/** Write file containing only cut atoms and energies as charges. */ int Action_Pairwise::WriteCutFrame(int frameNum, Topology const& Parm, AtomMask const& CutMask, Darray const& CutCharges, Frame const& frame, std::string const& outfilename) { if (CutMask.Nselected() != (int)CutCharges.size()) { mprinterr("Error: WriteCutFrame: # of charges (%u) != # mask atoms (%i)\n", CutCharges.size(), CutMask.Nselected()); return 1; } Frame CutFrame(frame, CutMask); Topology* CutParm = Parm.modifyStateByMask( CutMask ); if (CutParm == 0) return 1; // Set new charges for (int i = 0; i != CutParm->Natom(); i++) CutParm->SetAtom(i).SetCharge( CutCharges[i] ); int err = 0; Trajout_Single tout; if (tout.PrepareTrajWrite(outfilename, "multi", CutParm, CoordinateInfo(), 1, TrajectoryFile::MOL2FILE)) { mprinterr("Error: Could not set up cut mol2 file %s\n", outfilename.c_str()); err = 1; } else { tout.WriteSingle(frameNum, CutFrame); tout.EndTraj(); } delete CutParm; return err; }
// Analysis_Hist::Analyze() Analysis::RetType Analysis_Hist::Analyze() { // Set up dimensions // Size of histdata and dimensionArgs should be the same size_t total_bins = 0UL; for (unsigned int hd = 0; hd < N_dimensions_; hd++) { if ( setupDimension(dimensionArgs_[hd], *(histdata_[hd]), total_bins) ) return Analysis::ERR; } // dimensionArgs no longer needed dimensionArgs_.clear(); // Check that the number of data points in each dimension are equal std::vector<DataSet_1D*>::iterator ds = histdata_.begin(); size_t Ndata = (*ds)->Size(); ++ds; for (; ds != histdata_.end(); ++ds) { //mprintf("DEBUG: DS %s size %i\n",histdata[hd]->Name(),histdata[hd]->Xmax()+1); if (Ndata != (*ds)->Size()) { mprinterr("Error: Hist: Dataset %s has inconsistent # data points (%zu), expected %zu.\n", (*ds)->legend(), (*ds)->Size(), Ndata); return Analysis::ERR; } } mprintf("\tHist: %zu data points in each dimension.\n", Ndata); if (calcAMD_ && Ndata != amddata_->Size()) { mprinterr("Error: Hist: AMD data set size (%zu) does not match # expected data points (%zu).\n", amddata_->Size(), Ndata); return Analysis::ERR; } // Allocate bins mprintf("\tHist: Allocating histogram, total bins = %zu\n", total_bins); Bins_.resize( total_bins, 0.0 ); // Bin data for (size_t n = 0; n < Ndata; n++) { long int index = 0; HdimType::const_iterator dim = dimensions_.begin(); OffType::const_iterator bOff = binOffsets_.begin(); for (std::vector<DataSet_1D*>::iterator ds = histdata_.begin(); ds != histdata_.end(); ++ds, ++dim, ++bOff) { double dval = (*ds)->Dval( n ); // Check if data is out of bounds for this dimension. if (dval > dim->Max() || dval < dim->Min()) { index = -1L; break; } // Calculate index for this particular dimension (idx) long int idx = (long int)((dval - dim->Min()) / dim->Step()); if (debug_>1) mprintf(" [%s:%f (%li)],", dim->label(), dval, idx); // Calculate overall index in Bins, offset has already been calcd. index += (idx * (*bOff)); } // If index was successfully calculated, populate bin if (index > -1L && index < (long int)Bins_.size()) { if (debug_ > 1) mprintf(" |index=%li",index); if (calcAMD_) Bins_[index] += exp( amddata_->Dval(n) ); else Bins_[index]++; } else { mprintf("\tWarning: Frame %zu Coordinates out of bounds (%li)\n", n+1, index); } if (debug_>1) mprintf("}\n"); } // Calc free energy if requested if (calcFreeE_) CalcFreeE(); // Normalize if requested if (normalize_ != NO_NORM) Normalize(); if (nativeOut_) { // Use Histogram built-in output PrintBins(); } else { // Using