void ReferenceArguments::readArgumentsFromPDB( const PDB& pdb ) {
ReferenceAtoms* aref=dynamic_cast<ReferenceAtoms*>( this );
arg_names.resize( pdb.getArgumentNames().size() );
for(unsigned i=0; i<arg_names.size(); ++i) arg_names[i]=pdb.getArgumentNames()[i];
if( !aref && arg_names.size()==0 ) error("no arguments in input PDB file");
reference_args.resize( arg_names.size() ); arg_der_index.resize( arg_names.size() );
for(unsigned i=0; i<arg_names.size(); ++i) {
if( !pdb.getArgumentValue(arg_names[i], reference_args[i]) ) error("argument " + arg_names[i] + " was not set in pdb input");
arg_der_index[i]=i;
}
if( hasweights ) {
plumed_massert( !hasmetric, "should not have weights if we are using metric");
weights.resize( arg_names.size() ); sqrtweight.resize( arg_names.size() );
for(unsigned i=0; i<reference_args.size(); ++i) {
if( !pdb.getArgumentValue("sigma_" + arg_names[i], weights[i]) ) error("value sigma_" + arg_names[i] + " was not set in pdb input");
sqrtweight[i] = sqrt( weights[i] );
}
} else if( hasmetric ) {
plumed_massert( !hasweights, "should not have weights if we are using metric");
double thissig; metric.resize( arg_names.size(), arg_names.size() );
for(unsigned i=0; i<reference_args.size(); ++i) {
for(unsigned j=i; j<reference_args.size(); ++j) {
if( !pdb.getArgumentValue("sigma_" + arg_names[i] + "_" + arg_names[j], thissig) ) {
error("value sigma_" + arg_names[i] + "_" + arg_names[j] + " was not set in pdb input");
}
metric(i,j)=metric(j,i)=thissig;
}
}
} else {
weights.resize( arg_names.size() ); sqrtweight.resize( arg_names.size() );
for(unsigned i=0; i<weights.size(); ++i) sqrtweight[i]=weights[i]=1.0;
}
}
void MolDataClass::getBackboneForResidue( const std::string& type, const unsigned& residuenum, const PDB& mypdb, std::vector<AtomNumber>& atoms ){
std::string residuename=mypdb.getResidueName( residuenum );
plumed_massert( MolDataClass::allowedResidue( type, residuename ), "residue " + residuename + " unrecognized for molecule type " + type );
if( type=="protein" ){
if( residuename=="GLY"){
atoms.resize(5);
atoms[0]=mypdb.getNamedAtomFromResidue("N",residuenum);
atoms[1]=mypdb.getNamedAtomFromResidue("CA",residuenum);
atoms[2]=mypdb.getNamedAtomFromResidue("HA1",residuenum);
atoms[3]=mypdb.getNamedAtomFromResidue("C",residuenum);
atoms[4]=mypdb.getNamedAtomFromResidue("O",residuenum);
} else if( residuename=="ACE"){
atoms.resize(1);
atoms[0]=mypdb.getNamedAtomFromResidue("C",residuenum);
} else if( residuename=="NME"){
atoms.resize(1);
atoms[0]=mypdb.getNamedAtomFromResidue("N",residuenum);
} else {
atoms.resize(5);
atoms[0]=mypdb.getNamedAtomFromResidue("N",residuenum);
atoms[1]=mypdb.getNamedAtomFromResidue("CA",residuenum);
atoms[2]=mypdb.getNamedAtomFromResidue("CB",residuenum);
atoms[3]=mypdb.getNamedAtomFromResidue("C",residuenum);
atoms[4]=mypdb.getNamedAtomFromResidue("O",residuenum);
}
} else {
plumed_merror(type + " is not a valid molecule type");
}
}
void RMSD::set(const PDB&pdb, string mytype ){
setReference(pdb.getPositions());
setAlign(pdb.getOccupancy());
setDisplace(pdb.getBeta());
setType(mytype);
}
int main()
{
char szError[cbErrMax];
EC ec;
PDB* ppdb = PDB::Open("001.PDB", pdbWrite, 0, &ec, szError);
assert(ppdb);
DBI* pdbi = ppdb->OpenDBI(pdbWrite, "<target>");
assert(pdbi);
TS ts = pdbi->OpenTpi(pdbWrite);
assert(ts);
struct {
unsigned short len;
unsigned short leaf;
unsigned long signature;
unsigned long age;
unsigned char name[9];
} typeUseTypeServer = {
20,
LF_TYPESERVER,
123456789,
1,
"\x07""002.PDB"
};
struct {
unsigned short reclen;
unsigned short rectyp;
CV_uoff32_t off;
unsigned short seg;
CV_typ_t typind;
unsigned char name[5];
} aSymbol = {
16,
S_GDATA32,
0,
0,
0,
"\x03""ABC"
};
Mod* pmod = pdbi->OpenMod(ts, 1, "<mod>");
assert(pmod->AddTypes((PB)&typeUseTypeServer, 20));
for (TI ti = 0x1000; ti < 0x12e0; ti++) {
aSymbol.typind = ti;
assert(pmod->AddSymbols((PB)&aSymbol, 16));
}
pmod->Commit();
pmod->Close();
ts->Commit();
ts->Close();
ppdb->Commit();
pdbi->Close();
ppdb->Commit();
ppdb->Close();
return 0;
}
int main(int argc, char *argv[]) {
string hdr = invocationHeader(argc, argv);
opts::BasicOptions* bopts = new opts::BasicOptions;
opts::ModelWithCoords* mopts = new opts::ModelWithCoords;
ToolOptions* topts = new ToolOptions;
opts::AggregateOptions options;
options.add(bopts).add(mopts).add(topts);
if (!options.parse(argc, argv))
exit(-1);
AtomicGroup model = mopts->model;
if (topts->reimage) {
if (!model.isPeriodic()) {
cerr << "WARNING- Reimaging requested, but the model has no periodic box information\n";
} else {
if (!topts->bonds_name.empty()) {
AtomicGroup bonds = createSystem(topts->bonds_name);
copyBonds(model, bonds);
}
if (!model.hasBonds()) {
cerr << "WARNING- The model has no connectivity. Assigning bonds based on distance.\n";
model.findBonds();
}
}
}
AtomicGroup center_mol = selectAtoms(model, topts->center_sel);
GCoord center = center_mol.centroid();
AtomicGroup apply_mol = selectAtoms(model, topts->apply_sel);
GCoord offset = topts->translate - center;
if (topts->center_xy)
offset.z() = 0.0;
for (AtomicGroup::iterator atom = apply_mol.begin(); atom != apply_mol.end(); ++atom)
(*atom)->coords() += offset;
if (topts->reimage && model.isPeriodic()) {
vGroup molecules = model.splitByMolecule();
vGroup segments = model.splitByUniqueSegid();
for (vGroup::iterator seg = segments.begin(); seg != segments.end(); ++seg)
seg->reimage();
for (vGroup::iterator mol =molecules.begin(); mol != molecules.end(); ++mol)
mol->reimage();
}
AtomicGroup write_mol = selectAtoms(model, topts->write_sel);
PDB pdb = PDB::fromAtomicGroup(write_mol);
pdb.remarks().add(hdr);
cout << pdb;
}
void AdaptivePath::update() {
double weight2 = -1.*mypathv->dx;
double weight1 = 1.0 + mypathv->dx;
if( weight1>1.0 ) {
weight1=1.0; weight2=0.0;
} else if( weight2>1.0 ) {
weight1=0.0; weight2=1.0;
}
// Add projections to dispalcement accumulators
ReferenceConfiguration* myref = getReferenceConfiguration( mypathv->iclose1 );
myref->extractDisplacementVector( getPositions(), getArguments(), mypathv->cargs, false, displacement );
getReferenceConfiguration( mypathv->iclose2 )->extractDisplacementVector( myref->getReferencePositions(), getArguments(), myref->getReferenceArguments(), false, displacement2 );
displacement.addDirection( -mypathv->dx, displacement2 );
pdisplacements[mypathv->iclose1].addDirection( weight1, displacement );
pdisplacements[mypathv->iclose2].addDirection( weight2, displacement );
// Update weight accumulators
wsum[mypathv->iclose1] *= fadefact;
wsum[mypathv->iclose2] *= fadefact;
wsum[mypathv->iclose1] += weight1;
wsum[mypathv->iclose2] += weight2;
// This does the update of the path if it is time to
if( (getStep()>0) && (getStep()%update_str==0) ) {
wsum[fixedn[0]]=wsum[fixedn[1]]=0.;
for(unsigned inode=0; inode<getNumberOfReferencePoints(); ++inode) {
if( wsum[inode]>0 ) {
// First displace the node by the weighted direction
getReferenceConfiguration( inode )->displaceReferenceConfiguration( 1./wsum[inode], pdisplacements[inode] );
// Reset the displacement
pdisplacements[inode].zeroDirection();
}
}
// Now ensure all the nodes of the path are equally spaced
PathReparameterization myspacings( getPbc(), getArguments(), getAllReferenceConfigurations() );
myspacings.reparameterize( fixedn[0], fixedn[1], tolerance );
}
if( (getStep()>0) && (getStep()%wstride==0) ) {
pathfile.printf("# PATH AT STEP %d TIME %f \n", getStep(), getTime() );
std::vector<std::unique_ptr<ReferenceConfiguration>>& myconfs=getAllReferenceConfigurations();
std::vector<SetupMolInfo*> moldat=plumed.getActionSet().select<SetupMolInfo*>();
if( moldat.size()>1 ) error("you should only have one MOLINFO action in your input file");
SetupMolInfo* mymoldat=NULL; if( moldat.size()==1 ) mymoldat=moldat[0];
std::vector<std::string> argument_names( getNumberOfArguments() );
for(unsigned i=0; i<getNumberOfArguments(); ++i) argument_names[i] = getPntrToArgument(i)->getName();
PDB mypdb; mypdb.setArgumentNames( argument_names );
for(unsigned i=0; i<myconfs.size(); ++i) {
pathfile.printf("REMARK TYPE=%s\n", myconfs[i]->getName().c_str() );
mypdb.setAtomPositions( myconfs[i]->getReferencePositions() );
for(unsigned j=0; j<getNumberOfArguments(); ++j) mypdb.setArgumentValue( getPntrToArgument(j)->getName(), myconfs[i]->getReferenceArgument(j) );
mypdb.print( atoms.getUnits().getLength()/0.1, mymoldat, pathfile, ofmt );
}
pathfile.flush();
}
}
void ActionAtomistic::readAtomsFromPDB( const PDB& pdb ){
Colvar*cc=dynamic_cast<Colvar*>(this);
if(cc && cc->checkIsEnergy()) error("can't read energies from pdb files");
for(unsigned j=0;j<indexes.size();j++){
if( indexes[j].index()>pdb.size() ) error("there are not enough atoms in the input pdb file");
if( pdb.getAtomNumbers()[j].index()!=indexes[j].index() ) error("there are atoms missing in the pdb file");
positions[j]=pdb.getPositions()[indexes[j].index()];
}
for(unsigned j=0;j<indexes.size();j++) charges[j]=pdb.getBeta()[indexes[j].index()];
for(unsigned j=0;j<indexes.size();j++) masses[j]=pdb.getOccupancy()[indexes[j].index()];
}
void SingleDomainRMSD::readReference( const PDB& pdb ){
readAtomsFromPDB( pdb );
double wa=0, wd=0;
for(unsigned i=0;i<pdb.size();++i){ wa+=align[i]; wd+=displace[i]; }
Vector center;
for(unsigned i=0;i<pdb.size();++i){
align[i]=align[i] / wa; displace[i]=displace[i] / wd;
center+=reference_atoms[i]*align[i];
}
for(unsigned i=0;i<pdb.size();++i) reference_atoms[i]-=center;
}
PathMSDBase::PathMSDBase(const ActionOptions&ao):
PLUMED_COLVAR_INIT(ao),
neigh_size(-1),
neigh_stride(-1),
nframes(0)
{
parse("LAMBDA",lambda);
parse("NEIGH_SIZE",neigh_size);
parse("NEIGH_STRIDE",neigh_stride);
parse("REFERENCE",reference);
// open the file
FILE* fp=fopen(reference.c_str(),"r");
std::vector<AtomNumber> aaa;
if (fp!=NULL)
{
log<<"Opening reference file "<<reference.c_str()<<"\n";
bool do_read=true;
while (do_read){
PDB mypdb;
RMSD mymsd(log);
do_read=mypdb.readFromFilepointer(fp,plumed.getAtoms().usingNaturalUnits(),0.1/atoms.getUnits().getLength());
if(do_read){
unsigned nat=0;
nframes++;
if(mypdb.getAtomNumbers().size()==0) error("number of atoms in a frame should be more than zero");
if(nat==0) nat=mypdb.getAtomNumbers().size();
if(nat!=mypdb.getAtomNumbers().size()) error("frames should have the same number of atoms");
if(aaa.empty()) aaa=mypdb.getAtomNumbers();
if(aaa!=mypdb.getAtomNumbers()) error("frames should contain same atoms in same order");
log<<"Found PDB: "<<nframes<<" containing "<<mypdb.getAtomNumbers().size()<<" atoms\n";
pdbv.push_back(mypdb);
// requestAtoms(mypdb.getAtomNumbers()); // is done in non base classes
derivs_s.resize(mypdb.getAtomNumbers().size());
derivs_z.resize(mypdb.getAtomNumbers().size());
mymsd.set(mypdb,"OPTIMAL");
msdv.push_back(mymsd); // the vector that stores the frames
//log<<mypdb;
}else{break ;}
}
fclose (fp);
log<<"Found TOTAL "<<nframes<< " PDB in the file "<<reference.c_str()<<" \n";
if(nframes==0) error("at least one frame expected");
}
if(neigh_stride>0 || neigh_size>0){
if(neigh_size>int(nframes)){
log.printf(" List size required ( %d ) is too large: resizing to the maximum number of frames required: %u \n",neigh_size,nframes);
neigh_size=nframes;
}
log.printf(" Neighbor list enabled: \n");
log.printf(" size : %d elements\n",neigh_size);
log.printf(" stride : %d timesteps \n",neigh_stride);
}else{
log.printf(" Neighbor list NOT enabled \n");
}
}
bool CCPDB::parseFrame(void) {
if (ifs->eof())
return(false);
// We cheat here... Maybe it would be better to have a PDB::clear()
// or AtomicGroup::clear() member function???
