If you think that there is an error in how your package is being tested or represented, please file an issue at NewPkgEval.jl , making sure to read the FAQ first.
Results with Julia v1.2.0
Testing was successful .
Last evaluation was ago and took 13 minutes, 28 seconds.
Click here to download the log file.
Click here to show the log contents.
Resolving package versions...
Installed DataAPI ──────────────── v1.1.0
Installed Missings ─────────────── v0.4.3
Installed Showoff ──────────────── v0.3.1
Installed Contour ──────────────── v0.5.1
Installed LineSearches ─────────── v7.0.1
Installed Colors ───────────────── v0.9.6
Installed CoupledFields ────────── v0.1.0
Installed ProteinEnsembles ─────── v0.3.0
Installed BinaryProvider ───────── v0.5.8
Installed AbstractFFTs ─────────── v0.5.0
Installed PDMats ───────────────── v0.9.10
Installed Tokenize ─────────────── v0.5.7
Installed Measures ─────────────── v0.3.0
Installed CommonSubexpressions ─── v0.2.0
Installed Conda ────────────────── v1.3.0
Installed StatsBase ────────────── v0.32.0
Installed StatsFuns ────────────── v0.9.0
Installed URIParser ────────────── v0.4.0
Installed AxisAlgorithms ───────── v1.0.0
Installed DocStringExtensions ──── v0.7.0
Installed NLSolversBase ────────── v7.5.0
Installed ArgParse ─────────────── v0.6.2
Installed Compose ──────────────── v0.7.4
Installed CSTParser ────────────── v1.1.0
Installed Reexport ─────────────── v0.2.0
Installed Requires ─────────────── v0.5.2
Installed OffsetArrays ─────────── v0.11.2
Installed Rmath ────────────────── v0.5.1
Installed Compat ───────────────── v2.2.0
Installed ForwardDiff ──────────── v0.10.7
Installed Loess ────────────────── v0.5.0
Installed OrderedCollections ───── v1.1.0
Installed IterTools ────────────── v1.3.0
Installed Calculus ─────────────── v0.5.1
Installed KernelDensity ────────── v0.5.1
Installed FixedPointNumbers ────── v0.6.1
Installed TextWrap ─────────────── v0.3.0
Installed DataStructures ───────── v0.15.0
Installed FillArrays ───────────── v0.8.2
Installed DiffEqDiffTools ──────── v1.5.0
Installed Distributions ────────── v0.19.2
Installed Gadfly ───────────────── v1.1.0
Installed DiffRules ────────────── v0.1.0
Installed JSON ─────────────────── v0.20.0
Installed ArrayInterface ───────── v2.0.0
Installed Graphics ─────────────── v0.4.0
Installed Ratios ───────────────── v0.3.1
Installed StaticArrays ─────────── v0.12.1
Installed Media ────────────────── v0.5.0
Installed Cairo ────────────────── v0.8.0
Installed Juno ─────────────────── v0.7.2
Installed NaNMath ──────────────── v0.3.3
Installed FFTW ─────────────────── v1.1.0
Installed DiffResults ──────────── v0.0.4
Installed Interpolations ───────── v0.12.5
Installed Parameters ───────────── v0.12.0
Installed Hexagons ─────────────── v0.2.0
Installed QuadGK ───────────────── v2.1.1
Installed CategoricalArrays ────── v0.5.5
Installed WoodburyMatrices ─────── v0.4.1
Installed SortingAlgorithms ────── v0.3.1
Installed IndirectArrays ───────── v0.5.0
Installed VersionParsing ───────── v1.1.3
Installed Distances ────────────── v0.8.2
Installed MacroTools ───────────── v0.5.1
Installed PositiveFactorizations ─ v0.2.3
Installed ColorTypes ───────────── v0.8.0
Installed SpecialFunctions ─────── v0.8.0
Installed BinDeps ──────────────── v0.8.10
Installed ProgressMeter ────────── v1.2.0
Installed Optim ────────────────── v0.19.5
Installed Arpack ───────────────── v0.3.1
Updating `~/.julia/environments/v1.2/Project.toml`