DataFileList framework, set-up labels etc. if (N_dimensions_ == 1) { DataSet_double& dds = static_cast<DataSet_double&>( *hist_ ); // Since Allocate1D only reserves data, use assignment op. dds = Bins_; hist_->SetDim(Dimension::X, dimensions_[0]); } else if (N_dimensions_ == 2) { DataSet_MatrixDbl& mds = static_cast<DataSet_MatrixDbl&>( *hist_ ); mds.Allocate2D( dimensions_[0].Bins(), dimensions_[1].Bins() ); std::copy( Bins_.begin(), Bins_.end(), mds.begin() ); hist_->SetDim(Dimension::X, dimensions_[0]); hist_->SetDim(Dimension::Y, dimensions_[1]); outfile_->ProcessArgs("noxcol usemap nolabels"); } else if (N_dimensions_ == 3) { DataSet_GridFlt& gds = static_cast<DataSet_GridFlt&>( *hist_ ); //gds.Allocate3D( dimensions_[0].Bins(), dimensions_[1].Bins(), dimensions_[2].Bins() ); gds.Allocate_N_O_D( dimensions_[0].Bins(), dimensions_[1].Bins(), dimensions_[2].Bins(), Vec3(dimensions_[0].Min(), dimensions_[1].Min(), dimensions_[2].Min()), Vec3(dimensions_[0].Step(), dimensions_[1].Step(), dimensions_[2].Step()) ); //std::copy( Bins_.begin(), Bins_.end(), gds.begin() ); // FIXME: Copy will not work since in grids data is ordered with Z // changing fastest. Should the ordering in grid be changed? size_t idx = 0; for (size_t z = 0; z < gds.NZ(); z++) for (size_t y = 0; y < gds.NY(); y++) for (size_t x = 0; x < gds.NX(); x++) gds.SetElement( x, y, z, (float)Bins_[idx++] ); hist_->SetDim(Dimension::X, dimensions_[0]); hist_->SetDim(Dimension::Y, dimensions_[1]); hist_->SetDim(Dimension::Z, dimensions_[2]); outfile_->ProcessArgs("noxcol usemap nolabels"); // Create pseudo-topology/trajectory if (!traj3dName_.empty()) { Topology pseudo; pseudo.AddTopAtom(Atom("H3D", 0), Residue("H3D", 1, ' ', ' ')); pseudo.CommonSetup(); if (!parmoutName_.empty()) { ParmFile pfile; if (pfile.WriteTopology( pseudo, parmoutName_, ParmFile::UNKNOWN_PARM, 0 )) mprinterr("Error: Could not write pseudo topology to '%s'\n", parmoutName_.c_str()); } Trajout_Single out; if (out.PrepareTrajWrite(traj3dName_, ArgList(), &pseudo, CoordinateInfo(), Ndata, traj3dFmt_) == 0) { Frame outFrame(1); for (size_t i = 0; i < Ndata; ++i) { outFrame.ClearAtoms(); outFrame.AddVec3( Vec3(histdata_[0]->Dval(i), histdata_[1]->Dval(i), histdata_[2]->Dval(i)) ); out.WriteSingle(i, outFrame); } out.EndTraj(); } else mprinterr("Error: Could not set up '%s' for write.\n", traj3dName_.c_str()); } } } return Analysis::OK; }
int SequenceAlign(CpptrajState& State, ArgList& argIn) { std::string blastfile = argIn.GetStringKey("blastfile"); if (blastfile.empty()) { mprinterr("Error: 'blastfile' must be specified.\n"); return 1; } ReferenceFrame qref = State.DSL()->GetReferenceFrame(argIn); if (qref.error() || qref.empty()) { mprinterr("Error: Must specify reference structure for query.\n"); return 1; } std::string outfilename = argIn.GetStringKey("out"); if (outfilename.empty()) { mprinterr("Error: Must specify output file.\n"); return 1; } TrajectoryFile::TrajFormatType fmt = TrajectoryFile::GetFormatFromArg(argIn); if (fmt != TrajectoryFile::PDBFILE && fmt != TrajectoryFile::MOL2FILE) fmt = TrajectoryFile::PDBFILE; // Default to PDB int smaskoffset = argIn.getKeyInt("smaskoffset", 0) + 1; int qmaskoffset = argIn.getKeyInt("qmaskoffset", 0) + 1; // Load blast file mprintf("\tReading BLAST alignment from '%s'\n", blastfile.c_str()); BufferedLine infile; if (infile.OpenFileRead( blastfile )) return 1; // Seek down to first Query line. const char* ptr = infile.Line(); bool atFirstQuery = false; while (ptr != 0) { if (*ptr == 'Q') { if ( strncmp(ptr, "Query", 5) == 0 ) { atFirstQuery = true; break; } } ptr = infile.Line(); } if (!atFirstQuery) { mprinterr("Error: 'Query' not found.