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Add trp man torsions analysis to mk5 #112

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Add trp man torsions analysis to mk5 #112

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40f3eec
update torsions data json files to include TRP-MAN linkage
louholland Jan 13, 2025
45b3657
update code to consider TRP-MAN linkage torsions
louholland Jan 13, 2025
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2 changes: 1 addition & 1 deletion data/linkage_torsions/privateer_torsion_database.json
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2 changes: 1 addition & 1 deletion data/linkage_torsions/privateer_torsions_z_score_database.json
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24 changes: 22 additions & 2 deletions src/privateer/cpp/clipper-glyco.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -4999,6 +4999,7 @@ void MGlycan::Linkage::calculate_and_set_zscore(float Phi, float Psi, clipper::S
"NAG-1,3-FUC",
"MAN-1,2-NAG",
"NAG-1,4-GAL",
"TRP-1,1-MAN",
};
std::string linkage_name = donor_sugar + "-" + acceptor_position + "," + donor_position + "-" + acceptor_sugar;

Expand Down Expand Up @@ -5523,13 +5524,32 @@ void MGlycology::init ( const clipper::MiniMol& mmol, const clipper::MAtomNonBon
aa_atom_bravo.coord_orth() );


if ( psi < 0 )
psi = clipper::Util::twopi() + psi;
//if ( psi < 0 )
// psi = clipper::Util::twopi() + psi;


mg.set_glycosylation_torsions ( clipper::Util::rad2d(phi), clipper::Util::rad2d(psi) );
mg.add_torsions_for_detected_linkages(clipper::Util::rad2d(phi), clipper::Util::rad2d(psi), potential_c_roots[i].first.type().trim(), cd1, sugar.type().trim(), c1, potential_c_roots[i].first.seqnum(), sugar.seqnum());

if(!torsions_zscore_database.database_array.empty())
{
mg.set_protein_sugar_linkage_zscore_attempt_to_calculate(true);
std::string amino_acid = potential_c_roots[i].first.type().trim();
std::string donor_position = std::regex_replace(cd1.name().trim(), std::regex(R"([^\d])"), "");
std::string first_sugar = sugar.type().trim();
std::string acceptor_position = std::regex_replace(c1.name().trim(), std::regex(R"([^\d])"), "");
auto search_result_in_torsions_zscore_db = std::find_if(torsions_zscore_database.database_array.begin(), torsions_zscore_database.database_array.end(), [amino_acid, donor_position, acceptor_position, first_sugar](privateer::json::TorsionsZScoreDatabase& element)
{
return amino_acid == element.donor_sugar && donor_position == element.donor_end && acceptor_position == element.acceptor_end && first_sugar == element.acceptor_sugar;
});
if(search_result_in_torsions_zscore_db != std::end(torsions_zscore_database.database_array))
{
privateer::json::TorsionsZScoreDatabase& found_torsion_description = *search_result_in_torsions_zscore_db;
float linkage_score = mg.calculate_zscore(clipper::Util::rad2d(phi), clipper::Util::rad2d(psi), found_torsion_description);
mg.set_protein_sugar_linkage_zscore(linkage_score);
}
}

if ( linked[j].second.monomer()+3 < mmol[linked[j].second.polymer()].size() )
// Make sure that checks for consensus sequence do not occur outside the array, therefore causing segfaults.
{
Expand Down
15 changes: 14 additions & 1 deletion src/privateer/cpp/privateer-lib.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -1488,6 +1488,7 @@ bool privateer::util::do_report_linkage(std::string d_pos, std::string d_atom, s
"NAG-1,3-FUC",
"MAN-1,2-NAG",
"NAG-1,4-GAL",
"TRP-1,1-MAN",
};

std::string name = d_pos + "-" + d_atom + "," + a_atom + "-" + a_pos ;
Expand Down Expand Up @@ -2450,7 +2451,7 @@ bool privateer::glycanbuilderplot::Plot::plot_glycan ( clipper::MGlycan glycan )

const clipper::MGlycan::Node node = glycan.get_node ( 0 ); // get the first node

if(glycan.get_type() == "n-glycan")
if(glycan.get_type() == "n-glycan" || glycan.get_type() == "c-glycan")
{
if (node.get_sugar().type().trim() == "NAG" && glycan.get_root().first.type().trim() == "ASN")
{
Expand All @@ -2464,6 +2465,18 @@ bool privateer::glycanbuilderplot::Plot::plot_glycan ( clipper::MGlycan glycan )
add_shaded_link(new_shaded_bond);
}
}
else if (node.get_sugar().type().trim() == "MAN" && glycan.get_root().first.type().trim() == "TRP")
{
float link_zscore = glycan.get_protein_sugar_linkage_zscore();
if(link_zscore < -1 && link_zscore != 42069 && glycan.get_protein_sugar_linkage_zscore_attempt_to_calculate())
{
std::ostringstream os;
os << "Linkage Z-Score = " << std::setprecision(3) << link_zscore << "\nWarning: Sample size is small. Check torsion plot to validate.";
std::string message = os.str();
shadedBond * new_shaded_bond = new shadedBond( 2800, 1015, side, message, "shadedbond", mmdbsel );
add_shaded_link(new_shaded_bond);
}
}
else
{
if (glycan.get_protein_sugar_linkage_zscore_attempt_to_calculate())
Expand Down