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Fix off-by-one in 1-indexed loops in frag_picker + accounting (split 2/4 of #707) #731

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Merged
lyskov merged 1 commit into from
Jul 10, 2026
Merged

Fix off-by-one in 1-indexed loops in frag_picker + accounting (split 2/4 of #707) #731

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2 changes: 1 addition & 1 deletion source/src/protocols/canonical_sampling/mc_convergence_checks/HierarchicalLevel.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -307,7 +307,7 @@ HierarchicalLevel::num_matching_levels( utility::vector1< core::Size > & address
utility::vector1< core::Size > & address2 ){
runtime_assert( address1.size() == address2.size() );
core::Size num_matching_levels = 0;
for ( core::Size ii = 1; ii < address1.size(); ii++ ) {
for ( core::Size ii = 1; ii <= address1.size(); ii++ ) {
if ( address1[ ii ] == address2[ ii ] ) {
num_matching_levels++;
}
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2 changes: 1 addition & 1 deletion source/src/protocols/frag_picker/GrabAllCollector.hh
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Expand Up @@ -66,7 +66,7 @@ public:

inline void clear() override
{
for ( core::Size i=1; i<storage_.size(); ++i ) {
for ( core::Size i=1; i<=storage_.size(); ++i ) {
storage_[i].clear();
}
}
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2 changes: 1 addition & 1 deletion source/src/protocols/frag_picker/VallProvider.cc
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Expand Up @@ -66,7 +66,7 @@ VallChunkOP VallProvider::find_chunk(std::string pdb_id, char chain_id, core::Si
if ( c->get_chain_id() != chain_id ) {
continue;
}
for ( core::Size j = 1; j < c->size(); ++j ) {
for ( core::Size j = 1; j <= c->size(); ++j ) {
if ( c->at(j)->resi() == residue_id ) {
return c;
}
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10 changes: 5 additions & 5 deletions source/src/protocols/frag_picker/quota/QuotaCollector.cc
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Expand Up @@ -51,9 +51,9 @@ bool QuotaCollector::add(std::pair<FragmentCandidateOP, scores::FragmentScoreMap

void QuotaCollector::list_pools(std::ostream & where) const {

for ( core::Size i=1; i<storage_.size(); ++i ) {
for ( core::Size i=1; i<=storage_.size(); ++i ) {
where << std::setw(3) << i;
for ( core::Size j=1; j<storage_[i].size(); ++j ) {
for ( core::Size j=1; j<=storage_[i].size(); ++j ) {
where << std::setw(10) << storage_[i][j]->get_pool_name() << "(" << std::setw(3) << storage_[i][j]->total_size() << ") ";
}
where << std::endl;
Expand All @@ -64,7 +64,7 @@ void QuotaCollector::list_pools(std::ostream & where) const {
void QuotaCollector::clear() {

for ( core::Size i=1; i<=storage_.size(); ++i ) {
for ( core::Size j=1; j<storage_[i].size(); ++j ) {
for ( core::Size j=1; j<=storage_[i].size(); ++j ) {
storage_[i][j]->clear();
}
}
Expand All @@ -73,7 +73,7 @@ void QuotaCollector::clear() {
core::Size QuotaCollector::count_candidates(core::Size pos) const {

core::Size cnt = 0;
for ( core::Size j=1; j<storage_[pos].size(); ++j ) {
for ( core::Size j=1; j<=storage_[pos].size(); ++j ) {
cnt += storage_[pos][j]->count_candidates();
}

