// DataIO_Mdout::ID_DataFormat() bool DataIO_Mdout::ID_DataFormat(CpptrajFile& infile) { if (infile.OpenFile()) return false; bool isMdout = false; std::string line = infile.GetLine(); if (line[0] == '\n') { line = infile.GetLine(); if (line.compare(0, 15, " -----") == 0) { line = infile.GetLine(); if (line.compare(0, 15, " Amber") == 0) isMdout = true; } } infile.CloseFile(); return isMdout; }
bool Parm_CharmmPsf::ID_ParmFormat(CpptrajFile& fileIn) { // Assumes already set up if (fileIn.OpenFile()) return false; std::string nextLine = fileIn.GetLine(); if (nextLine.empty()) return false; bool isPSF = ( nextLine.compare(0, 3, "PSF") == 0 ); fileIn.CloseFile(); return isPSF; }
bool DataIO_OpenDx::ID_DataFormat( CpptrajFile& infile ) { bool isDX = false; if (!infile.OpenFile()) { std::string firstLine = infile.GetLine(); if (!firstLine.empty()) isDX = (firstLine.compare(0, 28, "object 1 class gridpositions") == 0); infile.CloseFile(); } return isDX; }
// PDBfile::ID_PDB() bool PDBfile::ID_PDB(CpptrajFile& fileIn) { // NOTE: ASSUME FILE SET UP FOR READ if (fileIn.OpenFile()) return false; std::string line1 = fileIn.GetLine(); std::string line2 = fileIn.GetLine(); fileIn.CloseFile(); if (!IsPDBkeyword( line1 )) return false; if (!IsPDBkeyword( line2 )) return false; return true; }
/** Determine if fileIn is a CIF file. Look for entries beginning with * an underscore (indicating data block), and a 'loop_' keyword or * '_entry.id' block. */ bool CIFfile::ID_CIF(CpptrajFile& fileIn) { // NOTE: ASSUME FILE SET UP FOR READ if (fileIn.OpenFile()) return false; int ndata = 0; // Number of '_XXX' entries seen bool foundLoop = false; bool foundEntryID = false; for (int i = 0; i < 10; i++) { std::string lineIn = fileIn.GetLine(); if (lineIn[0] == '_') ndata++; if (lineIn.compare(0,5,"loop_")==0) foundLoop = true; if (lineIn.compare(0,9,"_entry.id")==0) foundEntryID = true; } fileIn.CloseFile(); return ( ndata > 2 && (foundLoop || foundEntryID) ); }
// Traj_AmberCoord::ID_TrajFormat() bool Traj_AmberCoord::ID_TrajFormat(CpptrajFile& fileIn) { // File must already be set up for read if (fileIn.OpenFile()) return false; if (fileIn.NextLine()==0) return false; // Title std::string buffer2 = fileIn.GetLine(); // REMD header/coords fileIn.CloseFile(); // Check if second line contains REMD/HREMD, Amber Traj with REMD header if ( IsRemdHeader( buffer2.c_str() ) ) { if (debug_>0) mprintf(" AMBER TRAJECTORY with (H)REMD header.\n"); hasREMD_ = REMD_HEADER_SIZE + (size_t)fileIn.IsDos(); return true; } // Check if we can read at least 3 coords of width 8, Amber trajectory float TrajCoord[3]; if ( sscanf(buffer2.c_str(), "%8f%8f%8f", TrajCoord, TrajCoord+1, TrajCoord+2) == 3 ) { if (debug_>0) mprintf(" AMBER TRAJECTORY file\n"); return true; } return false; }
