.getKeyInt("backtrack",4);
increment_ = argIn.getKeyInt("increment",1);
max_factor_ = argIn.getKeyInt("maxfactor",2);
int iseed = argIn.getKeyInt("rseed",-1);
// Output file for # of problems
DataFile* problemFile = State.DFL().AddDataFile(argIn.GetStringKey("out"), argIn);
// Dataset to store number of problems
number_of_problems_ = State.DSL().AddSet(DataSet::INTEGER, argIn.GetStringNext(),"Nprob");
if (number_of_problems_==0) return CpptrajState::ERR;
// Add dataset to data file list
if (problemFile != 0) problemFile->AddDataSet(number_of_problems_);
// Check validity of args
if (cutoff_ < Constants::SMALL) {
mprinterr("Error: cutoff too small.\n");
return CpptrajState::ERR;
}
if (rescutoff_ < Constants::SMALL) {
mprinterr("Error: rescutoff too small.\n");
return CpptrajState::ERR;
}
if (backtrack_ < 0) {
mprinterr("Error: backtrack value must be >= 0\n");
return CpptrajState::ERR;
}
if ( increment_<1 || (360 % increment_)!=0 ) {
mprinterr("Error: increment must be a factor of 360.\n");
return CpptrajState::ERR;
}
// Calculate max increment
max_increment_ = 360 / increment_;
// Seed random number gen
RN_.rn_set( iseed );
// Print info
mprintf("\tDihedrals will be rotated to random values.\n");
if (iseed==-1)
mprintf("\tRandom number generator will be seeded using time.\n");
else
mprintf("\tRandom number generator will be seeded using %i\n",iseed);
if (check_for_clashes_) {
mprintf("\tWill attempt to recover from bad steric clashes.\n");
if (checkAllResidues_)
mprintf("\tAll residues will be checked.\n");
else
mprintf("\tResidues up to the currenly rotating dihedral will be checked.\n");
mprintf("\tAtom cutoff %.2f, residue cutoff %.2f, backtrack = %i\n",
cutoff_, rescutoff_, backtrack_);
mprintf("\tWhen clashes occur dihedral will be incremented by %i\n",increment_);
mprintf("\tMax # attempted rotations = %i times number dihedrals.\n",
max_factor_);
}
// Square cutoffs to compare to dist^2 instead of dist
cutoff_ *= cutoff_;
rescutoff_ *= rescutoff_;
// Increment backtrack by 1 since we need to skip over current res
++backtrack_;
// Initialize CheckStructure
if (checkStructure_.SetOptions( false, false, false, State.Debug(), "*", "", 0.8, 1.15, 4.0 )) {
mprinterr("Error: Could not set up structure check.\n");
return CpptrajState::ERR;
}
// Set up CheckStructure for this parm (false = nobondcheck)
if (checkStructure_.Setup(CRD->Top(), CRD->CoordsInfo().TrajBox()))
return CpptrajState::ERR;
}
// Determine from selected mask atoms which dihedrals will be rotated.
PermuteDihedralsType dst;
// If range is empty (i.e. no resrange arg given) look through all
// solute residues.
Range actualRange;
if (resRange.Empty())
actualRange = CRD->Top().SoluteResidues();
else
actualRange = resRange;
// Search for dihedrals
if (dihSearch.FindDihedrals(CRD->Top(), actualRange))
return CpptrajState::ERR;
// For each found dihedral, set up mask of atoms that will move upon
// rotation. Also set up mask of atoms in this residue that will not
// move, including atom2.
if (debug_>0)
mprintf("DEBUG: Dihedrals:\n");
for (DihedralSearch::mask_it dih = dihSearch.begin();
dih != dihSearch.end(); ++dih)
{
dst.checkAtoms.clear();
// Set mask of atoms that will move during dihedral rotation.
dst.Rmask = DihedralSearch::MovingAtoms(CRD->Top(), dih->A1(), dih->A2());
// If randomly rotating angles, check for atoms that are in the same
// residue as A1 but will not move. They need to be checked for clashes
// since further rotations will not help them.
if (mode_ == RANDOM && check_for_clashes_) {
CharMask cMask( dst.Rmask.ConvertToCharMask(), dst.Rmask.Nselected() );
int a1res = CRD->Top()[dih->A1()].ResNum();
for (int maskatom = CRD->Top().Res(a1res).FirstAtom();
maskatom < CRD->Top().Res(a1res).LastAtom(); ++maskatom)
if (!cMask.AtomInCharMask(maskatom))
dst.checkAtoms.push_back( maskatom );
dst.checkAtoms.push_back(dih->A1()); // TODO: Does this need to be added first?