// Note: For some reason, PDB newframe(*(ifs)) doesn't parse correctly...
PDB newframe;
newframe.read(*(ifs));
frame = newframe;
if (frame.size() == 0)
return(false);
return(true);
}
bool DataCollectionObject::transferDataToPDB( PDB& mypdb ) {
// Check if PDB contains argument names
std::vector<std::string> pdb_args( mypdb.getArgumentNames() );
// Now set the argument values
std::map<std::string,double>::iterator it;
for(unsigned i=0; i<pdb_args.size(); ++i) {
it=args.find( pdb_args[i] );
if( it==args.end() ) return false;
mypdb.setArgumentValue( pdb_args[i], it->second );
}
// Now set the atomic positions
std::vector<AtomNumber> pdb_pos( mypdb.getAtomNumbers() );
if( pdb_pos.size()==positions.size() ) mypdb.setAtomPositions( positions );
else if( pdb_pos.size()>0 ) plumed_merror("This feature is currently not ready");
return true;
}
TrigonometricPathVessel::TrigonometricPathVessel( const vesselbase::VesselOptions& da ):
StoreDataVessel(da),
projdir(ReferenceConfigurationOptions("DIRECTION")),
mydpack1( 1, getAction()->getNumberOfDerivatives() ),
mydpack2( 1, getAction()->getNumberOfDerivatives() ),
mydpack3( 1, getAction()->getNumberOfDerivatives() ),
mypack1( 0, 0, mydpack1 ),
mypack2( 0, 0, mydpack2 ),
mypack3( 0, 0, mydpack3 )
{
mymap=dynamic_cast<Mapping*>( getAction() );
plumed_massert( mymap, "Trigonometric path vessel can only be used with mappings");
// Retrieve the index of the property in the underlying mapping
if( mymap->getNumberOfProperties()!=1 ) error("cannot use trigonometric paths when there are multiple properties");
for(unsigned i=0; i<mymap->getFullNumberOfTasks(); ++i) {
if( mymap->getTaskCode(i)!=mymap->getPositionInFullTaskList(i) ) error("mismatched tasks and codes");
}
mymap->addComponentWithDerivatives("gspath"); mymap->componentIsNotPeriodic("gspath");
sp=mymap->copyOutput( mymap->getNumberOfComponents()-1 ); sp->resizeDerivatives( mymap->getNumberOfDerivatives() );
mymap->addComponentWithDerivatives("gzpath"); mymap->componentIsNotPeriodic("gzpath");
zp=mymap->copyOutput( mymap->getNumberOfComponents()-1 ); zp->resizeDerivatives( mymap->getNumberOfDerivatives() );
// Check we have PCA
ReferenceConfiguration* ref0=mymap->getReferenceConfiguration(0);
for(unsigned i=0; i<mymap->getFullNumberOfTasks(); ++i) {
if( !(mymap->getReferenceConfiguration(i))->pcaIsEnabledForThisReference() ) error("pca must be implemented in order to use trigometric path");
if( ref0->getName()!=(mymap->getReferenceConfiguration(i))->getName() ) error("cannot use mixed metrics");
if( mymap->getNumberOfAtoms()!=(mymap->getReferenceConfiguration(i))->getNumberOfReferencePositions() ) error("all frames must use the same set of atoms");
if( mymap->getNumberOfArguments()!=(mymap->getReferenceConfiguration(i))->getNumberOfReferenceArguments() ) error("all frames must use the same set of arguments");
}
cargs.resize( mymap->getNumberOfArguments() ); std::vector<std::string> argument_names( mymap->getNumberOfArguments() );
for(unsigned i=0; i<mymap->getNumberOfArguments(); ++i) argument_names[i] = (mymap->getPntrToArgument(i))->getName();
PDB mypdb; mypdb.setAtomNumbers( mymap->getAbsoluteIndexes() ); mypdb.addBlockEnd( mymap->getAbsoluteIndexes().size() );
if( argument_names.size()>0 ) mypdb.setArgumentNames( argument_names );
projdir.read( mypdb );
mypack1.resize( mymap->getNumberOfArguments(), mymap->getNumberOfAtoms() ); ref0->setupPCAStorage( mypack1 );
mypack2.resize( mymap->getNumberOfArguments(), mymap->getNumberOfAtoms() ); ref0->setupPCAStorage( mypack2 );
mypack3.resize( mymap->getNumberOfArguments(), mymap->getNumberOfAtoms() );
for(unsigned i=0; i<mymap->getNumberOfAtoms(); ++i) { mypack1.setAtomIndex(i,i); mypack2.setAtomIndex(i,i); mypack3.setAtomIndex(i,i); }
mypack1_stashd_atoms.resize( mymap->getNumberOfAtoms() ); mypack1_stashd_args.resize( mymap->getNumberOfArguments() );
}
int colvarproxy_namd::load_atoms(char const *pdb_filename,
cvm::atom_group &atoms,
std::string const &pdb_field_str,
double const pdb_field_value)
{
if (pdb_field_str.size() == 0)
cvm::error("Error: must define which PDB field to use "
"in order to define atoms from a PDB file.\n", INPUT_ERROR);
PDB *pdb = new PDB(pdb_filename);
size_t const pdb_natoms = pdb->num_atoms();
e_pdb_field pdb_field_index = pdb_field_str2enum(pdb_field_str);
for (size_t ipdb = 0; ipdb < pdb_natoms; ipdb++) {
double atom_pdb_field_value = 0.0;
switch (pdb_field_index) {
case e_pdb_occ:
atom_pdb_field_value = (pdb->atom(ipdb))->occupancy();
break;
case e_pdb_beta:
atom_pdb_field_value = (pdb->atom(ipdb))->temperaturefactor();
break;
case e_pdb_x:
atom_pdb_field_value = (pdb->atom(ipdb))->xcoor();
break;
case e_pdb_y:
atom_pdb_field_value = (pdb->atom(ipdb))->ycoor();
break;
case e_pdb_z:
atom_pdb_field_value = (pdb->atom(ipdb))->zcoor();
break;
default:
break;
}
if ( (pdb_field_value) &&
(atom_pdb_field_value != pdb_field_value) ) {
continue;
} else if (atom_pdb_field_value == 0.0) {
continue;
}
if (atoms.is_enabled(colvardeps::f_ag_scalable)) {
atoms.add_atom_id(ipdb);
} else {
atoms.add_atom(cvm::atom(ipdb+1));
}
}
delete pdb;
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}
void ReferenceAtoms::readAtomsFromPDB( const PDB& pdb, const bool allowblocks ){
if( !allowblocks && pdb.getNumberOfAtomBlocks()!=1 ) error("found multi-atom-block pdb format but expecting only one block of atoms");
for(unsigned i=0;i<pdb.size();++i){
indices.push_back( pdb.getAtomNumbers()[i] ); reference_atoms.push_back( pdb.getPositions()[i] );
align.push_back( pdb.getOccupancy()[i] ); displace.push_back( pdb.getBeta()[i] );
}
atom_der_index.resize( reference_atoms.size() );
}
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() );
}
int colvarproxy_namd::load_coords(char const *pdb_filename,
std::vector<cvm::atom_pos> &pos,
const std::vector<int> &indices,
std::string const &pdb_field_str,
double const pdb_field_value)
{
if (pdb_field_str.size() == 0 && indices.size() == 0) {
cvm::error("Bug alert: either PDB field should be defined or list of "
"atom IDs should be available when loading atom coordinates!\n", BUG_ERROR);
}
e_pdb_field pdb_field_index;
bool const use_pdb_field = (pdb_field_str.size() > 0);
if (use_pdb_field) {
pdb_field_index = pdb_field_str2enum(pdb_field_str);
}
// next index to be looked up in PDB file (if list is supplied)
std::vector<int>::const_iterator current_index = indices.begin();
PDB *pdb = new PDB(pdb_filename);
size_t const pdb_natoms = pdb->num_atoms();
if (pos.size() != pdb_natoms) {
bool const pos_allocated = (pos.size() > 0);
size_t ipos = 0, ipdb = 0;
for ( ; ipdb < pdb_natoms; ipdb++) {
if (use_pdb_field) {
// PDB field mode: skip atoms with wrong value in PDB field
double atom_pdb_field_value = 0.0;
switch (pdb_field_index) {
case e_pdb_occ:
atom_pdb_field_value = (pdb->atom(ipdb))->occupancy();
break;
case e_pdb_beta:
atom_pdb_field_value = (pdb->atom(ipdb))->temperaturefactor();
break;
case e_pdb_x:
atom_pdb_field_value = (pdb->atom(ipdb))->xcoor();
break;
case e_pdb_y:
atom_pdb_field_value = (pdb->atom(ipdb))->ycoor();
break;
case e_pdb_z:
atom_pdb_field_value = (pdb->atom(ipdb))->zcoor();
break;
default:
break;
}
if ( (pdb_field_value) &&
(atom_pdb_field_value != pdb_field_value) ) {
continue;
} else if (atom_pdb_field_value == 0.0) {
continue;
}
} else {
// Atom ID mode: use predefined atom IDs from the atom group
if (((int) ipdb) != *current_index) {
// Skip atoms not in the list
continue;
} else {
current_index++;
}
}
if (!pos_allocated) {
pos.push_back(cvm::atom_pos(0.0, 0.0, 0.0));
} else if (ipos >= pos.size()) {
cvm::error("Error: the PDB file \""+
std::string(pdb_filename)+
"\" contains coordinates for "
"more atoms than needed.\n", BUG_ERROR);
}
pos[ipos] = cvm::atom_pos((pdb->atom(ipdb))->xcoor(),
(pdb->atom(ipdb))->ycoor(),
(pdb->atom(ipdb))->zcoor());
ipos++;
if (!use_pdb_field && current_index == indices.end())
break;
}
if (ipos < pos.size() || (!use_pdb_field && current_index != indices.end())) {
size_t n_requested = use_pdb_field ? pos.size() : indices.size();
cvm::error("Error: number of matching records in the PDB file \""+
std::string(pdb_filename)+"\" ("+cvm::to_str(ipos)+
") does not match the number of requested coordinates ("+
cvm::to_str(n_requested)+").\n", INPUT_ERROR);
return COLVARS_ERROR;
}
} else {
// when the PDB contains exactly the number of atoms of the array,
// ignore the fields and just read coordinates
for (size_t ia = 0; ia < pos.size(); ia++) {
pos[ia] = cvm::atom_pos((pdb->atom(ia))->xcoor(),
(pdb->atom(ia))->ycoor(),
(pdb->atom(ia))->zcoor());
}
}
delete pdb;
return COLVARS_OK;
}
int main(int argc, char* argv[]) {
// findiff step: eps
double eps=1.e-6;
// various setups: com needs to be reset
bool remove_com=true;
// normalize weights or not (to check if the rmsd is proportional to weights)
bool normalize_weights=true;
// use msd instead of rmsd to check consistency
bool squared=false;
// enhance com to enphasize the issues with COM treatment
bool enhance_com=false;
// parse input instructions
// default task, calculate the RMSD of one frame respect to a set of others
vector<int> task(1);task[0]=0;
// this test wants to be only for OPTIMAL case
string type; type.assign("OPTIMAL");
// first parse the task: in this applications the tasks are simple integers that pass the action that is required
for(int i = 1; i < argc; i++){
task.push_back(atoi(argv[i]));
}
if(std::find(task.begin(), task.end(), -1)!=task.end()){cout<<"squared=true (default false)"<<endl;squared=true;}
