Package evaluation to test BiochemicalAlgorithms on Julia 1.14.0-DEV.1786 (45ee44a91e*) started at 2026-02-23T00:05:52.875 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 11.94s ################################################################################ # Installation # Installing BiochemicalAlgorithms... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [9d651bdf] + BiochemicalAlgorithms v0.6.0 Updating `~/.julia/environments/v1.14/Manifest.toml` [47edcb42] + ADTypes v1.21.0 [1520ce14] + AbstractTrees v0.4.5 [7d9f7c33] + Accessors v0.1.43 [79e6a3ab] + Adapt v4.4.0 [ec485272] + ArnoldiMethod v0.4.0 [4fba245c] + ArrayInterface v7.22.0 [15f4f7f2] + AutoHashEquals v2.2.0 [47718e42] + BioGenerics v0.1.5 [de9282ab] + BioStructures v4.7.1 [3c28c6f8] + BioSymbols v5.2.0 [9d651bdf] + BiochemicalAlgorithms v0.6.0 [e1450e63] + BufferedStreams v1.2.2 [336ed68f] + CSV v0.10.16 [49dc2e85] + Calculus v0.5.2 [69e1c6dd] + CellListMap v0.9.17 [ae650224] + ChunkSplitters v3.2.0 [944b1d66] + CodecZlib v0.7.8 [3da002f7] + ColorTypes v0.12.1 [5ae59095] + Colors v0.13.1 [38540f10] + CommonSolve v0.2.6 [34da2185] + Compat v4.18.1 [a33af91c] + CompositionsBase v0.1.2 [88cd18e8] + ConsoleProgressMonitor v0.1.2 [187b0558] + ConstructionBase v1.6.0 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.8.1 [864edb3b] + DataStructures v0.19.3 [e2d170a0] + DataValueInterfaces v1.0.0 [8bb1440f] + DelimitedFiles v1.9.1 [a0c0ee7d] + DifferentiationInterface v0.7.16 [ffbed154] + DocStringExtensions v0.9.5 [4e289a0a] + EnumX v1.0.6 [e2ba6199] + ExprTools v0.1.10 [55351af7] + ExproniconLite v0.10.14 [411431e0] + Extents v0.1.6 [9aa1b823] + FastClosures v0.3.2 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.16.0 [53c48c17] + FixedPointNumbers v0.8.5 [1fa38f19] + Format v1.3.7 [069b7b12] + FunctionWrappers v1.1.3 [77dc65aa] + FunctionWrappersWrappers v0.1.3 [46192b85] + GPUArraysCore v0.2.0 [5c1252a2] + GeometryBasics v0.5.10 [86223c79] + Graphs v1.13.4 [d25df0c9] + Inflate v0.1.5 [842dd82b] + InlineStrings v1.4.5 [8197267c] + IntervalSets v0.7.13 [3587e190] + InverseFunctions v0.1.17 [41ab1584] + InvertedIndices v1.3.1 [c8e1da08] + IterTools v1.10.0 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.1 [682c06a0] + JSON v1.4.0 [0f8b85d8] + JSON3 v1.14.3 [ae98c720] + Jieko v0.2.1 [5be7bae1] + LBFGSB v0.4.1 [b964fa9f] + LaTeXStrings v1.4.0 [1d6d02ad] + LeftChildRightSiblingTrees v0.2.1 [e6f89c97] + LoggingExtras v1.2.0 [1914dd2f] + MacroTools v0.5.16 [20f20a25] + MakieCore v0.10.0 [eff96d63] + Measurements v2.14.1 [c116f080] + Mendeleev v1.0.2 [626554b9] + MetaGraphs v0.9.0 [e1d29d7a] + Missings v1.2.0 [6c89ec66] + MolecularGraph v0.22.0 [2e0e35c7] + Moshi v0.3.7 [510215fc] + Observables v0.5.5 [7f7a1694] + Optimization v5.5.0 [bca83a33] + OptimizationBase v5.0.0 [22f7324a] + OptimizationLBFGSB v1.4.0 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.37 [d96e819e] + Parameters v0.12.3 [69de0a69] + Parsers v2.8.3 [5ad8b20f] + PhysicalConstants v0.2.4 [2dfb63ee] + PooledArrays v1.4.3 [d236fae5] + PreallocationTools v1.1.2 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.1 [08abe8d2] + PrettyTables v3.2.3 [33c8b6b6] + ProgressLogging v0.1.6 [92933f4c] + ProgressMeter v1.11.0 [94ee1d12] + Quaternions v0.7.7 [c1ae055f] + RealDot v0.1.0 [3cdcf5f2] + RecipesBase v1.3.4 [731186ca] + RecursiveArrayTools v3.48.0 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [f2b01f46] + Roots v2.2.12 [6038ab10] + Rotations v1.7.1 [7e49a35a] + RuntimeGeneratedFunctions v0.5.17 [6ef1bc8b] + Scanf v0.5.4 [0bca4576] + SciMLBase v2.142.1 [a6db7da4] + SciMLLogging v1.9.1 [c0aeaf25] + SciMLOperators v1.15.1 [431bcebd] + SciMLPublic v1.0.1 [53ae85a6] + SciMLStructures v1.10.0 [91c51154] + SentinelArrays v1.4.9 [efcf1570] + Setfield v1.1.2 [699a6c99] + SimpleTraits v0.9.5 [a2af1166] + SortingAlgorithms v1.2.2 [9f842d2f] + SparseConnectivityTracer v1.2.1 [0a514795] + SparseMatrixColorings v0.4.23 [90137ffa] + StaticArrays v1.9.17 [1e83bf80] + StaticArraysCore v1.4.4 [10745b16] + Statistics v1.11.1 [69024149] + StringEncodings v0.3.7 [892a3eda] + StringManipulation v0.4.2 [856f2bd8] + StructTypes v1.11.0 [ec057cc2] + StructUtils v2.6.3 [2efcf032] + SymbolicIndexingInterface v0.3.46 [ab02a1b2] + TableOperations v1.2.0 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [5d786b92] + TerminalLoggers v0.1.7 [1c621080] + TestItems v1.0.0 [3bb67fe8] + TranscodingStreams v0.11.3 [3a884ed6] + UnPack v1.0.2 [1986cc42] + Unitful v1.28.0 [a7773ee8] + UnitfulAtomic v1.0.0 [ea10d353] + WeakRefStrings v1.4.2 [76eceee3] + WorkerUtilities v1.6.1 [ddb6d928] + YAML v0.4.16 [5ae413db] + EarCut_jll v2.2.4+0 [81d17ec3] + L_BFGS_B_jll v3.0.1+0 [94ce4f54] + Libiconv_jll v1.18.0+0 [f6050b86] + coordgenlibs_jll v3.0.2+0 [172afb32] + libinchi_jll v1.6.0+0 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [f43a241f] + Downloads v1.7.