// Since only the second atom and atoms it is bonded to move during
// rotation, base the check on the residue of the second atom.
dst.resnum = a1res;
}
dst.atom0 = dih->A0(); // FIXME: This duplicates info
dst.atom1 = dih->A1();
dst.atom2 = dih->A2();
dst.atom3 = dih->A3();
BB_dihedrals_.push_back(dst);
// DEBUG: List dihedral info.
if (debug_ > 0) {
mprintf("\t%s-%s-%s-%s\n",
CRD->Top().TruncResAtomName(dih->A0()).c_str(),
CRD->Top().TruncResAtomName(dih->A1()).c_str(),
CRD->Top().TruncResAtomName(dih->A2()).c_str(),
CRD->Top().TruncResAtomName(dih->A3()).c_str() );
if (debug_ > 1 && mode_ == RANDOM && check_for_clashes_) {
mprintf("\t\tCheckAtoms=");
for (std::vector<int>::const_iterator ca = dst.checkAtoms.begin();
ca != dst.checkAtoms.end(); ++ca)
mprintf(" %i", *ca + 1);
mprintf("\n");
}
if (debug_ > 2) {
mprintf("\t\t");
dst.Rmask.PrintMaskAtoms("Rmask:");
}
}
}
// Set up simple structure check. First step is coarse; check distances
// between a certain atom in each residue (first, COM, CA, some other atom?)
// to see if residues are in each others neighborhood. Second step is to
// check the atoms in each close residue.
if (check_for_clashes_) {
ResidueCheckType rct;
int res = 0;
for (Topology::res_iterator residue = CRD->Top().ResStart();
residue != CRD->Top().ResEnd(); ++residue)
{
rct.resnum = res++;
rct.start = residue->FirstAtom();
rct.stop = residue->LastAtom();
rct.checkatom = rct.start;
ResCheck_.push_back(rct);
}
}
// Perform dihedral permute
Frame currentFrame = CRD->AllocateFrame();
for (unsigned int set = 0; set != CRD->Size(); set++)
{
CRD->GetFrame(set, currentFrame);
int n_problems = 0;
switch (mode_) {
case RANDOM:
RandomizeAngles(currentFrame, CRD->Top());
// Check the resulting structure
n_problems = checkStructure_.CheckOverlaps( currentFrame );
//mprintf("%i\tResulting structure has %i problems.\n",frameNum,n_problems);
number_of_problems_->Add(set, &n_problems);
if (outtraj_.IsInitialized()) outtraj_.WriteSingle(outframe_++, currentFrame);
if (crdout_ != 0) crdout_->AddFrame( currentFrame );
break;
case INTERVAL: IntervalAngles(currentFrame, CRD->Top(), interval_in_deg); break;
}
}
if (outtraj_.IsInitialized()) outtraj_.EndTraj();
return CpptrajState::OK;
}
/** Determine from selected mask atoms which dihedrals will be rotated. */
Action::RetType Action_DihedralScan::Setup(ActionSetup& setup) {
DihedralScanType dst;
// If range is empty (i.e. no resrange arg given) look through all
// solute residues.
