/** Read file as a Tripos Mol2 file. */ int Parm_Mol2::ReadParm(FileName const& fname, Topology &parmOut) { Mol2File infile; if (infile.OpenRead(fname)) return 1; mprintf(" Reading Mol2 file %s as topology file.\n",infile.Filename().base()); // Get @<TRIPOS>MOLECULE information if (infile.ReadMolecule()) return 1; parmOut.SetParmName( infile.Mol2Title(), infile.Filename() ); // Get @<TRIPOS>ATOM information if (infile.ScanTo( Mol2File::ATOM)) return 1; double XYZ[3]; for (int atom=0; atom < infile.Mol2Natoms(); atom++) { if ( infile.Mol2XYZ(XYZ) ) return 1; parmOut.AddTopAtom( infile.Mol2Atom(), infile.Mol2Residue(), XYZ ); } // Get @<TRIPOS>BOND information [optional] int at1 = 0; int at2 = 0; if (infile.ScanTo(Mol2File::BOND)==0) { for (int bond=0; bond < infile.Mol2Nbonds(); bond++) { if (infile.Mol2Bond(at1, at2)) return 1; // mol2 atom #s start from 1 parmOut.AddBond(at1-1, at2-1); } needsBondSearch_ = false; } else { mprintf(" Mol2 file does not contain bond information.\n"); needsBondSearch_ = true; } // No box parmOut.SetParmBox( Box() ); mprintf(" Mol2 contains %i atoms, %i residues,\n", parmOut.Natom(),parmOut.Nres()); //mprintf(" %i bonds to H, %i other bonds.\n", parmOut.NbondsWithH,parmOut.NbondsWithoutH); infile.CloseFile(); return 0; }
/** Read file as a Tinker file. */ int Parm_Tinker::ReadParm(FileName const& fname, Topology &parmOut) { TinkerFile infile; infile.SetTinkerName( fname ); if (infile.OpenTinker()) return 1; mprintf("\tReading Tinker file %s as topology file.\n",infile.Filename().base()); // Allocate memory for coordinates. double* Coords = new double[ infile.TinkerNatom() * 3 ]; std::vector<int> Bonds; std::vector<Atom> Atoms = infile.ReadTinkerAtoms(Coords, Bonds); if (Atoms.empty()) return 1; // Use up to first 3 chars of title as residue name. std::string resname; for (std::string::const_iterator c = infile.TinkerTitle().begin(); c != infile.TinkerTitle().end(); ++c) resname += *c; if (resname.size() > 3) resname.resize(3); Residue tinker_res( resname, 0, ' ', ' ' ); // Put atoms into topology const double* XYZ = Coords; for (std::vector<Atom>::const_iterator atom = Atoms.begin(); atom != Atoms.end(); ++atom, XYZ += 3) parmOut.AddTopAtom( *atom, tinker_res, XYZ ); delete[] Coords; // Add bond information for (std::vector<int>::const_iterator bond = Bonds.begin(); bond != Bonds.end(); bond += 2) parmOut.AddBond( *bond, *(bond+1) ); // Try to set up residue info based on bonds. if (parmOut.Setup_NoResInfo()) return 1; // Set topology box info. parmOut.SetParmBox( infile.TinkerBox() ); parmOut.SetParmName( infile.TinkerTitle(), infile.Filename() ); mprintf("\tTinker file contains %i atoms, %i residues,\n", parmOut.Natom(),parmOut.Nres()); //mprintf(" %i bonds to H, %i other bonds.\n", parmOut.NbondsWithH,parmOut.NbondsWithoutH); infile.CloseFile(); return 0; }
/** An atom pair list consists of 2 values for each entry, a beginning * index and ending index. For molecules and residues this is the first * and just beyond the last atom; for atoms it is just the atom itself * twice. */ Image::PairType Image::CreatePairList(Topology const& Parm, Mode modeIn, std::string const& maskExpression) { PairType atomPairs; // Set up mask based on desired imaging mode. if ( modeIn == BYMOL || modeIn == BYRES ) { CharMask cmask( maskExpression ); if ( Parm.SetupCharMask( cmask ) ) return atomPairs; cmask.MaskInfo(); if (cmask.None()) return atomPairs; // Set up atom range for each entity to be imaged. if (modeIn == BYMOL) { atomPairs.reserve( Parm.Nmol()*2 ); for (Topology::mol_iterator mol = Parm.MolStart(); mol != Parm.MolEnd(); ++mol) CheckRange( atomPairs, cmask, mol->BeginAtom(), mol->EndAtom()); } else { // BYRES atomPairs.reserve( Parm.Nres()*2 ); for (Topology::res_iterator residue = Parm.ResStart(); residue != Parm.ResEnd(); ++residue) CheckRange( atomPairs, cmask, residue->FirstAtom(), residue->LastAtom() ); } } else { // BYATOM AtomMask imask( maskExpression ); if ( Parm.SetupIntegerMask( imask ) ) return atomPairs; imask.MaskInfo(); if (imask.None()) return atomPairs; atomPairs.reserve( Parm.Natom()*2 ); for (AtomMask::const_iterator atom = imask.begin(); atom != imask.end(); ++atom) { atomPairs.push_back( *atom ); atomPairs.push_back( (*atom)+1 ); } } // mprintf("\tNumber of %ss to be imaged is %zu based on mask '%s'\n", // ModeString[modeIn], atomPairs.size()/2, maskIn.MaskString()); return atomPairs; }
// Parm_CIF::ReadParm() int Parm_CIF::ReadParm(FileName const& fname, Topology &TopIn) { CIFfile infile; CIFfile::DataBlock::data_it line; if (infile.Read( fname, debug_ )) return 1; CIFfile::DataBlock const& block = infile.GetDataBlock("_atom_site"); if (block.empty()) { mprinterr("Error: CIF data block '_atom_site' not found.\n"); return 1; } // Does this CIF contain multiple models? int Nmodels = 0; int model_col = block.ColumnIndex("pdbx_PDB_model_num"); if (model_col != -1) { line = block.end(); --line; Nmodels = convertToInteger( (*line)[model_col] ); if (Nmodels > 1) mprintf("Warning: CIF '%s' contains %i models. Using first model for topology.\n", fname.full(), Nmodels); } // Get essential columns int COL[NENTRY]; for (int i = 0; i < (int)NENTRY; i++) { COL[i] = block.ColumnIndex(Entries[i]); if (COL[i] == -1) { mprinterr("Error: In CIF file '%s' could not find entry '%s' in block '%s'\n", fname.full(), Entries[i], block.Header().c_str()); return 1; } if (debug_>0) mprintf("DEBUG: '%s' column = %i\n", Entries[i], COL[i]); } // Get optional columns int occ_col = block.ColumnIndex("occupancy"); int bfac_col = block.ColumnIndex("B_iso_or_equiv"); int icode_col = block.ColumnIndex("pdbx_PDB_ins_code"); int altloc_col = block.ColumnIndex("label_alt_id"); std::vector<AtomExtra> extra; // Loop over all atom sites int current_res = 0; double XYZ[3]; double occupancy = 1.0; double bfactor = 0.0; char altloc = ' '; char icode; icode = ' '; Frame Coords; for (line = block.begin(); line != block.end(); ++line) { // If more than 1 model check if we are done. if (Nmodels > 1) { if ( convertToInteger( (*line)[model_col] ) > 1 ) break; } if (occ_col != -1) occupancy = convertToDouble( (*line)[ occ_col ] ); if (bfac_col != -1) bfactor = convertToDouble( (*line)[ bfac_col ] ); if (altloc_col != -1) altloc = (*line)[ altloc_col ][0]; // '.' altloc means blank? if (altloc == '.') altloc = ' '; extra.push_back( AtomExtra(occupancy, bfactor, altloc) ); if (icode_col != -1) { icode = (*line)[ icode_col ][0]; // '?' icode means blank if (icode == '?') icode = ' '; } XYZ[0] = convertToDouble( (*line)[ COL[X] ] ); XYZ[1] = convertToDouble( (*line)[ COL[Y] ] ); XYZ[2] = convertToDouble( (*line)[ COL[Z] ] ); NameType currentResName( (*line)[ COL[RNAME] ] ); // It seems that in some CIF files, there doesnt have to be a residue // number. Check if residue name has changed. if ( (*line)[ COL[RNUM] ][0] == '.' ) { Topology::res_iterator lastResidue = TopIn.ResEnd(); --lastResidue; if ( currentResName != (*lastResidue).Name() ) current_res = TopIn.Nres() + 