Skip to content

D
dssp
Commit 056e4f8f by Maarten L. Hekkelman
Options

rename item from range_1 to range_id_1 

Update dictionary extensions to reflect changes in output
parent 5fb6af0d
Showing with 81 additions and 13 deletions
mmcif_pdbx/dssp-extension.dic
...@@ -477,6 +477,9 @@ save_dssp_struct_ladder ...@@ -477,6 +477,9 @@ save_dssp_struct_ladder
; ;
; ;
_dssp_struct_ladder.id A _dssp_struct_ladder.id A
_dssp_struct_ladder.sheet_id A
_dssp_struct_ladder.range_1 A
_dssp_struct_ladder.range_2 B
_dssp_struct_ladder.type anti-parallel _dssp_struct_ladder.type anti-parallel
_dssp_struct_ladder.beg_1_label_comp_id GLY _dssp_struct_ladder.beg_1_label_comp_id GLY
_dssp_struct_ladder.beg_1_label_asym_id A _dssp_struct_ladder.beg_1_label_asym_id A
...@@ -520,6 +523,39 @@ save__dssp_struct_ladder.id ...@@ -520,6 +523,39 @@ save__dssp_struct_ladder.id
_item_type.code code _item_type.code code
save_ save_
save__dssp_struct_ladder.sheet_id
_item.description
; This data item is a pointer to _struct_sheet.id in the
STRUCT_SHEET category.
;
_item.name '_dssp_struct_ladder.id'
_item.category_id dssp_struct_ladder
_item.mandatory_code yes
_item_type.code code
save_
save__dssp_struct_ladder.range_id_1
_item.description
; This data item is a pointer to _struct_sheet_range.id in
the STRUCT_SHEET_RANGE category.
;
_item.name '_dssp_struct_ladder.id'
_item.category_id dssp_struct_ladder
_item.mandatory_code yes
_item_type.code code
save_
save__dssp_struct_ladder.range_id_2
_item.description
; This data item is a pointer to _struct_sheet_range.id in
the STRUCT_SHEET_RANGE category.
;
_item.name '_dssp_struct_ladder.id'
_item.category_id dssp_struct_ladder
_item.mandatory_code yes
_item_type.code code
save_
save__dssp_struct_ladder.type save__dssp_struct_ladder.type
_item.description _item.description
; The type of the ladder, be it parallel or anti-parallel ; The type of the ladder, be it parallel or anti-parallel
...@@ -1466,9 +1502,10 @@ save_dssp_struct_summary ...@@ -1466,9 +1502,10 @@ save_dssp_struct_summary
_dssp_struct_summary.helix_pp . _dssp_struct_summary.helix_pp .
_dssp_struct_summary.bend S _dssp_struct_summary.bend S
_dssp_struct_summary.chirality + _dssp_struct_summary.chirality +
_dssp_struct_summary.sheet .
_dssp_struct_summary.strand .
_dssp_struct_summary.ladder_1 . _dssp_struct_summary.ladder_1 .
_dssp_struct_summary.ladder_2 . _dssp_struct_summary.ladder_2 .
_dssp_struct_summary.sheet .
_dssp_struct_summary.accessibility 23.1 _dssp_struct_summary.accessibility 23.1
_dssp_struct_summary.TCO 0.940 _dssp_struct_summary.TCO 0.940
_dssp_struct_summary.kappa 73.9 _dssp_struct_summary.kappa 73.9
...@@ -1655,31 +1692,43 @@ save__dssp_struct_summary.chirality ...@@ -1655,31 +1692,43 @@ save__dssp_struct_summary.chirality
'-' '-'
save_ save_
save__dssp_struct_summary.ladder_1 save__dssp_struct_summary.sheet
_item.description _item.description
; Label for the first beta bridge of which this residue is part. ; This data item is a pointer to _struct_sheet.id in
the STRUCT_SHEET category.
; ;
_item.name '_dssp_struct_summary.ladder_1' _item.name '_dssp_struct_summary.sheet'
_item.category dssp_struct_summary _item.category dssp_struct_summary
_item.mandatory_code no _item.mandatory_code no
_item_type.code code _item_type.code code
save_ save_
save__dssp_struct_summary.ladder_2 save__dssp_struct_summary.strand
_item.description _item.description
; Label for the second beta bridge of which this residue is part. ; This data item is a pointer to _struct_sheet_range.id in
the STRUCT_SHEET_RANGE category.