Range actualRange;
if (resRange_.Empty())
actualRange = setup.Top().SoluteResidues();
else
actualRange = resRange_;
// Search for dihedrals
if (dihSearch_.FindDihedrals(setup.Top(), actualRange))
return Action::ERR;
// For each found dihedral, set up mask of atoms that will move upon
// rotation. Also set up mask of atoms in this residue that will not
// move, including atom2.
if (debug_>0)
mprintf("DEBUG: Dihedrals:\n");
for (DihedralSearch::mask_it dih = dihSearch_.begin();
dih != dihSearch_.end(); ++dih)
{
dst.checkAtoms.clear();
// Set mask of atoms that will move during dihedral rotation.
dst.Rmask = DihedralSearch::MovingAtoms(setup.Top(), dih->A1(), dih->A2());
// If randomly rotating angles, check for atoms that are in the same
// residue as A1 but will not move. They need to be checked for clashes
// since further rotations will not help them.
if (mode_ == RANDOM && check_for_clashes_) {
CharMask cMask( dst.Rmask.ConvertToCharMask(), dst.Rmask.Nselected() );
int a1res = setup.Top()[dih->A1()].ResNum();
for (int maskatom = setup.Top().Res(a1res).FirstAtom();
maskatom < setup.Top().Res(a1res).LastAtom(); ++maskatom)
if (!cMask.AtomInCharMask(maskatom))
dst.checkAtoms.push_back( maskatom );
dst.checkAtoms.push_back(dih->A1()); // TODO: Does this need to be added first?
// Since only the second atom and atoms it is bonded to move during
// rotation, base the check on the residue of the second atom.
dst.resnum = a1res;
}
dst.atom0 = dih->A0(); // FIXME: This duplicates info
dst.atom1 = dih->A1();
dst.atom2 = dih->A2();
dst.atom3 = dih->A3();
BB_dihedrals_.push_back(dst);
// DEBUG: List dihedral info.
if (debug_ > 0) {
mprintf("\t%s-%s-%s-%s\n",
setup.Top().TruncResAtomName(dih->A0()).c_str(),
setup.Top().TruncResAtomName(dih->A1()).c_str(),
setup.Top().TruncResAtomName(dih->A2()).c_str(),
setup.Top().TruncResAtomName(dih->A3()).c_str() );
if (debug_ > 1 && mode_ == RANDOM && check_for_clashes_) {
mprintf("\t\tCheckAtoms=");
for (std::vector<int>::const_iterator ca = dst.checkAtoms.begin();
ca != dst.checkAtoms.end(); ++ca)
mprintf(" %i", *ca + 1);
mprintf("\n");
}
if (debug_ > 2) {
mprintf("\t\t");
dst.Rmask.PrintMaskAtoms("Rmask:");
}
}
}
// Set up CheckStructure for this parm (false = nobondcheck)
if (checkStructure_.SeparateSetup(setup.Top(),
setup.CoordInfo().TrajBox().Type(), false) != Action::OK)
return Action::ERR;
// Set the overall max number of rotations to try
max_rotations_ = (int) BB_dihedrals_.size();
max_rotations_ *= max_factor_;
// Set up simple structure check. First step is coarse; check distances
// between a certain atom in each residue (first, COM, CA, some other atom?)
// to see if residues are in each others neighborhood. Second step is to
// check the atoms in each close residue.
if (check_for_clashes_) {
ResidueCheckType rct;
int res = 0;
for (Topology::res_iterator residue = setup.Top().ResStart();
residue != setup.Top().ResEnd(); ++residue)
{
rct.resnum = res++;
rct.start = residue->FirstAtom();
rct.stop = residue->LastAtom();
rct.checkatom = rct.start;
ResCheck_.push_back(rct);
}
}
if (!outfilename_.empty() && CurrentParm_ == 0) // FIXME: Correct frames for # of rotations
outtraj_.SetupTrajWrite(setup.TopAddress(), setup.CoordInfo(), setup.Nframes());
CurrentParm_ = setup.TopAddress();
return Action::OK;
}
// 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;
}
// Action_MakeStructure::Init()
Action::RetType Action_MakeStructure::Init(ArgList& actionArgs, TopologyList* PFL, DataSetList* DSL, DataFileList* DFL, int debugIn)
{
debug_ = debugIn;
secstruct_.clear();
// Get all arguments
std::string ss_expr = actionArgs.GetStringNext();
while ( !ss_expr.empty() ) {
ArgList ss_arg(ss_expr, ":");
if (ss_arg.Nargs() < 2) {
mprinterr("Error: Malformed SS arg.\n");
Help();
return Action::ERR;
}
// Type is 1st arg, range is 2nd arg.