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.13.0 [b27032c2] + LibCURL v1.0.0 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.14.0 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.0.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.13.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] + LibCURL_jll v8.18.0+0 [e37daf67] + LibGit2_jll v1.9.2+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.12.2 [4536629a] + OpenBLAS_jll v0.3.30+0 [458c3c95] + OpenSSL_jll v3.5.5+0 [efcefdf7] + PCRE2_jll v10.47.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.68.0+1 [3f19e933] + p7zip_jll v17.7.0+0 Installation completed after 5.92s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling packages... 9382.0 ms ✓ BioStructures → BioStructuresDataFramesExt 3634.4 ms ✓ MetaGraphs 8230.2 ms ✓ MakieCore 4053.4 ms ✓ BioStructures → BioStructuresGraphsExt 23425.5 ms ✓ MolecularGraph 47836.8 ms ✓ BiochemicalAlgorithms 6 dependencies successfully precompiled in 100 seconds. 223 already precompiled. Precompilation completed after 121.32s ################################################################################ # Testing # Testing BiochemicalAlgorithms Status `/tmp/jl_yCozTl/Project.toml` [4c88cf16] Aqua v0.8.14 [15f4f7f2] AutoHashEquals v2.2.0 [de9282ab] BioStructures v4.7.1 [3c28c6f8] BioSymbols v5.2.0 [9d651bdf] BiochemicalAlgorithms v0.6.0 [336ed68f] CSV v0.10.16 [69e1c6dd] CellListMap v0.9.17 [a93c6f00] DataFrames v1.8.1 [864edb3b] DataStructures v0.19.3 [ffbed154] DocStringExtensions v0.9.5 [4e289a0a] EnumX v1.0.6 [86223c79] Graphs v1.13.4 [0f8b85d8] JSON3 v1.14.3 [c116f080] Mendeleev v1.0.2 [626554b9] MetaGraphs v0.9.0 [6c89ec66] MolecularGraph v0.22.0 [510215fc] Observables v0.5.5 [7f7a1694] Optimization v5.5.0 [22f7324a] OptimizationLBFGSB v1.4.0 [5ad8b20f] PhysicalConstants v0.2.4 [08abe8d2] PrettyTables v3.2.3 [94ee1d12] Quaternions v0.7.7 [6038ab10] Rotations v1.7.1 [6ef1bc8b] Scanf v0.5.4 [90137ffa] StaticArrays v1.9.17 [10745b16] Statistics v1.11.1 [856f2bd8] StructTypes v1.11.0 [ab02a1b2] TableOperations v1.2.0 [bd369af6] Tables v1.12.1 [f8b46487] TestItemRunner v1.1.4 [1986cc42] Unitful v1.28.0 [a7773ee8] UnitfulAtomic v1.0.0 [ade2ca70] Dates v1.11.0 [37e2e46d] LinearAlgebra v1.13.0 [de0858da] Printf v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_yCozTl/Manifest.toml` [47edcb42] ADTypes v1.21.0 [1520ce14] AbstractTrees v0.4.5 [7d9f7c33] Accessors v0.1.43 [79e6a3ab] Adapt v4.4.0 [4c88cf16] Aqua v0.8.14 [ec485272] ArnoldiMethod v0.4.0 [4fba245c] ArrayInterface v7.22.0 [15f4f7f2] AutoHashEquals v2.2.0 [47718e42] BioGenerics v0.1.5 [de9282ab] BioStructures v4.7.1 [3c28c6f8] BioSymbols v5.2.0 [9d651bdf] BiochemicalAlgorithms v0.6.0 [e1450e63] BufferedStreams v1.2.2 [336ed68f] CSV v0.10.16 [49dc2e85] Calculus v0.5.2 [69e1c6dd] CellListMap v0.9.17 [ae650224] ChunkSplitters v3.2.0 [944b1d66] CodecZlib v0.7.8 [3da002f7] ColorTypes v0.12.1 [5ae59095] Colors v0.13.1 [38540f10] CommonSolve v0.2.6 [34da2185] Compat v4.18.1 [a33af91c] CompositionsBase v0.1.2 [88cd18e8] ConsoleProgressMonitor v0.1.2 [187b0558] ConstructionBase v1.6.0 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.1 [864edb3b] DataStructures v0.19.3 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [a0c0ee7d] DifferentiationInterface v0.7.16 [ffbed154] DocStringExtensions v0.9.5 [4e289a0a] EnumX v1.0.6 [e2ba6199] ExprTools v0.1.10 [55351af7] ExproniconLite v0.10.14 [411431e0] Extents v0.1.6 [9aa1b823] FastClosures v0.3.2 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.16.0 [53c48c17] FixedPointNumbers v0.8.5 [1fa38f19] Format v1.3.7 [069b7b12] FunctionWrappers v1.1.3 [77dc65aa] FunctionWrappersWrappers v0.1.3 [46192b85] GPUArraysCore v0.2.0 [5c1252a2] GeometryBasics v0.5.10 [86223c79] Graphs v1.13.4 [d25df0c9] Inflate v0.1.5 [842dd82b] InlineStrings v1.4.5 [8197267c] IntervalSets v0.7.13 [3587e190] InverseFunctions v0.1.17 [41ab1584] InvertedIndices v1.3.1 [c8e1da08] IterTools v1.10.0 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.1 [682c06a0] JSON v1.4.0 [0f8b85d8] JSON3 v1.14.3 [ae98c720] Jieko v0.2.1 [5be7bae1] LBFGSB v0.4.1 [b964fa9f] LaTeXStrings v1.4.0 [1d6d02ad] LeftChildRightSiblingTrees v0.2.1 [e6f89c97] LoggingExtras v1.2.0 [1914dd2f] MacroTools v0.5.16 [20f20a25] MakieCore v0.10.0 [eff96d63] Measurements v2.14.1 [c116f080] Mendeleev v1.0.2 [626554b9] MetaGraphs v0.9.0 [e1d29d7a] Missings v1.2.0 [6c89ec66] MolecularGraph v0.22.0 [2e0e35c7] Moshi v0.3.7 [510215fc] Observables v0.5.5 [7f7a1694] Optimization v5.5.0 [bca83a33] OptimizationBase v5.0.0 [22f7324a] OptimizationLBFGSB v1.4.0 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.37 [d96e819e] Parameters v0.12.3 [69de0a69] Parsers v2.8.3 [5ad8b20f] PhysicalConstants v0.2.4 [2dfb63ee] PooledArrays v1.4.3 [d236fae5] PreallocationTools v1.1.2 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.1 [08abe8d2] PrettyTables v3.2.3 [33c8b6b6] ProgressLogging v0.1.6 [92933f4c] ProgressMeter v1.11.0 [94ee1d12] Quaternions v0.7.7 [c1ae055f] RealDot v0.1.0 [3cdcf5f2] RecipesBase v1.3.4 [731186ca] RecursiveArrayTools v3.48.0 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [f2b01f46] Roots v2.2.12 [6038ab10] Rotations v1.7.1 [7e49a35a] RuntimeGeneratedFunctions v0.5.17 [6ef1bc8b] Scanf v0.5.4 [0bca4576] SciMLBase v2.142.1 [a6db7da4] SciMLLogging v1.9.1 [c0aeaf25] SciMLOperators v1.15.1 [431bcebd] SciMLPublic v1.0.1 [53ae85a6] SciMLStructures v1.10.0 [91c51154] SentinelArrays v1.4.9 [efcf1570] Setfield v1.1.2 [699a6c99] SimpleTraits v0.9.5 [a2af1166] SortingAlgorithms v1.2.2 [9f842d2f] SparseConnectivityTracer v1.2.1 [0a514795] SparseMatrixColorings v0.4.23 [90137ffa] StaticArrays v1.9.17 [1e83bf80] StaticArraysCore v1.4.4 [10745b16] Statistics v1.11.1 [69024149] StringEncodings v0.3.7 [892a3eda] StringManipulation v0.4.2 [856f2bd8] StructTypes v1.11.0 [ec057cc2] StructUtils v2.6.3 [2efcf032] SymbolicIndexingInterface v0.3.46 [ab02a1b2] TableOperations v1.2.0 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [5d786b92] TerminalLoggers v0.1.7 [f8b46487] TestItemRunner v1.1.4 [1c621080] TestItems v1.0.0 [3bb67fe8] TranscodingStreams v0.11.3 [3a884ed6] UnPack v1.0.2 [1986cc42] Unitful v1.28.0 [a7773ee8] UnitfulAtomic v1.0.0 [ea10d353] WeakRefStrings v1.4.2 [76eceee3] WorkerUtilities v1.6.1 [ddb6d928] YAML v0.4.16 [5ae413db] EarCut_jll v2.2.4+0 [81d17ec3] L_BFGS_B_jll v3.0.1+0 [94ce4f54] Libiconv_jll v1.18.0+0 [f6050b86] coordgenlibs_jll v3.0.2+0 [172afb32] libinchi_jll v1.6.0+0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [f43a241f] Downloads v1.7.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.13.0 [b27032c2] LibCURL v1.0.0 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.13.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.14.0 [de0858da] Printf v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.0.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.13.0 [4607b0f0] SuiteSparse [fa267f1f] TOML v1.0.3 [a4e569a6] Tar v1.10.0 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] LibCURL_jll v8.18.0+0 [e37daf67] LibGit2_jll v1.9.2+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.12.2 [4536629a] OpenBLAS_jll v0.3.30+0 [458c3c95] OpenSSL_jll v3.5.5+0 [efcefdf7] PCRE2_jll v10.47.0+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.68.0+1 [3f19e933] p7zip_jll v17.7.0+0 Testing Running tests... ┌ Error: illegal HIN file in line 31: cannot finalize bond (29, 30, BiochemicalAlgorithms.BondOrder.Single)! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/fileformats/hinfile.jl:232 ┌ Error: illegal HIN file in line 31: cannot finalize bond (29, 30, BiochemicalAlgorithms.BondOrder.Single)! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/fileformats/hinfile.jl:232 ┌ Warning: Atom names in HIN files cannot contain spaces! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/fileformats/hinfile.jl:446 ┌ Warning: Atom names in HIN files cannot contain spaces! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/fileformats/hinfile.jl:446 [ Info: reconstruct_fragments!(): added 0 atoms. [ Info: build_bonds!