Skip to content

Fix off-by-one in 1-indexed loops in docking/membrane/misc (split 4/4 of #707) #733

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
lyskov merged 1 commit into from
Jul 23, 2026
Merged

Fix off-by-one in 1-indexed loops in docking/membrane/misc (split 4/4 of #707) #733

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion source/src/protocols/antibody/residue_selector/CDRResidueSelector.cc
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -130,7 +130,7 @@ void
CDRResidueSelector::set_cdrs( utility::vector1< CDRNameEnum > cdrs ){
cdrs_.clear();
cdrs_.resize(8, false);
for ( core::Size i = 1; i < cdrs.size(); ++i ) {
for ( core::Size i = 1; i <= cdrs.size(); ++i ) {
cdrs_[ cdrs[ i ] ] = true;
}
}
Expand Down
4 changes: 2 additions & 2 deletions source/src/protocols/cartesian/md.cc
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1275,7 +1275,7 @@ void MolecularDynamics::applyForces_ConjugateGradient(

}
} else { // this block is for Step == 0 - its just a standard SD Step
for ( core::Size i = 1; i < cartom.size(); i++ ) {
for ( core::Size i = 1; i <= cartom.size(); i++ ) {
cartom[i].old_position = cartom[i].position; // save position (old position = current position)
cartom[i].old_force = cartom[i].force * forcemul; // save old forces
cartom[i].old_velocity = -cartom[i].force * forcemul; // save old directions, equal to old force
Expand Down Expand Up @@ -1483,7 +1483,7 @@ void MolecularDynamics::testCartesianDerivatives( core::scoring::ScoreFunction c
}


for ( core::Size i = 1; i < cartom.size(); i++ ) {
for ( core::Size i = 1; i <= cartom.size(); i++ ) {

if ( ( fabs( cartom[i].force.x() - numeriv[i].x() ) > 0.1 ) ||
( fabs( cartom[i].force.y() - numeriv[i].y() ) > 0.1 ) ||
Expand Down
2 changes: 1 addition & 1 deletion source/src/protocols/cutoutdomain/CutOutDomain.cc
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -90,7 +90,7 @@ core::Size
CutOutDomain::find_nearest_res( core::pose::Pose const & source, core::pose::Pose const & target, core::Size const res, core::Size const chain/*=0*/ ){
core::Real min_dist( 100000 ); core::Size nearest_res( 0 );
core::Size i;
for ( i = 1; i < target.size(); ++i ) {
for ( i = 1; i <= target.size(); ++i ) {
if ( target.residue( i ).is_ligand() ) continue;
if ( chain && target.residue( i ).chain() != chain ) continue;
// TR<<"the residue examnied is:"<<i<<target.residue(i).name1()<<std::endl;
Expand Down
4 changes: 2 additions & 2 deletions source/src/protocols/docking/DockingEnsemblePrepackProtocol.cc
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -304,7 +304,7 @@ void DockingEnsemblePrepackProtocol::check_ensemble_member_compatibility() {

// if the chain identities are not equivalent, error!
// assuming ensemble 1 chains are first reported in parterns flag
for ( core::Size k=1; k<chains.size(); ++k ) {
for ( core::Size k=1; k<=chains.size(); ++k ) {
if ( chains[k] != partners.partner1[k] ) {
std::string exit_message = "Ensemble 1 member differs in chain identity from partners flag!\n";
exit_message = exit_message + "Member " + std::to_string(i) + ": " + chains[k] + " vs. " + partners.partner1[k] + "\n";
Expand All @@ -328,7 +328,7 @@ void DockingEnsemblePrepackProtocol::check_ensemble_member_compatibility() {

// if the chain identities are not equivalent, error!
// assuming ensemble 2 chains are second reported in parterns flag
for ( core::Size k=1; k<chains.size(); ++k ) {
for ( core::Size k=1; k<=chains.size(); ++k ) {
if ( chains[k] != partners.partner2[k] ) {
std::string exit_message = "Ensemble 2 member differs in chain identity from partners flag!\n";
exit_message = exit_message + "Member " + std::to_string(i) + ": " + chains[k] + " vs. " + partners.partner2[k] + "\n";
Expand Down
4 changes: 2 additions & 2 deletions source/src/protocols/docking/metrics.cc
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -521,7 +521,7 @@ calc_Fnonnat( const core::pose::Pose & pose, const core::pose::Pose & native_pos

//generate list of interface residues for partner 1 and partner 2
core::Size cutpoint = 0;
for ( core::Size i = 1; i < pose.size(); i++ ) {
for ( core::Size i = 1; i <= pose.size(); i++ ) {
if ( !temp_part( i ) ) {
cutpoint = i;
break;
Expand Down Expand Up @@ -596,7 +596,7 @@ calc_Fnonnat( const core::pose::Pose & pose, std::string const& list_file, DockJ
ObjexxFCL::FArray1D_bool temp_part ( pose.size(), false );
pose.fold_tree().partition_by_jump( rb_jump, temp_part );
core::Size cutpoint = 0;
for ( core::Size i = 1; i < pose.size(); i++ ) {
for ( core::Size i = 1; i <= pose.size(); i++ ) {
if ( !temp_part( i ) ) {
cutpoint = i;
break;
Expand Down
2 changes: 1 addition & 1 deletion source/src/protocols/enzdes/EnzRepackMinimize.cc
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -134,7 +134,7 @@ EnzRepackMinimize::apply( pose::Pose & pose )
core::kinematics::MoveMapOP movemap = enzprot->create_enzdes_movemap( pose, task_, minimize_prot_jumps_ );
core::scoring::ScoreFunctionCOP br_scorefxn = scorefxn_minimize_;
utility::vector1<core::Size> residues;
for ( core::Size i =1; i<pose.size(); ++i ) {
for ( core::Size i =1; i<=pose.size(); ++i ) {
if ( movemap->get_bb(i) ) residues.push_back(i);
}
TR<<"Now Backrub minimizing: min_sc "<<min_sc_<<" min_bb "<< min_bb_<<std::endl;
Expand Down
6 changes: 3 additions & 3 deletions source/src/protocols/loops/util.cc
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -224,7 +224,7 @@ void addScoresForLoopParts(

core::Size nres = pose.size();
utility::vector1< core::Size > all_loop_list;
for ( core::Size i = 1; i < nres; i ++ ) {
for ( core::Size i = 1; i <= nres; i ++ ) {
if ( loops.is_loop_residue(i) ) all_loop_list.push_back( i );
}
scorefxn(pose);
Expand All @@ -241,7 +241,7 @@ void addScoresForLoopParts(
}
utility::vector1< core::Size > loop_list;
utility::vector1< core::Size > non_loop_list;
for ( core::Size i = 1; i < nres; i ++ ) {
for ( core::Size i = 1; i <= nres; i ++ ) {
if ( ( i < loops[l].start() ) || ( i > loops[l].stop() ) ) {
loop_list.push_back( i );
} else {
Expand Down Expand Up @@ -544,7 +544,7 @@ protocols::loops::Loops find_non_protein_chunks(core::pose::Pose const & pose) {
Loop new_loop;
bool chunk_started = false;

for ( core::Size ires = 1; ires < pose.size(); ++ires ) {
for ( core::Size ires = 1; ires <= pose.size(); ++ires ) {
if ( pose.residue_type(ires).is_protein() ) continue;
if ( !chunk_started ) {
new_loop.set_start(ires);
Expand Down
2 changes: 1 addition & 1 deletion source/src/protocols/match/output/UpstreamDownstreamCollisionFilter.cc
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -158,7 +158,7 @@ bool UpstreamDownstreamCollisionFilter::passes_etable_filter( match_dspos1 const

using namespace core::scoring;
EnergyMap emap;
for ( core::Size ii = 1; ii < m.upstream_hits.size(); ++ii ) {
for ( core::Size ii = 1; ii <= m.upstream_hits.size(); ++ii ) {
if ( ii == m.originating_geom_cst_for_dspos ) continue; // don't collision check since we've presumably done so already
if ( us_ds_chemical_bond_[ ii ] ) continue;
for ( core::Size jj = 1; jj <= downstream_pose_->size(); ++jj ) {
Expand Down
4 changes: 2 additions & 2 deletions source/src/protocols/membrane/MPLipidAccessibility.cc
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -227,7 +227,7 @@ void MPLipidAccessibility::apply( core::pose::Pose & pose ){
}

// go through slices
for ( core::Size s = 1; s < slice_zmin_.size(); ++s ) {
for ( core::Size s = 1; s <= slice_zmin_.size(); ++s ) {

// go through residues
for ( core::Size r = 1; r <= resi_[ s ].size(); ++r ) {
Expand Down Expand Up @@ -502,7 +502,7 @@ void MPLipidAccessibility::fill_up_slices( core::pose::Pose & pose ) {
void MPLipidAccessibility::compute_slice_com(){

// go through slices and compute COMs
for ( core::Size s = 1; s < slice_zmin_.size(); ++s ) {
for ( core::Size s = 1; s <= slice_zmin_.size(); ++s ) {

core::Vector com( 0, 0, 0 );

Expand Down
1 change: 1 addition & 0 deletions source/src/protocols/membrane/util.cc
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -616,6 +616,7 @@ core::Size create_membrane_foldtree_anchor_com( core::pose::Pose & pose ) {
utility::vector1< core::Size > anchors;

// get residues closest to COMs for all chains which will be new jump anchor residues
// needs to < chains.size() because the MEM is an additional chain
for ( core::Size i = 1; i < chains.size(); ++i ) {
core::Size anchor = rsd_closest_to_chain_com( pose, chains[ i ] );
anchors.push_back( anchor );
Expand Down
2 changes: 1 addition & 1 deletion source/src/protocols/moves/PyMOLMover.cc
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -548,7 +548,7 @@ void PyMOLMover::send_membrane_planes( Pose const & pose ) {
// Compute radius of gyration of the pose
utility::vector1< bool > relevant_residues;
relevant_residues.resize( pose.size() );
for ( core::Size i = 1; i < relevant_residues.size(); ++i ) {
for ( core::Size i = 1; i <= relevant_residues.size(); ++i ) {
relevant_residues[i] = true;
}

Expand Down