PDBResidue *PDBChain::
FindResidue(const char *residue_name, int residue_sequence, int residue_insertion_code) const
{
// Check all residues
for (int i = 0; i < NResidues(); i++) {
PDBResidue *residue = Residue(i);
if ((residue_sequence == residue->Sequence()) &&
(residue_insertion_code == residue->InsertionCode()) &&
(!strcmp(residue_name, residue->Name()))) {
return residue;
}
}
return NULL;
}
Residue get_residue(Atom d, bool nothrow) {
Hierarchy mhd(d.get_particle());
do {
mhd= mhd.get_parent();
if (mhd== Hierarchy()) {
if (nothrow) return Residue();
else {
IMP_THROW("Atom is not the child of a residue " << d,
ValueException);
}
}
} while (!Residue::particle_is_instance(mhd.get_particle()));
Residue rd(mhd.get_particle());
return rd;
}
fasta::Residue fasta::make_residue(const std::string& codon) {
std::vector<std::string> features;
if (codon.size() >= 5 && codon[4] != 'A') {
features.push_back(ptm_code_map.at(codon[4]));
}
if (codon.size() > 1
&& strct_code_map.find(codon[1]) != strct_code_map.end()) {
features.push_back(strct_code_map.at(codon[1]));
}
if (codon.size() >= 7 && codon.substr(5, 2) != "AA") {
features.push_back("m_" + codon.substr(5, 2));
}
if (codon.size() >= 4 && codon.substr(2, 2) != "AA") {
features.push_back("d_" + codon.substr(2, 2));
}
return Residue(codon, features);
}
CHARMMTopology *CHARMMParameters::create_topology(Hierarchy hierarchy) const {
IMP_OBJECT_LOG;
IMP_NEW(CHARMMTopology, topology, (this));
Hierarchies chains = get_by_type(hierarchy, CHAIN_TYPE);
for (Hierarchies::iterator chainit = chains.begin(); chainit != chains.end();
++chainit) {
IMP_NEW(CHARMMSegmentTopology, segment, ());
Hierarchies residues = get_by_type(*chainit, RESIDUE_TYPE);
for (Hierarchies::iterator resit = residues.begin();
resit != residues.end(); ++resit) {
ResidueType restyp = Residue(*resit).get_residue_type();
try {
IMP_NEW(CHARMMResidueTopology, residue, (get_residue_topology(restyp)));
segment->add_residue(residue);
}
catch (base::ValueException) {
// If residue type is unknown, add empty topology for this residue
IMP_WARN_ONCE(
restyp.get_string(),
"Residue type "
<< restyp
<< " was not found in "
"topology library; using empty topology for this residue",
warn_context_);
IMP_NEW(CHARMMResidueTopology, residue, (restyp));
segment->add_residue(residue);
}
}
topology->add_segment(segment);
}
// keep clang happy
bool dumped = false;
IMP_IF_LOG(VERBOSE) {
dumped = true;
warn_context_.dump_warnings();
}
if (!dumped) {
warn_context_.clear_warnings();
}
// Topology objects are not designed to be added into other containers
topology->set_was_used(true);
return topology.release();
}
// Analysis_Hist::Analyze()
Analysis::RetType Analysis_Hist::Analyze() {
// Set up dimensions
// Size of histdata and dimensionArgs should be the same
size_t total_bins = 0UL;
for (unsigned int hd = 0; hd < N_dimensions_; hd++) {
if ( setupDimension(dimensionArgs_[hd], *(histdata_[hd]), total_bins) )
return Analysis::ERR;
}
// dimensionArgs no longer needed
dimensionArgs_.clear();
// Check that the number of data points in each dimension are equal
std::vector<DataSet_1D*>::iterator ds = histdata_.begin();
size_t Ndata = (*ds)->Size();
++ds;
for (; ds != histdata_.end(); ++ds)
{
//mprintf("DEBUG: DS %s size %i\n",histdata[hd]->Name(),histdata[hd]->Xmax()+1);
if (Ndata != (*ds)->Size()) {
mprinterr("Error: Hist: Dataset %s has inconsistent # data points (%zu), expected %zu.\n",
(*ds)->legend(), (*ds)->Size(), Ndata);
return Analysis::ERR;
}
}
mprintf("\tHist: %zu data points in each dimension.\n", Ndata);
if (calcAMD_ && Ndata != amddata_->Size()) {
mprinterr("Error: Hist: AMD data set size (%zu) does not match # expected data points (%zu).\n",
amddata_->Size(), Ndata);
return Analysis::ERR;
}
// Allocate bins
mprintf("\tHist: Allocating histogram, total bins = %zu\n", total_bins);
Bins_.resize( total_bins, 0.0 );
// Bin data
for (size_t n = 0; n < Ndata; n++) {
long int index = 0;
HdimType::const_iterator dim = dimensions_.begin();
OffType::const_iterator bOff = binOffsets_.begin();
for (std::vector<DataSet_1D*>::iterator ds = histdata_.begin();
ds != histdata_.end(); ++ds, ++dim, ++bOff)
{
double dval = (*ds)->Dval( n );
// Check if data is out of bounds for this dimension.
if (dval > dim->Max() || dval < dim->Min()) {
index = -1L;
break;
}
// Calculate index for this particular dimension (idx)
long int idx = (long int)((dval - dim->Min()) / dim->Step());
if (debug_>1) mprintf(" [%s:%f (%li)],", dim->label(), dval, idx);
// Calculate overall index in Bins, offset has already been calcd.
index += (idx * (*bOff));
}
// If index was successfully calculated, populate bin
if (index > -1L && index < (long int)Bins_.size()) {
if (debug_ > 1) mprintf(" |index=%li",index);
if (calcAMD_)
Bins_[index] += exp( amddata_->Dval(n) );
else
Bins_[index]++;
} else {
mprintf("\tWarning: Frame %zu Coordinates out of bounds (%li)\n", n+1, index);
}
if (debug_>1) mprintf("}\n");
}
// Calc free energy if requested
if (calcFreeE_) CalcFreeE();
// Normalize if requested
if (normalize_ != NO_NORM) Normalize();
if (nativeOut_) {
// Use Histogram built-in output
PrintBins();
} else {
// Using DataFileList framework, set-up labels etc.
if (N_dimensions_ == 1) {
DataSet_double& dds = static_cast<DataSet_double&>( *hist_ );
// Since Allocate1D only reserves data, use assignment op.
dds = Bins_;
hist_->SetDim(Dimension::X, dimensions_[0]);
} else if (N_dimensions_ == 2) {
DataSet_MatrixDbl& mds = static_cast<DataSet_MatrixDbl&>( *hist_ );
mds.Allocate2D( dimensions_[0].Bins(), dimensions_[1].Bins() );
std::copy( Bins_.begin(), Bins_.end(), mds.begin() );
hist_->SetDim(Dimension::X, dimensions_[0]);
hist_->SetDim(Dimension::Y, dimensions_[1]);
outfile_->ProcessArgs("noxcol usemap nolabels");
} else if (N_dimensions_ == 3) {
DataSet_GridFlt& gds = static_cast<DataSet_GridFlt&>( *hist_ );
//gds.Allocate3D( dimensions_[0].Bins(), dimensions_[1].Bins(), dimensions_[2].Bins() );
gds.Allocate_N_O_D( dimensions_[0].Bins(), dimensions_[1].Bins(), dimensions_[2].Bins(),
Vec3(dimensions_[0].Min(), dimensions_[1].Min(), dimensions_[2].Min()),
Vec3(dimensions_[0].Step(), dimensions_[1].Step(), dimensions_[2].Step())
);
//std::copy( Bins_.begin(), Bins_.end(), gds.begin() );
// FIXME: Copy will not work since in grids data is ordered with Z
// changing fastest. Should the ordering in grid be changed?
