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FragmentDB: add more fragments #264

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1145419
FragmentDB: add DOD fragment
tkemmer Mar 11, 2026
300e763
FragmentDB: add PO4 fragment
tkemmer Mar 11, 2026
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2 changes: 2 additions & 0 deletions data/fragmentdb/FragmentDB.json
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Original file line number Diff line number Diff line change
Expand Up @@ -26,8 +26,10 @@
"NME": "fragments/NME.json",
"CA": "fragments/CA.json",
"MG": "fragments/MG.json",
"PO4": "fragments/PO4.json",
"ZN": "fragments/ZN.json",
"HOH": "fragments/HOH.json",
"DOD": "fragments/DOD.json",
"A": "fragments/A.json",
"C": "fragments/C.json",
"G": "fragments/G.json",
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56 changes: 56 additions & 0 deletions data/fragmentdb/fragments/DOD.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,56 @@
{
"name": "DOD",
"names": [
"Deuterated water"
],
"type": "None",
"atoms": [
{
"name": "O",
"element": "O",
"r": [
42.646,
44.869,
64.255
]
},
{
"name": "D1",
"element": "H",
"r": [
43.596,
44.869,
64.255
]
},
{
"name": "D2",
"element": "H",
"r": [
42.408,
44.869,
65.175
]
}
],
"bonds": [
{
"number": 1,
"a1": "O",
"a2": "D1",
"order": "Single"
},
{
"number": 2,
"a1": "O",
"a2": "D2",
"order": "Single"
}
],
"connections": [],
"variants": [
{
"name": "DOD"
}
]
}
86 changes: 86 additions & 0 deletions data/fragmentdb/fragments/PO4.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,86 @@
{
"name": "PO4",
"names": [
"Phosphate ion"
],
"type": "None",
"atoms": [
{
"name": "P",
"element": "P",
"r": [
0.0,
0.0,
0.0
]
},
{
"name": "O1",
"element": "O",
"r": [
0.0,
-1.288,
-0.911
]
},
{
"name": "O2",
"element": "O",
"r": [
0.0,
1.288,
-0.911
]
},
{
"name": "O3",
"element": "O",
"r": [
-1.288,
0.0,
0.911
]
},
{
"name": "O4",
"element": "O",
"r": [
1.288,
0.0,
0.911
]
}
],
"bonds": [
{
"number": 1,
"a1": "P",
"a2": "O1",
"order": "Double"
},
{
"number": 1,
"a1": "P",
"a2": "O2",
"order": "Single"
},
{
"number": 1,
"a1": "P",
"a2": "O3",
"order": "Single"
},
{
"number": 1,
"a1": "P",
"a2": "O4",
"order": "Single"
}
],
"connections": [],
"variants": [
{
"name": "PO4"
}
]
}
4 changes: 2 additions & 2 deletions test/preprocessing/test_fragmentdb.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
using BiochemicalAlgorithms: get_reference_fragment

for fdb in (default_fragmentdb(), FragmentDB(), FragmentDB{Float32}(), FragmentDB{Float64}())
@test length(fdb.fragments) == 33
@test length(fdb.fragments) == 35
@test length(fdb.name_mappings) == 6
@test length(fdb.defaults) == 1
@test fdb.defaults["Naming"] == "PDB"
Expand Down Expand Up @@ -52,7 +52,7 @@
end

# show method
@test contains(repr(fdb), "33 fragments")
@test contains(repr(fdb), "35 fragments")
end
end

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