[186d2b2d] + ProteinEnsembles v0.3.0
Updating `~/.julia/environments/v1.2/Manifest.toml`
[621f4979] + AbstractFFTs v0.5.0
[c7e460c6] + ArgParse v0.6.2
[7d9fca2a] + Arpack v0.3.1
[4fba245c] + ArrayInterface v2.0.0
[13072b0f] + AxisAlgorithms v1.0.0
[9e28174c] + BinDeps v0.8.10
[b99e7846] + BinaryProvider v0.5.8
[00ebfdb7] + CSTParser v1.1.0
[159f3aea] + Cairo v0.8.0
[49dc2e85] + Calculus v0.5.1
[324d7699] + CategoricalArrays v0.5.5
[3da002f7] + ColorTypes v0.8.0
[5ae59095] + Colors v0.9.6
[bbf7d656] + CommonSubexpressions v0.2.0
[34da2185] + Compat v2.2.0
[a81c6b42] + Compose v0.7.4
[8f4d0f93] + Conda v1.3.0
[d38c429a] + Contour v0.5.1
[7ad07ef1] + CoupledFields v0.1.0
[9a962f9c] + DataAPI v1.1.0
[864edb3b] + DataStructures v0.15.0
[01453d9d] + DiffEqDiffTools v1.5.0
[163ba53b] + DiffResults v0.0.4
[b552c78f] + DiffRules v0.1.0
[b4f34e82] + Distances v0.8.2
[31c24e10] + Distributions v0.19.2
[ffbed154] + DocStringExtensions v0.7.0
[7a1cc6ca] + FFTW v1.1.0
[1a297f60] + FillArrays v0.8.2
[53c48c17] + FixedPointNumbers v0.6.1
[f6369f11] + ForwardDiff v0.10.7
[c91e804a] + Gadfly v1.1.0
[a2bd30eb] + Graphics v0.4.0
[a1b4810d] + Hexagons v0.2.0
[9b13fd28] + IndirectArrays v0.5.0
[a98d9a8b] + Interpolations v0.12.5
[c8e1da08] + IterTools v1.3.0
[682c06a0] + JSON v0.20.0
[e5e0dc1b] + Juno v0.7.2
[5ab0869b] + KernelDensity v0.5.1
[d3d80556] + LineSearches v7.0.1
[4345ca2d] + Loess v0.5.0
[1914dd2f] + MacroTools v0.5.1
[442fdcdd] + Measures v0.3.0
[e89f7d12] + Media v0.5.0
[e1d29d7a] + Missings v0.4.3
[d41bc354] + NLSolversBase v7.5.0
[77ba4419] + NaNMath v0.3.3
[6fe1bfb0] + OffsetArrays v0.11.2
[429524aa] + Optim v0.19.5
[bac558e1] + OrderedCollections v1.1.0
[90014a1f] + PDMats v0.9.10
[d96e819e] + Parameters v0.12.0
[85a6dd25] + PositiveFactorizations v0.2.3
[92933f4c] + ProgressMeter v1.2.0
[186d2b2d] + ProteinEnsembles v0.3.0
[1fd47b50] + QuadGK v2.1.1
[c84ed2f1] + Ratios v0.3.1
[189a3867] + Reexport v0.2.0
[ae029012] + Requires v0.5.2
[79098fc4] + Rmath v0.5.1
[992d4aef] + Showoff v0.3.1
[a2af1166] + SortingAlgorithms v0.3.1
[276daf66] + SpecialFunctions v0.8.0
[90137ffa] + StaticArrays v0.12.1
[2913bbd2] + StatsBase v0.32.0
[4c63d2b9] + StatsFuns v0.9.0
[b718987f] + TextWrap v0.3.0
[0796e94c] + Tokenize v0.5.7
[30578b45] + URIParser v0.4.0
[81def892] + VersionParsing v1.1.3
[efce3f68] + WoodburyMatrices v0.4.1
[2a0f44e3] + Base64
[ade2ca70] + Dates
[8bb1440f] + DelimitedFiles
[8ba89e20] + Distributed
[9fa8497b] + Future
[b77e0a4c] + InteractiveUtils
[76f85450] + LibGit2
[8f399da3] + Libdl
[37e2e46d] + LinearAlgebra
[56ddb016] + Logging
[d6f4376e] + Markdown
[a63ad114] + Mmap
[44cfe95a] + Pkg
[de0858da] + Printf
[9abbd945] + Profile
[3fa0cd96] + REPL
[9a3f8284] + Random
[ea8e919c] + SHA
[9e88b42a] + Serialization
[1a1011a3] + SharedArrays
[6462fe0b] + Sockets
[2f01184e] + SparseArrays
[10745b16] + Statistics
[4607b0f0] + SuiteSparse
[8dfed614] + Test
[cf7118a7] + UUIDs
[4ec0a83e] + Unicode
Building Conda ───────────→ `~/.julia/packages/Conda/kLXeC/deps/build.log`
Building Rmath ───────────→ `~/.julia/packages/Rmath/4wt82/deps/build.log`
Building Cairo ───────────→ `~/.julia/packages/Cairo/ZbzIH/deps/build.log`
Building FFTW ────────────→ `~/.julia/packages/FFTW/loJ3F/deps/build.log`
Building SpecialFunctions → `~/.julia/packages/SpecialFunctions/ne2iw/deps/build.log`
Building Arpack ──────────→ `~/.julia/packages/Arpack/cu5By/deps/build.log`
Testing ProteinEnsembles
Resolving package versions...