size_t idx = 0;
for (size_t z = 0; z < gds.NZ(); z++)
for (size_t y = 0; y < gds.NY(); y++)
for (size_t x = 0; x < gds.NX(); x++)
gds.SetElement( x, y, z, (float)Bins_[idx++] );
hist_->SetDim(Dimension::X, dimensions_[0]);
hist_->SetDim(Dimension::Y, dimensions_[1]);
hist_->SetDim(Dimension::Z, dimensions_[2]);
outfile_->ProcessArgs("noxcol usemap nolabels");
// Create pseudo-topology/trajectory
if (!traj3dName_.empty()) {
Topology pseudo;
pseudo.AddTopAtom(Atom("H3D", 0), Residue("H3D", 1, ' ', ' '));
pseudo.CommonSetup();
if (!parmoutName_.empty()) {
ParmFile pfile;
if (pfile.WriteTopology( pseudo, parmoutName_, ParmFile::UNKNOWN_PARM, 0 ))
mprinterr("Error: Could not write pseudo topology to '%s'\n", parmoutName_.c_str());
}
Trajout_Single out;
if (out.PrepareTrajWrite(traj3dName_, ArgList(), &pseudo, CoordinateInfo(),
Ndata, traj3dFmt_) == 0)
{
Frame outFrame(1);
for (size_t i = 0; i < Ndata; ++i) {
outFrame.ClearAtoms();
outFrame.AddVec3( Vec3(histdata_[0]->Dval(i),
histdata_[1]->Dval(i),
histdata_[2]->Dval(i)) );
out.WriteSingle(i, outFrame);
}
out.EndTraj();
} else
mprinterr("Error: Could not set up '%s' for write.\n", traj3dName_.c_str());
}
}
}
return Analysis::OK;
}
void Coder_ld8h(
Word16 ana[], /* (o) : analysis parameters */
Word16 rate /* input : rate selector/frame =0 6.4kbps , =1 8kbps,= 2 11.8 kbps*/
)
{
/* LPC analysis */
Word16 r_l_fwd[MP1], r_h_fwd[MP1]; /* Autocorrelations low and hi (forward) */
Word32 r_bwd[M_BWDP1]; /* Autocorrelations (backward) */
Word16 r_l_bwd[M_BWDP1]; /* Autocorrelations low (backward) */
Word16 r_h_bwd[M_BWDP1]; /* Autocorrelations high (backward) */
Word16 rc_fwd[M]; /* Reflection coefficients : forward analysis */
Word16 rc_bwd[M_BWD]; /* Reflection coefficients : backward analysis */
Word16 A_t_fwd[MP1*2]; /* A(z) forward unquantized for the 2 subframes */
Word16 A_t_fwd_q[MP1*2]; /* A(z) forward quantized for the 2 subframes */
Word16 A_t_bwd[2*M_BWDP1]; /* A(z) backward for the 2 subframes */
Word16 *Aq; /* A(z) "quantized" for the 2 subframes */
Word16 *Ap; /* A(z) "unquantized" for the 2 subframes */
Word16 *pAp, *pAq;
Word16 Ap1[M_BWDP1]; /* A(z) with spectral expansion */
Word16 Ap2[M_BWDP1]; /* A(z) with spectral expansion */
Word16 lsp_new[M], lsp_new_q[M]; /* LSPs at 2th subframe */
Word16 lsf_int[M]; /* Interpolated LSF 1st subframe. */
Word16 lsf_new[M];
Word16 lp_mode; /* Backward / Forward Indication mode */
Word16 m_ap, m_aq, i_gamma;
Word16 code_lsp[2];
/* Other vectors */
Word16 h1[L_SUBFR]; /* Impulse response h1[] */
Word16 xn[L_SUBFR]; /* Target vector for pitch search */
Word16 xn2[L_SUBFR]; /* Target vector for codebook search */
Word16 code[L_SUBFR]; /* Fixed codebook excitation */
Word16 y1[L_SUBFR]; /* Filtered adaptive excitation */
Word16 y2[L_SUBFR]; /* Filtered fixed codebook excitation */
Word16 g_coeff[4]; /* Correlations between xn & y1 */
Word16 res2[L_SUBFR]; /* residual after long term prediction*/
Word16 g_coeff_cs[5];
Word16 exp_g_coeff_cs[5]; /* Correlations between xn, y1, & y2
<y1,y1>, -2<xn,y1>,
<y2,y2>, -2<xn,y2>, 2<y1,y2> */
/* Scalars */
Word16 i, j, k, i_subfr;
Word16 T_op, T0, T0_min, T0_max, T0_frac;
Word16 gain_pit, gain_code, index;
Word16 taming, pit_sharp;
Word16 sat_filter;
Word32 L_temp;
Word16 freq_cur[M];
Word16 temp;
/*------------------------------------------------------------------------*
* - Perform LPC analysis: *
* * autocorrelation + lag windowing *
* * Levinson-durbin algorithm to find a[] *
* * convert a[] to lsp[] *
* * quantize and code the LSPs *
* * find the interpolated LSPs and convert to a[] for the 2 *
* subframes (both quantized and unquantized) *
*------------------------------------------------------------------------*/
/* ------------------- */
/* LP Forward analysis */
/* ------------------- */
Autocorr(p_window, M, r_h_fwd, r_l_fwd); /* Autocorrelations */
Lag_window(M, r_h_fwd, r_l_fwd); /* Lag windowing */
Levinsone(M, r_h_fwd, r_l_fwd, &A_t_fwd[MP1], rc_fwd, old_A_fwd, old_rc_fwd); /* Levinson Durbin */
Az_lsp(&A_t_fwd[MP1], lsp_new, lsp_old); /* From A(z) to lsp */
/* -------------------- */
/* LP Backward analysis */
/* -------------------- */
/* -------------------- */
/* LP Backward analysis */
/* -------------------- */
if ( rate== G729E) {
/* LPC recursive Window as in G728 */
autocorr_hyb_window(synth, r_bwd, rexp); /* Autocorrelations */
Lag_window_bwd(r_bwd, r_h_bwd, r_l_bwd); /* Lag windowing */
/* Fixed Point Levinson (as in G729) */
Levinsone(M_BWD, r_h_bwd, r_l_bwd, &A_t_bwd[M_BWDP1], rc_bwd,
old_A_bwd, old_rc_bwd);
/* Tests saturation of A_t_bwd */
sat_filter = 0;
for (i=M_BWDP1; i<2*M_BWDP1; i++) if (A_t_bwd[i] >= 32767) sat_filter = 1;
if (sat_filter == 1) Copy(A_t_bwd_mem, &A_t_bwd[M_BWDP1], M_BWDP1);
else Copy(&A_t_bwd[M_BWDP1], A_t_bwd_mem, M_BWDP1);
/* Additional bandwidth expansion on backward filter */
Weight_Az(&A_t_bwd[M_BWDP1], GAMMA_BWD, M_BWD, &A_t_bwd[M_BWDP1]);
}
/*--------------------------------------------------*
* Update synthesis signal for next frame. *
*--------------------------------------------------*/
Copy(&synth[L_FRAME], &synth[0], MEM_SYN_BWD);
/*--------------------------------------------------------------------*
* Find interpolated LPC parameters in all subframes (unquantized). *
* The interpolated parameters are in array A_t[] of size (M+1)*4 *
*--------------------------------------------------------------------*/
if( prev_lp_mode == 0) {
Int_lpc(lsp_old, lsp_new, lsf_int, lsf_new, A_t_fwd);
}
else {
/* no interpolation */
/* unquantized */
Lsp_Az(lsp_new, A_t_fwd); /* Subframe 1 */
Lsp_lsf(lsp_new, lsf_new, M); /* transformation from LSP to LSF (freq.domain) */
Copy(lsf_new, lsf_int, M); /* Subframe 1 */
}
/* ---------------- */
/* LSP quantization */
/* ---------------- */
Qua_lspe(lsp_new, lsp_new_q, code_lsp, freq_prev, freq_cur);
/*--------------------------------------------------------------------*
* Find interpolated LPC parameters in all subframes (quantized) *
* the quantized interpolated parameters are in array Aq_t[] *
*--------------------------------------------------------------------*/
if( prev_lp_mode == 0) {
Int_qlpc(lsp_old_q, lsp_new_q, A_t_fwd_q);
}
else {
/* no interpolation */