1; } else current_res = convertToInteger( (*line)[ COL[RNUM] ] ); TopIn.AddTopAtom( Atom((*line)[ COL[ANAME] ], " "), Residue(currentResName, current_res, icode, (*line)[ COL[CHAINID] ][0]) ); Coords.AddXYZ( XYZ ); } if (TopIn.SetExtraAtomInfo( 0, extra )) return 1; // Search for bonds // FIXME nobondsearch? BondSearch( TopIn, Coords, Offset_, debug_ ); // Get title. CIFfile::DataBlock const& entryblock = infile.GetDataBlock("_entry"); std::string ciftitle; if (!entryblock.empty()) ciftitle = entryblock.Data("id"); TopIn.SetParmName( ciftitle, infile.CIFname() ); // Get unit cell parameters if present. CIFfile::DataBlock const& cellblock = infile.GetDataBlock("_cell"); if (!cellblock.empty()) { double cif_box[6]; cif_box[0] = convertToDouble( cellblock.Data("length_a") ); cif_box[1] = convertToDouble( cellblock.Data("length_b") ); cif_box[2] = convertToDouble( cellblock.Data("length_c") ); cif_box[3] = convertToDouble( cellblock.Data("angle_alpha") ); cif_box[4] = convertToDouble( cellblock.Data("angle_beta" ) ); cif_box[5] = convertToDouble( cellblock.Data("angle_gamma") ); mprintf("\tRead cell info from CIF: a=%g b=%g c=%g alpha=%g beta=%g gamma=%g\n", cif_box[0], cif_box[1], cif_box[2], cif_box[3], cif_box[4], cif_box[5]); TopIn.SetParmBox( Box(cif_box) ); } 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 }
/** Open the Charmm PSF file specified by filename and set up topology data. * Mask selection requires natom, nres, names, resnames, resnums. */ int Parm_CharmmPsf::ReadParm(FileName const& fname, Topology &parmOut) { const size_t TAGSIZE = 10; char tag[TAGSIZE]; tag[0]='\0'; CpptrajFile infile; if (infile.OpenRead(fname)) return 1; mprintf(" Reading Charmm PSF file %s as topology file.\n",infile.Filename().base()); // Read the first line, should contain PSF... const char* buffer = 0; if ( (buffer=infile.NextLine()) == 0 ) return 1; // Advance to <ntitle> !NTITLE int ntitle = FindTag(tag, "!NTITLE", 7, infile); // Only read in 1st title. Skip any asterisks. std::string psftitle; if (ntitle > 0) { buffer = infile.NextLine(); const char* ptr = buffer; while (*ptr != '\0' && (*ptr == ' ' || *ptr == '*')) ++ptr; psftitle.assign( ptr ); } parmOut.SetParmName( NoTrailingWhitespace(psftitle), infile.Filename() ); // Advance to <natom> !NATOM int natom = FindTag(tag, "!NATOM", 6, infile); if (debug_>0) mprintf("\tPSF: !NATOM tag found, natom=%i\n", natom); // If no atoms, probably issue with PSF file if (natom < 1) { mprinterr("Error: No atoms in PSF file.\n"); return 1; } // Read the next natom lines int psfresnum = 0; char psfresname[6]; char psfname[6]; char psftype[6]; double psfcharge; double psfmass; for (int atom=0; atom < natom; atom++) { if ( (buffer=infile.NextLine()) == 0 ) { mprinterr("Error: ReadParmPSF(): Reading atom %i\n",atom+1); return 1; } // Read line // ATOM# SEGID RES# RES ATNAME ATTYPE CHRG MASS (REST OF COLUMNS ARE LIKELY FOR CMAP AND CHEQ) sscanf(buffer,"%*i %*s %i %s %s %s %lf %lf",&psfresnum, psfresname, psfname, psftype, &psfcharge, &psfmass); parmOut.AddTopAtom( Atom( psfname, psfcharge, psfmass, psftype), Residue( psfresname, psfresnum, ' ', ' '), 0 ); } // END loop over atoms // Advance to <nbond> !NBOND int bondatoms[9]; int nbond = FindTag(tag, "!NBOND", 6, infile); if (nbond > 0) { if (debug_>0) mprintf("\tPSF: !NBOND tag found, nbond=%i\n", nbond); int nlines = nbond / 4; if ( (nbond % 4) != 0) nlines++; for (int bondline=0; bondline < nlines; bondline++) { if ( (buffer=infile.NextLine()) == 0 ) { mprinterr("Error: ReadParmPSF(): Reading bond line %i\n",bondline+1); return 1; } // Each line has 4 pairs of atom numbers int nbondsread = sscanf(buffer,"%i %i %i %i %i %i %i %i",bondatoms,bondatoms+1, bondatoms+2,bondatoms+3, bondatoms+4,bondatoms+5, bondatoms+6,bondatoms+7); // NOTE: Charmm atom nums start from 1 for (int bondidx=0; bondidx < nbondsread; bondidx+=2) parmOut.AddBond(bondatoms[bondidx]-1, bondatoms[bondidx+1]-1); } } else mprintf("Warning: PSF has no bonds.