if(std::find(task.begin(), task.end(), -2)!=task.end()){cout<<"normalize_weights=false (default true)"<<endl;normalize_weights=false;}
if(std::find(task.begin(), task.end(), -3)!=task.end()){cout<<"remove_com=false (default true)"<<endl; remove_com=false;}
if(std::find(task.begin(), task.end(), -4)!=task.end()){cout<<"OPTIMAL-FAST (default OPTIMAL)"<<endl; type.assign("OPTIMAL-FAST");}
if(std::find(task.begin(), task.end(), -5)!=task.end()){cout<<"enhance_com=true (default false) include option -3 (no com removal) "<<endl;enhance_com=true ; }
if(enhance_com)remove_com=false;
cout<<"ARGUMENTS: \n";
cout<<"OPTIONS that go on top of tasks:\n";
cout<<" -1 : squared=true (default=false)\n";
cout<<" -2 : normalize_weights=false (default=true)\n";
cout<<" -3 : remove_com=false (default=true) \n";
cout<<" -4 : OPTIMAL-FAST (default=OPTIMAL) \n";
cout<<" -5 : enhance_com=true (default false) automatically set option -3 (i.e. check the trouble with com when you do not remove it)\n";
cout<<"TASKS (can choose more than one):\n";
cout<<" 0 : normal rmsd/msd calculation and derivative dumps (default: always done)\n";
cout<<" 1 : findiff test for d msd / d position (inhomogenehous weights)\n";
cout<<" 2 : findiff test for d msd / d reference (inhomogenehous weights)\n";
cout<<" 3 : findiff test for d msd / d position (homogenehous weights)\n";
cout<<" 4 : findiff test for d msd / d reference (homogenehous weights)\n";
cout<<" 5 : findiff test for d Rot / d position (inhomogenehous weights) (reference->position)\n";
cout<<" 6 : findiff test for d Rot / d reference (inhomogenehous weights) (reference->position)\n";
cout<<" 7 : consistency check for MSD proportionality (works with squared=true through option -1 )\n";
cout<<" 8 : do some timings for all the above routines and for a growing number of atoms\n";
cout<<" 9 : test the rotation order: print position.pdb reference.pdb aligned.pdb and check that it makes sense(should be reference aligned onto positions)\n";
cout<<" 10 : findiff test for d Rot / d position ( position -> reference ) \n";
cout<<" 11 : findiff test for d Rot / d position (homogenehous weights) (reference->position)\n";
cout<<" 12 : findiff test for d Rot / d reference (homogenehous weights) (reference->position)\n";
cout<<" 13 : do timings only for the most common use (aligment +derivatives) and repeat for homogeneous weights\n";
cout<<" 20 : a simple test calculating only derivative of positions which is needed to compare new version and old version (need to compile with -DOLDRMSD both plumed and the test)\n";
PDB pdbref;
// now create the object: does not do anything but set the typer to SIMPLE
PLMD::RMSD* rmsd=new RMSD();
// set the reference pdb
string reference; reference.assign("1GB1_mdl1_rototranslated.pdb");
PDB pdb;
if( !pdb.read(reference,false,0.1) )
cout<<"missing input file 1GB1_mdl1_rototranslated.pdb "<<"\n";
if (enhance_com){
vector<Vector> v=pdb.getPositions();
for(unsigned i=0;i<v.size();i++){v[i][0]+=10.;v[i][1]+=20.;v[i][2]+=30.;}
pdb.setPositions(v);
}
cout<<"NOW CREATING THE RMSD OBJECT... with set() method";
// remember that "set" method parses the reference, align and displace from the PDB by calling the following methods
// setReference(pdb.getPositions()); -> set the reference and put the weights as 1/n, remove the com according to such weight
// setAlign(pdb.getOccupancy()); -> normalizes, set the alignment vector and remove the Com using such weights
// setDisplace(pdb.getBeta()); -> normalizes and set the displacement vector
// setType(mytype);
rmsd->set(pdb,type,remove_com,normalize_weights);
// store other vectors from further manipulation
std::vector<Vector> ref ; ref=pdb.getPositions() ;
std::vector<double> align; align=pdb.getOccupancy(); // non-normalized !
std::vector<double> displace; displace=pdb.getBeta(); // non-normalized !
cout<<"DONE!"<<endl;
// now take another conformation to compare with: the running frame
PDB pdbrun;
// mimic gromacs: do it in nm
if( !pdbrun.read("1GB1_mdl2.pdb",false,0.1) )
cout<<"missing input file 1GB1_mdl2.pdb\n" ;
std::vector<Vector> run ; run=pdbrun.getPositions() ;
std::vector<Vector> derivatives ;
if (enhance_com){
for(unsigned i=0;i<run.size();i++){run[i][0]-=10.;run[i][1]-=20.;run[i][2]-=30.;}
}
// Task 0: calculate the alignment and dump some data
if(std::find(task.begin(), task.end(), 0)!=task.end()){
cout<<"Task 0: calculates the alignment and retrieve some data"<<endl;
double r=rmsd->calculate( run, derivatives, squared );
cout<<"RMSD IS "<<r<<"\n";
// now dump some more information
ofstream myfile;
myfile.open ("output_rmsd");
myfile<<"RMSD ";
myfile.setf( std::ios::fixed, std:: ios::floatfield );
myfile.width(12);myfile.precision(6); myfile<<std::right<<r<<"\n";
// the derivatives
for(unsigned int i=0;i<run.size();++i){
myfile<<"DDIST_DPOS "<<std::setw(5)<<i<<" X= "<<std::setw(18)<<std::right<<derivatives[i][0]<<" Y= "<<std::setw(18)<<std::right<<derivatives[i][1]<<" Z= "<<std::setw(18)<<std::right<<derivatives[i][2]<<"\n";
}
std::vector<Vector> DDistDRef; DDistDRef.resize(align.size());
r=rmsd->calc_DDistDRef( run,derivatives,DDistDRef,squared);
for(unsigned int i=0;i<run.size();++i){
myfile<<"DDIST_DREF "<<std::setw(5)<<i<<" X= "<<std::setw(18)<<std::right<<DDistDRef[i][0]<<" Y= "<<std::setw(18)<<std::right<<DDistDRef[i][1]<<" Z= "<<std::setw(18)<<std::right<<DDistDRef[i][2]<<"\n";
}
myfile.close();
}
// Task 1: calculate findiff of running frame
if(std::find(task.begin(), task.end(), 1)!=task.end()){
cout<<"Task 1: calculates the finite difference for the running frame"<<endl;
double r_old=rmsd->calculate( run, derivatives, squared );
std::vector<Vector> run_save=run;
for(unsigned int comp=0;comp<3;comp++){
for(unsigned int i=0;i<run.size();++i){
//change the position
run[i][comp]+=eps;
double r=rmsd->calculate( run, derivatives, squared );
cout<<"DDIST_DPOS COMPONENT "<<comp<<" "<<(r-r_old)/(run[i][comp]-run_save[i][comp])<<" "<<derivatives[i][comp]<<"\n";
// restore the old position
run=run_save;
}
}
}
#ifndef OLDRMSD
// Task 2: calculate findiff of reference frame
if(std::find(task.begin(), task.end(), 2)!=task.end()){
cout<<"Task 2: calculates the finite difference for the reference frame"<<endl;
double r_old=rmsd->calculate( run, derivatives, squared );
std::vector<Vector> ref_save=ref;
std::vector<Vector> DDistDRef;
rmsd->clear();
rmsd->set(align, displace, ref,type,remove_com,normalize_weights );
for(unsigned int comp=0;comp<3;comp++){
for(unsigned int i=0;i<run.size();++i){
//change the position
ref[i][comp]+=eps;
// the asymmetry between reference and positions requires that
// in order to modify the reference one has to reset the rmsd object
rmsd->clear();
rmsd->set(align, displace, ref,type,remove_com,normalize_weights );
double r=rmsd->calc_DDistDRef( run, derivatives, DDistDRef, squared);
cout<<"DDIST_DREF COMPONENT "<<comp<<" "<<(r-r_old)/(ref[i][comp]-ref_save[i][comp])<<" "<<DDistDRef[i][comp]<<"\n";
// restore the old position
ref=ref_save;
}
}
}
// Task 3 calculate findiff of running frame for alEqDis version (align=displace)
if(std::find(task.begin(), task.end(), 3)!=task.end()){
std::vector<double> newalign(run.size(),1.);
std::vector<double> newdisplace(run.size(),1.);
rmsd->clear();
rmsd->set(newalign, newdisplace, ref,type,remove_com,normalize_weights );
cout<<"Task 3: calculates the finite difference for the running frame (fast version)"<<endl;
double r_old=rmsd->calculate( run, derivatives, squared );
std::vector<Vector> run_save=run;
for(unsigned int comp=0;comp<3;comp++){
for(unsigned int i=0;i<run.size();++i){
//change the position
run[i][comp]+=eps;
double r=rmsd->calculate( run, derivatives, squared );
cout<<"DDIST_DPOS_FAST COMPONENT "<<comp<<" "<<(r-r_old)/(run[i][comp]-run_save[i][comp])<<" "<<derivatives[i][comp]<<"\n";
// restore the old position
run=run_save;
}
}
}
// Task 4: calculate findiff of reference frame for alEqDis version (align=displace)
if(std::find(task.begin(), task.end(), 4)!=task.end()){
cout<<"Task 4: calculates the finite difference for the reference frame"<<endl;
std::vector<double> newalign(run.size(),1.);
std::vector<double> newdisplace(run.size(),1.);
rmsd->clear();
rmsd->set(newalign, newdisplace, ref,type,remove_com,normalize_weights);
double r_old=rmsd->calculate( run, derivatives, squared );
std::vector<Vector> DDistDRef;
std::vector<Vector> ref_save=ref;
for(unsigned int comp=0;comp<3;comp++){
for(unsigned int i=0;i<run.size();++i){
//change the position
ref[i][comp]+=eps;
// this function below also reset the com of the reference (but not of the running frame)
rmsd->clear();
rmsd->set(newalign, newdisplace, ref,type,remove_com,normalize_weights );
double r=rmsd->calc_DDistDRef( run, derivatives,DDistDRef, squared);
cout<<"DDIST_DREF_FAST COMPONENT "<<comp<<" "<<(r-r_old)/(ref[i][comp]-ref_save[i][comp])<<" "<<DDistDRef[i][comp]<<" "<<r<<" "<<r_old<<"\n";
// restore the old position
ref=ref_save;
}
}
}
// Task 5: calculate findiff of derivative of the rotation matrix respect to running frame
if(std::find(task.begin(), task.end(), 5)!=task.end()){
cout<<"Task 5: calculates the finite difference for derivative of the rotation matrix respect to the the running frame"<<endl;
rmsd->clear();
rmsd->set(align, displace, ref,type,remove_com,normalize_weights );
Tensor Rotation,OldRotation;
Matrix<std::vector<Vector> > DRotDPos(3,3);
std::vector<Vector> DDistDRef;
rmsd->calc_DDistDRef_Rot_DRotDPos( run, derivatives, DDistDRef, OldRotation, DRotDPos, squared );
std::vector<Vector> run_save=run;