Status `/tmp/jl_7pHx91/Manifest.toml`
[621f4979] AbstractFFTs v0.5.0
[c7e460c6] ArgParse v0.6.2
[7d9fca2a] Arpack v0.3.1
[4fba245c] ArrayInterface v2.0.0
[13072b0f] AxisAlgorithms v1.0.0
[9e28174c] BinDeps v0.8.10
[b99e7846] BinaryProvider v0.5.8
[00ebfdb7] CSTParser v1.1.0
[159f3aea] Cairo v0.8.0
[49dc2e85] Calculus v0.5.1
[324d7699] CategoricalArrays v0.5.5
[3da002f7] ColorTypes v0.8.0
[5ae59095] Colors v0.9.6
[bbf7d656] CommonSubexpressions v0.2.0
[34da2185] Compat v2.2.0
[a81c6b42] Compose v0.7.4
[8f4d0f93] Conda v1.3.0
[d38c429a] Contour v0.5.1
[7ad07ef1] CoupledFields v0.1.0
[9a962f9c] DataAPI v1.1.0
[864edb3b] DataStructures v0.15.0
[01453d9d] DiffEqDiffTools v1.5.0
[163ba53b] DiffResults v0.0.4
[b552c78f] DiffRules v0.1.0
[b4f34e82] Distances v0.8.2
[31c24e10] Distributions v0.19.2
[ffbed154] DocStringExtensions v0.7.0
[7a1cc6ca] FFTW v1.1.0
[1a297f60] FillArrays v0.8.2
[53c48c17] FixedPointNumbers v0.6.1
[f6369f11] ForwardDiff v0.10.7
[c91e804a] Gadfly v1.1.0
[a2bd30eb] Graphics v0.4.0
[a1b4810d] Hexagons v0.2.0
[9b13fd28] IndirectArrays v0.5.0
[a98d9a8b] Interpolations v0.12.5
[c8e1da08] IterTools v1.3.0
[682c06a0] JSON v0.20.0
[e5e0dc1b] Juno v0.7.2
[5ab0869b] KernelDensity v0.5.1
[d3d80556] LineSearches v7.0.1
[4345ca2d] Loess v0.5.0
[1914dd2f] MacroTools v0.5.1
[442fdcdd] Measures v0.3.0
[e89f7d12] Media v0.5.0
[e1d29d7a] Missings v0.4.3
[d41bc354] NLSolversBase v7.5.0
[77ba4419] NaNMath v0.3.3
[6fe1bfb0] OffsetArrays v0.11.2
[429524aa] Optim v0.19.5
[bac558e1] OrderedCollections v1.1.0
[90014a1f] PDMats v0.9.10
[d96e819e] Parameters v0.12.0
[85a6dd25] PositiveFactorizations v0.2.3
[92933f4c] ProgressMeter v1.2.0
[186d2b2d] ProteinEnsembles v0.3.0
[1fd47b50] QuadGK v2.1.1
[c84ed2f1] Ratios v0.3.1
[189a3867] Reexport v0.2.0
[ae029012] Requires v0.5.2
[79098fc4] Rmath v0.5.1
[992d4aef] Showoff v0.3.1
[a2af1166] SortingAlgorithms v0.3.1
[276daf66] SpecialFunctions v0.8.0
[90137ffa] StaticArrays v0.12.1
[2913bbd2] StatsBase v0.32.0
[4c63d2b9] StatsFuns v0.9.0
[b718987f] TextWrap v0.3.0
[0796e94c] Tokenize v0.5.7
[30578b45] URIParser v0.4.0
[81def892] VersionParsing v1.1.3
[efce3f68] WoodburyMatrices v0.4.1
[2a0f44e3] Base64 [`@stdlib/Base64`]
[ade2ca70] Dates [`@stdlib/Dates`]
[8bb1440f] DelimitedFiles [`@stdlib/DelimitedFiles`]
[8ba89e20] Distributed [`@stdlib/Distributed`]
[9fa8497b] Future [`@stdlib/Future`]
[b77e0a4c] InteractiveUtils [`@stdlib/InteractiveUtils`]
[76f85450] LibGit2 [`@stdlib/LibGit2`]
[8f399da3] Libdl [`@stdlib/Libdl`]
[37e2e46d] LinearAlgebra [`@stdlib/LinearAlgebra`]
[56ddb016] Logging [`@stdlib/Logging`]
[d6f4376e] Markdown [`@stdlib/Markdown`]
[a63ad114] Mmap [`@stdlib/Mmap`]
[44cfe95a] Pkg [`@stdlib/Pkg`]
[de0858da] Printf [`@stdlib/Printf`]