Lsp_Az(lsp_new_q, &A_t_fwd_q[MP1]); /* Subframe 2 */
Copy(&A_t_fwd_q[MP1], A_t_fwd_q, MP1); /* Subframe 1 */
}
/*---------------------------------------------------------------------*
* - Decision for the switch Forward / Backward *
*---------------------------------------------------------------------*/
if(rate == G729E) {
set_lpc_modeg(speech, A_t_fwd_q, A_t_bwd, &lp_mode,
lsp_new, lsp_old, &bwd_dominant, prev_lp_mode, prev_filter,
&C_int, &glob_stat, &stat_bwd, &val_stat_bwd);
}
else {
update_bwd( &lp_mode, &bwd_dominant, &C_int, &glob_stat);
}
/* ---------------------------------- */
/* update the LSPs for the next frame */
/* ---------------------------------- */
Copy(lsp_new, lsp_old, M);
/*----------------------------------------------------------------------*
* - Find the weighted input speech w_sp[] for the whole speech frame *
*----------------------------------------------------------------------*/
if(lp_mode == 0) {
m_ap = M;
if (bwd_dominant == 0) Ap = A_t_fwd;
else Ap = A_t_fwd_q;
perc_var(gamma1, gamma2, lsf_int, lsf_new, rc_fwd);
}
else {
if (bwd_dominant == 0) {
m_ap = M;
Ap = A_t_fwd;
}
else {
m_ap = M_BWD;
Ap = A_t_bwd;
}
perc_vare(gamma1, gamma2, bwd_dominant);
}
pAp = Ap;
for (i=0; i<2; i++) {
Weight_Az(pAp, gamma1[i], m_ap, Ap1);
Weight_Az(pAp, gamma2[i], m_ap, Ap2);
Residue(m_ap, Ap1, &speech[i*L_SUBFR], &wsp[i*L_SUBFR], L_SUBFR);
Syn_filte(m_ap, Ap2, &wsp[i*L_SUBFR], &wsp[i*L_SUBFR], L_SUBFR,
&mem_w[M_BWD-m_ap], 0);
for(j=0; j<M_BWD; j++) mem_w[j] = wsp[i*L_SUBFR+L_SUBFR-M_BWD+j];
pAp += m_ap+1;
}
*ana++ = rate+ (Word16)2; /* bit rate mode */
if(lp_mode == 0) {
m_aq = M;
Aq = A_t_fwd_q;
/* update previous filter for next frame */
Copy(&Aq[MP1], prev_filter, MP1);
for(i=MP1; i <M_BWDP1; i++) prev_filter[i] = 0;
for(j=MP1; j<M_BWDP1; j++) ai_zero[j] = 0;
}
else {
m_aq = M_BWD;
Aq = A_t_bwd;
if (bwd_dominant == 0) {
for(j=MP1; j<M_BWDP1; j++) ai_zero[j] = 0;
}
/* update previous filter for next frame */
Copy(&Aq[M_BWDP1], prev_filter, M_BWDP1);
}
if (rate == G729E) *ana++ = lp_mode;
/*----------------------------------------------------------------------*
* - Find the weighted input speech w_sp[] for the whole speech frame *
* - Find the open-loop pitch delay *
*----------------------------------------------------------------------*/
if( lp_mode == 0) {
Copy(lsp_new_q, lsp_old_q, M);
Lsp_prev_update(freq_cur, freq_prev);
*ana++ = code_lsp[0];
*ana++ = code_lsp[1];
}
/* Find open loop pitch lag */
T_op = Pitch_ol(wsp, PIT_MIN, PIT_MAX, L_FRAME);
/* Range for closed loop pitch search in 1st subframe */
T0_min = sub(T_op, 3);
if (sub(T0_min,PIT_MIN)<0) {
T0_min = PIT_MIN;
}
T0_max = add(T0_min, 6);
if (sub(T0_max ,PIT_MAX)>0)
{
T0_max = PIT_MAX;
T0_min = sub(T0_max, 6);
}
/*------------------------------------------------------------------------*
* Loop for every subframe in the analysis frame *
*------------------------------------------------------------------------*
* To find the pitch and innovation parameters. The subframe size is *
* L_SUBFR and the loop is repeated 2 times. *
* - find the weighted LPC coefficients *
* - find the LPC residual signal res[] *
* - compute the target signal for pitch search *
* - compute impulse response of weighted synthesis filter (h1[]) *
* - find the closed-loop pitch parameters *
* - encode the pitch delay *
* - update the impulse response h1[] by including fixed-gain pitch *
* - find target vector for codebook search *
* - codebook search *
* - encode codebook address *
* - VQ of pitch and codebook gains *
* - find synthesis speech *
* - update states of weighting filter *
*------------------------------------------------------------------------*/
pAp = Ap; /* pointer to interpolated "unquantized"LPC parameters */
pAq = Aq; /* pointer to interpolated "quantized" LPC parameters */
i_gamma = 0;
for (i_subfr = 0; i_subfr < L_FRAME; i_subfr += L_SUBFR) {
/*---------------------------------------------------------------*
* Find the weighted LPC coefficients for the weighting filter. *
*---------------------------------------------------------------*/
Weight_Az(pAp, gamma1[i_gamma], m_ap, Ap1);
Weight_Az(pAp, gamma2[i_gamma], m_ap, Ap2);
/*---------------------------------------------------------------*
* Compute impulse response, h1[], of weighted synthesis filter *
*---------------------------------------------------------------*/
for (i = 0; i <=m_ap; i++) ai_zero[i] = Ap1[i];
Syn_filte(m_aq, pAq, ai_zero, h1, L_SUBFR, zero, 0);
Syn_filte(m_ap, Ap2, h1, h1, L_SUBFR, zero, 0);
/*------------------------------------------------------------------------*
* *
* Find the target vector for pitch search: *
* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ *
* *
* |------| res[n] *
* speech[n]---| A(z) |-------- *
* |------| | |--------| error[n] |------| *
* zero -- (-)--| 1/A(z) |-----------| W(z) |-- target *
* exc |--------| |------| *
* *
* Instead of subtracting the zero-input response of filters from *
* the weighted input speech, the above configuration is used to *
* compute the target vector. This configuration gives better performance *
* with fixed-point implementation. The memory of 1/A(z) is updated by *
* filtering (res[n]-exc[n]) through 1/A(z), or simply by subtracting *
* the synthesis speech from the input speech: *
* error[n] = speech[n] - syn[n]. *
* The memory of W(z) is updated by filtering error[n] through W(z), *
* or more simply by subtracting the filtered adaptive and fixed *
* codebook excitations from the target: *
* target[n] - gain_pit*y1[n] - gain_code*y2[n] *
* as these signals are already available. *
* *
*------------------------------------------------------------------------*/
Residue(m_aq, pAq, &speech[i_subfr], &exc[i_subfr], L_SUBFR); /* LPC residual */
for (i=0; i<L_SUBFR; i++) res2[i] = exc[i_subfr+i];
Syn_filte(m_aq, pAq, &exc[i_subfr], error, L_SUBFR,
&mem_err[M_BWD-m_aq], 0);
Residue(m_ap, Ap1, error, xn, L_SUBFR);
Syn_filte(m_ap, Ap2, xn, xn, L_SUBFR, &mem_w0[M_BWD-m_ap], 0); /* target signal xn[]*/
/*----------------------------------------------------------------------*
* Closed-loop fractional pitch search *
*----------------------------------------------------------------------*/
T0 = Pitch_fr3cp(&exc[i_subfr], xn, h1, L_SUBFR, T0_min, T0_max,
i_subfr, &T0_frac, rate);
index = Enc_lag3cp(T0, T0_frac, &T0_min, &T0_max,PIT_MIN,PIT_MAX,
i_subfr, rate);
*ana++ = index;
if ( (i_subfr == 0) && (rate != G729D) ) {
*ana = Parity_Pitch(index);
if( rate == G729E) {
*ana ^= (shr(index, 1) & 0x0001);
}
ana++;
}
/*-----------------------------------------------------------------*
* - find unity gain pitch excitation (adaptive codebook entry) *
* with fractional interpolation. *
* - find filtered pitch exc. y1[]=exc[] convolve with h1[]) *
* - compute pitch gain and limit between 0 and 1.2 *
* - update target vector for codebook search *
* - find LTP residual. *
*-----------------------------------------------------------------*/
Pred_lt_3(&exc[i_subfr], T0, T0_frac, L_SUBFR);
Convolve(&exc[i_subfr], h1, y1, L_SUBFR);
gain_pit = G_pitch(xn, y1, g_coeff, L_SUBFR);
/* clip pitch gain if taming is necessary */
taming = test_err(T0, T0_frac);
if( taming == 1){
if (sub(gain_pit, GPCLIP) > 0) {
gain_pit = GPCLIP;
}
}
/* xn2[i] = xn[i] - y1[i] * gain_pit */
for (i = 0; i < L_SUBFR; i++) {
L_temp = L_mult(y1[i], gain_pit);
L_temp = L_shl(L_temp, 1); /* gain_pit in Q14 */
xn2[i] = sub(xn[i], extract_h(L_temp));
}
/*-----------------------------------------------------*
* - Innovative codebook search. *
*-----------------------------------------------------*/
switch (rate) {
case G729: /* 8 kbit/s */
{
/* case 8 kbit/s */
index = ACELP_Codebook(xn2, h1, T0, sharp, i_subfr, code, y2, &i);
*ana++ = index; /* Positions index */
*ana++ = i; /* Signs index */
break;
}
case G729D: /* 6.4 kbit/s */
{
index = ACELP_CodebookD(xn2, h1, T0, sharp, code, y2, &i);
*ana++ = index; /* Positions index */
*ana++ = i; /* Signs index */
break;
}
case G729E: /* 11.8 kbit/s */
{
/*-----------------------------------------------------------------*
* Include fixed-gain pitch contribution into impulse resp. h[] *
*-----------------------------------------------------------------*/
pit_sharp = shl(sharp, 1); /* From Q14 to Q15 */
if(T0 < L_SUBFR) {
for (i = T0; i < L_SUBFR; i++){ /* h[i] += pitch_sharp*h[i-T0] */
h1[i] = add(h1[i], mult(h1[i-T0], pit_sharp));
}
}
/* calculate residual after long term prediction */
/* res2[i] -= exc[i+i_subfr] * gain_pit */
for (i = 0; i < L_SUBFR; i++) {
L_temp = L_mult(exc[i+i_subfr], gain_pit);
L_temp = L_shl(L_temp, 1); /* gain_pit in Q14 */
res2[i] = sub(res2[i], extract_h(L_temp));
}
if (lp_mode == 0) ACELP_10i40_35bits(xn2, res2, h1, code, y2, ana); /* Forward */
else ACELP_12i40_44bits(xn2, res2, h1, code, y2, ana); /* Backward */
ana += 5;
/*-----------------------------------------------------------------*
* Include fixed-gain pitch contribution into code[]. *
*-----------------------------------------------------------------*/
if(T0 < L_SUBFR) {
for (i = T0; i < L_SUBFR; i++) { /* code[i] += pitch_sharp*code[i-T0] */
code[i] = add(code[i], mult(code[i-T0], pit_sharp));
}
}
break;
}
default : {
printf("Unrecognized bit rate\n");
exit(-1);
}
} /* end of switch */
/*-----------------------------------------------------*
* - Quantization of gains. *
*-----------------------------------------------------*/
g_coeff_cs[0] = g_coeff[0]; /* <y1,y1> */
exp_g_coeff_cs[0] = negate(g_coeff[1]); /* Q-Format:XXX -> JPN */
g_coeff_cs[1] = negate(g_coeff[2]); /* (xn,y1) -> -2<xn,y1> */
exp_g_coeff_cs[1] = negate(add(g_coeff[3], 1)); /* Q-Format:XXX -> JPN */
Corr_xy2( xn, y1, y2, g_coeff_cs, exp_g_coeff_cs ); /* Q0 Q0 Q12 ^Qx ^Q0 */
/* g_coeff_cs[3]:exp_g_coeff_cs[3] = <y2,y2> */
/* g_coeff_cs[4]:exp_g_coeff_cs[4] = -2<xn,y2> */
/* g_coeff_cs[5]:exp_g_coeff_cs[5] = 2<y1,y2> */
if (rate == G729D)
index = Qua_gain_6k(code, g_coeff_cs, exp_g_coeff_cs, L_SUBFR,
&gain_pit, &gain_code, taming, past_qua_en);
else
index = Qua_gain_8k(code, g_coeff_cs, exp_g_coeff_cs, L_SUBFR,
&gain_pit, &gain_code, taming, past_qua_en);
*ana++ = index;
/*------------------------------------------------------------*
* - Update pitch sharpening "sharp" with quantized gain_pit *
*------------------------------------------------------------*/
sharp = gain_pit;
if (sub(sharp, SHARPMAX) > 0) sharp = SHARPMAX;
else {
if (sub(sharp, SHARPMIN) < 0) sharp = SHARPMIN;
}
/*------------------------------------------------------*
* - Find the total excitation *
* - find synthesis speech corresponding to exc[] *
* - update filters memories for finding the target *
* vector in the next subframe *
* (update error[-m..-1] and mem_w_err[]) *
* update error function for taming process *
*------------------------------------------------------*/
for (i = 0; i < L_SUBFR; i++) {
/* exc[i] = gain_pit*exc[i] + gain_code*code[i]; */
/* exc[i] in Q0 gain_pit in Q14 */
/* code[i] in Q13 gain_cod in Q1 */
L_temp = L_mult(exc[i+i_subfr], gain_pit);
L_temp = L_mac(L_temp, code[i], gain_code);
L_temp = L_shl(L_temp, 1);
exc[i+i_subfr] = round(L_temp);
}
update_exc_err(gain_pit, T0);
Syn_filte(m_aq, pAq, &exc[i_subfr], &synth_ptr[i_subfr], L_SUBFR,
&mem_syn[M_BWD-m_aq], 0);
for(j=0; j<M_BWD; j++) mem_syn[j] = synth_ptr[i_subfr+L_SUBFR-M_BWD+j];
for (i = L_SUBFR-M_BWD, j = 0; i < L_SUBFR; i++, j++) {
mem_err[j] = sub(speech[i_subfr+i], synth_ptr[i_subfr+i]);
temp = extract_h(L_shl( L_mult(y1[i], gain_pit), 1) );
k = extract_h(L_shl( L_mult(y2[i], gain_code), 2) );
mem_w0[j] = sub(xn[i], add(temp, k));
}
pAp += m_ap+1;
pAq += m_aq+1;
i_gamma = add(i_gamma,1);
}
/*--------------------------------------------------*
* Update signal for next frame. *
* -> shift to the left by L_FRAME: *
* speech[], wsp[] and exc[] *
*--------------------------------------------------*/
Copy(&old_speech[L_FRAME], &old_speech[0], L_TOTAL-L_FRAME);
Copy(&old_wsp[L_FRAME], &old_wsp[0], PIT_MAX);
Copy(&old_exc[L_FRAME], &old_exc[0], PIT_MAX+L_INTERPOL);
prev_lp_mode = lp_mode;
return;
}
// Parm_CIF::ReadParm()
int Parm_CIF::ReadParm(FileName const& fname, Topology &TopIn) {
CIFfile infile;
CIFfile::DataBlock::data_it line;
if (infile.Read( fname, debug_ )) return 1;
CIFfile::DataBlock const& block = infile.GetDataBlock("_atom_site");
if (block.empty()) {
mprinterr("Error: CIF data block '_atom_site' not found.\n");
return 1;
}
// Does this CIF contain multiple models?