for(unsigned int a=0;a<3;a++){
for(unsigned int b=0;b<3;b++){
for(unsigned int comp=0;comp<3;comp++){
for(unsigned int i=0;i<run.size();++i){
//change the position
run[i][comp]+=eps;
rmsd->calc_DDistDRef_Rot_DRotDPos( run, derivatives ,DDistDRef, Rotation, DRotDPos, squared );
cout<<"DROT_DPOS COMPONENT "<<comp<<" "<<(Rotation[a][b]-OldRotation[a][b])/(run[i][comp]-run_save[i][comp])<<" "<<DRotDPos[a][b][i][comp]<<"\n";
// restore the old position
run=run_save;
}
}
}
}
}
// Task 6: calculate findiff of derivative of the rotation matrix respect to reference frame
if(std::find(task.begin(), task.end(), 6)!=task.end()){
cout<<"Task 6: calculates the finite difference for derivative of the rotation matrix respect to the the reference frame"<<endl;
rmsd->clear();
rmsd->set(align, displace, ref,type,remove_com,normalize_weights );
Tensor Rotation,OldRotation;
Matrix<std::vector<Vector> > DRotDPos(3,3),DRotDRef(3,3);
std::vector<Vector> DDistDRef;
rmsd->calc_DDistDRef_Rot_DRotDPos_DRotDRef( run, derivatives, DDistDRef, OldRotation , DRotDPos , DRotDRef , squared);
std::vector<Vector> ref_save=ref;
for(unsigned int a=0;a<3;a++){
for(unsigned int b=0;b<3;b++){
for(unsigned int comp=0;comp<3;comp++){
for(unsigned int i=0;i<run.size();++i){
//change the position
ref[i][comp]+=eps;
// this function below also reset the com of the reference (but not of the running frame)
rmsd->clear();
rmsd->set(align, displace, ref,type,remove_com,normalize_weights );
rmsd->calc_DDistDRef_Rot_DRotDPos_DRotDRef( run, derivatives, DDistDRef, Rotation , DRotDPos, DRotDRef ,squared );
cout<<"DROT_DREF COMPONENT "<<comp<<" "<<(Rotation[a][b]-OldRotation[a][b])/(ref[i][comp]-ref_save[i][comp])<<" "<<DRotDRef[a][b][i][comp]<<"\n";
// restore the old position
ref=ref_save;
}
}
}
}
}
// Task 7: check weight consistency
if(std::find(task.begin(), task.end(), 7)!=task.end()){
cout<<"Task 7: calculates the weight (displacement) consistency: all these should same result when weights are normalized in input by setReferenceAtoms otherwise they should be proportional when squared=true \n When squared=false, each factor of 2 in weights should produce a factor of sqrt(2) in the total value "<<endl;
rmsd->clear();
rmsd->set(align, displace, ref,type,remove_com, false );
double r=rmsd->calculate( run, derivatives, squared );
cout<<"STANDARD WEIGHT "<<r<<"\n";
std::vector<double> newdisplace=displace;for(std::vector<double>::iterator p=newdisplace.begin();p!=newdisplace.end();++p ){(*p)*=2.;}
rmsd->clear();
rmsd->set(align, newdisplace, ref,type,remove_com, false );
r=rmsd->calculate( run, derivatives, squared );
cout<<"DOUBLE WEIGHT "<<r<<"\n";
newdisplace=displace;for(std::vector<double>::iterator p=newdisplace.begin();p!=newdisplace.end();++p ){(*p)*=4.;}
rmsd->clear();
rmsd->set(align,newdisplace, ref,type,remove_com, false );
r=rmsd->calculate( run, derivatives, squared );
cout<<"FOUR WEIGHT "<<r<<"\n";
}
// Task 8: do some timings to get a flavor
if(std::find(task.begin(), task.end(), 8)!=task.end()){
cout<<"Task 8: makes some timings for increasing atoms and different routines "<<endl;
rmsd->clear();
rmsd->set(align, displace, ref,type,remove_com,normalize_weights );
vector<Vector> r_run,r_ref;
vector<double> r_al,r_disp;
for (unsigned int i=0;i<10;i++){r_run.push_back(run[i]);r_ref.push_back(ref[i]);r_al.push_back(align[i]);r_disp.push_back(displace[i]);}
for(unsigned int i=0;i<10;i++){
cout<<"NUMBER OF ATOMS : "<<r_run.size()<<endl;
unsigned ntest; ntest=100;
// test the fast routine
rmsd->clear();
rmsd->set(r_al,r_disp, r_ref, type,remove_com, normalize_weights );
Stopwatch sw;
sw.start();
for(unsigned int j=0;j<ntest;j++)rmsd->calculate( r_run, derivatives, squared );
sw.stop();
cout<<"SIMPLE ROUTINE \n"<<sw<<endl;
std::vector<Vector> DDistDRef;
Stopwatch sw2;
sw2.start();
for(unsigned int j=0;j<ntest;j++)rmsd->calc_DDistDRef( r_run, derivatives,DDistDRef, squared);
sw2.stop();
cout<<"WITH REFERENCE FRAME: \n"<<sw2<<endl;
Tensor Rotation;
Matrix<std::vector<Vector> > DRotDPos(3,3);
Stopwatch sw3;
sw3.start();
for(unsigned int j=0;j<ntest;j++)rmsd->calc_DDistDRef_Rot_DRotDPos( r_run, derivatives,DDistDRef, Rotation , DRotDPos, squared);
sw3.stop();
cout<<"WITH ROTATION MATRIX DERIVATIVE: \n"<<sw3<<endl;
Matrix<std::vector<Vector> > DRotDRef(3,3);
Stopwatch sw4;
sw4.start();
for(unsigned int j=0;j<ntest;j++)rmsd->calc_DDistDRef_Rot_DRotDPos_DRotDRef( r_run, derivatives ,DDistDRef, Rotation , DRotDPos, DRotDRef, squared);
sw4.stop();
cout<<"WITH ROTATION MATRIX DERIVATIVE OF REEFERENCE: \n"<<sw4<<endl;
// duplicate the atoms
unsigned s=r_run.size();
for (unsigned int i=0;i<s;i++){r_run.push_back(r_run[i]);r_ref.push_back(r_ref[i]);r_al.push_back(r_al[i]);r_disp.push_back(r_disp[i]);}
}
}
// Task 9: check the rotation
if(std::find(task.begin(), task.end(), 9)!=task.end()){
cout<<"Task 9: dump some pdbs so to check if all makes sense when using inverse transform. In particular positions_aligned.pdb should overlap with reference_centered.pdb "<<endl;
rmsd->clear();
rmsd->set(align, displace, ref,type,remove_com,normalize_weights );
// dump the reference
ofstream myfile;
myfile.open ("reference.pdb");
std::vector<AtomNumber> at=pdb.getAtomNumbers();
std::vector<Vector> pos=pdb.getPositions();
unsigned k=0;
for(std::vector<AtomNumber>::iterator i=at.begin(); i!=at.end(); i++){
myfile<<"ATOM";
myfile.width(7);myfile<<std::right<<(*i).serial()<<" ";
myfile.width(4);myfile<<std::left<<pdb.getAtomName(*i);
myfile.width(4);myfile<<std::right<<pdb.getResidueName(*i)<<" A";
myfile.width(4);myfile<<std::right<<pdb.getResidueNumber(*i)<<" ";
myfile.setf( std::ios::fixed, std:: ios::floatfield );
myfile.width(8);myfile.precision(3); myfile<<std::right<<pos[k][0]*10;
myfile.width(8);myfile.precision(3); myfile<<std::right<<pos[k][1]*10;
myfile.width(8);myfile.precision(3); myfile<<std::right<<pos[k][2]*10<<" 1.00 1.00\n";
k++;
}
myfile.close();
// dump the position
myfile.open ("positions.pdb");
at=pdbrun.getAtomNumbers();
std::vector<Vector> runpos=pdbrun.getPositions();
k=0;
for(std::vector<AtomNumber>::iterator i=at.begin(); i!=at.end(); i++){
myfile<<"ATOM";
myfile.width(7);myfile<<std::right<<(*i).serial()<<" ";
myfile.width(4);myfile<<std::left<<pdbrun.getAtomName(*i);
myfile.width(4);myfile<<std::right<<pdbrun.getResidueName(*i)<<" A";
myfile.width(4);myfile<<std::right<<pdbrun.getResidueNumber(*i)<<" ";
myfile.setf( std::ios::fixed, std:: ios::floatfield );
myfile.width(8);myfile.precision(3); myfile<<std::right<<runpos[k][0]*10;
myfile.width(8);myfile.precision(3); myfile<<std::right<<runpos[k][1]*10;
myfile.width(8);myfile.precision(3); myfile<<std::right<<runpos[k][2]*10<<" 1.00 1.00\n";
k++;
}
myfile.close();
// now do the alignment
Tensor Rotation;
Matrix<std::vector<Vector> > DRotDPos(3,3);
std::vector<Vector> DDistDRef;
std::vector<Vector> alignedpos;
std::vector<Vector> centeredpos;
std::vector<Vector> centeredref;
std::vector<Vector> ddistdpos;
rmsd->calc_PCAelements( run, derivatives, Rotation , DRotDPos , alignedpos ,centeredpos, centeredref ,squared);
myfile.open ("positions_aligned.pdb");
k=0;
for(std::vector<AtomNumber>::iterator i=at.begin(); i!=at.end(); i++){
myfile<<"ATOM";
myfile.width(7);myfile<<std::right<<(*i).serial()<<" ";
myfile.width(4);myfile<<std::left<<pdbrun.getAtomName(*i);
myfile.width(4);myfile<<std::right<<pdbrun.getResidueName(*i)<<" A";
myfile.width(4);myfile<<std::right<<pdbrun.getResidueNumber(*i)<<" ";
myfile.setf( std::ios::fixed, std:: ios::floatfield );
myfile.width(8);myfile.precision(3); myfile<<std::right<<alignedpos[k][0]*10;
myfile.width(8);myfile.precision(3); myfile<<std::right<<alignedpos[k][1]*10;
myfile.width(8);myfile.precision(3); myfile<<std::right<<alignedpos[k][2]*10<<" 1.00 1.00\n";
k++;
}
myfile.close();
// dump the aligned
myfile.open ("reference_centered.pdb");
k=0;
for(std::vector<AtomNumber>::iterator i=at.begin(); i!=at.end(); i++){
myfile<<"ATOM";
myfile.width(7);myfile<<std::right<<(*i).serial()<<" ";
myfile.width(4);myfile<<std::left<<pdbrun.getAtomName(*i);
myfile.width(4);myfile<<std::right<<pdbrun.getResidueName(*i)<<" A";
myfile.width(4);myfile<<std::right<<pdbrun.getResidueNumber(*i)<<" ";
myfile.setf( std::ios::fixed, std:: ios::floatfield );
myfile.width(8);myfile.precision(3); myfile<<std::right<<centeredref[k][0]*10;
myfile.width(8);myfile.precision(3); myfile<<std::right<<centeredref[k][1]*10;
myfile.width(8);myfile.precision(3); myfile<<std::right<<centeredref[k][2]*10<<" 1.00 1.00\n";
k++;
}
myfile.close();
}
// Task 10: derivative of the rotation matrix (in case of reverse transition)
if(std::find(task.begin(), task.end(), 10)!=task.end()){
cout<<"Task 10: calculates the finite difference for derivative of the rotation matrix respect to the the running frame"<<endl;
rmsd->clear();
rmsd->set(align, displace, ref,type,remove_com,normalize_weights );
Tensor Rotation,OldRotation;
Matrix<std::vector<Vector> > DRotDPos(3,3);
std::vector<Vector> DDistDRef;
std::vector<Vector> alignedpos;
std::vector<Vector> centeredpos;
std::vector<Vector> centeredref;
std::vector<Vector> ddistdpos;
rmsd->calc_PCAelements( run, derivatives, OldRotation , DRotDPos , alignedpos ,centeredpos, centeredref, squared );
std::vector<Vector> run_save=run;
for(unsigned int a=0;a<3;a++){
for(unsigned int b=0;b<3;b++){
for(unsigned int comp=0;comp<3;comp++){
for(unsigned int i=0;i<run.size();++i){
//change the position
run[i][comp]+=eps;
rmsd->calc_PCAelements( run, derivatives, Rotation ,DRotDPos , alignedpos ,centeredpos, centeredref , squared);