Expand All @@ -83,7 +83,7 @@ core::Size QuotaCollector::count_candidates(core::Size pos) const {
core::Size QuotaCollector::count_candidates() const {
core::Size cnt = 0;
for ( core::Size i=1; i<=storage_.size(); ++i ) {
for ( core::Size j=1; j<storage_[i].size(); ++j ) {
for ( core::Size j=1; j<=storage_[i].size(); ++j ) {
cnt += storage_[i][j]->count_candidates();
}
}
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4 changes: 2 additions & 2 deletions source/src/protocols/frag_picker/scores/AtomBasedConstraintsScore.cc
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Expand Up @@ -46,7 +46,7 @@ AtomBasedConstraintsScore::AtomBasedConstraintsScore(core::Size priority,
CachingScoringMethod(priority, lowest_acceptable_value, use_lowest, score_name) {

query_size_ = query_size;
for ( core::Size i = 1; i < constrainable_atoms.size(); ++i ) {
for ( core::Size i = 1; i <= constrainable_atoms.size(); ++i ) {
constrainable_atoms_.insert(std::pair<std::string, core::Size>(
constrainable_atoms[i], i));
}
Expand Down Expand Up @@ -97,7 +97,7 @@ void AtomBasedConstraintsScore::do_caching(VallChunkOP chunk) {
utility::vector1<bool> flag_row(constrainable_atoms_.size());
utility::vector1<numeric::xyzVector<core::Real> > row(
constrainable_atoms_.size());
for ( core::Size j = 1; j < constrainable_atoms_.size(); ++j ) {
for ( core::Size j = 1; j <= constrainable_atoms_.size(); ++j ) {
flag_row[j] = false;
row[j] = empty_one;
}
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2 changes: 1 addition & 1 deletion source/src/protocols/jd3/JobGenealogist.cc
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Expand Up @@ -437,7 +437,7 @@ JobGenealogist::newick_tree() const {
utility::vector1< std::list< JGResultNodeCAP > > parentless_results_for_input_source;
parentless_results_for_input_source.resize( num_input_sources_ );

for ( unsigned int i = 1; i < job_nodes_for_dag_node_.size(); ++i ) {
for ( unsigned int i = 1; i <= job_nodes_for_dag_node_.size(); ++i ) {
for ( auto const & job_node_cop : job_nodes_for_dag_node_[ i ] ) {
debug_assert( job_node_cop != nullptr );
if ( job_node_cop->parents().empty() ) {
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2 changes: 1 addition & 1 deletion source/src/protocols/pose_metric_calculators/DecomposeAndReweightEnergiesCalculator.cc
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Expand Up @@ -418,7 +418,7 @@ DecomposeAndReweightEnergiesCalculator::nonzero_weight_score_types() const
utility::vector1<core::scoring::ScoreType> score_types;

for ( int i = 1; i < core::scoring::n_score_types; ++i ) {
for ( core::Size j = 1; j < weight_map_vector.size(); ++j ) {
for ( core::Size j = 1; j <= weight_map_vector.size(); ++j ) {
if ( weight_map_vector[j][core::scoring::ScoreType(i)] ) {
score_types.push_back(core::scoring::ScoreType(i));
break;
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2 changes: 1 addition & 1 deletion source/src/protocols/pose_metric_calculators/SurfaceCalculator.cc
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Expand Up @@ -82,7 +82,7 @@ SurfaceCalculator::print( std::string const & key ) const {
} else if ( key == "residue_surface" ) {
std::ostringstream ss;
ss << "[";
for ( core::Size ii=1; ii < residue_surface_energy_.size(); ++ii ) {
for ( core::Size ii=1; ii <= residue_surface_energy_.size(); ++ii ) {
ss << ii << ":";
if ( residue_surface_energy_[ ii ] != 0.00 ) {
ss << ObjexxFCL::format::F(8,4, residue_surface_energy_[ ii ]);
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2 changes: 1 addition & 1 deletion source/src/protocols/unfolded_state_energy_calculator/UnfoldedStateEnergyCalculatorMover.cc
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Expand Up @@ -116,7 +116,7 @@ UnfoldedStateEnergyCalculatorMover::create_random_fragments( Pose & pose, vector
{
// get number of protein residues
core::Size num_protein_res( 0 );
for ( core::Size i = 1; i < pose.size(); ++i ) {
for ( core::Size i = 1; i <= pose.size(); ++i ) {
if ( pose.residue( i ).type().is_protein() ) {
num_protein_res++;
}
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