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Resolve trp man conf issue webapp #79

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merged 5 commits into from
Jan 9, 2024
Merged

Resolve trp man conf issue webapp #79

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cb5510c
move trp man conformation condition to library functions to match main
louholland Jan 9, 2024
da59b31
move trp man conformation condition to library functions to match main
louholland Jan 9, 2024
03e14f2
fix trp man conformation issue in webapp glycan plot
louholland Jan 9, 2024
52f3f95
fix trp man conformation issue in webapp glycan plot
louholland Jan 9, 2024
e24dfad
fix trp man conformation issue in webapp glycan plot
louholland Jan 9, 2024
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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);
}
}
Expand Down
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