// 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;
}