\n"); // Advance to <nangles> !NTHETA int nangle = FindTag(tag, "!NTHETA", 7, infile); if (nangle > 0) { if (debug_>0) mprintf("\tPSF: !NTHETA tag found, nangle=%i\n", nangle); int nlines = nangle / 3; if ( (nangle % 3) != 0) nlines++; for (int angleline=0; angleline < nlines; angleline++) { if ( (buffer=infile.NextLine()) == 0) { mprinterr("Error: Reading angle line %i\n", angleline+1); return 1; } // Each line has 3 groups of 3 atom numbers int nanglesread = sscanf(buffer,"%i %i %i %i %i %i %i %i %i",bondatoms,bondatoms+1, bondatoms+2,bondatoms+3, bondatoms+4,bondatoms+5, bondatoms+6,bondatoms+7, bondatoms+8); for (int angleidx=0; angleidx < nanglesread; angleidx += 3) parmOut.AddAngle( bondatoms[angleidx ]-1, bondatoms[angleidx+1]-1, bondatoms[angleidx+2]-1 ); } } else mprintf("Warning: PSF has no angles.\n"); // Advance to <ndihedrals> !NPHI int ndihedral = FindTag(tag, "!NPHI", 5, infile); if (ndihedral > 0) { if (debug_>0) mprintf("\tPSF: !NPHI tag found, ndihedral=%i\n", ndihedral); int nlines = ndihedral / 2; if ( (ndihedral % 2) != 0) nlines++; for (int dihline = 0; dihline < nlines; dihline++) { if ( (buffer=infile.NextLine()) == 0) { mprinterr("Error: Reading dihedral line %i\n", dihline+1); return 1; } // Each line has 2 groups of 4 atom numbers int ndihread = sscanf(buffer,"%i %i %i %i %i %i %i %i",bondatoms,bondatoms+1, bondatoms+2,bondatoms+3, bondatoms+4,bondatoms+5, bondatoms+6,bondatoms+7); for (int dihidx=0; dihidx < ndihread; dihidx += 4) parmOut.AddDihedral( bondatoms[dihidx ]-1, bondatoms[dihidx+1]-1, bondatoms[dihidx+2]-1, bondatoms[dihidx+3]-1 ); } } else mprintf("Warning: PSF has no dihedrals.\n"); mprintf("\tPSF contains %i atoms, %i residues.\n", parmOut.Natom(), parmOut.Nres()); infile.CloseFile(); return 0; }
/** Perform setup required for per residue rmsd calculation. * Need to set up a target mask, reference mask, and dataset for each * residue specified in ResRange. * NOTE: Residues in the range arguments from user start at 1, internal * res nums start from 0. */ int Action_Rmsd::perResSetup(Topology const& currentParm, Topology const& refParm) { Range tgt_range; // Selected target residues Range ref_range; // Selected reference residues // If no target range previously specified do all solute residues if (TgtRange_.Empty()) { tgt_range = currentParm.SoluteResidues(); tgt_range.ShiftBy(1); // To match user range arg which would start from 1 } else tgt_range = TgtRange_; // If the reference range is empty, set it to match the target range if (RefRange_.Empty()) ref_range = tgt_range; else ref_range = RefRange_; // Check that the number of reference residues matches number of target residues if (tgt_range.Size() != ref_range.Size()) { mprintf("Warning: Number of target residues %i does not match\n" "Warning: number of reference residues %i.