SecStructHolder ss_holder(ss_arg[1], FindSStype(ss_arg[0]));
if (ss_arg.Nargs() == 2) {
// Find SS type: <ss type>:<range>
if (ss_holder.sstype_idx == SS_EMPTY) {
mprinterr("Error: SS type %s not found.\n", ss_arg[0].c_str());
return Action::ERR;
}
ss_holder.dihSearch_.SearchFor(MetaData::PHI);
ss_holder.dihSearch_.SearchFor(MetaData::PSI);
secstruct_.push_back( ss_holder );
} else if (ss_arg[0] == "ref") {
// Use dihedrals from reference structure
if (ss_arg.Nargs() < 3) {
mprinterr("Error: Invalid 'ref' arg. Requires 'ref:<range>:<refname>[:<ref range>]'\n");
return Action::ERR;
}
ss_arg.MarkArg(0);
ss_arg.MarkArg(1);
// Sanity check: Currently only unique args of this type are allowed
if (ss_holder.sstype_idx != SS_EMPTY) {
mprinterr("Error: Ref backbone types must be unique [%s]\n", ss_arg[0].c_str());
return Action::ERR;
}
// Use backbone phi/psi from reference structure
ss_holder.dihSearch_.SearchFor(MetaData::PHI);
ss_holder.dihSearch_.SearchFor(MetaData::PSI);
// Get reference structure
DataSet_Coords_REF* REF = (DataSet_Coords_REF*)
DSL->FindSetOfType(ss_arg.GetStringNext(),
DataSet::REF_FRAME); // ss_arg[2]
if (REF == 0) {
mprinterr("Error: Could not get reference structure [%s]\n", ss_arg[2].c_str());
return Action::ERR;
}
// Get reference residue range, or use resRange
Range refRange(ss_arg.GetStringNext(), -1); // ss_arg[3]
if (!refRange.Empty()) {
if (ss_holder.resRange.Size() != refRange.Size()) {
mprinterr("Error: Reference range [%s] must match residue range [%s]\n",
refRange.RangeArg(), ss_holder.resRange.RangeArg());
return Action::ERR;
}
} else
refRange = ss_holder.resRange;
// Look for phi/psi only in reference
DihedralSearch refSearch;
refSearch.SearchFor(MetaData::PHI);
refSearch.SearchFor(MetaData::PSI);
if (refSearch.FindDihedrals( REF->Top(), refRange )) return Action::ERR;
// For each found dihedral, set theta
for (DihedralSearch::mask_it dih = refSearch.begin(); dih != refSearch.end(); ++dih)
{
double torsion = Torsion( REF->RefFrame().XYZ(dih->A0()),
REF->RefFrame().XYZ(dih->A1()),
REF->RefFrame().XYZ(dih->A2()),
REF->RefFrame().XYZ(dih->A3()) );
ss_holder.thetas_.push_back( (float)torsion );
}
secstruct_.push_back( ss_holder );
} else if (ss_arg.Nargs() == 4 && isalpha(ss_arg[2][0])) {
// Single dihedral type: <name>:<range>:<dih type>:<angle>
DihedralSearch::DihedralType dtype = DihedralSearch::GetType(ss_arg[2]);
if (ss_holder.sstype_idx == SS_EMPTY) {
// Type not yet defined. Create new type.
if (dtype == MetaData::UNDEFINED) {
mprinterr("Error: Dihedral type %s not found.\n", ss_arg[2].c_str());
return Action::ERR;
}
if (!validDouble(ss_arg[3])) {
mprinterr("Error: 4th arg (angle) is not a valid number.\n");
return Action::ERR;
}
SS.push_back( SS_TYPE(convertToDouble(ss_arg[3]), 0.0, 0.0, 0.0, 2, ss_arg[0]) );
ss_holder.sstype_idx = (int)(SS.size() - 1);
}
ss_holder.dihSearch_.SearchFor( dtype );
secstruct_.push_back( ss_holder );
} else if (ss_arg.Nargs() == 7 || ss_arg.Nargs() == 8) {
// Single custom dihedral type: <name>:<range>:<at0>:<at1>:<at2>:<at3>:<angle>[:<offset>]
if (ss_holder.sstype_idx == SS_EMPTY) {
// Type not yet defined. Create new type.
