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Bugfix for RosettaCM and branched glycans #221

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Bugfix for RosettaCM and branched glycans #221

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52536df
Bugfix for RosettaCM and branched glycans
Oct 23, 2024
992a400
Beautification to fix indentations
Oct 24, 2024
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39 changes: 28 additions & 11 deletions source/src/core/conformation/util.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@

// Unit headers
#include <core/conformation/util.hh>
#include <core/conformation/carbohydrates/util.hh>

// Package headers
#include <core/conformation/Conformation.hh>
Expand Down Expand Up @@ -319,20 +320,36 @@ idealize_position(

if ( rsd.is_polymer() ) {
// add polymer nbrs?
if ( seqpos > 1 && !rsd.is_lower_terminus() && !conformation.fold_tree().is_cutpoint( seqpos-1 ) ) {
lower_connect = true;
ResidueOP prev_rsd( ResidueFactory::create_residue( conformation.residue( seqpos-1 ).type() ) );
idl.prepend_polymer_residue_before_seqpos( *prev_rsd, 1, true );
idl_pos = 2;
}
if ( rsd.is_carbohydrate() ) {
if ( seqpos > 1 && !rsd.is_lower_terminus() ) {
lower_connect = true;
core::Size parent_res_seqpos( conformation::carbohydrates::find_seqpos_of_saccharides_parent_residue( rsd ) );
ResidueOP prev_rsd( ResidueFactory::create_residue( conformation.residue( parent_res_seqpos ).type() ) );
idl.prepend_polymer_residue_before_seqpos( *prev_rsd, 1, true );
idl_pos = 2;
}

if ( seqpos < conformation.size() && !rsd.is_upper_terminus() && !conformation.fold_tree().is_cutpoint( seqpos ) ) {
upper_connect = true;
core::Size child_res_seqpos( conformation::carbohydrates::find_seqpos_of_saccharides_mainchain_child( rsd ) );
ResidueOP next_rsd( ResidueFactory::create_residue( conformation.residue( child_res_seqpos ).type() ) );
idl.append_polymer_residue_after_seqpos( *next_rsd, idl_pos, true );
}
} else {
if ( seqpos > 1 && !rsd.is_lower_terminus() && !conformation.fold_tree().is_cutpoint( seqpos-1 ) ) {
lower_connect = true;
ResidueOP prev_rsd( ResidueFactory::create_residue( conformation.residue( seqpos-1 ).type() ) );
idl.prepend_polymer_residue_before_seqpos( *prev_rsd, 1, true );
idl_pos = 2;
}

if ( seqpos < conformation.size() && !rsd.is_upper_terminus() && !conformation.fold_tree().is_cutpoint( seqpos ) ) {
upper_connect = true;
ResidueOP next_rsd( ResidueFactory::create_residue( conformation.residue( seqpos+1 ).type() ) );
idl.append_polymer_residue_after_seqpos( *next_rsd, idl_pos, true );
if ( seqpos < conformation.size() && !rsd.is_upper_terminus() && !conformation.fold_tree().is_cutpoint( seqpos ) ) {
upper_connect = true;
ResidueOP next_rsd( ResidueFactory::create_residue( conformation.residue( seqpos+1 ).type() ) );
idl.append_polymer_residue_after_seqpos( *next_rsd, idl_pos, true );
}
}
}

//// now set the torsion angles in the ideal conformation... This is to prepare for replacing rsd with
//// the idealized version

Expand Down
39 changes: 38 additions & 1 deletion source/src/protocols/hybridization/HybridizeProtocol.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -79,6 +79,7 @@

#include <core/conformation/Residue.hh>
#include <core/conformation/util.hh>
#include <core/conformation/carbohydrates/util.hh>