cout<<"DROT_DPOS_INVERSE_TRANSFORM COMPONENT "<<comp<<" "<<(Rotation[a][b]-OldRotation[a][b])/(run[i][comp]-run_save[i][comp])<<" "<<DRotDPos[a][b][i][comp]<<"\n";
// restore the old position
run=run_save;
}
}
}
}
}
// Task 11: calculate findiff of derivative of the rotation matrix respect to running frame (homogenehous weights)
if(std::find(task.begin(), task.end(), 11)!=task.end()){
cout<<"Task 11: calculates the finite difference for derivative of the rotation matrix respect to the the running frame (homogeneous weights)"<<endl;
std::vector<double> newalign(run.size(),1.);
std::vector<double> newdisplace(run.size(),1.);
rmsd->clear();
rmsd->set(newalign, newdisplace, ref,type,remove_com,normalize_weights );
Tensor Rotation,OldRotation;
Matrix<std::vector<Vector> > DRotDPos(3,3);
std::vector<Vector> DDistDRef;
std::vector<Vector> alignedpos;
std::vector<Vector> centeredpos;
std::vector<Vector> centeredref;
rmsd->calc_DDistDRef_Rot_DRotDPos( run,derivatives, DDistDRef, OldRotation , DRotDPos, squared );
//rmsd->calc_PCAelements( run, derivatives, OldRotation , DRotDPos , alignedpos ,centeredpos, centeredref ,squared);
std::vector<Vector> run_save=run;
for(unsigned int a=0;a<3;a++){
for(unsigned int b=0;b<3;b++){
for(unsigned int comp=0;comp<3;comp++){
for(unsigned int i=0;i<run.size();++i){
//change the position
run[i][comp]+=eps;
rmsd->calc_DDistDRef_Rot_DRotDPos( run, derivatives , DDistDRef, Rotation , DRotDPos, squared );
//rmsd->calc_PCAelements( run, derivatives, Rotation , DRotDPos , alignedpos ,centeredpos, centeredref ,squared);
cout<<"DROT_DPOS COMPONENT "<<comp<<" "<<(Rotation[a][b]-OldRotation[a][b])/(run[i][comp]-run_save[i][comp])<<" "<<DRotDPos[a][b][i][comp]<<"\n";
// restore the old position
run=run_save;
}
}
}
}
}
// Task 12: calculate findiff of derivative of the rotation matrix respect to reference frame
if(std::find(task.begin(), task.end(), 12)!=task.end()){
cout<<"Task 12: calculates the finite difference for derivative of the rotation matrix respect to the the reference frame (homogeneous weights)"<<endl;
std::vector<double> newalign(run.size(),1.);
std::vector<double> newdisplace(run.size(),1.);
rmsd->clear();
rmsd->set(newalign, newdisplace, ref,type,remove_com,normalize_weights );
Tensor Rotation,OldRotation;
Matrix<std::vector<Vector> > DRotDPos(3,3),DRotDRef(3,3);
std::vector<Vector> DDistDRef;
rmsd->calc_DDistDRef_Rot_DRotDPos_DRotDRef( run, derivatives, DDistDRef, OldRotation , DRotDPos , DRotDRef ,squared);
std::vector<Vector> ref_save=ref;
for(unsigned int a=0;a<3;a++){
for(unsigned int b=0;b<3;b++){
for(unsigned int comp=0;comp<3;comp++){
for(unsigned int i=0;i<run.size();++i){
//change the position
ref[i][comp]+=eps;
// this function below also reset the com of the reference (but not of the running frame)
rmsd->clear();
rmsd->set(newalign, newdisplace, ref,type,remove_com,normalize_weights );
rmsd->calc_DDistDRef_Rot_DRotDPos_DRotDRef( run, derivatives, DDistDRef, Rotation , DRotDPos, DRotDRef ,squared );
cout<<"DROT_DREF COMPONENT "<<comp<<" "<<(Rotation[a][b]-OldRotation[a][b])/(ref[i][comp]-ref_save[i][comp])<<" "<<DRotDRef[a][b][i][comp]<<"\n";
// restore the old position
ref=ref_save;
}
}
}
}
}
// Task 13: do some timings to get a flavor (only on alignment+derivatives)
if(std::find(task.begin(), task.end(), 13)!=task.end()){
cout<<"Task 13: timings for the most common use (only on alignment+derivatives) "<<endl;
vector<Vector> r_run,r_ref;
vector<double> r_al,r_disp;
for (unsigned int i=0;i<10;i++){r_run.push_back(run[i]);r_ref.push_back(ref[i]);r_al.push_back(align[i]);r_disp.push_back(displace[i]);}
for(unsigned int i=0;i<10;i++){
cout<<"NUMBER OF ATOMS : "<<r_run.size()<<endl;
unsigned ntest; ntest=100;
// test the fast routine
rmsd->clear();
rmsd->set(r_al, r_disp, r_ref, type,remove_com,normalize_weights );
Stopwatch sw;
sw.start();
for(unsigned int j=0;j<ntest;j++)rmsd->calculate( r_run, derivatives, squared );
sw.stop();
cout<<"TIME \n"<<sw<<endl;
// duplicate the atoms
unsigned s=r_run.size();
for (unsigned int i=0;i<s;i++){r_run.push_back(r_run[i]);r_ref.push_back(r_ref[i]);r_al.push_back(r_al[i]);r_disp.push_back(r_disp[i]);}
}
cout <<"NOW HOMOGENEOUS WEIGHTS\n";
std::vector<double> newalign(10,1.);
std::vector<double> newdisplace(10,1.);
r_run.resize(0);
r_ref.resize(0);
r_al.resize(0);
r_disp.resize(0);
for (unsigned int i=0;i<10;i++){r_run.push_back(run[i]);r_ref.push_back(ref[i]);r_al.push_back(newalign[i]);r_disp.push_back(newdisplace[i]);}
rmsd->clear();
rmsd->set(r_al,r_disp , r_ref ,type,remove_com,normalize_weights );
for(unsigned int i=0;i<10;i++){
cout<<"NUMBER OF ATOMS : "<<r_run.size()<<endl;
unsigned ntest; ntest=100;
// test the fast routine
rmsd->clear();
rmsd->set(r_al, r_disp, r_ref, type,remove_com,normalize_weights );
derivatives.resize(r_al.size());
Stopwatch sw;
sw.start();
for(unsigned int j=0;j<ntest;j++)rmsd->calculate( r_run, derivatives, squared );
sw.stop();
cout<<"TIME \n"<<sw<<endl;
// duplicate the atoms
unsigned s=r_run.size();
for (unsigned int i=0;i<s;i++){r_run.push_back(r_run[i]);r_ref.push_back(r_ref[i]);r_al.push_back(r_al[i]);r_disp.push_back(r_disp[i]);}
}
}
#endif
// Task 20: do some timings to get a flavor
if(std::find(task.begin(), task.end(), 20)!=task.end()){
cout<<"Task 8: makes some timings for increasing atoms to compare new and old rmsd (need to be recompiled with -DOLDRMSD) "<<endl;
vector<Vector> r_run,r_ref;
vector<double> r_al,r_disp;
for (unsigned int i=0;i<10;i++){r_run.push_back(run[i]);r_ref.push_back(ref[i]);r_al.push_back(align[i]);r_disp.push_back(displace[i]);}
for(unsigned int i=0;i<10;i++){
cout<<"NUMBER OF ATOMS : "<<r_run.size()<<endl;
unsigned ntest; ntest=100;
// test the fast routine
rmsd->clear();
rmsd->set(r_al,r_disp, r_ref, type,remove_com, normalize_weights );
Stopwatch sw;
sw.start();
for(unsigned int j=0;j<ntest;j++)rmsd->calculate( r_run, derivatives, squared );
sw.stop();
cout<<"SIMPLE ROUTINE \n"<<sw<<endl;
unsigned s=r_run.size();
for (unsigned int i=0;i<s;i++){r_run.push_back(r_run[i]);r_ref.push_back(r_ref[i]);r_al.push_back(r_al[i]);r_disp.push_back(r_disp[i]);}
}
}
return 0;
}
int main(int argc, char *argv[]) {
string hdr = invocationHeader(argc, argv);
cout << "# " << hdr << endl;
parseArgs(argc, argv);
DoubleMatrix eigvals;
readAsciiMatrix(eigvals_name, eigvals);
DoubleMatrix eigvecs;
readAsciiMatrix(eigvecs_name, eigvecs);
if (modes.empty())
for (uint i=0; i<eigvals.rows(); ++i)
modes.push_back(i);
uint n = modes.size();
uint m = eigvecs.rows();
// V = m x n matrix of eigenvectors
DoubleMatrix V(m, n);
for (uint i=0; i<n; ++i)
for (uint j=0; j<m; ++j)
V(j, i) = eigvecs(j, modes[i]);
// Make a copy and scale by the appropriate eigenvalue,
// remembering that eigenvalues are inverted for ENM,
// or squaring and not inverting in the case of PCA
DoubleMatrix VS = V.copy();
for (uint i=0; i<n; ++i) {
double e = eigvals[modes[i]];
double s = (pca_input) ? (scale * e * e): (scale / e);
for (uint j=0; j<m; ++j)
VS(j, i) *= s;
}
// U = Covariance matrix
DoubleMatrix U = loos::Math::MMMultiply(VS,V,false,true);
// B-factors come from trace of diagonal 3x3 superblocks
vector<double> B;
double prefactor = 8.0 * M_PI * M_PI / 3.0;
for (uint i=0; i<m; i += 3) {
double b = prefactor * (U(i,i) + U(i+1, i+1) + U(i+2, i+2));
B.push_back(b);
cout << boost::format("%-8d %g\n") % (i/3) % b;
}
if (!pdb_name.empty()) {
AtomicGroup model = createSystem(pdb_name);
AtomicGroup subset = selectAtoms(model, selection);
if ((unsigned int)subset.size() != B.size()) {
cerr << boost::format("Error- selection has %d atoms, but %d were expected.\n") % subset.size() % B.size();
exit(-10);
}
for (uint i=0; i<B.size(); ++i)
subset[i]->bfactor(B[i]);
PDB pdb = PDB::fromAtomicGroup(model);
pdb.remarks().add(hdr);
ofstream ofs(out_name.c_str());
ofs << pdb;
}
}
bool processSinglePDBFile(const char* filename,
Options& opts,
ofstream& output_file,
ofstream& pairlistfile,
const char* chains)
{
int numRes1 = opts.residue1.size();
int numRes2 = opts.residue2.size();
// Read in the PDB file
// This function actually reads and stores more information than
// we really need, but the files are relatively small so it isn't
// taking up much RAM (from what I saw, < 5MB each PDB file)
// with a few exceptions
PDB PDBfile_whole(filename, opts.resolution);
if( PDBfile_whole.fail() )
{
//cerr << red << "Error" << reset << ": Parsing PDB file failed!" << endl;
PDBfile_whole.printFailure();
return false;
}
for(unsigned int model=0; model < PDBfile_whole.models.size(); model++)
{
PDB PDBfile = PDBfile_whole.models[model];
PDBfile.filename = PDBfile_whole.filename;
PDBfile.resolution = PDBfile_whole.resolution;
PDBfile.setResiduesToFind(&opts.residue1, &opts.residue2);
if(opts.numLigands)
{
PDBfile.setLigandsToFind(&opts.ligands);
}
PDBfile.populateChains(false);
if( opts.numLigands )
{
PDBfile.findLigands( opts.ligands );
}
//If we're searching for triplets, then do that here
if(opts.triplets == true){
//this triple for loop is set up so that it searches through each
//unique combination of chains. e.g. if there are 3 chains labeled 1, 2, and 3
//it will search through the combinations: 111 112 113 122 123 133 222 223 233 333
for(unsigned int i = 0; i < PDBfile.chains.size(); i++)
{
if(opts.sameChain){
searchTripletInformation(PDBfile,opts,i,i,i,output_file,pairlistfile);
return true;
}
// in the future we may have the below double for loop go through each chain combination.
