// Iterate from an initial state
void DynSysModel::Iterate( NTuple& initial_state, size_t length, TimeSeries& result )
{
// Make sure the result is empty
result.clear();
// Save the initial state as the first time series entry
result.push_back( initial_state );
mState = initial_state;
NTuple next_state;
PolyModelIter iter;
size_t i,k;
for( i = length-1; i > 0; --i )
{
k = 1;
// For each polynomial;
next_state.Reset();
iter = mModel.begin();
while( iter != mModel.end() )
{
// Evaluate the k'th polynomial at the current state
// to produce a new value for the k'th variable
next_state.Assign( k, mModel[k-1].Evaluate( mState ) );
// next polynomial
++iter; ++k;
}
// Update the current state to be the newly compute state
mState = next_state;
result.push_back( next_state );
}
}
// Iterate only the k'th variable with respect to the given reference time series
size_t DynSysModel::Iterate( TimeSeries& ref_series, size_t k, TimeSeries& result, size_t kov )
{
// Make sure the result is empty
result.clear();
// Hamming distance for bit k
size_t h = 0;
TimeSeriesIter t_iter = ref_series.begin();
// Empty series in => empty series out
if( t_iter == ref_series.end() ) return h;
// Save the initial state as the first state in the result
mState = *t_iter;
// Force the knockout variable to zero - no longer needed, corrected when file is read in
// if( kov != 0 ) mState.Reset(kov);
result.push_back( mState );
bool f;
while( true )
{
// Merge the next state from the time series with the function evaluation
// (a) increment iterator and check for end of time series
++t_iter;
if( t_iter == ref_series.end() ) break;
// Evaluate the k'th polynomial at the current state
// to produce a new value for the k'th variable for time i+1
f = mModel[k-1].Evaluate( mState );
// (b) assign value pointed to by iterator to mState (t[i+1])
mState = *t_iter;
// Force the knockout variable to zero - no longer needed, corrected when file is read in
// if( kov != 0 ) mState.Reset(kov);
// Accumulate Hamming Distance = t'[i+1][k] - t[i+1][k]
h += (mState[k] ^ f) ? 1 : 0;
// (c) create t'[i+1] = t[i+1] with k'th element replaced by f(t'[i])
mState.Assign( k, f );
// Save t'[i+1]
result.push_back( mState );
}
return h;
}
Datum blocker(const RealMatrix& Ua, const RealMatrix sa, const vGroup& ensemble, const uint blocksize, uint repeats, ExtractPolicy& policy) {
TimeSeries<double> coverlaps;
for (uint i=0; i<repeats; ++i) {
vector<uint> picks = pickFrames(ensemble.size(), blocksize);
if (debug) {
cerr << "***Block " << blocksize << ", replica " << i << ", picks " << picks.size() << endl;
dumpPicks(picks);
}
vGroup subset = subgroup(ensemble, picks);
boost::tuple<RealMatrix, RealMatrix> pca_result = pca(subset, policy);
RealMatrix s = boost::get<0>(pca_result);
RealMatrix U = boost::get<1>(pca_result);
if (length_normalize)
for (uint j=0; j<s.rows(); ++j)
s[j] /= blocksize;
coverlaps.push_back(covarianceOverlap(sa, Ua, s, U));
}
return( Datum(coverlaps.average(), coverlaps.variance(), coverlaps.size()) );
}
// Iterate from an initial state with the k'th function knocked out
void DynSysModel::KoIterate( NTuple& initial_state, size_t length, TimeSeries& result, size_t kov )
{
// Make sure the result is empty
result.clear();
// Force k'th entry to zero in the initial state - no longer needed, corrected when file is read in
// NTuple state1 = initial_state;
// state1.Reset( kov );
// Save the initial state as the first time series entry
result.push_back( initial_state );
mState = initial_state;
NTuple next_state;
PolyModelIter iter;
size_t i,k;
for( i = length-1; i > 0; --i )
{
k = 1;
// For each polynomial
next_state.Reset();
iter = mModel.begin();
while( iter != mModel.end() )
{
// Force the knockout function result to zero
if( k == kov )
{
next_state.Assign( k, 0 );
}
else
{
// Evaluate the k'th polynomial at the current state
// to produce a new value for the k'th variable
next_state.Assign( k, mModel[k-1].Evaluate( mState ) );
}
// next polynomial
++iter; ++k;
}
// Update the current state to be the newly compute state
mState = next_state;
result.push_back( next_state );
}
}
void BFFindMotif::FindMotifSub(std::deque<Point> &window)
{
size_t i = 0;
for(i = 0; i < window.size() - m_MotifLength; ++i)
{
double distance = 0.0;
bool newMotif = true;
TimeSeries ts;
ts.reserve(m_MotifLength);