if (!validDouble(ss_arg[6])) {
mprinterr("Error: 7th arg (angle) is not a valid number.\n");
return Action::ERR;
}
SS.push_back( SS_TYPE(convertToDouble(ss_arg[6]), 0.0, 0.0, 0.0, 2, ss_arg[0]) );
ss_holder.sstype_idx = (int)(SS.size() - 1);
}
int offset = 0;
if (ss_arg.Nargs() == 8) {
if (!validInteger(ss_arg[7])) {
mprinterr("Error: 8th arg (offset) is not a valid number.\n");
return Action::ERR;
}
offset = convertToInteger(ss_arg[7]);
}
ss_holder.dihSearch_.SearchForNewType(offset,ss_arg[2],ss_arg[3],ss_arg[4],ss_arg[5],
ss_arg[0]);
secstruct_.push_back( ss_holder );
} else if (ss_arg.Nargs() == 4 || ss_arg.Nargs() == 6) {
// Custom SS/turn type: <name>:<range>:<phi1>:<psi1>[:<phi2>:<psi2>]
if (ss_holder.sstype_idx == SS_EMPTY) {
// Type not yet defined. Create new type.
if (!validDouble(ss_arg[2]) || !validDouble(ss_arg[3])) {
mprinterr("Error: 3rd or 4th arg (phi1/psi1) is not a valid number.\n");
return Action::ERR;
}
double phi1 = convertToDouble(ss_arg[2]);
double psi1 = convertToDouble(ss_arg[3]);
int isTurn = 0;
double phi2 = 0.0;
double psi2 = 0.0;
if (ss_arg.Nargs() == 6) {
isTurn = 1;
if (!validDouble(ss_arg[4]) || !validDouble(ss_arg[5])) {
mprinterr("Error: 5th or 6th arg (phi2/psi2) is not a valid number.\n");
return Action::ERR;
}
phi2 = convertToDouble(ss_arg[4]);
psi2 = convertToDouble(ss_arg[5]);
}
SS.push_back(SS_TYPE(phi1, psi1, phi2, psi2, isTurn, ss_arg[0] ));
ss_holder.sstype_idx = (int)(SS.size() - 1);
}
ss_holder.dihSearch_.SearchFor(MetaData::PHI);
ss_holder.dihSearch_.SearchFor(MetaData::PSI);
secstruct_.push_back( ss_holder );
} else {
mprinterr("Error: SS arg type [%s] not recognized.\n", ss_arg[0].c_str());
return Action::ERR;
}
ss_expr = actionArgs.GetStringNext();
} // End loop over args
if (secstruct_.empty()) {
mprinterr("Error: No SS types defined.\n");
return Action::ERR;
}
mprintf(" MAKESTRUCTURE:\n");
for (std::vector<SecStructHolder>::iterator ss = secstruct_.begin();
ss != secstruct_.end(); ++ss)
{
if (ss->sstype_idx != SS_EMPTY) {
const SS_TYPE& myType = SS[ss->sstype_idx];
switch ( myType.isTurn ) {
case 0:
mprintf("\tSS type %s will be applied to residue(s) %s\n",
myType.type_arg.c_str(), ss->resRange.RangeArg());
break;
case 1:
mprintf("\tTurn type %s will be applied to residue(s) %s\n",
myType.type_arg.c_str(), ss->resRange.RangeArg());
break;
case 2:
mprintf("\tDihedral value of %.2f will be applied to %s dihedrals in residue(s) %s\n",
myType.phi, myType.type_arg.c_str(), ss->resRange.RangeArg());
}
} else
mprintf("\tBackbone angles from reference will be applied to residue(s) %s\n",
ss->resRange.RangeArg());
}
return Action::OK;
}