// Traj_AmberCoord::ID_TrajFormat() bool Traj_AmberCoord::ID_TrajFormat(CpptrajFile& fileIn) { // File must already be set up for read if (fileIn.OpenFile()) return false; if (fileIn.NextLine()==0) return false; // Title std::string buffer2 = fileIn.GetLine(); // REMD header/coords fileIn.CloseFile(); // Check if second line contains REMD/HREMD, Amber Traj with REMD header if ( IsRemdHeader( buffer2.c_str() ) ) { if (debug_>0) mprintf(" AMBER TRAJECTORY with (H)REMD header.\n"); headerSize_ = REMD_HEADER_SIZE + (size_t)fileIn.IsDos(); tStart_ = 33; // 42 - 8 - 1 tEnd_ = 41; // 42 - 1 return true; } // TODO: Read these in as indices instead of temperatures if ( IsRxsgldHeader( buffer2.c_str() ) ) { mprintf(" AMBER TRAJECTORY with RXSGLD header.\n"); headerSize_ = RXSGLD_HEADER_SIZE + (size_t)fileIn.IsDos(); tStart_ = 35; // 44 - 8 - 1 tEnd_ = 43; // 44 - 1 return true; } // Check if we can read 3, 6, 9, or 10 coords (corresponding to 1, 2, 3 or // > 3 atoms) of width 8; Amber trajectory. float TrajCoord[10]; int nscan = sscanf(buffer2.c_str(), "%8f%8f%8f%8f%8f%8f%8f%8f%8f%8f", TrajCoord, TrajCoord+1, TrajCoord+2, TrajCoord+3, TrajCoord+4, TrajCoord+5, TrajCoord+6, TrajCoord+7, TrajCoord+8, TrajCoord+9); if (nscan == 3 || nscan == 6 || nscan == 9 || nscan == 10) { if (debug_>0) mprintf(" AMBER TRAJECTORY file\n"); return true; } return false; }
// Action_Spam::init() Action::RetType Action_Spam::Init(ArgList& actionArgs, TopologyList* PFL, DataSetList* DSL, DataFileList* DFL, int debugIn) { // Always use imaged distances InitImaging(true); // This is needed everywhere in this function scope FileName filename; // See if we're doing pure water. If so, we don't need a peak file purewater_ = actionArgs.hasKey("purewater"); if (purewater_) { // We still need the cutoff double cut = actionArgs.getKeyDouble("cut", 12.0); cut2_ = cut * cut; doublecut_ = 2 * cut; onecut2_ = 1 / cut2_; // See if we write to a data file datafile_ = actionArgs.GetStringKey("out"); // Generate the data set name, and hold onto the master data set list std::string ds_name = actionArgs.GetStringKey("name"); if (ds_name.empty()) ds_name = myDSL_.GenerateDefaultName("SPAM"); // We only have one data set averaging over every water. Add it here myDSL_.AddSet(DataSet::DOUBLE, ds_name, NULL); solvname_ = actionArgs.GetStringKey("solv"); if (solvname_.empty()) solvname_ = std::string("WAT"); }else { // Get the file name with the peaks defined in it filename.SetFileName( actionArgs.GetStringNext() ); if (filename.empty() || !File::Exists(filename)) { mprinterr("Spam: Error: Peak file [%s] does not exist!\n", filename.full()); return Action::ERR; } // Get the remaining optional arguments solvname_ = actionArgs.GetStringKey("solv"); if (solvname_.empty()) solvname_ = std::string("WAT"); reorder_ = actionArgs.hasKey("reorder"); bulk_ = actionArgs.getKeyDouble("bulk", 0.0); double cut = actionArgs.getKeyDouble("cut", 12.0); cut2_ = cut * cut; doublecut_ = 2 * cut; onecut2_ = 1 / cut2_; std::string infoname = actionArgs.GetStringKey("info"); if (infoname.empty()) infoname = std::string("spam.info"); infofile_ = DFL->AddCpptrajFile(infoname, "SPAM info"); if (infofile_ == 0) return Action::ERR; // The default maskstr is the Oxygen atom of the solvent summaryfile_ = actionArgs.GetStringKey("summary"); // Divide site size by 2 to make it half the edge length (or radius) site_size_ = actionArgs.getKeyDouble("site_size", 2.5) / 2.0; sphere_ = actionArgs.hasKey("sphere"); // If it's a sphere, square the radius to compare with if (sphere_) site_size_ *= site_size_; datafile_ = actionArgs.GetStringKey("out"); std::string ds_name = actionArgs.GetStringKey("name"); if (ds_name.empty()) ds_name = myDSL_.GenerateDefaultName("SPAM"); // Parse through the peaks file and extract the peaks CpptrajFile peakfile; if (peakfile.OpenRead(filename)) { mprinterr("SPAM: Error: Could not open %s for reading!