\n", tgt_range.Size(), ref_range.Size()); return 1; } // Setup a dataset, target mask, and reference mask for each residue. int maxNatom = 0; Range::const_iterator ref_it = ref_range.begin(); MetaData md(rmsd_->Meta().Name(), "res"); md.SetScalarMode( MetaData::M_RMS ); for (Range::const_iterator tgt_it = tgt_range.begin(); tgt_it != tgt_range.end(); ++tgt_it, ++ref_it) { int tgtRes = *tgt_it; int refRes = *ref_it; // Check if either the residue num or the reference residue num out of range. if ( tgtRes < 1 || tgtRes > currentParm.Nres()) { mprintf("Warning: Specified residue # %i is out of range.\n", tgtRes); continue; } if ( refRes < 1 || refRes > refParm.Nres() ) { mprintf("Warning: Specified reference residue # %i is out of range.\n", refRes); continue; } // Check if a perResType has been set for this residue # yet. perResArray::iterator PerRes; for (PerRes = ResidueRMS_.begin(); PerRes != ResidueRMS_.end(); ++PerRes) if ( PerRes->data_->Meta().Idx() == tgtRes ) break; // If necessary, create perResType for residue if (PerRes == ResidueRMS_.end()) { perResType p; md.SetIdx( tgtRes ); md.SetLegend( currentParm.TruncResNameNum(tgtRes-1) ); p.data_ = (DataSet_1D*)masterDSL_->AddSet(DataSet::DOUBLE, md); if (p.data_ == 0) { mprinterr("Internal Error: Could not set up per residue data set.\n"); return 2; } if (perresout_ != 0) perresout_->AddDataSet( p.data_ ); // Setup mask strings. Note that masks are based off user residue nums p.tgtResMask_.SetMaskString(":" + integerToString(tgtRes) + perresmask_); p.refResMask_.SetMaskString(":" + integerToString(refRes) + perresmask_); ResidueRMS_.push_back( p ); PerRes = ResidueRMS_.end() - 1; } PerRes->isActive_ = false; // Setup the reference mask if (refParm.SetupIntegerMask(PerRes->refResMask_)) { mprintf("Warning: Could not setup reference mask for residue %i\n",refRes); continue; } if (PerRes->refResMask_.None()) { mprintf("Warning: No atoms selected for reference residue %i\n",refRes); continue; } // Setup the target mask if (currentParm.SetupIntegerMask(PerRes->tgtResMask_)) { mprintf("Warning: Could not setup target mask for residue %i\n",tgtRes); continue; } if (PerRes->tgtResMask_.None()) { mprintf("Warning: No atoms selected for target residue %i\n",tgtRes); continue; } // Check that # atoms in target and reference masks match if (PerRes->tgtResMask_.Nselected() != PerRes->refResMask_.Nselected()) { mprintf("Warning: Res %i: # atoms in Tgt (%i) != # atoms in Ref (%i)\n", tgtRes, PerRes->tgtResMask_.Nselected(), PerRes->refResMask_.Nselected()); if (debug_ > 0) { mprintf(" Target Atoms:\n"); for (AtomMask::const_iterator t = PerRes->tgtResMask_.begin(); t != PerRes->tgtResMask_.end(); ++t) mprintf("\t%s\n", currentParm.AtomMaskName(*t).c_str()); mprintf(" Ref Atoms:\n"); for (AtomMask::const_iterator r = PerRes->refResMask_.begin(); r != PerRes->refResMask_.end(); ++r) mprintf("\t%s\n", refParm.AtomMaskName(*r).c_str()); } continue; } if ( PerRes->tgtResMask_.Nselected() > maxNatom ) maxNatom = PerRes->tgtResMask_.Nselected(); // Indicate that these masks were properly set up PerRes->isActive_ = true; } mprintf("\tMax # selected atoms in residues: %i\n", maxNatom); // Allocate memory for target and reference residue frames. // Although initial masses are wrong this is OK since the number of atoms // and masses will be assigned when residue RMSD is actually being calcd. if (maxNatom > 0) { std::vector<Atom> temp( maxNatom ); ResTgtFrame_.SetupFrameM( temp ); ResRefFrame_.SetupFrameM( temp ); } else { mprintf("Warning: No residues selected for per-residue calculation.\n"); return 1; } return 0; }
// ----- 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; }