int Nmodels = 0;
int model_col = block.ColumnIndex("pdbx_PDB_model_num");
if (model_col != -1) {
line = block.end();
--line;
Nmodels = convertToInteger( (*line)[model_col] );
if (Nmodels > 1)
mprintf("Warning: CIF '%s' contains %i models. Using first model for topology.\n",
fname.full(), Nmodels);
}
// Get essential columns
int COL[NENTRY];
for (int i = 0; i < (int)NENTRY; i++) {
COL[i] = block.ColumnIndex(Entries[i]);
if (COL[i] == -1) {
mprinterr("Error: In CIF file '%s' could not find entry '%s' in block '%s'\n",
fname.full(), Entries[i], block.Header().c_str());
return 1;
}
if (debug_>0) mprintf("DEBUG: '%s' column = %i\n", Entries[i], COL[i]);
}
// Get optional columns
int occ_col = block.ColumnIndex("occupancy");
int bfac_col = block.ColumnIndex("B_iso_or_equiv");
int icode_col = block.ColumnIndex("pdbx_PDB_ins_code");
int altloc_col = block.ColumnIndex("label_alt_id");
std::vector<AtomExtra> extra;
// Loop over all atom sites
int current_res = 0;
double XYZ[3];
double occupancy = 1.0;
double bfactor = 0.0;
char altloc = ' ';
char icode;
icode = ' ';
Frame Coords;
for (line = block.begin(); line != block.end(); ++line) {
// If more than 1 model check if we are done.
if (Nmodels > 1) {
if ( convertToInteger( (*line)[model_col] ) > 1 )
break;
}
if (occ_col != -1) occupancy = convertToDouble( (*line)[ occ_col ] );
if (bfac_col != -1) bfactor = convertToDouble( (*line)[ bfac_col ] );
if (altloc_col != -1) altloc = (*line)[ altloc_col ][0];
// '.' altloc means blank?
if (altloc == '.') altloc = ' ';
extra.push_back( AtomExtra(occupancy, bfactor, altloc) );
if (icode_col != -1) {
icode = (*line)[ icode_col ][0];
// '?' icode means blank
if (icode == '?') icode = ' ';
}
XYZ[0] = convertToDouble( (*line)[ COL[X] ] );
XYZ[1] = convertToDouble( (*line)[ COL[Y] ] );
XYZ[2] = convertToDouble( (*line)[ COL[Z] ] );
NameType currentResName( (*line)[ COL[RNAME] ] );
// It seems that in some CIF files, there doesnt have to be a residue
// number. Check if residue name has changed.
if ( (*line)[ COL[RNUM] ][0] == '.' ) {
Topology::res_iterator lastResidue = TopIn.ResEnd();
--lastResidue;
if ( currentResName != (*lastResidue).Name() )
current_res = TopIn.Nres() + 1;
} else
current_res = convertToInteger( (*line)[ COL[RNUM] ] );
TopIn.AddTopAtom( Atom((*line)[ COL[ANAME] ], " "),
Residue(currentResName, current_res, icode,
(*line)[ COL[CHAINID] ][0]) );
Coords.AddXYZ( XYZ );
}
if (TopIn.SetExtraAtomInfo( 0, extra )) return 1;
// Search for bonds // FIXME nobondsearch?
BondSearch( TopIn, Coords, Offset_, debug_ );
// Get title.
CIFfile::DataBlock const& entryblock = infile.GetDataBlock("_entry");
std::string ciftitle;
if (!entryblock.empty())
ciftitle = entryblock.Data("id");
TopIn.SetParmName( ciftitle, infile.CIFname() );
// Get unit cell parameters if present.
CIFfile::DataBlock const& cellblock = infile.GetDataBlock("_cell");
if (!cellblock.empty()) {
double cif_box[6];
cif_box[0] = convertToDouble( cellblock.Data("length_a") );
cif_box[1] = convertToDouble( cellblock.Data("length_b") );
cif_box[2] = convertToDouble( cellblock.Data("length_c") );
cif_box[3] = convertToDouble( cellblock.Data("angle_alpha") );
cif_box[4] = convertToDouble( cellblock.Data("angle_beta" ) );
cif_box[5] = convertToDouble( cellblock.Data("angle_gamma") );
mprintf("\tRead cell info from CIF: a=%g b=%g c=%g alpha=%g beta=%g gamma=%g\n",
cif_box[0], cif_box[1], cif_box[2], cif_box[3], cif_box[4], cif_box[5]);
TopIn.SetParmBox( Box(cif_box) );
}
return 0;
}
int SequenceAlign(CpptrajState& State, ArgList& argIn) {
std::string blastfile = argIn.GetStringKey("blastfile");
if (blastfile.empty()) {
mprinterr("Error: 'blastfile' must be specified.\n");
return 1;
}
ReferenceFrame qref = State.DSL()->GetReferenceFrame(argIn);
if (qref.error() || qref.empty()) {
mprinterr("Error: Must specify reference structure for query.\n");
return 1;
}
std::string outfilename = argIn.GetStringKey("out");
if (outfilename.empty()) {
mprinterr("Error: Must specify output file.\n");
return 1;
}
TrajectoryFile::TrajFormatType fmt = TrajectoryFile::GetFormatFromArg(argIn);
if (fmt != TrajectoryFile::PDBFILE && fmt != TrajectoryFile::MOL2FILE)
fmt = TrajectoryFile::PDBFILE; // Default to PDB
int smaskoffset = argIn.getKeyInt("smaskoffset", 0) + 1;
int qmaskoffset = argIn.getKeyInt("qmaskoffset", 0) + 1;
// Load blast file
mprintf("\tReading BLAST alignment from '%s'\n", blastfile.c_str());
BufferedLine infile;
if (infile.OpenFileRead( blastfile )) return 1;
// Seek down to first Query line.
const char* ptr = infile.Line();
bool atFirstQuery = false;
while (ptr != 0) {
if (*ptr == 'Q') {
if ( strncmp(ptr, "Query", 5) == 0 ) {
atFirstQuery = true;
break;
}
}
ptr = infile.Line();
}
if (!atFirstQuery) {
mprinterr("Error: 'Query' not found.\n");
return 1;
}
// Read alignment. Replacing query with subject.