\n"); return 1; } // Read alignment. Replacing query with subject. typedef std::vector<char> Carray; typedef std::vector<int> Iarray; Carray Query; // Query residues Carray Sbjct; // Sbjct residues Iarray Smap; // Smap[Sbjct index] = Query index while (ptr != 0) { const char* qline = ptr; // query line const char* aline = infile.Line(); // alignment line const char* sline = infile.Line(); // subject line if (aline == 0 || sline == 0) { mprinterr("Error: Missing alignment line or subject line after Query:\n"); mprinterr("Error: %s", qline); return 1; } for (int idx = 12; qline[idx] != ' '; idx++) { if (qline[idx] == '-') { // Sbjct does not have corresponding res in Query Smap.push_back(-1); Sbjct.push_back( sline[idx] ); } else if (sline[idx] == '-') { // Query does not have a corresponding res in Sbjct Query.push_back( qline[idx] ); } else { // Direct Query to Sbjct map Smap.push_back( Query.size() ); Sbjct.push_back( sline[idx] ); Query.push_back( qline[idx] ); } } // Scan to next Query ptr = infile.Line(); while (ptr != 0) { if (*ptr == 'Q') { if ( strncmp(ptr, "Query", 5) == 0 ) break; } ptr = infile.Line(); } } // DEBUG std::string SmaskExp, QmaskExp; if (State.Debug() > 0) mprintf(" Map of Sbjct to Query:\n"); for (int sres = 0; sres != (int)Sbjct.size(); sres++) { if (State.Debug() > 0) mprintf("%-i %3s %i", sres+smaskoffset, Residue::ConvertResName(Sbjct[sres]), Smap[sres]+qmaskoffset); const char* qres = ""; if (Smap[sres] != -1) { qres = Residue::ConvertResName(Query[Smap[sres]]); if (SmaskExp.empty()) SmaskExp.assign( integerToString(sres+smaskoffset) ); else SmaskExp.append( "," + integerToString(sres+smaskoffset) ); if (QmaskExp.empty()) QmaskExp.assign( integerToString(Smap[sres]+qmaskoffset) ); else QmaskExp.append( "," + integerToString(Smap[sres]+qmaskoffset) ); } if (State.Debug() > 0) mprintf(" %3s\n", qres); } mprintf("Smask: %s\n", SmaskExp.c_str()); mprintf("Qmask: %s\n", QmaskExp.c_str()); // Check that query residues match reference. for (unsigned int sres = 0; sres != Sbjct.size(); sres++) { int qres = Smap[sres]; if (qres != -1) { if (Query[qres] != qref.Parm().Res(qres).SingleCharName()) { mprintf("Warning: Potential residue mismatch: Query %s reference %s\n", Residue::ConvertResName(Query[qres]), qref.Parm().Res(qres).c_str()); } } } // Build subject using coordinate from reference. //AtomMask sMask; // Contain atoms that should be in sTop Topology sTop; Frame sFrame; Iarray placeHolder; // Atom indices of placeholder residues. for (unsigned int sres = 0; sres != Sbjct.size(); sres++) { int qres = Smap[sres]; NameType SresName( Residue::ConvertResName(Sbjct[sres]) ); if (qres != -1) { Residue const& QR = qref.Parm().Res(qres); Residue SR(SresName, sres+1, ' ', QR.ChainID()); if (Query[qres] == Sbjct[sres]) { // Exact match. All non-H atoms. for (int qat = QR.FirstAtom(); qat != QR.LastAtom(); qat++) { if (qref.Parm()[qat].Element() != Atom::HYDROGEN) sTop.AddTopAtom( qref.Parm()[qat], SR ); sFrame.AddXYZ( qref.Coord().XYZ(qat) ); //sMask.AddAtom(qat); } } else { // Partial match. Copy only backbone and CB. for (int qat = QR.FirstAtom(); qat != QR.LastAtom(); qat++) { if ( qref.Parm()[qat].Name().Match("N" ) || qref.Parm()[qat].Name().Match("CA") || qref.Parm()[qat].Name().Match("CB") || qref.Parm()[qat].Name().Match("C" ) || qref.Parm()[qat].Name().Match("O" ) ) { sTop.AddTopAtom( qref.Parm()[qat], SR ); sFrame.AddXYZ( qref.Coord().XYZ(qat) ); } } } } else { // Residue in query does not exist for subject. Just put placeholder CA for now. Vec3 Zero(0.0); placeHolder.push_back( sTop.Natom() ); sTop.AddTopAtom( Atom("CA", "C "), Residue(SresName, sres+1, ' ', ' ') ); sFrame.AddXYZ( Zero.Dptr() ); } } //sTop.PrintAtomInfo("*"); mprintf("\tPlaceholder residue indices:"); for (Iarray::const_iterator p = placeHolder.begin(); p != placeHolder.end(); ++p) mprintf(" %i", *p + 1); mprintf("\n"); // Try to give placeholders more reasonable coordinates. if (!placeHolder.empty()) { Iarray current_indices; unsigned int pidx = 0; while (pidx < placeHolder.size()) { if (current_indices.empty()) { current_indices.push_back( placeHolder[pidx++] ); // Search for the end of this segment for (; pidx != placeHolder.size(); pidx++) { if (placeHolder[pidx] - current_indices.back() > 1) break; current_indices.push_back( placeHolder[pidx] ); } // DEBUG mprintf("\tSegment:"); for (Iarray::const_iterator it = current_indices.begin(); it != current_indices.end(); ++it) mprintf(" %i", *it + 1); // Get coordinates of residues bordering segment. int prev_res = sTop[current_indices.front()].ResNum() - 1; int next_res = sTop[current_indices.back() ].ResNum() + 1; mprintf(" (prev_res=%i, next_res=%i)\n", prev_res+1, next_res+1); Vec3 prev_crd(sFrame.XYZ(current_indices.front() - 1)); Vec3 next_crd(sFrame.XYZ(current_indices.back() + 1)); prev_crd.Print("prev_crd"); next_crd.Print("next_crd"); Vec3 crd_step = (next_crd - prev_crd) / (double)(current_indices.size()+1); crd_step.Print("crd_step"); double* xyz = sFrame.xAddress() + (current_indices.front() * 3); for (unsigned int i = 0; i != current_indices.size(); i++, xyz += 3) { prev_crd += crd_step; xyz[0] = prev_crd[0]; xyz[1] = prev_crd[1]; xyz[2] = prev_crd[2]; } current_indices.clear(); } } } //Topology* sTop = qref.Parm().partialModifyStateByMask( sMask ); //if (sTop == 0) return 1; //Frame sFrame(qref.Coord(), sMask); // Write output traj Trajout_Single trajout; if (trajout.PrepareTrajWrite(outfilename, argIn, &sTop, CoordinateInfo(), 1, fmt)) return 1; if (trajout.WriteSingle(0, sFrame)) return 1; trajout.EndTraj(); return 0; }
// 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 }
// ----- M A I N --------------------------------------------------------------- int main(int argc, char** argv) { SetWorldSilent(true); // No STDOUT output from cpptraj routines. std::string topname, crdname, title, bres, pqr, sybyltype, writeconect; std::string aatm(" pdbatom"), ter_opt(" terbyres"), box(" sg \"P 1\""); TrajectoryFile::TrajFormatType fmt = TrajectoryFile::PDBFILE; bool ctr_origin = false; bool useExtendedInfo = false; int res_offset = 0; int debug = 0; int numSoloArgs = 0; for (int i = 1; i < argc; ++i) { std::string arg( argv[i] ); if (arg == "-p" && i+1 != argc && topname.empty()) // Topology topname = std::string( argv[++i] ); else if (arg == "-c" && i+1 != argc && crdname.empty()) // Coords crdname = std::string( argv[++i] ); else if (arg == "-tit" && i+1 != argc && title.empty()) // Title title = " title " + std::string( argv[++i] ); else if (arg == "-offset" && i+1 != argc) // Residue # offset res_offset = convertToInteger( argv[++i] ); else if ((arg == "-d" || arg == "--debug") && i+1 != argc) // Debug level debug = convertToInteger( argv[++i] ); else if (arg == "-h" || arg == "--help") { // Help Help(argv[0], true); return 0; } else if (arg == "-v" || arg == "--version") { // Version info WriteVersion(); return 0; } else if (arg == "-aatm") // Amber atom names, include extra pts aatm.assign(" include_ep"); else if (arg == "-sybyl") // Amber atom types to SYBYL sybyltype.assign(" sybyltype"); else if (arg == "-conect") // Write CONECT records from bond info writeconect.assign(" conect"); else if (arg == "-ep") // PDB atom names, include extra pts aatm.append(" include_ep"); else if (arg == "-bres") // PDB residue names bres.assign(" pdbres"); else if (arg == "-ext") // Use extended PDB info from Topology useExtendedInfo = true; else if (arg == "-ctr") // Center on origin ctr_origin = true; else if (arg == "-noter") // No TER cards ter_opt.assign(" noter"); else if (arg == "-nobox") // No CRYST1 record box.assign(" nobox"); else if (arg == "-pqr") { // Charge/Radii in occ/bfactor cols pqr.assign(" dumpq"); ++numSoloArgs; } else if (arg == "-mol2") { // output as mol2 fmt = TrajectoryFile::MOL2FILE; ++numSoloArgs; } else if (Unsupported(arg)) { mprinterr("Error: Option '%s' is not yet supported.\n\n", arg.c_str()); return 1; } else { mprinterr("Error: Unrecognized option '%s'\n", arg.c_str()); Help(argv[0], false); return 1; } } if (debug > 0) WriteVersion(); // Check command line for errors. if (topname.empty()) topname.assign("prmtop"); if (debug > 0 && crdname.empty()) mprinterr("| Reading Amber restart from STDIN\n"); if (numSoloArgs > 1) { mprinterr("Error: Only one alternate output format option may be specified (found %i)\n", numSoloArgs); Help(argv[0], true); return 1; } if (!sybyltype.empty() && fmt != TrajectoryFile::MOL2FILE) { mprinterr("Warning: -sybyl is only valid for MOL2 file output.\n"); sybyltype.clear(); } if (debug > 0) { mprinterr("Warning: debug is %i; debug info will be written to STDOUT.\n", debug); SetWorldSilent(false); } // Topology ParmFile pfile; Topology parm; if (pfile.ReadTopology(parm, topname, debug)) { if (topname == "prmtop") Help(argv[0], false); return 1; } if (!useExtendedInfo) parm.ResetPDBinfo(); if (res_offset != 0) for (int r = 0; r < parm.Nres(); r++) parm.SetRes(r).SetOriginalNum( parm.Res(r).OriginalResNum() + res_offset ); ArgList trajArgs; // Input coords Frame TrajFrame; CoordinateInfo cInfo; if (!crdname.empty()) { Trajin_Single trajin; if (trajin.SetupTrajRead(crdname, trajArgs, &parm)) return 1; cInfo = trajin.TrajCoordInfo(); TrajFrame.SetupFrameV(parm.Atoms(), cInfo); trajin.BeginTraj(); if (trajin.ReadTrajFrame(0, TrajFrame)) return 1; trajin.EndTraj(); } else { // Assume Amber restart from STDIN // Check that input is from a redirect. if ( isatty(fileno(stdin)) ) { mprinterr("Error: No coordinates specified with '-c' and no STDIN '<'.\n"); return 1; } Traj_AmberRestart restartIn; restartIn.SetDebug( debug ); //restartIn.processReadArgs( trajArgs ); int total_frames = restartIn.setupTrajin("", &parm); if (total_frames < 1) return 1; cInfo = restartIn.CoordInfo(); TrajFrame.SetupFrameV(parm.Atoms(), cInfo); if (restartIn.openTrajin()) return 1; if (restartIn.readFrame(0, TrajFrame)) return 1; restartIn.closeTraj(); } if (ctr_origin) TrajFrame.CenterOnOrigin(false); // Output coords Trajout_Single trajout; trajArgs.SetList( aatm + bres + pqr + title + ter_opt + box + sybyltype + writeconect, " " ); if ( trajout.PrepareStdoutTrajWrite(trajArgs, &parm, cInfo, 1, fmt) ) return 1; trajout.WriteSingle(0, TrajFrame); trajout.EndTraj(); return 0; }