\n", filename.full()); return Action::ERR; } std::string line = peakfile.GetLine(); int npeaks = 0; while (!line.empty()) { if (sscanf(line.c_str(), "%d", &npeaks) != 1) { line = peakfile.GetLine(); continue; } line = peakfile.GetLine(); break; } while (!line.empty()) { double x, y, z, dens; if (sscanf(line.c_str(), "C %lg %lg %lg %lg", &x, &y, &z, &dens) != 4) { line = peakfile.GetLine(); continue; } line = peakfile.GetLine(); peaks_.push_back(Vec3(x, y, z)); } peakfile.CloseFile(); // Check that our initial number of peaks matches our parsed peaks. Warn // otherwise if (npeaks != (int)peaks_.size()) mprinterr("SPAM: Warning: %s claims to have %d peaks, but really has %d!\n", filename.full(), npeaks, peaks_.size()); // Now add all of the data sets MetaData md(ds_name); for (int i = 0; i < (int)peaks_.size(); i++) { md.SetAspect( integerToString(i+1) ); // TODO: Should this be Idx? if (myDSL_.AddSet(DataSet::DOUBLE, md) == 0) return Action::ERR; // Add a new list of integers to keep track of omitted frames std::vector<int> vec; peakFrameData_.push_back(vec); } } // Print info now if (purewater_) { mprintf("SPAM: Calculating bulk value for pure solvent\n"); if (!datafile_.empty()) mprintf("SPAM: Printing solvent energies to %s\n", datafile_.c_str()); mprintf("SPAM: Using a %.2f Angstrom non-bonded cutoff with shifted EEL.\n", sqrt(cut2_)); if (reorder_) mprintf("SPAM: Warning: Re-ordering makes no sense for pure solvent.\n"); if (!summaryfile_.empty()) mprintf("SPAM: Printing solvent SPAM summary to %s\n", summaryfile_.c_str()); }else { mprintf("SPAM: Solvent [%s] density peaks taken from %s.\n", solvname_.c_str(), filename.base()); mprintf("SPAM: %d density peaks will be analyzed from %s.\n", peaks_.size(), filename.base()); mprintf("SPAM: Occupation information printed to %s.\n", infofile_->Filename().full()); mprintf("SPAM: Sites are "); if (sphere_) mprintf("spheres with diameter %.3lf\n", site_size_); else mprintf("boxes with edge length %.3lf\n", site_size_); if (reorder_) { mprintf("SPAM: Re-ordering trajectory so each site always has "); mprintf("the same water molecule.\n"); } if (summaryfile_.empty() && datafile_.empty()) { if (!reorder_) { mprinterr("SPAM: Error: Not re-ordering trajectory or calculating energies. "); mprinterr("Nothing to do!\n"); return Action::ERR; } mprintf("SPAM: Not calculating any SPAM energies\n"); }else { mprintf("SPAM: Using a non-bonded cutoff of %.2lf Ang. with a EEL shifting function.\n", sqrt(cut2_)); mprintf("SPAM: Bulk solvent SPAM energy taken as %.3lf kcal/mol\n", bulk_); } } mprintf("#Citation: Cui, G.; Swails, J.M.; Manas, E.S.; \"SPAM: A Simple Approach\n" "# for Profiling Bound Water Molecules\"\n" "# J. Chem. Theory Comput., 2013, 9 (12), pp 5539–5549.\n"); return Action::OK; }