void SecondaryStructureRMSD::setSecondaryStructure( std::vector<Vector>& structure, double bondlength, double units ){
// If we are in natural units get conversion factor from nm into natural length units
if( plumed.getAtoms().usingNaturalUnits() ){
error("cannot use this collective variable when using natural units");
}
plumed_massert( !(align_strands && align_atom_1==0 && align_atom_2==0), "you must use setAtomsFromStrands with strands cutoff");
// Convert into correct units
for(unsigned i=0;i<structure.size();++i){
structure[i][0]*=units; structure[i][1]*=units; structure[i][2]*=units;
}
if( references.size()==0 ){
finishTaskListUpdate();
readVesselKeywords();
if( getNumberOfVessels()==0 ){
double r0; parse("R_0",r0); double d0; parse("D_0",d0);
int nn; parse("NN",nn); int mm; parse("MM",mm);
std::ostringstream ostr;
ostr<<"RATIONAL R_0="<<r0<<" D_0="<<d0<<" NN="<<nn<<" MM="<<mm;
std::string input=ostr.str(); addVessel( "LESS_THAN", input, -1 ); // -1 here means that this value will be named getLabel()
readVesselKeywords(); // This makes sure resizing is done
}
}
// Set the reference structure
references.push_back( metricRegister().create<SingleDomainRMSD>( alignType ) );
unsigned nn=references.size()-1;
std::vector<double> align( structure.size(), 1.0 ), displace( structure.size(), 1.0 );
references[nn]->setBoundsOnDistances( true , bondlength ); // We always use pbc
references[nn]->setReferenceAtoms( structure, align, displace );
// references[nn]->setNumberOfAtoms( structure.size() );
}
void MultiReferenceBase::readFrame( PDB& mypdb ) {
wasSet=true;
// If skipchecks are enabled metric types must be specified in the input file
ReferenceConfiguration* mymsd=metricRegister().create<ReferenceConfiguration>( mtype, mypdb );
// Save everything
frames.push_back( mymsd );
// Do reading in derived class
readRestOfFrame();
// Check readin was succesfull
mymsd->checkRead();
}
void MultiReferenceBase::copyFrame( ReferenceConfiguration* frameToCopy ) {
// Create a reference configuration of the appropriate type
ReferenceConfiguration* mymsd=metricRegister().create<ReferenceConfiguration>( frameToCopy->getName() );
// Copy names of arguments and and indexes
mymsd->setNamesAndAtomNumbers( frameToCopy->getAbsoluteIndexes(), frameToCopy->getArgumentNames() );
// Copy reference positions, reference arguments and reference metric
mymsd->setReferenceConfig( frameToCopy->getReferencePositions(), frameToCopy->getReferenceArguments(), frameToCopy->getReferenceMetric() );
// Copy weight
mymsd->setWeight( frameToCopy->getWeight() );
// Easy bit - copy the frame
frames.push_back( mymsd );
// This resizes the low dim array
resizeRestOfFrame();
}
void MultiDomainRMSD::read( const PDB& pdb ) {
unsigned nblocks = pdb.getNumberOfAtomBlocks();
if( nblocks<2 ) error("multidomain RMSD only has one block of atoms");
std::vector<Vector> positions; std::vector<double> align, displace;
std::string num; blocks.resize( nblocks+1 ); blocks[0]=0;
for(unsigned i=0; i<nblocks; ++i) blocks[i+1]=pdb.getAtomBlockEnds()[i];
double tmp, lower=0.0, upper=std::numeric_limits<double>::max( );
if( pdb.getArgumentValue("LOWER_CUTOFF",tmp) ) lower=tmp;
if( pdb.getArgumentValue("UPPER_CUTOFF",tmp) ) upper=tmp;
bool nopbc=pdb.hasFlag("NOPBC");
domains.resize(0); weights.resize(0);
for(unsigned i=1; i<=nblocks; ++i) {
Tools::convert(i,num);
if( ftype=="RMSD" ) {
// parse("TYPE"+num, ftype );
lower=0.0; upper=std::numeric_limits<double>::max( );
if( pdb.getArgumentValue("LOWER_CUTOFF"+num,tmp) ) lower=tmp;
if( pdb.getArgumentValue("UPPER_CUTOFF"+num,tmp) ) upper=tmp;
nopbc=pdb.hasFlag("NOPBC");
}
domains.emplace_back( metricRegister().create<SingleDomainRMSD>( ftype ) );
positions.resize( blocks[i] - blocks[i-1] );
align.resize( blocks[i] - blocks[i-1] );
displace.resize( blocks[i] - blocks[i-1] );
unsigned n=0;
for(unsigned j=blocks[i-1]; j<blocks[i]; ++j) {
positions[n]=pdb.getPositions()[j];
align[n]=pdb.getOccupancy()[j];
displace[n]=pdb.getBeta()[j];
n++;
}
domains[i-1]->setBoundsOnDistances( !nopbc, lower, upper );
domains[i-1]->setReferenceAtoms( positions, align, displace );
domains[i-1]->setupRMSDObject();
double ww=0;
if( !pdb.getArgumentValue("WEIGHT"+num,ww) ) weights.push_back( 1.0 );
else weights.push_back( ww );
}
// And set the atom numbers for this object
indices.resize(0); atom_der_index.resize(0);
for(unsigned i=0; i<pdb.size(); ++i) { indices.push_back( pdb.getAtomNumbers()[i] ); atom_der_index.push_back(i); }
// setAtomNumbers( pdb.getAtomNumbers() );
}
void MultiDomainRMSD::read( const PDB& pdb ){
unsigned nblocks = pdb.getNumberOfAtomBlocks();
if( nblocks<2 ) error("multidomain RMSD only has one block of atoms");
std::vector<AtomNumber> atomnumbers;
std::vector<Vector> positions; std::vector<double> align, displace;
std::string num; blocks.resize( nblocks+1 ); blocks[0]=0;
for(unsigned i=0;i<nblocks;++i) blocks[i+1]=pdb.getAtomBlockEnds()[i];
double lower=0.0, upper=std::numeric_limits<double>::max( );
parse("LOWER_CUTOFF",lower,true);
parse("UPPER_CUTOFF",upper,true);
for(unsigned i=1;i<=nblocks;++i){
Tools::convert(i,num);
if( ftype=="RMSD" ){
parse("TYPE"+num, ftype );
parse("LOWER_CUTOFF"+num,lower,true);
parse("UPPER_CUTOFF"+num,upper,true);
}
domains.push_back( metricRegister().create<SingleDomainRMSD>( ftype ) );
positions.resize( blocks[i] - blocks[i-1] + 1 );
align.resize( blocks[i] - blocks[i-1] + 1 );
displace.resize( blocks[i] - blocks[i-1] + 1 );
unsigned n=0;
for(unsigned j=blocks[i-1];j<blocks[i];++j){
positions[n]=pdb.getPositions()[j];
align[n]=pdb.getOccupancy()[j];
displace[n]=pdb.getBeta()[j];
n++;
}
domains[i-1]->setBoundsOnDistances( true, lower, upper ); // Currently no option for nopbc
domains[i-1]->setReferenceAtoms( positions, align, displace );
domains[i-1]->setNumberOfAtoms( positions.size() );
double ww=0; parse("WEIGHT"+num, ww, true );
if( ww==0 ) weights.push_back( 1.0 );
else weights.push_back( ww );
}
// And set the atom numbers for this object
setAtomNumbers( pdb.getAtomNumbers() );
}