; ;
_item.name '_dssp_struct_summary.ladder_2' _item.name '_dssp_struct_summary.sheet'
_item.category dssp_struct_summary _item.category dssp_struct_summary
_item.mandatory_code no _item.mandatory_code no
_item_type.code code _item_type.code code
save_ save_
save__dssp_struct_summary.sheet save__dssp_struct_summary.ladder_1
_item.description _item.description
; Label for the sheet of which this residue is part. ; Label for the first beta bridge of which this residue is part.
; ;
_item.name '_dssp_struct_summary.sheet' _item.name '_dssp_struct_summary.ladder_1'
_item.category dssp_struct_summary
_item.mandatory_code no
_item_type.code code
save_
save__dssp_struct_summary.ladder_2
_item.description
; Label for the second beta bridge of which this residue is part.
;
_item.name '_dssp_struct_summary.ladder_2'
_item.category dssp_struct_summary _item.category dssp_struct_summary
_item.mandatory_code no _item.mandatory_code no
_item_type.code code _item_type.code code
......
src/dssp-io.cpp
...@@ -818,8 +818,8 @@ void writeLadders(cif::datablock &db, const dssp &dssp) ...@@ -818,8 +818,8 @@ void writeLadders(cif::datablock &db, const dssp &dssp)
dssp_struct_ladder.emplace({ dssp_struct_ladder.emplace({
{ "id", cif::cif_id_for_number(l.ladder) }, { "id", cif::cif_id_for_number(l.ladder) },
{ "sheet_id", cif::cif_id_for_number(l.sheet) }, { "sheet_id", cif::cif_id_for_number(l.sheet) },
{ "range_1", cif::cif_id_for_number(beg1.strand() - 1) }, { "range_id_1", cif::cif_id_for_number(beg1.strand() - 1) },
{ "range_2", cif::cif_id_for_number(beg2.strand() - 1) }, { "range_id_2", cif::cif_id_for_number(beg2.strand() - 1) },
{ "type", l.parallel ? "parallel" : "anti-parallel" }, { "type", l.parallel ? "parallel" : "anti-parallel" },
{ "beg_1_label_comp_id", beg1.compound_id() }, { "beg_1_label_comp_id", beg1.compound_id() },
...@@ -951,7 +951,10 @@ void writeSummary(cif::datablock &db, const dssp &dssp) ...@@ -951,7 +951,10 @@ void writeSummary(cif::datablock &db, const dssp &dssp)
// prime the category with the field labels we need, this is to ensure proper order in writing out the data. // prime the category with the field labels we need, this is to ensure proper order in writing out the data.
for (auto label : { "entry_id", "label_comp_id", "label_asym_id", "label_seq_id", "secondary_structure", "ss_bridge", "helix_3_10", "helix_alpha", "helix_pi", "helix_pp", "bend", "chirality", "sheet", "strand", "ladder_1", "ladder_2", "accessibility", "TCO", "kappa", "alpha", "phi", "psi", "x_ca", "y_ca", "z_ca"}) for (auto label : { "entry_id", "label_comp_id", "label_asym_id", "label_seq_id", "secondary_structure",
"ss_bridge", "helix_3_10", "helix_alpha", "helix_pi", "helix_pp", "bend", "chirality", "sheet",
"strand", "ladder_1", "ladder_2", "accessibility", "TCO", "kappa", "alpha", "phi", "psi",
"x_ca", "y_ca", "z_ca"})
dssp_struct_summary.add_column(label); dssp_struct_summary.add_column(label);
for (auto res : dssp) for (auto res : dssp)
......
test/unit-test-dssp.cpp
...@@ -226,3 +226,18 @@ BOOST_AUTO_TEST_CASE(dssp_2) ...@@ -226,3 +226,18 @@ BOOST_AUTO_TEST_CASE(dssp_2)
BOOST_CHECK_EQUAL((char)ri.type(), secstr.front()); BOOST_CHECK_EQUAL((char)ri.type(), secstr.front());
} }
} }
// --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(dssp_3)
{
cif::file f(gTestDir / "1cbs.cif.gz");
BOOST_ASSERT(f.is_valid());
dssp dssp(f.front(), 1, 3, true);
dssp.annotate(f.front(), true, true);
BOOST_TEST(f.is_valid());
}
\ No newline at end of file
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment