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Merge pull request #79 from glycojones/resolve-trp-man-conf-issue-webapp
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Resolve trp man conf issue webapp
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@Dialpuri
Dialpuri authored Jan 9, 2024
2 parents 1fe17a4 + e24dfad commit c1c48c9
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Showing 5 changed files with 79 additions and 8,359 deletions.
92 changes: 52 additions & 40 deletions src/privateer/cpp/privateer-lib.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -1068,6 +1068,10 @@ void privateer::util::print_monosaccharide_summary (bool batch, bool showGeom, i
}
else if ( ligandList[index].second.get_context() == "c-glycan" )
{
if ( (ligandList[index].second.type().trim() == "MAN" ) && (ligandList[index].second.conformation_name() == "1c4"))
{
ligandList[index].second.override_conformation_diag ( true );
}
fprintf ( output, "\t(c) " );
}
else if ( ligandList[index].second.get_context() == "o-glycan" )
Expand Down Expand Up @@ -1163,6 +1167,10 @@ void privateer::util::print_monosaccharide_summary (bool batch, bool showGeom, i
}
else if ( ligandList[index].second.get_context() == "c-glycan" )
{
if ( (ligandList[index].second.type().trim() == "MAN" ) && (ligandList[index].second.conformation_name() == "1c4"))
{
ligandList[index].second.override_conformation_diag ( true );
}
std::cout << "\t(c) ";
}
else if ( ligandList[index].second.get_context() == "o-glycan" )
Expand Down Expand Up @@ -1277,6 +1285,10 @@ void privateer::util::print_monosaccharide_summary_python (bool batch, bool show
}
else if ( ligandList[index].second.get_context() == "c-glycan" )
{
if ( (ligandList[index].second.type().trim() == "MAN" ) && (ligandList[index].second.conformation_name() == "1c4"))
{
ligandList[index].second.override_conformation_diag ( true );
}
std::cout << "\t(c) ";
}
else if ( ligandList[index].second.get_context() == "o-glycan" )
Expand Down Expand Up @@ -2441,7 +2453,7 @@ bool privateer::glycanbuilderplot::Plot::plot_glycan ( clipper::MGlycan glycan,
void privateer::glycanbuilderplot::Plot::recursive_paint ( clipper::MGlycan mg, clipper::MGlycan::Node node, int x, int y, bool oxford_angles, GlycanErrorCount* errors)
{
const clipper::MSugar& sugar = node.get_sugar();
GlycanErrorCount node_errors = privateer::glycanbuilderplot::get_error_counts(sugar);
GlycanErrorCount node_errors = privateer::glycanbuilderplot::get_error_counts(sugar, mg);

errors->torsion_err += node_errors.torsion_err;
errors->conformation_err += node_errors.conformation_err;
Expand All @@ -2456,197 +2468,197 @@ void privateer::glycanbuilderplot::Plot::recursive_paint ( clipper::MGlycan mg,
bool node_contains_issue_with_sugar = false;
int branches = node.number_of_connections();

node_contains_issue_with_sugar = sugar_contains_issues(sugar);
node_contains_issue_with_sugar = sugar_contains_issues(sugar,mg);


if ( sugname == "Glc" )
{
Glc * glc = new Glc (x, y, get_svg_tooltip ( sugar, validation ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
Glc * glc = new Glc (x, y, get_svg_tooltip ( sugar, validation, mg), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
add_block ( glc );
if (node_contains_issue_with_sugar && this->potential_issue_shading)
{
shadedCircle * shCrcl = new shadedCircle (x, y, get_svg_tooltip ( sugar, validation ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
shadedCircle * shCrcl = new shadedCircle (x, y, get_svg_tooltip ( sugar, validation, mg ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
add_shaded_node (shCrcl);
}
}
else if ( sugname == "Gal" )
{
Gal * gal = new Gal (x, y, get_svg_tooltip ( sugar, validation ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
Gal * gal = new Gal (x, y, get_svg_tooltip ( sugar, validation, mg ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
add_block ( gal );
if (node_contains_issue_with_sugar && this->potential_issue_shading )
{
shadedCircle * shCrcl = new shadedCircle (x, y, get_svg_tooltip ( sugar, validation ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
shadedCircle * shCrcl = new shadedCircle (x, y, get_svg_tooltip ( sugar, validation, mg ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
add_shaded_node (shCrcl);
}
}
else if ( sugname == "Man" )
{
Man * man = new Man (x, y, get_svg_tooltip ( sugar, validation ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
Man * man = new Man (x, y, get_svg_tooltip ( sugar, validation, mg ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
add_block ( man );
if (node_contains_issue_with_sugar && this->potential_issue_shading )
{
shadedCircle * shCrcl = new shadedCircle (x, y, get_svg_tooltip ( sugar, validation ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
shadedCircle * shCrcl = new shadedCircle (x, y, get_svg_tooltip ( sugar, validation, mg ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
add_shaded_node (shCrcl);
}

}
else if ( sugname == "Fuc" )
{
Fuc * fuc = new Fuc (x, y, get_svg_tooltip ( sugar, validation ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
Fuc * fuc = new Fuc (x, y, get_svg_tooltip ( sugar, validation, mg ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
add_block ( fuc );
if (node_contains_issue_with_sugar && this->potential_issue_shading )
{
shadedTriangle * shTrngl = new shadedTriangle (x, y, get_svg_tooltip ( sugar, validation ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
shadedTriangle * shTrngl = new shadedTriangle (x, y, get_svg_tooltip ( sugar, validation, mg ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
add_shaded_node (shTrngl);
}
}
else if ( sugname == "Xyl" )
{
Xyl * xyl = new Xyl (x, y, get_svg_tooltip ( sugar, validation ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
Xyl * xyl = new Xyl (x, y, get_svg_tooltip ( sugar, validation, mg ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
add_block ( xyl );
if (node_contains_issue_with_sugar && this->potential_issue_shading )
{
shadedStar * shStar = new shadedStar (x, y, get_svg_tooltip ( sugar, validation ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
shadedStar * shStar = new shadedStar (x, y, get_svg_tooltip ( sugar, validation, mg ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
add_shaded_node (shStar);
}
}
else if ( sugname == "GlcN" )
{
GlcN * glcn = new GlcN (x, y, get_svg_tooltip ( sugar, validation ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
GlcN * glcn = new GlcN (x, y, get_svg_tooltip ( sugar, validation, mg ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
add_block ( glcn );
if (node_contains_issue_with_sugar && this->potential_issue_shading )
{
shadedSquare * shSqr = new shadedSquare (x, y, get_svg_tooltip ( sugar, validation ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
shadedSquare * shSqr = new shadedSquare (x, y, get_svg_tooltip ( sugar, validation, mg ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
add_shaded_node (shSqr);
}
}
else if ( sugname == "GalN" )
{
GalN * galn = new GalN (x, y, get_svg_tooltip ( sugar, validation ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
GalN * galn = new GalN (x, y, get_svg_tooltip ( sugar, validation, mg ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
add_block ( galn );
if (node_contains_issue_with_sugar && this->potential_issue_shading )
{
shadedSquare * shSqr = new shadedSquare (x, y, get_svg_tooltip ( sugar, validation ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
shadedSquare * shSqr = new shadedSquare (x, y, get_svg_tooltip ( sugar, validation, mg ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
add_shaded_node (shSqr);
}
}
else if ( sugname == "ManN" )
{
ManN * mann = new ManN (x, y, get_svg_tooltip ( sugar, validation ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
ManN * mann = new ManN (x, y, get_svg_tooltip ( sugar, validation, mg ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
add_block ( mann );
if (node_contains_issue_with_sugar && this->potential_issue_shading )
{
shadedSquare * shSqr = new shadedSquare (x, y, get_svg_tooltip ( sugar, validation ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
shadedSquare * shSqr = new shadedSquare (x, y, get_svg_tooltip ( sugar, validation, mg ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
add_shaded_node (shSqr);
}
}
else if ( sugname == "GlcNAc" )
{
GlcNAc * glcnac = new GlcNAc (x, y, get_svg_tooltip ( sugar, validation ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
GlcNAc * glcnac = new GlcNAc (x, y, get_svg_tooltip ( sugar, validation, mg ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
add_block ( glcnac );
if (node_contains_issue_with_sugar && this->potential_issue_shading )
{
shadedSquare * shSqr = new shadedSquare (x, y, get_svg_tooltip ( sugar, validation ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
shadedSquare * shSqr = new shadedSquare (x, y, get_svg_tooltip ( sugar, validation, mg ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
add_shaded_node (shSqr);
}
}
else if ( sugname == "GalNAc" )
{
GalNAc * galnac = new GalNAc (x, y, get_svg_tooltip ( sugar, validation ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
GalNAc * galnac = new GalNAc (x, y, get_svg_tooltip ( sugar, validation, mg ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
add_block ( galnac );
if (node_contains_issue_with_sugar && this->potential_issue_shading )
{
shadedSquare * shSqr = new shadedSquare (x, y, get_svg_tooltip ( sugar, validation ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
shadedSquare * shSqr = new shadedSquare (x, y, get_svg_tooltip ( sugar, validation, mg ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
add_shaded_node (shSqr);
}
}
else if ( sugname == "ManNAc" )
{
ManNAc * mannac = new ManNAc (x, y, get_svg_tooltip ( sugar, validation ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
ManNAc * mannac = new ManNAc (x, y, get_svg_tooltip ( sugar, validation, mg ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
add_block ( mannac );
if (node_contains_issue_with_sugar && this->potential_issue_shading )
{
shadedSquare * shSqr = new shadedSquare (x, y, get_svg_tooltip ( sugar, validation ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
shadedSquare * shSqr = new shadedSquare (x, y, get_svg_tooltip ( sugar, validation, mg ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
add_shaded_node (shSqr);
}
}
else if ( sugname == "GlcA" )
{
GlcA * glca = new GlcA (x, y, get_svg_tooltip ( sugar, validation ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
GlcA * glca = new GlcA (x, y, get_svg_tooltip ( sugar, validation, mg ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
