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 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");
}
}
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;
}