typedef std::vector<char> Carray;
typedef std::vector<int> Iarray;
Carray Query; // Query residues
Carray Sbjct; // Sbjct residues
Iarray Smap; // Smap[Sbjct index] = Query index
while (ptr != 0) {
const char* qline = ptr; // query line
const char* aline = infile.Line(); // alignment line
const char* sline = infile.Line(); // subject line
if (aline == 0 || sline == 0) {
mprinterr("Error: Missing alignment line or subject line after Query:\n");
mprinterr("Error: %s", qline);
return 1;
}
for (int idx = 12; qline[idx] != ' '; idx++) {
if (qline[idx] == '-') {
// Sbjct does not have corresponding res in Query
Smap.push_back(-1);
Sbjct.push_back( sline[idx] );
} else if (sline[idx] == '-') {
// Query does not have a corresponding res in Sbjct
Query.push_back( qline[idx] );
} else {
// Direct Query to Sbjct map
Smap.push_back( Query.size() );
Sbjct.push_back( sline[idx] );
Query.push_back( qline[idx] );
}
}
// Scan to next Query
ptr = infile.Line();
while (ptr != 0) {
if (*ptr == 'Q') {
if ( strncmp(ptr, "Query", 5) == 0 ) break;
}
ptr = infile.Line();
}
}
// DEBUG
std::string SmaskExp, QmaskExp;
if (State.Debug() > 0) mprintf(" Map of Sbjct to Query:\n");
for (int sres = 0; sres != (int)Sbjct.size(); sres++) {
if (State.Debug() > 0)
mprintf("%-i %3s %i", sres+smaskoffset, Residue::ConvertResName(Sbjct[sres]),
Smap[sres]+qmaskoffset);
const char* qres = "";
if (Smap[sres] != -1) {
qres = Residue::ConvertResName(Query[Smap[sres]]);
if (SmaskExp.empty())
SmaskExp.assign( integerToString(sres+smaskoffset) );
else
SmaskExp.append( "," + integerToString(sres+smaskoffset) );
if (QmaskExp.empty())
QmaskExp.assign( integerToString(Smap[sres]+qmaskoffset) );
else
QmaskExp.append( "," + integerToString(Smap[sres]+qmaskoffset) );
}
if (State.Debug() > 0) mprintf(" %3s\n", qres);
}
mprintf("Smask: %s\n", SmaskExp.c_str());
mprintf("Qmask: %s\n", QmaskExp.c_str());
// Check that query residues match reference.
for (unsigned int sres = 0; sres != Sbjct.size(); sres++) {
int qres = Smap[sres];
if (qres != -1) {
if (Query[qres] != qref.Parm().Res(qres).SingleCharName()) {
mprintf("Warning: Potential residue mismatch: Query %s reference %s\n",
Residue::ConvertResName(Query[qres]), qref.Parm().Res(qres).c_str());
}
}
}
// Build subject using coordinate from reference.
//AtomMask sMask; // Contain atoms that should be in sTop
Topology sTop;
Frame sFrame;
Iarray placeHolder; // Atom indices of placeholder residues.
for (unsigned int sres = 0; sres != Sbjct.size(); sres++) {
int qres = Smap[sres];
NameType SresName( Residue::ConvertResName(Sbjct[sres]) );
if (qres != -1) {
Residue const& QR = qref.Parm().Res(qres);
Residue SR(SresName, sres+1, ' ', QR.ChainID());
if (Query[qres] == Sbjct[sres]) { // Exact match. All non-H atoms.
for (int qat = QR.FirstAtom(); qat != QR.LastAtom(); qat++)
{
if (qref.Parm()[qat].Element() != Atom::HYDROGEN)
sTop.AddTopAtom( qref.Parm()[qat], SR );
sFrame.AddXYZ( qref.Coord().XYZ(qat) );
//sMask.AddAtom(qat);
}
} else { // Partial match. Copy only backbone and CB.
for (int qat = QR.FirstAtom(); qat != QR.LastAtom(); qat++)
{
if ( qref.Parm()[qat].Name().Match("N" ) ||
qref.Parm()[qat].Name().Match("CA") ||
qref.Parm()[qat].Name().Match("CB") ||
qref.Parm()[qat].Name().Match("C" ) ||
qref.Parm()[qat].Name().Match("O" ) )
{
sTop.AddTopAtom( qref.Parm()[qat], SR );
sFrame.AddXYZ( qref.Coord().XYZ(qat) );
}
}
}
} else {
// Residue in query does not exist for subject. Just put placeholder CA for now.
Vec3 Zero(0.0);
placeHolder.push_back( sTop.Natom() );
sTop.AddTopAtom( Atom("CA", "C "), Residue(SresName, sres+1, ' ', ' ') );
sFrame.AddXYZ( Zero.Dptr() );
}
}
//sTop.PrintAtomInfo("*");
mprintf("\tPlaceholder residue indices:");
for (Iarray::const_iterator p = placeHolder.begin(); p != placeHolder.end(); ++p)
mprintf(" %i", *p + 1);
mprintf("\n");
// Try to give placeholders more reasonable coordinates.
if (!placeHolder.empty()) {
Iarray current_indices;
unsigned int pidx = 0;
while (pidx < placeHolder.size()) {
if (current_indices.empty()) {
current_indices.push_back( placeHolder[pidx++] );
// Search for the end of this segment
for (; pidx != placeHolder.size(); pidx++) {
if (placeHolder[pidx] - current_indices.back() > 1) break;
current_indices.push_back( placeHolder[pidx] );
}
// DEBUG
mprintf("\tSegment:");
for (Iarray::const_iterator it = current_indices.begin();
it != current_indices.end(); ++it)
mprintf(" %i", *it + 1);
// Get coordinates of residues bordering segment.
int prev_res = sTop[current_indices.front()].ResNum() - 1;
int next_res = sTop[current_indices.back() ].ResNum() + 1;
mprintf(" (prev_res=%i, next_res=%i)\n", prev_res+1, next_res+1);
Vec3 prev_crd(sFrame.XYZ(current_indices.front() - 1));
Vec3 next_crd(sFrame.XYZ(current_indices.back() + 1));
prev_crd.Print("prev_crd");
next_crd.Print("next_crd");
Vec3 crd_step = (next_crd - prev_crd) / (double)(current_indices.size()+1);
crd_step.Print("crd_step");
double* xyz = sFrame.xAddress() + (current_indices.front() * 3);
for (unsigned int i = 0; i != current_indices.size(); i++, xyz += 3) {
prev_crd += crd_step;
xyz[0] = prev_crd[0];
xyz[1] = prev_crd[1];
xyz[2] = prev_crd[2];
}
current_indices.clear();
}
}
}
//Topology* sTop = qref.Parm().partialModifyStateByMask( sMask );
//if (sTop == 0) return 1;
//Frame sFrame(qref.Coord(), sMask);
// Write output traj
Trajout_Single trajout;
if (trajout.PrepareTrajWrite(outfilename, argIn, &sTop, CoordinateInfo(), 1, fmt)) return 1;
if (trajout.WriteSingle(0, sFrame)) return 1;
trajout.EndTraj();
return 0;
}
Hierarchy
create_simplified_along_backbone(Chain in,
const IntRanges& residue_segments,
bool keep_detailed) {
IMP_USAGE_CHECK(in.get_is_valid(true), "Chain " << in
<< " is not valid.");
if (in.get_number_of_children() ==0 || residue_segments.empty()) {
IMP_LOG_TERSE( "Nothing to simplify in " << (in? in->get_name(): "nullptr")
<< " with " << residue_segments.size() << " segments.\n");
return Hierarchy();
}
for (unsigned int i=0; i< residue_segments.size(); ++i) {
IMP_USAGE_CHECK(residue_segments[i].first < residue_segments[i].second,
"Residue intervals must be non-empty");
}
IMP_IF_LOG(VERBOSE) {
for (unsigned int i=0; i < residue_segments.size(); ++i) {
IMP_LOG_VERBOSE( "[" << residue_segments[i].first
<< "..." << residue_segments[i].second << ") ");
}
IMP_LOG_VERBOSE( std::endl);
}
unsigned int cur_segment=0;
Hierarchies cur;
Hierarchy root=create_clone_one(in);
for (unsigned int i=0; i< in.get_number_of_children(); ++i) {
Hierarchy child=in.get_child(i);
int index= Residue(child).get_index();
IMP_LOG_VERBOSE( "Processing residue " << index
<< " with range " << residue_segments[cur_segment].first
<< " " << residue_segments[cur_segment].second << std::endl);
if (index >= residue_segments[cur_segment].first
&& index < residue_segments[cur_segment].second) {
} else if (!cur.empty()) {
IMP_LOG_VERBOSE( "Added particle for "
<< residue_segments[cur_segment].first
<< "..." << residue_segments[cur_segment].second
<< std::endl);
Hierarchy cur_approx=create_approximation_of_residues(cur);
root.add_child(cur_approx);
if (keep_detailed) {
for (unsigned int j=0; j< cur.size(); ++j) {
cur[j].get_parent().remove_child(cur[j]);
cur_approx.add_child(cur[j]);
}
}
cur.clear();
++cur_segment;
}
cur.push_back(child);
}
if (!cur.empty()) {
root.add_child(create_approximation_of_residues(cur));
}
/*#ifdef IMP_ATOM_USE_IMP_CGAL
double ov= get_volume(in);
double cv= get_volume(root);
double scale=1;
ParticlesTemp rt= get_by_type(root, XYZR_TYPE);
Floats radii(rt.size());
for (unsigned int i=0; i< rt.size(); ++i) {
core::XYZR d(rt[i]);
radii[i]=d.get_radius();
}
do {
show(root);
double f= ov/cv*scale;
scale*=.95;
IMP_LOG_TERSE( "Bumping radius by " << f << std::endl);
for (unsigned int i=0; i< rt.size(); ++i) {
core::XYZR d(rt[i]);
d.set_radius(radii[i]*f);
}
double nv=get_volume(root);
IMP_LOG_TERSE( "Got volume " << nv << " " << ov << std::endl);
if (nv < ov) {
break;
}
} while (true);
#else
#endif*/
IMP_INTERNAL_CHECK(root.get_is_valid(true),
"Invalid hierarchy produced " << root);
return root;
}
void set_lpc_modeg ( Word16 *signal_ptr, /* I Input signal */
Word16 *a_fwd, /* I Forward LPC filter */
Word16 *a_bwd, /* I Backward LPC filter */
Word16 *mode, /* O Backward / forward Indication */
Word16 *lsp_new, /* I LSP vector current frame */
Word16 *lsp_old, /* I LSP vector previous frame */
Word16 *bwd_dominant,/* O Bwd dominant mode indication */
Word16 prev_mode, /* I previous frame Backward / forward Indication */
Word16 *prev_filter, /* I previous frame filter */
Word16 *C_int, /*I/O filter interpolation parameter */
Word16 *glob_stat, /* I/O Mre of global stationnarity Q8 */
Word16 *stat_bwd, /* I/O Number of consecutive backward frames */
Word16 *val_stat_bwd/* I/O Value associated with stat_bwd */
)
{
Word16 i;
Word16 res[L_FRAME];
Word16 *pa_bwd;
Word16 gap;
Word16 gpred_f, gpred_b, gpred_bint;
Word16 tmp;
Word32 thresh_lpc_L;
Word32 tmp_L;
Word32 dist_lsp, energy;
pa_bwd = a_bwd + M_BWDP1;
/* Backward filter prediction gain (no interpolation ) */
/* --------------------------------------------------- */
Residue(M_BWD,pa_bwd, signal_ptr, res, L_FRAME);
gpred_b = ener_dB(signal_ptr, L_FRAME) - ener_dB(res, L_FRAME);
/* Interpolated LPC filter for transition forward -> backward */
/* (used during 10 frames) ( for the second sub-frame ) */
/* Interpolated backward filter for the first sub-frame */
/* ---------------------------------------------------------- */
Int_bwd(a_bwd, prev_filter, C_int);
/* Interpolated backward filter prediction gain */
/* -------------------------------------------- */
Residue(M_BWD,a_bwd, signal_ptr, res, L_SUBFR);
Residue(M_BWD,pa_bwd, &signal_ptr[L_SUBFR], &res[L_SUBFR], L_SUBFR);
gpred_bint = ener_dB(signal_ptr, L_FRAME) - ener_dB(res, L_FRAME);
/* Forward filter prediction gain */
/* ------------------------------ */
Residue(M, a_fwd, signal_ptr, res, L_SUBFR);
Residue(M, &a_fwd[MP1], &signal_ptr[L_SUBFR], &res[L_SUBFR], L_SUBFR);
gpred_f = ener_dB(signal_ptr, L_FRAME) - ener_dB(res, L_FRAME);
/* -------------------------------------------------------------- */
/* BACKWARD / FORWARD DECISION */
/* */
/* The Main criterion is based on the prediction gains : */
/* The global stationnarity index is used to adapt the threshold */
/* value " GAP ". */
/* This adaptation is used to favour one mode according to the */
/* stationnarity of the input signal (backward for music and */
/* forward for speech) which avoids too many switches. */
/* */
/* A second criterion based on the LSPs is used to avoid switches */
/* if the successive LPC forward filters are very stationnary */
/* (which is measured a Euclidean distance on LSPs). */
/* */
/* -------------------------------------------------------------- */
/* 1st criterion with prediction gains */
/* ----------------------------------- */
/* Threshold adaptation according to the global stationnarity indicator */
tmp = shr(*glob_stat, 7);
tmp_L = L_mult(tmp, 3);
tmp_L = L_shr(tmp_L, 1);
tmp = extract_l(tmp_L);
gap = add(tmp, 205);
if ( (gpred_bint > gpred_f - gap)&&
(gpred_b > gpred_f - gap)&&
(gpred_b > 0)&&
(gpred_bint > 0) ) *mode = 1;
else *mode = 0;
if (*glob_stat < 13000) *mode = 0; /* => Forward mode imposed */
/* 2nd criterion with a distance between 2 successive LSP vectors */
/* -------------------------------------------------------------- */
/* Computation of the LPC distance */
dist_lsp = 0;
for(i=0; i<M; i++){
tmp = sub(lsp_old[i],lsp_new[i]);
dist_lsp = L_mac(dist_lsp, tmp, tmp);
}
/* Adaptation of the LSPs thresholds */
if (*glob_stat < 32000) {
thresh_lpc_L = 0L;
}
else {
thresh_lpc_L = 64424509L;
}
/* Switching backward -> forward forbidden in case of a LPC stationnary */
if ((dist_lsp < thresh_lpc_L)&&(*mode == 0)&&(prev_mode == 1)&&(gpred_b > 0)&&(gpred_bint > 0)) {
*mode = 1;
}
/* Low energy frame => Forward mode chosen */
/* --------------------------------------- */
energy = ener_dB(signal_ptr, L_FRAME);
if (energy < 8192) {
*mode = 0;
if (*glob_stat > 13000) *glob_stat = 13000;
}
else tst_bwd_dominant(bwd_dominant, *mode);
/* Adaptation of the global stationnarity indicator */
/* ------------------------------------------------ */
if (energy >= 8192) calc_stat(gpred_b, gpred_f, *mode, prev_mode,
glob_stat, stat_bwd, val_stat_bwd);
if(*mode == 0) *C_int = 4506;
return;
}
/** Open the Charmm PSF file specified by filename and set up topology data.
* Mask selection requires natom, nres, names, resnames, resnums.
