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Fix off-by-one loops + self-distance bug in SEWING/splice/de novo/RNA (split 3/4 of #707) #732

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Fix off-by-one loops + self-distance bug in SEWING/splice/de novo/RNA (split 3/4 of #707) #732

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2 changes: 1 addition & 1 deletion source/src/protocols/denovo_design/components/FoldGraph.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -852,7 +852,7 @@ FoldGraph::compute_best_solution( SegmentNames const & staple_loops ) const
solutions[sol].push_back( new_visited );
} else {
Solution tmpset;
for ( core::Size t=1; t<solutions[sol].size(); ++t ) {
for ( core::Size t=1; t<=solutions[sol].size(); ++t ) {
tmpset.push_back( solutions[sol][t] );
}
tmpset.push_back( new_visited );
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4 changes: 2 additions & 2 deletions source/src/protocols/features/strand_assembly/StrandBundleFeatures.cc
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Expand Up @@ -934,8 +934,8 @@ StrandBundleFeatures::shortest_dis_sidechain(

for ( core::Size strand_j_res=0; strand_j_res < strand_j.get_size(); strand_j_res++ ) {
core::Size j_resnum = strand_j.get_start()+strand_j_res;
for ( core::Size i_AtomNum=1; i_AtomNum < pose.residue(i_resnum).natoms(); i_AtomNum++ ) {
for ( core::Size j_AtomNum=1; j_AtomNum < pose.residue(j_resnum).natoms(); j_AtomNum++ ) {
for ( core::Size i_AtomNum=1; i_AtomNum <= pose.residue(i_resnum).natoms(); i_AtomNum++ ) {
for ( core::Size j_AtomNum=1; j_AtomNum <= pose.residue(j_resnum).natoms(); j_AtomNum++ ) {
Real dis_sc_sc = pose.residue(i_resnum).xyz(i_AtomNum).distance(pose.residue(j_resnum).xyz(j_AtomNum));
if ( temp_shortest_dis > dis_sc_sc ) {
temp_shortest_dis = dis_sc_sc;
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4 changes: 2 additions & 2 deletions source/src/protocols/fldsgn/MatchResidues.cc
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Expand Up @@ -62,7 +62,7 @@ core::Real
MatchResidues::compute_comb( core::pose::Pose const & pose, VecSize const & comb ) const
{
std::map< core::id::AtomID, core::id::AtomID > atom_id_map;
for ( core::Size i = 1; i < comb.size(); i++ ) {
for ( core::Size i = 1; i <= comb.size(); i++ ) {
const core::id::AtomID mod_id(pose.residue_type( comb[i] ).atom_index( "CA" ), comb[i] );
const core::id::AtomID ref_id(pose.residue_type( reference_residues_indexes_[i] ).atom_index( "CA" ), reference_residues_indexes_[i]);
atom_id_map.insert( std::make_pair(mod_id, ref_id) );
Expand All @@ -75,7 +75,7 @@ MatchResidues::superimpose_comb( core::pose::Pose & pose, VecSize const & comb )
{
core::id::AtomID_Map< core::id::AtomID > atom_map;
core::pose::initialize_atomid_map( atom_map, pose, core::id::AtomID::BOGUS_ATOM_ID() );
for ( core::Size i = 1; i < comb.size(); ++i ) {
for ( core::Size i = 1; i <= comb.size(); ++i ) {
const core::id::AtomID mod_id(pose.residue_type( comb[i] ).atom_index( "CA" ), comb[i] );
const core::id::AtomID ref_id(pose.residue_type( reference_residues_indexes_[i] ).atom_index( "CA" ), reference_residues_indexes_[i]);
atom_map.set( mod_id, ref_id);
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4 changes: 2 additions & 2 deletions source/src/protocols/legacy_sewing/conformation/Assembly.cc
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Expand Up @@ -1259,7 +1259,7 @@ Assembly::natives_select(
utility::vector1<core::Size>
Assembly::pose_loop_anchors() const {
utility::vector1<core::Size> loop_anchors;
for ( core::Size i=1; i<segments_.size(); ++i ) {
for ( core::Size i=1; i<=segments_.size(); ++i ) {
if ( !segments_.has_next(i) ) {
loop_anchors.push_back(pose_num(segments_[i].model_id_, segments_[i].residues_.back().resnum_));
}
Expand All @@ -1271,7 +1271,7 @@ Assembly::pose_loop_anchors() const {
utility::vector1<core::Size>
Assembly::disconnected_segments() const {
utility::vector1<core::Size> disconnected_segments;
for ( core::Size i=1; i<segments_.size(); ++i ) {
for ( core::Size i=1; i<=segments_.size(); ++i ) {
if ( !segments_.has_next(i) ) {
disconnected_segments.push_back(i);
}
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8 changes: 4 additions & 4 deletions source/src/protocols/pose_sewing/movers/BlockwiseAnalysisMover.cc
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Expand Up @@ -92,11 +92,11 @@ BlockwiseAnalysisMover::apply( core::pose::Pose& pose){

std::pair<core::Size, core::Size> helix_pair;

for ( core::Size upstream_res = 1; upstream_res < pose.size(); ++upstream_res ) {
for ( core::Size upstream_res = 1; upstream_res <= pose.size(); ++upstream_res ) {
if ( pose.secstruct(upstream_res) == 'H' ) {
for ( core::Size downstream_res = upstream_res+1; downstream_res <= pose.size(); ++downstream_res ) {
if ( pose.secstruct(downstream_res) == 'H' ) {
if ( element_blocks[upstream_res] != element_blocks[downstream_res] && pose.residue(upstream_res).xyz(2).distance(pose.residue(upstream_res).xyz(2)) <= crit_dist_ ) {
if ( element_blocks[upstream_res] != element_blocks[downstream_res] && pose.residue(upstream_res).xyz(2).distance(pose.residue(downstream_res).xyz(2)) <= crit_dist_ ) {
helix_pair.first = element_blocks[upstream_res];
helix_pair.second = element_blocks[downstream_res];
helix_pairs.insert(helix_pair);
Expand All @@ -117,7 +117,7 @@ BlockwiseAnalysisMover::apply( core::pose::Pose& pose){
//core::Size label_res = 1;
for ( auto current_pair : helix_pairs ) {
scc.Reset(); // this may not be needed anymore, but I'm leaving it here for safety
for ( core::Size current_res = 1; current_res < pose.size(); ++current_res ) {
for ( core::Size current_res = 1; current_res <= pose.size(); ++current_res ) {
if ( element_blocks[current_res] == current_pair.first ) {
scc.AddResidue( 0, pose.residue(current_res) );
}
Expand All @@ -134,7 +134,7 @@ BlockwiseAnalysisMover::apply( core::pose::Pose& pose){
d_median = r.distance;
has_disulfide = false;
core::Size last_upstream_res = 1;
for ( core::Size upstream_res = 1; upstream_res <pose.size(); ++upstream_res ) {
for ( core::Size upstream_res = 1; upstream_res <= pose.size(); ++upstream_res ) {
if ( pose.residue(upstream_res).type().is_disulfide_bonded() && element_blocks[upstream_res] == current_pair.first ) {
for ( core::Size downstream_res = upstream_res+2; downstream_res <= pose.size(); ++downstream_res ) {
if ( pose.residue(downstream_res).type().is_disulfide_bonded() && pose.residue(upstream_res).is_bonded(pose.residue(downstream_res)) && element_blocks[downstream_res] == current_pair.second ) {
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8 changes: 4 additions & 4 deletions source/src/protocols/pose_sewing/movers/OmnibusDisulfideAnalysisLabelerMover.cc
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Expand Up @@ -132,7 +132,7 @@ OmnibusDisulfideAnalysisLabelerMover::apply( core::pose::Pose& pose){
std::string label;

//pose.pdb_info()->add_reslabel(1,label);
for ( core::Size upstream_res = 1; upstream_res <pose.size(); ++upstream_res ) {
for ( core::Size upstream_res = 1; upstream_res <= pose.size(); ++upstream_res ) {
if ( pose.residue(upstream_res).type().is_disulfide_bonded() ) {
for ( core::Size downstream_res = upstream_res+2; downstream_res <= pose.size(); ++downstream_res ) {
if ( pose.residue(downstream_res).type().is_disulfide_bonded() && pose.residue(upstream_res).is_bonded(pose.residue(downstream_res)) ) {
Expand Down Expand Up @@ -170,11 +170,11 @@ OmnibusDisulfideAnalysisLabelerMover::apply( core::pose::Pose& pose){

std::pair<core::Size, core::Size> helix_pair;