add_block ( glca );
if (node_contains_issue_with_sugar && this->potential_issue_shading )
{
shadedSquare * shSqr = new shadedSquare (x, y, get_svg_tooltip ( sugar, validation ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
shadedSquare * shSqr = new shadedSquare (x, y, get_svg_tooltip ( sugar, validation, mg ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
add_shaded_node (shSqr);
}
}
else if ( sugname == "GalA" )
{
GalA * gala = new GalA (x, y, get_svg_tooltip ( sugar, validation ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
GalA * gala = new GalA (x, y, get_svg_tooltip ( sugar, validation, mg ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
add_block ( gala );
if (node_contains_issue_with_sugar && this->potential_issue_shading )
{
shadedSquare * shSqr = new shadedSquare (x, y, get_svg_tooltip ( sugar, validation ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
shadedSquare * shSqr = new shadedSquare (x, y, get_svg_tooltip ( sugar, validation, mg ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
add_shaded_node (shSqr);
}
}
else if ( sugname == "ManA" )
{
ManA * mana = new ManA (x, y, get_svg_tooltip ( sugar, validation ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
ManA * mana = new ManA (x, y, get_svg_tooltip ( sugar, validation, mg ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
add_block ( mana );
if (node_contains_issue_with_sugar && this->potential_issue_shading )
{
shadedSquare * shSqr = new shadedSquare (x, y, get_svg_tooltip ( sugar, validation ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
shadedSquare * shSqr = new shadedSquare (x, y, get_svg_tooltip ( sugar, validation, mg ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
add_shaded_node (shSqr);
}
}
else if ( sugname == "Neu5Gc" )
{
Neu5Gc *neu5gc = new Neu5Gc ( x, y, get_svg_tooltip ( sugar, validation ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
Neu5Gc *neu5gc = new Neu5Gc ( x, y, get_svg_tooltip ( sugar, validation, mg ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
add_block ( neu5gc );
if (node_contains_issue_with_sugar && this->potential_issue_shading )
{
shadedDiamond * shDiam = new shadedDiamond (x, y, get_svg_tooltip ( sugar, validation ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
shadedDiamond * shDiam = new shadedDiamond (x, y, get_svg_tooltip ( sugar, validation, mg ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
add_shaded_node (shDiam);
}
}
else if ( sugname == "Neu5Ac" )
{
Neu5Ac *neu5ac = new Neu5Ac ( x, y, get_svg_tooltip ( sugar, validation ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
Neu5Ac *neu5ac = new Neu5Ac ( x, y, get_svg_tooltip ( sugar, validation, mg ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
add_block ( neu5ac );
if (node_contains_issue_with_sugar && this->potential_issue_shading )
{
shadedDiamond * shDiam = new shadedDiamond (x, y, get_svg_tooltip ( sugar, validation ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
shadedDiamond * shDiam = new shadedDiamond (x, y, get_svg_tooltip ( sugar, validation, mg ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
add_shaded_node (shDiam);
}
}
else if ( sugname == "IdoA" )
{
IdoA *idoa = new IdoA ( x, y, get_svg_tooltip ( sugar, validation ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
IdoA *idoa = new IdoA ( x, y, get_svg_tooltip ( sugar, validation, mg ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
add_block ( idoa );
if (node_contains_issue_with_sugar && this->potential_issue_shading )
{
shadedDiamond * shDiam = new shadedDiamond (x, y, get_svg_tooltip ( sugar, validation ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
shadedDiamond * shDiam = new shadedDiamond (x, y, get_svg_tooltip ( sugar, validation, mg ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
add_shaded_node (shDiam);
}
}
else if ( sugname == "KDN" )
{
KDN *kdn = new KDN ( x, y, get_svg_tooltip ( sugar, validation ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
KDN *kdn = new KDN ( x, y, get_svg_tooltip ( sugar, validation, mg ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
add_block ( kdn );
if (node_contains_issue_with_sugar && this->potential_issue_shading )
{
shadedDiamond * shDiam = new shadedDiamond (x, y, get_svg_tooltip ( sugar, validation ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
shadedDiamond * shDiam = new shadedDiamond (x, y, get_svg_tooltip ( sugar, validation, mg ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
add_shaded_node (shDiam);
}
}
else
{
Unk *unk = new Unk ( x, y, *(sugar.type().substr(0,1).c_str()), get_svg_tooltip ( sugar, validation ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
Unk *unk = new Unk ( x, y, *(sugar.type().substr(0,1).c_str()), get_svg_tooltip ( sugar, validation, mg ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
add_block ( unk );
if (node_contains_issue_with_sugar && this->potential_issue_shading )
{
shadedHexagon * shHex = new shadedHexagon (x, y, get_svg_tooltip ( sugar, validation ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
shadedHexagon * shHex = new shadedHexagon (x, y, get_svg_tooltip ( sugar, validation, mg ), sugar.chain_id().trim(), sugar.short_name().trim(), sugar.get_seqnum(), mmdbsel );
add_shaded_node (shHex);
}
}
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