*/
int Parm_CharmmPsf::ReadParm(FileName const& fname, Topology &parmOut) {
const size_t TAGSIZE = 10;
char tag[TAGSIZE];
tag[0]='\0';
CpptrajFile infile;
if (infile.OpenRead(fname)) return 1;
mprintf(" Reading Charmm PSF file %s as topology file.\n",infile.Filename().base());
// Read the first line, should contain PSF...
const char* buffer = 0;
if ( (buffer=infile.NextLine()) == 0 ) return 1;
// Advance to <ntitle> !NTITLE
int ntitle = FindTag(tag, "!NTITLE", 7, infile);
// Only read in 1st title. Skip any asterisks.
std::string psftitle;
if (ntitle > 0) {
buffer = infile.NextLine();
const char* ptr = buffer;
while (*ptr != '\0' && (*ptr == ' ' || *ptr == '*')) ++ptr;
psftitle.assign( ptr );
}
parmOut.SetParmName( NoTrailingWhitespace(psftitle), infile.Filename() );
// Advance to <natom> !NATOM
int natom = FindTag(tag, "!NATOM", 6, infile);
if (debug_>0) mprintf("\tPSF: !NATOM tag found, natom=%i\n", natom);
// If no atoms, probably issue with PSF file
if (natom < 1) {
mprinterr("Error: No atoms in PSF file.\n");
return 1;
}
// Read the next natom lines
int psfresnum = 0;
char psfresname[6];
char psfname[6];
char psftype[6];
double psfcharge;
double psfmass;
for (int atom=0; atom < natom; atom++) {
if ( (buffer=infile.NextLine()) == 0 ) {
mprinterr("Error: ReadParmPSF(): Reading atom %i\n",atom+1);
return 1;
}
// Read line
// ATOM# SEGID RES# RES ATNAME ATTYPE CHRG MASS (REST OF COLUMNS ARE LIKELY FOR CMAP AND CHEQ)
sscanf(buffer,"%*i %*s %i %s %s %s %lf %lf",&psfresnum, psfresname,
psfname, psftype, &psfcharge, &psfmass);
parmOut.AddTopAtom( Atom( psfname, psfcharge, psfmass, psftype),
Residue( psfresname, psfresnum, ' ', ' '), 0 );
} // END loop over atoms
// Advance to <nbond> !NBOND
int bondatoms[9];
int nbond = FindTag(tag, "!NBOND", 6, infile);
if (nbond > 0) {
if (debug_>0) mprintf("\tPSF: !NBOND tag found, nbond=%i\n", nbond);
int nlines = nbond / 4;
if ( (nbond % 4) != 0) nlines++;
for (int bondline=0; bondline < nlines; bondline++) {
if ( (buffer=infile.NextLine()) == 0 ) {
mprinterr("Error: ReadParmPSF(): Reading bond line %i\n",bondline+1);
return 1;
}
// Each line has 4 pairs of atom numbers
int nbondsread = sscanf(buffer,"%i %i %i %i %i %i %i %i",bondatoms,bondatoms+1,
bondatoms+2,bondatoms+3, bondatoms+4,bondatoms+5,
bondatoms+6,bondatoms+7);
// NOTE: Charmm atom nums start from 1
for (int bondidx=0; bondidx < nbondsread; bondidx+=2)
parmOut.AddBond(bondatoms[bondidx]-1, bondatoms[bondidx+1]-1);
}
} else
mprintf("Warning: PSF has no bonds.\n");
// Advance to <nangles> !NTHETA
int nangle = FindTag(tag, "!NTHETA", 7, infile);
if (nangle > 0) {
if (debug_>0) mprintf("\tPSF: !NTHETA tag found, nangle=%i\n", nangle);
int nlines = nangle / 3;
if ( (nangle % 3) != 0) nlines++;
for (int angleline=0; angleline < nlines; angleline++) {
if ( (buffer=infile.NextLine()) == 0) {
mprinterr("Error: Reading angle line %i\n", angleline+1);
return 1;
}
// Each line has 3 groups of 3 atom numbers
int nanglesread = sscanf(buffer,"%i %i %i %i %i %i %i %i %i",bondatoms,bondatoms+1,
bondatoms+2,bondatoms+3, bondatoms+4,bondatoms+5,
bondatoms+6,bondatoms+7, bondatoms+8);
for (int angleidx=0; angleidx < nanglesread; angleidx += 3)
parmOut.AddAngle( bondatoms[angleidx ]-1,
bondatoms[angleidx+1]-1,
bondatoms[angleidx+2]-1 );
}
} else
mprintf("Warning: PSF has no angles.\n");
// Advance to <ndihedrals> !NPHI
int ndihedral = FindTag(tag, "!NPHI", 5, infile);
if (ndihedral > 0) {
if (debug_>0) mprintf("\tPSF: !NPHI tag found, ndihedral=%i\n", ndihedral);
int nlines = ndihedral / 2;
if ( (ndihedral % 2) != 0) nlines++;
for (int dihline = 0; dihline < nlines; dihline++) {
if ( (buffer=infile.NextLine()) == 0) {
mprinterr("Error: Reading dihedral line %i\n", dihline+1);
return 1;
}
// Each line has 2 groups of 4 atom numbers
int ndihread = sscanf(buffer,"%i %i %i %i %i %i %i %i",bondatoms,bondatoms+1,
bondatoms+2,bondatoms+3, bondatoms+4,bondatoms+5,
bondatoms+6,bondatoms+7);
for (int dihidx=0; dihidx < ndihread; dihidx += 4)
parmOut.AddDihedral( bondatoms[dihidx ]-1,
bondatoms[dihidx+1]-1,
bondatoms[dihidx+2]-1,
bondatoms[dihidx+3]-1 );
}
} else
mprintf("Warning: PSF has no dihedrals.\n");
mprintf("\tPSF contains %i atoms, %i residues.\n", parmOut.Natom(), parmOut.Nres());
infile.CloseFile();
return 0;
}
/*----------------------------------------------------------------------------
* Post - adaptive postfilter main function
*----------------------------------------------------------------------------
*/
void Poste(
Word16 t0, /* input : pitch delay given by coder */
Word16 *signal_ptr, /* input : input signal (pointer to current subframe */
Word16 *coeff, /* input : LPC coefficients for current subframe */
Word16 *sig_out, /* output: postfiltered output */
Word16 *vo, /* output: voicing decision 0 = uv, > 0 delay */
Word16 gamma1, /* input: short term postfilt. den. weighting factor*/
Word16 gamma2, /* input: short term postfilt. num. weighting factor*/
Word16 gamma_harm, /* input: long term postfilter weighting factor*/
Word16 long_h_st, /* input: impulse response length*/
Word16 m_pst, /* input: LPC order */
Word16 Vad
)
{
/* Local variables and arrays */
Word16 apond1[M_BWDP1]; /* s.t. denominator coeff. */
Word16 sig_ltp[L_SUBFRP1]; /* H0 output signal */
Word16 *sig_ltp_ptr;
Word16 parcor0;
/* Compute weighted LPC coefficients */
Weight_Az(coeff, gamma1, m_pst, apond1);
Weight_Az(coeff, gamma2, m_pst, apond2);
Set_zero(&apond2[m_pst+1], (Word16)(M_BWD-m_pst));
/* Compute A(gamma2) residual */
Residue(m_pst, apond2, signal_ptr, res2_ptr, L_SUBFR);
/* Harmonic filtering */
sig_ltp_ptr = sig_ltp + 1;
if (sub(Vad,1) > 0)
pst_ltpe(t0, res2_ptr, sig_ltp_ptr, vo, gamma_harm);
else {
*vo = 0;
Copy(res2_ptr, sig_ltp_ptr, L_SUBFR);
}
/* Save last output of 1/A(gamma1) */
/* (from preceding subframe) */
sig_ltp[0] = *ptr_mem_stp;
/* Controls short term pst filter gain and compute parcor0 */
calc_st_filte(apond2, apond1, &parcor0, sig_ltp_ptr, long_h_st, m_pst);
/* 1/A(gamma1) filtering, mem_stp is updated */
Syn_filte(m_pst, apond1, sig_ltp_ptr, sig_ltp_ptr, L_SUBFR,
&mem_stp[M_BWD-m_pst], 0);
Copy(&sig_ltp_ptr[L_SUBFR-M_BWD], mem_stp, M_BWD);
/* Tilt filtering */
filt_mu(sig_ltp, sig_out, parcor0);
/* Gain control */
scale_st(signal_ptr, sig_out, &gain_prec);
/**** Update for next subframe */
Copy(&res2[L_SUBFR], &res2[0], MEM_RES2);
return;
}