if(m_SlideWindow.size() >= m_MotifLength) // Only process slide window larger than motif length
{
// Get time series
for(size_t j = i; j < i + m_MotifLength; ++j)
{
ts.push_back(window[j].second);
}
// Compare with candidate motif
for(size_t j = 0; j < m_CandidateMotif.size(); ++j)
{
distance = EuclideanDistance(m_CandidateMotif[j].second, ts);
if((2 * m_Radius > distance) && (m_Radius < distance)) // Neither new motif nor similar motif
{
newMotif = false;
}
else if(m_Radius > distance) // Similar motif
{
m_CandidateMotif[j].first++;
i += m_Step;
newMotif = false;
break; // Impossible to be similar with other candidates
}
}
if(true == newMotif) // New motif
{
m_CandidateMotif.push_back(make_pair<long long, TimeSeries>(1, ts));
i += m_Step;
}
}
else
{
cerr << "Window size:" << m_SlideWindow.size() << endl;
}
}
for(size_t k = 0; k < i; ++k)
{
window.pop_front();
}
}
void SIMMA:: FindMotifSub(long &bufferCount)
{
long lLastSize = m_K; // last size of candidate motif buffer
long step = 32;
size_t i = 0;
for(i = 0; i < m_SlideWindow.size() - m_MotifLength; ++i)
{
double distance = 0.0;
bool newMotif = true;
TimeSeries ts;
ts.reserve(m_MotifLength);
++bufferCount;
// Check buffer when size big enough
if(true == m_bBufferCheck)
{
if((2 * m_K < bufferCount) && (5 * m_K < (int)m_CandidateMotif.size()))
{
this->BufferCheck();
lLastSize = m_SlideWindow.size();
bufferCount = 0;
}
}
if(m_SlideWindow.size() >= m_MotifLength) // Only process slide window larger than motif length
{
// Get time series
for(size_t j = i; j < i + m_MotifLength; ++j)
{
ts.push_back(m_SlideWindow[j].second);
}
// Compare with candidate motif
for(size_t j = 0; j < m_CandidateMotif.size(); ++j)
{
distance = EuclideanDistance(m_CandidateMotif[j].second, ts);
if((2 * m_Radius > distance) && (m_Radius < distance)) // Neither new motif nor similar motif
{
newMotif = false;
}
else if(m_Radius > distance) // Similar motif
{
m_CandidateMotif[j].first++;
long jump = this->NonTrivialStep(i);
if(0 != jump)
i += jump;
else
i = m_SlideWindow.size() - m_MotifLength;
newMotif = false;
break; // Impossible to be similar with other candidates
}
}
// Check whether current time series is new motif
if(true == newMotif)
{
m_CandidateMotif.push_back(make_pair<long long, TimeSeries>(1, ts));
long jump = this->NonTrivialStep(i);
if(0 != jump)
i += jump;
else
i = m_SlideWindow.size() - m_MotifLength;
}
}
}
// Remove used elements
for(size_t k = 0; k < i; ++k)
{
m_SlideWindow.pop_front();
}
}
int main(int argc, char *argv[]) {
if (argc < 4 || argc > 6) {
cerr << "Usage- block_avgconv model traj sel [range [1 = do not align trajectory]]\n";
cerr << fullHelpMessage();
exit(-1);
}
string hdr = invocationHeader(argc, argv);
int k = 1;
AtomicGroup model = createSystem(argv[k++]);
pTraj traj = createTrajectory(argv[k++], model);
AtomicGroup subset = selectAtoms(model, argv[k++]);
vector<uint> sizes;
bool do_align = true;
if (argc == k) {
uint step = traj->nframes() / default_starting_number_of_blocks;
for (uint i=step; i<traj->nframes() * default_fraction_of_trajectory; i += step)
sizes.push_back(i);
} else {
sizes = parseRangeList<uint>(argv[k++]);
if (argc == k+1)
do_align = (argv[k][0] != '1');
}
cout << "# " << hdr << endl;
cout << "# n\tavg\tvar\tblocks\tstderr\n";
vector<AtomicGroup> ensemble;
cerr << "Reading trajectory...\n";
readTrajectory(ensemble, subset, traj);
if (do_align) {
cerr << "Aligning trajectory...\n";
boost::tuple<vector<XForm>, greal, int> result = iterativeAlignment(ensemble);
} else
cerr << "Trajectory is already aligned!\n";
cerr << "Processing- ";
for (uint block = 0; block < sizes.size(); ++block) {
if (block % 50)
cerr << ".";
uint blocksize = sizes[block];
vector<AtomicGroup> averages;
for (uint i=0; i<ensemble.size() - blocksize; i += blocksize) {
vector<uint> indices(blocksize);
for (uint j=0; j<blocksize; ++j)
indices[j] = i+j;
averages.push_back(averageSelectedSubset(ensemble, indices));
}
TimeSeries<double> rmsds;
for (uint j=0; j<averages.size() - 1; ++j)
for (uint i=j+1; i<averages.size(); ++i) {
AtomicGroup left = averages[j];
AtomicGroup right = averages[i];
left.alignOnto(right);
rmsds.push_back(left.rmsd(right));
}
double v = rmsds.variance();
uint n = averages.size();
cout << boost::format("%d\t%f\t%f\t%d\t%f\n") % blocksize % rmsds.average() % v % n % sqrt(v/n);
}
cerr << "\nDone!\n";
}