(): built 22 bonds ┌ Warning: 2 warnings occurred during setup that were suppressed: │ - Torsion: 2 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/forcefields/common/forcefield.jl:231 ┌ Warning: 5 warnings occurred during setup that were suppressed: │ - Torsion: 5 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/forcefields/common/forcefield.jl:231 ┌ Warning: 20 warnings occurred during setup that were suppressed: │ - QuadraticBondStretch: 3 warnings │ - QuadraticAngleBend : 12 warnings │ - Torsion : 5 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/forcefields/common/forcefield.jl:231 ┌ Warning: 5 warnings occurred during setup that were suppressed: │ - Torsion: 5 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/forcefields/common/forcefield.jl:231 ┌ Warning: 5 warnings occurred during setup that were suppressed: │ - Torsion: 5 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/forcefields/common/forcefield.jl:231 ┌ Warning: 20 warnings occurred during setup that were suppressed: │ - QuadraticBondStretch: 3 warnings │ - QuadraticAngleBend : 12 warnings │ - Torsion : 5 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/forcefields/common/forcefield.jl:231 ┌ Warning: 5 warnings occurred during setup that were suppressed: │ - Torsion: 5 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/forcefields/common/forcefield.jl:231 [ Info: reconstruct_fragments!(): added 0 atoms. [ Info: build_bonds!(): built 22 bonds ┌ Warning: 2 warnings occurred during setup that were suppressed: │ - Torsion: 2 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/forcefields/common/forcefield.jl:231 [ Info: reconstruct_fragments!(): added 0 atoms. [ Info: build_bonds!(): built 22 bonds ┌ Warning: 2 warnings occurred during setup that were suppressed: │ - Torsion: 2 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/forcefields/common/forcefield.jl:231 [ Info: build_bonds!(): built 18 bonds ┌ Warning: Cannot calculate psi angle, no previous or next fragment found └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/core/fragment.jl:707 ┌ Warning: Cannot calculate phi angle, no previous or next fragment found └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/core/fragment.jl:752 ┌ Warning: Cannot calculate omega angle, no previous or next fragment found └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/core/fragment.jl:798 [ Info: build_bonds!(): built 18 bonds ┌ Warning: Cannot calculate psi angle, no previous or next fragment found └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/core/fragment.jl:707 ┌ Warning: Cannot calculate phi angle, no previous or next fragment found └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/core/fragment.jl:752 ┌ Warning: Cannot calculate omega angle, no previous or next fragment found └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/core/fragment.jl:798 [ Info: build_bonds!(): built 18 bonds [ Info: build_bonds!(): built 18 bonds [ Info: reconstruct_fragments!(): added 1423 atoms. [ Info: build_bonds!(): built 3839 bonds [ Info: reconstruct_fragments!(): added 1423 atoms. [ Info: build_bonds!(): built 3839 bonds [ Info: reconstruct_fragments!(): added 0 atoms. [ Info: build_bonds!(): built 22 bonds [ Info: reconstruct_fragments!(): added 0 atoms. [ Info: build_bonds!(): built 22 bonds [ Info: reconstruct_fragments!(): added 0 atoms. [ Info: build_bonds!(): built 897 bonds [ Info: Added 30 hydrogen bonds. ┌ Warning: reconstruct_fragments!(): could not find reference fragment for PO4:70 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for UNX:324 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:80 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:101 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:102 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:105 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:110 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:111 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:112 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:113 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:116 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:117 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:119 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:121 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:122 