for ( core::Size upstream_res = 1; upstream_res < pose.size(); ++upstream_res ) {
for ( core::Size upstream_res = 1; upstream_res <= pose.size(); ++upstream_res ) {
if ( pose.secstruct(upstream_res) == 'H' ) {
for ( core::Size downstream_res = upstream_res+2; downstream_res <= pose.size(); ++downstream_res ) {
if ( pose.secstruct(downstream_res) == 'H' ) {
if ( element_blocks[upstream_res] != element_blocks[downstream_res] && pose.residue(upstream_res).xyz(2).distance(pose.residue(upstream_res).xyz(2)) <= crit_dist_ ) {
if ( element_blocks[upstream_res] != element_blocks[downstream_res] && pose.residue(upstream_res).xyz(2).distance(pose.residue(downstream_res).xyz(2)) <= crit_dist_ ) {
helix_pair.first = element_blocks[upstream_res];
helix_pair.second = element_blocks[downstream_res];
helix_pairs.insert(helix_pair);
Expand All @@ -195,7 +195,7 @@ OmnibusDisulfideAnalysisLabelerMover::apply( core::pose::Pose& pose){
utility::vector1< core::Size > selection1;
utility::vector1< core::Size > selection2;

for ( core::Size current_res = 1; current_res < pose.size(); ++current_res ) {
for ( core::Size current_res = 1; current_res <= pose.size(); ++current_res ) {
if ( element_blocks[current_res] == current_pair.first ) {
selection1.push_back(current_res);
}
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2 changes: 1 addition & 1 deletion source/src/protocols/rna/movers/RNAIdealizeMover.cc
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Expand Up @@ -237,7 +237,7 @@ RNAIdealizeMover::apply( pose::Pose & pose )
suite_mm->set_jump( true );
protocols::minimization_packing::MinMoverOP minm = utility::pointer::make_shared< protocols::minimization_packing::MinMover >( suite_mm, scorefxn, "lbfgs_armijo_nonmonotone", 0.001, true );

for ( Size ii = 1; ii < ideal_pose.size(); ++ii ) {
for ( Size ii = 1; ii <= ideal_pose.size(); ++ii ) {

for ( Size jj = 1; jj <= ideal_pose.residue_type( ii ).natoms(); ++jj ) {
ConstraintOP constraint = utility::pointer::make_shared< CoordinateConstraint >( core::id::AtomID( jj, ii ), core::id::AtomID( 1, my_anchor ),
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4 changes: 2 additions & 2 deletions source/src/protocols/splice/SampleRotamersFromPDB.cc
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Expand Up @@ -229,7 +229,7 @@ void SampleRotamersFromPDB_RotamerSetOperation::fill_rotamer_matrix_from_db_file
}
//new_res->set_all_chi(Rots_real);
bool res_exsits_in_db = false;
for ( core::Size i=1; i<resi_vec_[resi_num].size(); i++ ) {
for ( core::Size i=1; i<=resi_vec_[resi_num].size(); i++ ) {
res_exsits_in_db = is_identical_rotamer(resi_vec_[resi_num][i],new_res);
if ( res_exsits_in_db ) break;
//TR<<"Found identical residue"<<std::endl;
Expand Down Expand Up @@ -780,7 +780,7 @@ rot_matrix RotLibdb::fill_rotamer_matrix_from_db_file(std::string fname) {
}

bool res_exsits_in_db = false;
for ( core::Size i=1; i<resi_mat[resi_num].size(); i++ ) {
for ( core::Size i=1; i<=resi_mat[resi_num].size(); i++ ) {
res_exsits_in_db = is_identical_rotamer(resi_mat[resi_num][i],new_res);
if ( res_exsits_in_db ) break;
//TR<<"Found identical residue"<<std::endl;
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2 changes: 1 addition & 1 deletion source/src/protocols/splice/SpliceManager.cc
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Expand Up @@ -333,7 +333,7 @@ SpliceManager::update_pose_stem_positions() {
}

void SpliceManager::check_sequence_profile(core::pose::Pose & pose, core::id::SequenceMappingOP smap, core::sequence::SequenceProfileOP seqprof){
for ( core::Size row = 1; row < seqprof->size(); row++ ) { //go over all the PSSM sements provided by the user
for ( core::Size row = 1; row <= seqprof->size(); row++ ) { //go over all the PSSM sements provided by the user
utility::vector1< core::Size > cur_prof_row = seqprof->prof_row(row);


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2 changes: 1 addition & 1 deletion source/src/protocols/stepwise/legacy/modeler/rna/StepWiseRNA_WorkingParametersSetup.cc
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Expand Up @@ -233,7 +233,7 @@ StepWiseWorkingParametersSetup::get_user_input_alignment_res_list( core::Size co

ObjexxFCL::FArray1D < bool > const & partition_definition = working_parameters_->partition_definition();
bool contain_non_root_partition_seq_num = false;
for ( core::Size ii = 1; ii < working_alignment.size(); ii++ ) {
for ( core::Size ii = 1; ii <= working_alignment.size(); ii++ ) {
if ( partition_definition( working_alignment[ii] ) != partition_definition( root_res ) ) contain_non_root_partition_seq_num = true;
}

Expand Down