for(unsigned int j = i; j < PDBfile.chains.size(); j++)
{
for(unsigned int k = j; k < PDBfile.chains.size(); k++)
{
searchTripletInformation(PDBfile,opts,i,j,k,output_file,pairlistfile);
}
}
}
return true; //end here if we're processing triplets
}
// Searching for interations within each chain
for(unsigned int i = 0; i < PDBfile.chains.size(); i++)
{
// Check if we are supposed to look at certain chains
if( chains )
{
if( !strchr(chains,PDBfile.chains[i].id) )
{
continue;
}
}
// if we want to look for interactions between the ith chain
// and each of the other chains, we set the indices to loop
// through all the chains
unsigned int start = 0;
unsigned int end = PDBfile.chains.size();
// otherwise we just set the indices to go through the ith chain
if(opts.sameChain)
{
start = i;
end = i+1;
}
for(unsigned int j = start; j < end; j++)
{
for(int ii = 0; ii < numRes1; ii++)
{
for(int jj = 0; jj < numRes2; jj++)
{
// Search for different residue combinations
searchChainInformation(PDBfile,
i,
j,
opts.residue1[ii],
opts.residue2[jj],
opts,
output_file);
}
}
}
// Go through the ligands, if there are any
for(unsigned int j = 0; j<PDBfile.ligands.size(); j++)
{
for(int ii=0; ii<numRes1; ii++)
{
searchLigandsInformation(PDBfile,
*PDBfile.ligands[j],
i,
opts.residue1[ii],
opts,
output_file);
}
}
}
}
return true;
}
void PDB::parsePDBstream(istream& PDBfile, float resolution)
{
string line; // this is a temp var to hold the current line from the file
int count = 0;
bool rflag = false;
PDB model;
int modelnum=1;
// For each line in the file
while( getline(PDBfile, line) && !failure)
{
count++;
// Check to see if there are more than one model
// If there is, we will just skip the file altogether because
// it is less of a hassle to deal with.
// So here, we check the model number, if it is greater
// than 1, we will just break from this loop and print
// a note
int found = line.find("MODEL");
if( found == 0 )
{
int model_number;
if(line.substr(10,4) == " ")
{
continue;
}
else if( !from_string<int>(model_number, line.substr(10,4), dec) )
{
failure = true;
failflag = MODEL_TO_NUMBER_FAILED;
continue;
}
else if( model_number > 1 )
{
model.model_number = modelnum;
models.push_back(model);
model.clear();
modelnum++;
}
}
// Check the resolution of the PDB
found = line.find("REMARK 2 RESOLUTION.");
if( found == 0 )
{
this->resolution = 0;
if(line.substr(23, 7) == "NOT APP")
{
//failure = true;
//failflag = RESOLUTION_NOT_APPLICABLE;
this->resolution = -1;
}
else if(line.substr(23, 7) == " ")
{
failure = true;
failflag = RESOLUTION_BLANK;
}
else
{
if(!from_string<float>(this->resolution, line.substr(23,7), dec))
{
failure = true;
failflag = RESOLUTION_TO_NUMBER_FAILED;
}
if(this->resolution > resolution)
{
failure = true;
failflag = RESOLUTION_TOO_HIGH;
}
}
continue;
}
// Parse the line if we are on an ATOM line
found = line.find("ATOM");
if( found == 0 )
{
Atom a(line, count);
failure = a.fail();
atoms.push_back(a);
model.atoms.push_back(a);
continue;
}
// Parse the line if we are on a HETATM line
// Used to find ligands
found = line.find("HETATM");
if( found == 0 )
{
Atom h(line, count);
failure = h.fail();
hetatms.push_back(h);
model.hetatms.push_back(h);
continue;
}
// Parse the line if we are on a CONECT line
// Used to find ligands
found = line.find("CONECT");
if( found == 0 )
{
conect.push_back(line);
model.conect.push_back(line);
continue;
}
}
// This checks to see if we even had a resolution line
// in the PDB. If we don't, we are skipping it
if( this->resolution == -2 )
{
failure = true;
failflag = NO_RESOLUTION;
}
// This ensures that we have the last model
// we parsed in out model list
model.model_number = modelnum;
models.push_back(model);
}
int Driver<real>::main(FILE* in,FILE*out,Communicator& pc){
Units units;
PDB pdb;
// Parse everything
bool printhelpdebug; parseFlag("--help-debug",printhelpdebug);
if( printhelpdebug ){
fprintf(out,"%s",
"Additional options for debug (only to be used in regtest):\n"
" [--debug-float] : turns on the single precision version (to check float interface)\n"
" [--debug-dd] : use a fake domain decomposition\n"
" [--debug-pd] : use a fake particle decomposition\n"
);
return 0;
}
// Are we reading trajectory data
bool noatoms; parseFlag("--noatoms",noatoms);
std::string fakein;
bool debugfloat=parse("--debug-float",fakein);
if(debugfloat && sizeof(real)!=sizeof(float)){
CLTool* cl=cltoolRegister().create(CLToolOptions("driver-float")); //new Driver<float>(*this);
cl->setInputData(this->getInputData());
int ret=cl->main(in,out,pc);
delete cl;
return ret;
}
bool debug_pd=parse("--debug-pd",fakein);
bool debug_dd=parse("--debug-dd",fakein);
if( debug_pd || debug_dd ){
if(noatoms) error("cannot debug without atoms");
}
// set up for multi replica driver:
int multi=0;
parse("--multi",multi);
Communicator intracomm;
Communicator intercomm;
if(multi){
int ntot=pc.Get_size();
int nintra=ntot/multi;
if(multi*nintra!=ntot) error("invalid number of processes for multi environment");
pc.Split(pc.Get_rank()/nintra,pc.Get_rank(),intracomm);
pc.Split(pc.Get_rank()%nintra,pc.Get_rank(),intercomm);
} else {
intracomm.Set_comm(pc.Get_comm());
}
// set up for debug replica exchange:
bool debug_grex=parse("--debug-grex",fakein);
int grex_stride=0;
FILE*grex_log=NULL;
if(debug_grex){
if(noatoms) error("must have atoms to debug_grex");
if(multi<2) error("--debug_grex needs --multi with at least two replicas");
Tools::convert(fakein,grex_stride);
string n; Tools::convert(intercomm.Get_rank(),n);
string file;
parse("--debug-grex-log",file);
if(file.length()>0){
file+="."+n;
grex_log=fopen(file.c_str(),"w");
}
}
// Read the plumed input file name
string plumedFile; parse("--plumed",plumedFile);
// the timestep
double t; parse("--timestep",t);
real timestep=real(t);
// the stride
unsigned stride; parse("--trajectory-stride",stride);
// are we writing forces
string dumpforces(""), dumpforcesFmt("%f");;
if(!noatoms) parse("--dump-forces",dumpforces);
if(dumpforces!="") parse("--dump-forces-fmt",dumpforcesFmt);
string trajectory_fmt;
// Read in an xyz file
string trajectoryFile(""), pdbfile("");
bool pbc_cli_given=false; vector<double> pbc_cli_box(9,0.0);
if(!noatoms){
std::string traj_xyz; parse("--ixyz",traj_xyz);
std::string traj_gro; parse("--igro",traj_gro);
if(traj_xyz.length()>0 && traj_gro.length()>0){
fprintf(stderr,"ERROR: cannot provide more than one trajectory file\n");
if(grex_log)fclose(grex_log);
return 1;
}
if(traj_xyz.length()>0 && trajectoryFile.length()==0){
trajectoryFile=traj_xyz;
trajectory_fmt="xyz";
}
if(traj_gro.length()>0 && trajectoryFile.length()==0){
trajectoryFile=traj_gro;
trajectory_fmt="gro";
}
if(trajectoryFile.length()==0){
fprintf(stderr,"ERROR: missing trajectory data\n");
if(grex_log)fclose(grex_log);
return 1;
}
string lengthUnits(""); parse("--length-units",lengthUnits);
if(lengthUnits.length()>0) units.setLength(lengthUnits);
parse("--pdb",pdbfile);
if(pdbfile.length()>0){
bool check=pdb.read(pdbfile,false,1.0);
if(!check) error("error reading pdb file");
}
string pbc_cli_list; parse("--box",pbc_cli_list);
if(pbc_cli_list.length()>0) {
pbc_cli_given=true;
vector<string> words=Tools::getWords(pbc_cli_list,",");
if(words.size()==3){
for(int i=0;i<3;i++) sscanf(words[i].c_str(),"%100lf",&(pbc_cli_box[4*i]));
} else if(words.size()==9) {
for(int i=0;i<9;i++) sscanf(words[i].c_str(),"%100lf",&(pbc_cli_box[i]));
} else {
string msg="ERROR: cannot parse command-line box "+pbc_cli_list;
fprintf(stderr,"%s\n",msg.c_str());
return 1;
}
}
}
if( debug_dd && debug_pd ) error("cannot use debug-dd and debug-pd at the same time");
if(debug_pd || debug_dd){
if( !Communicator::initialized() ) error("needs mpi for debug-pd");
}
Plumed p;
int rr=sizeof(real);
p.cmd("setRealPrecision",&rr);
int checknatoms=-1;
int step=0;
if(Communicator::initialized()){
if(multi){
if(intracomm.Get_rank()==0) p.cmd("GREX setMPIIntercomm",&intercomm.Get_comm());
p.cmd("GREX setMPIIntracomm",&intracomm.Get_comm());
p.cmd("GREX init");
}
p.cmd("setMPIComm",&intracomm.Get_comm());
}
p.cmd("setMDLengthUnits",&units.getLength());
p.cmd("setMDEngine","driver");
p.cmd("setTimestep",×tep);
p.cmd("setPlumedDat",plumedFile.c_str());
p.cmd("setLog",out);
if(multi){
string n;
Tools::convert(intercomm.Get_rank(),n);
trajectoryFile+="."+n;
}
FILE* fp=NULL; FILE* fp_forces=NULL;
if(!noatoms){
if (trajectoryFile=="-")
fp=in;
else {
fp=fopen(trajectoryFile.c_str(),"r");
if(!fp){
string msg="ERROR: Error opening XYZ file "+trajectoryFile;
fprintf(stderr,"%s\n",msg.c_str());
return 1;
}
}
if(dumpforces.length()>0){
if(Communicator::initialized() && pc.Get_size()>1){
string n;
Tools::convert(pc.Get_rank(),n);