#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/MoveMap.hh>
Expand Down Expand Up @@ -1292,12 +1293,48 @@ void HybridizeProtocol::apply( core::pose::Pose & pose )
for ( core::Size ires=1; ires <= templates_[initial_template_index]->size(); ++ires ) {
if ( templates_[initial_template_index]->pdb_info()->number(ires) > (int)nres_tgt ) {
TR.Debug << "Insert hetero residue: " << templates_[initial_template_index]->residue(ires).name3() << std::endl;
if ( templates_[initial_template_index]->residue(ires).is_polymer()
if ( templates_[initial_template_index]->residue(ires).is_carbohydrate() ) {
if ( !templates_[initial_template_index]->residue(ires).is_lower_terminus() ) {
core::Size offset = pose.size() + 1 - ires;
core::Size parent_res_seqpos( conformation::carbohydrates::find_seqpos_of_saccharides_parent_residue( templates_[initial_template_index]->residue(ires) ) );
int self_lower=0;
int parent_upper=0;
//self_lower = templates_[initial_template_index]->residue(ires).lower_connect_id();
//parent_upper = templates_[initial_template_index]->residue(parent_res_seqpos).connect_atom( templates_[initial_template_index]->residue(ires) );
for ( core::Size i(1); i <= templates_[initial_template_index]->residue(ires).connect_map_size(); ++i ) {
TR.Debug<<" "<<i<<" "<<templates_[initial_template_index]->residue(ires).residue_connection_partner(i)<<" "<<templates_[initial_template_index]->residue(ires).residue_connection_conn_id(i)<<std::endl;
if ( templates_[initial_template_index]->residue(ires).connect_map( i ).resid() == parent_res_seqpos ) {
//self_lower = templates_[initial_template_index]->residue(ires).connect_map( i ).connid();
self_lower = i;
parent_upper=templates_[initial_template_index]->residue(ires).connect_map( i ).connid();
//parent_upper=templates_[initial_template_index]->residue(ires).residue_connection_conn_id(i);
}
}
parent_res_seqpos += offset;
TR.Debug <<" appending by bond "<<pose.size()+1<<" lower "<<self_lower<<" anchor "<<parent_res_seqpos<<" parent upper "<<parent_upper<<std::endl;
pose.append_residue_by_bond(templates_[initial_template_index]->residue(ires), false, self_lower, parent_res_seqpos, parent_upper, false, false);
} else {
TR.Debug <<" appending by jump "<<ires<<" is Polymer "<<templates_[initial_template_index]->residue(ires).is_polymer()<<" is Lower "<<templates_[initial_template_index]->residue(ires).is_lower_terminus()<<" is Upper "<<pose.residue(pose.size()).is_upper_terminus()<<std::endl;
for ( core::Size i(1); i <= templates_[initial_template_index]->residue(ires).connect_map_size(); ++i ) {
TR.Debug<<" "<<i<<" "<<templates_[initial_template_index]->residue(ires).residue_connection_partner(i)<<" "<<templates_[initial_template_index]->residue(ires).residue_connection_conn_id(i)<<std::endl;
}
pose.append_residue_by_jump(templates_[initial_template_index]->residue(ires), 1);

}
} else if ( templates_[initial_template_index]->residue(ires).is_polymer()
&& !templates_[initial_template_index]->residue(ires).is_lower_terminus()
&& !pose.residue(pose.size()).is_upper_terminus() ) {
TR.Debug <<" appending by bond "<<ires<<std::endl;
pose.append_residue_by_bond(templates_[initial_template_index]->residue(ires));
for ( core::Size i(1); i <= templates_[initial_template_index]->residue(ires).connect_map_size(); ++i ) {
TR.Debug<<" "<<i<<" "<<templates_[initial_template_index]->residue(ires).residue_connection_partner(i)<<" "<<templates_[initial_template_index]->residue(ires).residue_connection_conn_id(i)<<std::endl;
}
} else {
TR.Debug <<" appending by jump "<<ires<<" is Polymer "<<templates_[initial_template_index]->residue(ires).is_polymer()<<" is Lower "<<templates_[initial_template_index]->residue(ires).is_lower_terminus()<<" is Upper "<<pose.residue(pose.size()).is_upper_terminus()<<std::endl;
pose.append_residue_by_jump(templates_[initial_template_index]->residue(ires), 1);
for ( core::Size i(1); i <= templates_[initial_template_index]->residue(ires).connect_map_size(); ++i ) {
TR.Debug<<" "<<i<<" "<<templates_[initial_template_index]->residue(ires).residue_connection_partner(i)<<" "<<templates_[initial_template_index]->residue(ires).residue_connection_conn_id(i)<<std::endl;
}
}
hetatms.push_back( std::make_pair( ires, pose.size() ) );
}
Expand Down