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:125 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:126 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:127 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:129 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:133 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:134 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:138 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:140 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:143 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:144 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:145 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:146 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:156 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:157 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:158 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:159 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:160 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:200 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:201 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:202 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:203 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:204 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:205 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:209 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:210 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:211 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:212 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:214 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:216 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:217 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:218 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:219 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:220 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:223 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:225 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:302 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:304 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:310 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:311 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:312 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:313 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:314 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:315 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:316 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:317 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:318 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:319 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:320 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:321 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:322 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 [ Info: reconstruct_fragments!(): added 103 atoms. ┌ Warning: build_bonds!(): could not find reference fragment for PO4. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for UNX. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 [ Info: build_bonds!(): built 903 bonds [ Info: Added 30 hydrogen bonds. [ Info: reconstruct_fragments!(): added 0 atoms. [ Info: build_bonds!(): built 897 bonds [ Info: Added 30 hydrogen bonds. ┌ Warning: reconstruct_fragments!(): could not find reference fragment for PO4:70 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for UNX:324 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:80 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:101 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:102 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:105 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:110 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:111 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:112 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:113 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:116 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:117 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:119 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:121 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:122 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:125 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:126 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:127 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:129 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:133 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:134 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:138 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:140 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:143 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:144 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:145 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:146 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:156 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:157 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:158 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:159 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:160 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:200 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:201 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:202 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:203 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:204 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:205 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:209 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:210 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:211 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:212 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:214 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:216 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:217 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:218 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:219 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:220 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:223 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:225 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:302 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:304 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:310 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:311 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:312 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:313 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:314 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:315 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:316 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:317 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:318 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:319 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:320 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:321 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:322 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/reconstruct_fragments.jl:177 [ Info: reconstruct_fragments!(): added 103 atoms. ┌ Warning: build_bonds!(): could not find reference fragment for PO4. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for UNX. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/preprocessing/build_bonds.jl:14 [ Info: build_bonds!(): built 903 bonds [ Info: Added 30 hydrogen bonds. [ Info: reconstruct_fragments!(): added 0 atoms. [ Info: build_bonds!(): built 22 bonds [ Info: Added 1 atoms. [ Info: reconstruct_fragments!(): added 0 atoms. [ Info: build_bonds!(): built 22 bonds [ Info: Added 1 atoms. ┌ Warning: Correlation matrix is not positive definit! Computing rotation through `RMSDMinimizerCoutsias` instead! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/mappings/rigid_mapping.jl:176 ┌ Warning: Correlation matrix is not positive definit! Computing rotation through `RMSDMinimizerCoutsias` instead! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/mappings/rigid_mapping.jl:176 ┌ Warning: Correlation matrix is not positive definit! Computing rotation through `RMSDMinimizerCoutsias` instead! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/mappings/rigid_mapping.jl:176 ┌ Warning: Correlation matrix is not positive definit! Computing rotation through `RMSDMinimizerCoutsias` instead! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/mappings/rigid_mapping.jl:176 ┌ Warning: Correlation matrix is not positive definit! Computing rotation through `RMSDMinimizerCoutsias` instead! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/mappings/rigid_mapping.jl:176 ┌ Warning: Correlation matrix is not positive definit! Computing rotation through `RMSDMinimizerCoutsias` instead! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/BxXu8/src/mappings/rigid_mapping.jl:176 [ Info: 1 records exported. [ Info: 11 records exported. [ Info: 1 records exported. [ Info: 11 records exported. [ Info: reconstruct_fragments!(): added 21 atoms. [ Info: reconstruct_fragments!(): added 21 atoms. Test Summary: | Pass Total Time Package | 8352 8352 23m25.8s test/core/test_chain.jl | 462 462 1m13.6s ChainTable | 206 206 57.6s Chain | 256 256 16.0s test/substructures/test_smarts.jl | 30 30 1m29.7s SMARTS | 30 30 1m29.7s test/aqua.jl | 11 11 4m15.8s Aqua | 11 11 4m15.8s Method ambiguity | 1 1 40.5s Unbound type parameters | 1 1 0.1s Undefined exports | 1 1 0.0s Compare Project.toml and test/Project.toml | 1 1 0.0s Stale dependencies | 1 1 31.7s Compat bounds | 4 4 0.7s Piracy | 1 1 1m00.9s Persistent tasks | 1 1 1m32.6s test/substructures/test_substructure.jl | 6 6 10.7s Substructure | 6 6 10.7s test/fileformats/test_hinfile.jl | 52 52 17.4s Read HIN | 48 48 6.9s Write HIN | 4 4 10.5s test/forcefields/AMBER/test_amberff.jl | 1951 1951 4m13.5s AmberFF | 1951 1951 4m13.5s test/core/test_atom.jl | 606 606 27.4s AtomTable | 308 308 9.6s Atom | 298 298 17.7s test/optimization/test_optimize_structure.jl | 6 6 14.7s Optimize structure | 3 3 10.0s Optimize hydrogen positions | 3 3 4.7s test/core/test_element.jl | 126 126 0.2s Element | 126 126 0.2s test/core/test_fragment.jl | 1840 1840 1m52.7s FragmentTable | 266 266 11.3s FragmentTable/None | 178 178 1.5s FragmentTable/Nucleotide | 178 178 1.8s FragmentTable/Residue | 178 178 1.7s Fragment | 118 118 4.5s Fragment/None | 272 272 14.6s Fragment/Nucleotide | 272 272 13.5s Fragment/Residue | 272 272 13.4s Fragment/*_torsion | 60 60 42.3s Fragment/calculate_torsion_angle | 4 4 0.3s Fragment/calculate_bond_angle | 6 6 1.9s Fragment/apply_torsion_angle | 36 36 6.0s test/core/test_amino_acid.jl | 63 63 0.4s AminoAcid | 63 63 0.4s test/core/test_secondary_structure.jl | 514 514 28.2s SecondaryStructureTable | 240 240 8.5s SecondaryStructure | 274 274 19.7s test/fileformats/test_pdb.jl | 130 130 2m14.5s Read PDB | 56 56 14.1s Write PDB | 42 42 1m01.3s Read PDBx/mmCIF | 18 18 46.9s Write PDBx/mmCIF | 14 14 12.1s test/core/test_types.jl | 106 106 2.0s Vector3 | 51 51 1.0s Matrix3 | 51 51 1.0s Properties | 2 2 0.0s Flags | 2 2 0.0s test/core/test_tables.jl | 8 8 21.3s AbstractColumnTable | 8 8 21.3s test/core/test_system.jl | 664 664 2m50.3s System | 664 664 2m50.3s test/core/test_bond_order.jl | 8 8 0.0s Bond Order | 8 8 0.0s test/core/test_moleculargraph_wrapper.jl | 162 162 2.3s Convert to SDFMolGraph | 162 162 2.3s test/preprocessing/test_predict_secondary_structure.jl | 6 6 59.9s predict secondary structure | 6 6 59.9s test/core/test_system_component_table.jl | 78 78 1.3s SystemComponentTableCol | 78 78 1.3s test/substructures/test_sssr.jl | 3 3 14.9s Ring Perception | 3 3 14.9s test/core/test_molecule.jl | 834 834 21.6s MoleculeTable | 238 238 10.0s MoleculeTable/None | 146 146 1.6s MoleculeTable/Protein | 146 146 1.5s Molecule | 68 68 1.1s Molecule/None | 118 118 4.6s Molecule/Protein | 118 118 2.7s test/preprocessing/test_add_hydrogens.jl | 2 2 35.6s FragmentDB | 2 2 35.6s test/core/test_bond.jl | 312 312 8.4s BondTable | 176 176 4.2s Bond | 136 136 4.3s test/fileformats/test_pubchem_json.jl | 106 106 5.1s Read PubChem | 106 106 5.1s test/mappings/test_mappings.jl | 224 224 26.2s TrivialAtomBijection | 8 8 0.5s RigidTransform | 16 16 0.5s translate! | 88 88 2.2s rigid_transform! | 44 44 3.8s compute_rmsd | 14 14 3.3s compute_rmsd_minimizer | 42 42 12.4s map_rigid! | 12 12 3.3s test/preprocessing/test_fragmentdb.jl | 4 4 1.7s FragmentDB | 4 4 1.7s test/fileformats/test_sdfile.jl | 32 32 15.7s Read SDFile | 30 30 3.4s Write SDFile | 2 2 12.3s test/preprocessing/test_reconstruct_fragments.jl | 6 6 0.5s reconstruct_fragments!() | 6 6 0.5s Testing BiochemicalAlgorithms tests passed Testing completed after 1457.18s PkgEval succeeded after 1614.02s