dumpforces+="."+n;
}
fp_forces=fopen(dumpforces.c_str(),"w");
}
}
std::string line;
std::vector<real> coordinates;
std::vector<real> forces;
std::vector<real> masses;
std::vector<real> charges;
std::vector<real> cell;
std::vector<real> virial;
// variables to test particle decomposition
int pd_nlocal;
int pd_start;
// variables to test random decomposition (=domain decomposition)
std::vector<int> dd_gatindex;
std::vector<int> dd_g2l;
std::vector<real> dd_masses;
std::vector<real> dd_charges;
std::vector<real> dd_forces;
std::vector<real> dd_coordinates;
int dd_nlocal;
// random stream to choose decompositions
Random rnd;
while(true){
if(!noatoms){
if(!Tools::getline(fp,line)) break;
}
int natoms;
bool first_step=false;
if(!noatoms){
if(trajectory_fmt=="gro") if(!Tools::getline(fp,line)) error("premature end of trajectory file");
sscanf(line.c_str(),"%100d",&natoms);
}
if(checknatoms<0 && !noatoms){
pd_nlocal=natoms;
pd_start=0;
first_step=true;
masses.assign(natoms,real(1.0));
charges.assign(natoms,real(0.0));
if(pdbfile.length()>0){
for(unsigned i=0;i<pdb.size();++i){
AtomNumber an=pdb.getAtomNumbers()[i];
unsigned index=an.index();
if( index>=unsigned(natoms) ) error("atom index in pdb exceeds the number of atoms in trajectory");
masses[index]=pdb.getOccupancy()[i];
charges[index]=pdb.getBeta()[i];
}
}
} else if( checknatoms<0 && noatoms ){
natoms=0;
}
if( checknatoms<0 ){
checknatoms=natoms;
p.cmd("setNatoms",&natoms);
p.cmd("init");
}
if(checknatoms!=natoms){
std::string stepstr; Tools::convert(step,stepstr);
error("number of atoms in frame " + stepstr + " does not match number of atoms in first frame");
}
coordinates.assign(3*natoms,real(0.0));
forces.assign(3*natoms,real(0.0));
cell.assign(9,real(0.0));
virial.assign(9,real(0.0));
if( first_step || rnd.U01()>0.5){
if(debug_pd){
int npe=intracomm.Get_size();
vector<int> loc(npe,0);
vector<int> start(npe,0);
for(int i=0;i<npe-1;i++){
int cc=(natoms*2*rnd.U01())/npe;
if(start[i]+cc>natoms) cc=natoms-start[i];
loc[i]=cc;
start[i+1]=start[i]+loc[i];
}
loc[npe-1]=natoms-start[npe-1];
intracomm.Bcast(loc,0);
intracomm.Bcast(start,0);
pd_nlocal=loc[intracomm.Get_rank()];
pd_start=start[intracomm.Get_rank()];
if(intracomm.Get_rank()==0){
fprintf(out,"\nDRIVER: Reassigning particle decomposition\n");
fprintf(out,"DRIVER: "); for(int i=0;i<npe;i++) fprintf(out,"%d ",loc[i]); printf("\n");
fprintf(out,"DRIVER: "); for(int i=0;i<npe;i++) fprintf(out,"%d ",start[i]); printf("\n");
}
p.cmd("setAtomsNlocal",&pd_nlocal);
p.cmd("setAtomsContiguous",&pd_start);
} else if(debug_dd){
int npe=intracomm.Get_size();
int rank=intracomm.Get_rank();
dd_charges.assign(natoms,0.0);
dd_masses.assign(natoms,0.0);
dd_gatindex.assign(natoms,-1);
dd_g2l.assign(natoms,-1);
dd_coordinates.assign(3*natoms,0.0);
dd_forces.assign(3*natoms,0.0);
dd_nlocal=0;
for(int i=0;i<natoms;++i){
double r=rnd.U01()*npe;
int n; for(n=0;n<npe;n++) if(n+1>r)break;
plumed_assert(n<npe);
if(n==rank){
dd_gatindex[dd_nlocal]=i;
dd_g2l[i]=dd_nlocal;
dd_charges[dd_nlocal]=charges[i];
dd_masses[dd_nlocal]=masses[i];
dd_nlocal++;
}
}
if(intracomm.Get_rank()==0){
fprintf(out,"\nDRIVER: Reassigning particle decomposition\n");
}
p.cmd("setAtomsNlocal",&dd_nlocal);
p.cmd("setAtomsGatindex",&dd_gatindex[0]);
}
}
int plumedStopCondition=0;
p.cmd("setStep",&step);
p.cmd("setStopFlag",&plumedStopCondition);
if(!noatoms){
if(trajectory_fmt=="xyz"){
if(!Tools::getline(fp,line)) error("premature end of trajectory file");
std::vector<double> celld(9,0.0);
if(pbc_cli_given==false) {
std::vector<std::string> words;
words=Tools::getWords(line);
if(words.size()==3){
sscanf(line.c_str(),"%100lf %100lf %100lf",&celld[0],&celld[4],&celld[8]);
} else if(words.size()==9){
sscanf(line.c_str(),"%100lf %100lf %100lf %100lf %100lf %100lf %100lf %100lf %100lf",
&celld[0], &celld[1], &celld[2],
&celld[3], &celld[4], &celld[5],
&celld[6], &celld[7], &celld[8]);
} else error("needed box in second line of xyz file");
} else { // from command line
celld=pbc_cli_box;
}
for(unsigned i=0;i<9;i++)cell[i]=real(celld[i]);
}
int ddist=0;
// Read coordinates
for(int i=0;i<natoms;i++){
bool ok=Tools::getline(fp,line);
if(!ok) error("premature end of trajectory file");
double cc[3];
if(trajectory_fmt=="xyz"){
char dummy[1000];
std::sscanf(line.c_str(),"%999s %100lf %100lf %100lf",dummy,&cc[0],&cc[1],&cc[2]);
} else if(trajectory_fmt=="gro"){
// do the gromacs way
if(!i){
//
// calculate the distance between dots (as in gromacs gmxlib/confio.c, routine get_w_conf )
//
const char *p1, *p2, *p3;
p1 = strchr(line.c_str(), '.');
if (p1 == NULL) error("seems there are no coordinates in the gro file");
p2 = strchr(&p1[1], '.');
if (p2 == NULL) error("seems there is only one coordinates in the gro file");
ddist = p2 - p1;
p3 = strchr(&p2[1], '.');
if (p3 == NULL)error("seems there are only two coordinates in the gro file");
if (p3 - p2 != ddist)error("not uniform spacing in fields in the gro file");
}
Tools::convert(line.substr(20,ddist),cc[0]);
Tools::convert(line.substr(20+ddist,ddist),cc[1]);
Tools::convert(line.substr(20+ddist+ddist,ddist),cc[2]);
} else plumed_error();
if(!debug_pd || ( i>=pd_start && i<pd_start+pd_nlocal) ){
coordinates[3*i]=real(cc[0]);
coordinates[3*i+1]=real(cc[1]);
coordinates[3*i+2]=real(cc[2]);
}
}
if(trajectory_fmt=="gro"){
if(!Tools::getline(fp,line)) error("premature end of trajectory file");
std::vector<string> words=Tools::getWords(line);
if(words.size()<3) error("cannot understand box format");
Tools::convert(words[0],cell[0]);
Tools::convert(words[1],cell[4]);
Tools::convert(words[2],cell[8]);
if(words.size()>3) Tools::convert(words[3],cell[1]);
if(words.size()>4) Tools::convert(words[4],cell[2]);
if(words.size()>5) Tools::convert(words[5],cell[3]);
if(words.size()>6) Tools::convert(words[6],cell[5]);
if(words.size()>7) Tools::convert(words[7],cell[6]);
if(words.size()>8) Tools::convert(words[8],cell[7]);
}
if(debug_dd){
for(int i=0;i<dd_nlocal;++i){
int kk=dd_gatindex[i];
dd_coordinates[3*i+0]=coordinates[3*kk+0];
dd_coordinates[3*i+1]=coordinates[3*kk+1];
dd_coordinates[3*i+2]=coordinates[3*kk+2];
}
p.cmd("setForces",&dd_forces[0]);
p.cmd("setPositions",&dd_coordinates[0]);
p.cmd("setMasses",&dd_masses[0]);
p.cmd("setCharges",&dd_charges[0]);
} else {
p.cmd("setForces",&forces[3*pd_start]);
p.cmd("setPositions",&coordinates[3*pd_start]);
p.cmd("setMasses",&masses[pd_start]);
p.cmd("setCharges",&charges[pd_start]);
}
p.cmd("setBox",&cell[0]);
p.cmd("setVirial",&virial[0]);
}
p.cmd("calc");
// this is necessary as only processor zero is adding to the virial:
intracomm.Bcast(virial,0);
if(debug_pd) intracomm.Sum(forces);
if(debug_dd){
for(int i=0;i<dd_nlocal;i++){
forces[3*dd_gatindex[i]+0]=dd_forces[3*i+0];
forces[3*dd_gatindex[i]+1]=dd_forces[3*i+1];
forces[3*dd_gatindex[i]+2]=dd_forces[3*i+2];
}
dd_forces.assign(3*natoms,0.0);
intracomm.Sum(forces);
}
if(debug_grex &&step%grex_stride==0){
p.cmd("GREX savePositions");
if(intracomm.Get_rank()>0){
p.cmd("GREX prepare");
} else {
int r=intercomm.Get_rank();
int n=intercomm.Get_size();
int partner=r+(2*((r+step/grex_stride)%2))-1;
if(partner<0)partner=0;
if(partner>=n) partner=n-1;
p.cmd("GREX setPartner",&partner);
p.cmd("GREX calculate");
p.cmd("GREX shareAllDeltaBias");
for(int i=0;i<n;i++){
string s; Tools::convert(i,s);
real a; s="GREX getDeltaBias "+s; p.cmd(s.c_str(),&a);
if(grex_log) fprintf(grex_log," %f",a);
}
if(grex_log) fprintf(grex_log,"\n");
}
}
if(fp_forces){
fprintf(fp_forces,"%d\n",natoms);
string fmt=dumpforcesFmt+" "+dumpforcesFmt+" "+dumpforcesFmt+"\n";
fprintf(fp_forces,fmt.c_str(),virial[0],virial[4],virial[8]);
fmt="X "+fmt;
for(int i=0;i<natoms;i++)
fprintf(fp_forces,fmt.c_str(),forces[3*i],forces[3*i+1],forces[3*i+2]);
}
if(noatoms && plumedStopCondition) break;
step+=stride;
}
p.cmd("runFinalJobs");
if(fp_forces) fclose(fp_forces);
if(fp && fp!=in)fclose(fp);
if(grex_log) fclose(grex_log);
return 0;
}
int main(int argc, char *argv[]) {
string hdr = invocationHeader(argc, argv);
opts::BasicOptions* bopts = new opts::BasicOptions(fullHelpMessage());
ToolOptions* topts = new ToolOptions;
opts::RequiredArguments* ropts = new opts::RequiredArguments;
ropts->addArgument("matrix", "matrix-file");
opts::AggregateOptions options;
options.add(bopts).add(topts).add(ropts);
if (!options.parse(argc, argv))
exit(-1);
string matrix_name = ropts->value("matrix");
RealMatrix A;
readAsciiMatrix(matrix_name, A);
uint m = A.rows();
if (rows.empty())
for (uint i=0; i<m; ++i)
rows.push_back(i);
uint resid = 1;
uint total_chunks = rows.size() / (chunksize ? chunksize : rows.size());
uint chunk = 1;
AtomicGroup model;
// Warn about pymol...
if (rows.size() >= 100000 && bonds)
cerr << "Warning- PyMol may not correctly handle the CONECT records generated by this tool.\n";
for (uint atomid = 0; atomid < rows.size(); ++atomid, ++resid) {
if (chunksize && resid > chunksize) {
if (bonds) {
for (uint i=atomid - chunksize; i<atomid-1; ++i)
model[i]->addBond(model[i+1]);
}
resid = 1;
++chunk;
}
GCoord c(scales[0] * A(rows[atomid], columns[0]),
scales[1] * A(rows[atomid], columns[1]),
scales[2] * A(rows[atomid], columns[2]));
pAtom pa(new Atom(atomid+1, atom_name, c));
pa->resid(resid);
pa->resname(residue_name);
ostringstream segstream;
segstream << boost::format(segid_fmt) % chunk;
pa->segid(segstream.str());
double b;
double q = 0.0;
if (chunksize) {
b = (100.0 * (resid-1)) / chunksize;
q = static_cast<double>(chunk-1) / total_chunks;
} else
b = 100.0 * atomid / rows.size();
pa->bfactor(b);
pa->occupancy(q);
model.append(pa);
}
if (bonds) {
if (chunksize && resid > 1)
for (uint i=rows.size() - chunksize; i<rows.size()-1; ++i)
model[i]->addBond(model[i+1]);
else if (!chunksize)
for (uint i=0; i<rows.size()-1; ++i)
model[i]->addBond(model[i+1]);
}
PDB pdb = PDB::fromAtomicGroup(model);
pdb.remarks().add(hdr);
cout << pdb;
}
// Open the TypeServer referenced by *pts and initialize a TMTS from it.
// Set *ptm and return TRUE if successful, FALSE otherwise.
//
BOOL DBI1::fOpenTmts(lfTypeServer* pts, SZ_CONST szObjFile, TM** pptm)
{
#pragma message("TODO - DBCS")
*pptm = 0; // 0 means use 'to' PDB
char szPDBTo[_MAX_PATH];
ppdb1->QueryPDBName(szPDBTo);
if (_strnicmp(szPDBTo, (char*)(pts->name + 1), *(PB)pts->name) == 0) {
// PDB filenames match, reference to the 'to' PDB
return TRUE;
}
char szPDBFrom[_MAX_PATH];
strncpy(szPDBFrom, (char*)(pts->name + 1), *(PB)pts->name);
szPDBFrom[*(PB)pts->name] = 0;
if (pts->signature == ppdb1->QuerySignature() && pts->age <= ppdb1->QueryAge()) {
// PDB signature and age match; this 'from' PDB must contain equivalent
// information (even if it is a copy on some other path). However, we
// may have the highly unlikely case of distinct PDBs with equal
// signatures; to feel better about this case, we won't conclude
// equivalence unless the PDB base names also match. In practice this
// should be exactly conservative enough to avoid false positives and
// yet prevent accidental reopening of the 'to' PDB.
#pragma message("TODO: DBCS review")
char* pchBaseFrom = strrchr(szPDBFrom, '\\'); // REVIEW: international?
char* pchBaseTo = strrchr(szPDBTo, '\\');
if (_tcsicmp(pchBaseFrom, pchBaseTo) == 0) {
// even the base names match; reference to the 'to' PDB
return TRUE;
}
}
// Alas, probably a reference to a different type server. Open it.
EC ec;
char szError[cbErrMax];
PDB* ppdbFrom;
char szPathBuf[_MAX_PATH+_MAX_DRIVE];
char szFullPath[_MAX_PATH+_MAX_DRIVE];
_fullpath(szFullPath, szObjFile, _MAX_PATH+_MAX_DRIVE);
_splitpath(szFullPath, szPathBuf, szPathBuf + _MAX_DRIVE, NULL, NULL);
SZ szPath;
if (szPathBuf[0] == 0) {
// no drive spec - set up path without it
szPath = szPathBuf + _MAX_DRIVE;
}
else {
// concatenate drive and dir to form full path
szPathBuf[2] = szPathBuf[1];
szPathBuf[1] = szPathBuf[0];
szPath = szPathBuf + 1;
}
if (!PDB::OpenValidate(szPDBFrom, szPath, ppdb1->fFullBuild ? (pdbRead pdbGetRecordsOnly pdbFullBuild) :(pdbRead pdbGetRecordsOnly),
pts->signature, pts->age, &ec, szError, &ppdbFrom)) {
ppdb1->setLastError(ec, szError);
return FALSE;
}
// Check again that the PDB we found along the lib path is the same as the
// target PDB.
ppdbFrom->QueryPDBName(szPDBFrom);
if (_tcsicmp(szPDBTo, szPDBFrom) == 0) {
// PDB filenames match, reference to the 'to' PDB
ppdbFrom->Close();
return TRUE;
}
// Create and initialize the TMTS.
TMTS* ptmts = new TMTS(ppdb1, this, ppdb1->ptpi1);
if (!ptmts) {
ppdb1->setOOMError();
return FALSE;
}
if (!ptmts->fInit(ppdbFrom))
return FALSE;
*pptm = ptmts;
return TRUE;
}
void MolDataClass::specialSymbol( const std::string& type, const std::string& symbol, const PDB& mypdb, std::vector<AtomNumber>& numbers ){
if( type=="protein" ){
if( symbol.find("phi")!=std::string::npos ){
std::size_t dash=symbol.find_first_of('-');
unsigned resnum; Tools::convert( symbol.substr(dash+1), resnum );
std::string resname = mypdb.getResidueName(resnum);
if( !allowedResidue( type, resname ) || isTerminalGroup( type, resname ) ) return ;
numbers.resize(4);
numbers[0]=mypdb.getNamedAtomFromResidue("C",resnum-1);
numbers[1]=mypdb.getNamedAtomFromResidue("N",resnum);
numbers[2]=mypdb.getNamedAtomFromResidue("CA",resnum);
numbers[3]=mypdb.getNamedAtomFromResidue("C",resnum);
} else if( symbol.find("psi")!=std::string::npos ){
std::size_t dash=symbol.find_first_of('-');
unsigned resnum; Tools::convert( symbol.substr(dash+1), resnum );
std::string resname = mypdb.getResidueName(resnum);
if( !allowedResidue( type, resname ) || isTerminalGroup( type, resname ) ) return ;
numbers.resize(4);
numbers[0]=mypdb.getNamedAtomFromResidue("N",resnum);
numbers[1]=mypdb.getNamedAtomFromResidue("CA",resnum);
numbers[2]=mypdb.getNamedAtomFromResidue("C",resnum);
numbers[3]=mypdb.getNamedAtomFromResidue("N",resnum+1);
} else if( symbol.find("omega")!=std::string::npos ){
std::size_t dash=symbol.find_first_of('-');
unsigned resnum; Tools::convert( symbol.substr(dash+1), resnum );
std::string resname = mypdb.getResidueName(resnum);
if( !allowedResidue( type, resname ) || isTerminalGroup( type, resname ) ) return ;
numbers.resize(4);
numbers[0]=mypdb.getNamedAtomFromResidue("CA",resnum);
numbers[1]=mypdb.getNamedAtomFromResidue("C",resnum);
numbers[2]=mypdb.getNamedAtomFromResidue("N",resnum+1);
numbers[3]=mypdb.getNamedAtomFromResidue("CA",resnum+1);
}
} else {
plumed_merror(type + " is not a valid molecule type");
}
}
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() );
}
Mapping::Mapping(const ActionOptions&ao):
Action(ao),
ActionAtomistic(ao),
ActionWithArguments(ao),
ActionWithValue(ao),
ActionWithVessel(ao)
{
// Read the input
std::string mtype; parse("TYPE",mtype);
bool skipchecks; parseFlag("DISABLE_CHECKS",skipchecks);
// Setup the object that does the mapping
mymap = new PointWiseMapping( mtype, skipchecks );
// Read the properties we require
if( keywords.exists("PROPERTY") ){
std::vector<std::string> property;
parseVector("PROPERTY",property);
if(property.size()==0) error("no properties were specified");
mymap->setPropertyNames( property, false );
} else {
std::vector<std::string> property(1);
property[0]="sss";
mymap->setPropertyNames( property, true );
}
// Open reference file
std::string reference; parse("REFERENCE",reference);
FILE* fp=fopen(reference.c_str(),"r");
if(!fp) error("could not open reference file " + reference );
// Read all reference configurations
bool do_read=true; std::vector<double> weights;
unsigned nfram=0, wnorm=0., ww;
while (do_read){
PDB mypdb;
// Read the pdb file
do_read=mypdb.readFromFilepointer(fp,plumed.getAtoms().usingNaturalUnits(),0.1/atoms.getUnits().getLength());
// Fix argument names
expandArgKeywordInPDB( mypdb );
if(do_read){
mymap->readFrame( mypdb ); ww=mymap->getWeight( nfram );
weights.push_back( ww );
wnorm+=ww; nfram++;
} else {
break;
}
}
fclose(fp);
if(nfram==0 ) error("no reference configurations were specified");
log.printf(" found %d configurations in file %s\n",nfram,reference.c_str() );
for(unsigned i=0;i<weights.size();++i) weights[i] /= wnorm;
mymap->setWeights( weights );
// Finish the setup of the mapping object
// Get the arguments and atoms that are required
std::vector<AtomNumber> atoms; std::vector<std::string> args;
mymap->getAtomAndArgumentRequirements( atoms, args );
requestAtoms( atoms ); std::vector<Value*> req_args;
interpretArgumentList( args, req_args ); requestArguments( req_args );
// Duplicate all frames (duplicates are used by sketch-map)
mymap->duplicateFrameList();
fframes.resize( 2*nfram, 0.0 ); dfframes.resize( 2*nfram, 0.0 );
plumed_assert( !mymap->mappingNeedsSetup() );
// Resize all derivative arrays
mymap->setNumberOfAtomsAndArguments( atoms.size(), args.size() );
// Resize forces array
if( getNumberOfAtoms()>0 ){
forcesToApply.resize( 3*getNumberOfAtoms() + 9 + getNumberOfArguments() );
} else {
forcesToApply.resize( getNumberOfArguments() );
}
}