[9abbd945] Profile [`@stdlib/Profile`]
[3fa0cd96] REPL [`@stdlib/REPL`]
[9a3f8284] Random [`@stdlib/Random`]
[ea8e919c] SHA [`@stdlib/SHA`]
[9e88b42a] Serialization [`@stdlib/Serialization`]
[1a1011a3] SharedArrays [`@stdlib/SharedArrays`]
[6462fe0b] Sockets [`@stdlib/Sockets`]
[2f01184e] SparseArrays [`@stdlib/SparseArrays`]
[10745b16] Statistics [`@stdlib/Statistics`]
[4607b0f0] SuiteSparse [`@stdlib/SuiteSparse`]
[8dfed614] Test [`@stdlib/Test`]
[cf7118a7] UUIDs [`@stdlib/UUIDs`]
[4ec0a83e] Unicode [`@stdlib/Unicode`]
Test Summary: | Pass Total
Types | 8 8
Could not find element for atom with name X
Test Summary: | Pass Total
Atoms | 26 26
Read 214 residues from DSSP file
Read 1336 atoms from PDB file
Read 141 residues from DSSP file
Read 3312 atoms from PDB file
Read 3804 atoms from PDB file
Read 3312 atoms from PDB file
Read 3312 atoms from PDB file
Read 476 pocket points from pocket points PDB file
Read 43 pocket centres from LIGSITEcs output PDB file
Test Summary: | Pass Total
IO | 31 31
Read 2035 atoms from PDB file
Read 214 residues from DSSP file
Found distance constraints from single structure
Found combined distance constraints from two structures
Test Summary: | Pass Total
Interactions | 41 41
Kept lowest scoring 2 out of 4 structures
Scores range from 10.0 to 20.0
Test Summary: | Pass Total
Generate | 12 12
Test Summary: | Pass Total
Align | 11 11
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read in protein ensemble
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read in protein ensemble
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read in protein ensemble
Test Summary: | Pass Total
PCA | 10 10
Found 2 interactions between the modulator and the protein
Read 395 pocket points from LIGSITEcs pocket points PDB file
Read 43 pocket centres from LIGSITEcs output PDB file
Assigned all points
Wrote pocket number assignments to file "/tmp/jl_QT8AwW"
Test Summary: | Pass Total
Perturb | 9 9
-- ExProSE --
Arguments:
i1 - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CLL_H.pdb
d1 - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CLL.dssp
i2 - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CTR_H.pdb
d2 - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CTR.dssp
out_dir - /tmp/exprose_out
n_strucs - 4
tolerance_weight - 0.3
other_ratio - 20.0
extra_pdbs - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CFF_1.pdb, /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CFF_2.pdb
mod_path - nothing
n_mods - 0
Making output directory "/tmp/exprose_out"
Proceeding with two structures
Read 1367 atoms from PDB file
Read 1336 atoms from PDB file
Read 144 residues from DSSP file
Read 141 residues from DSSP file
Found interactions:
Covalently bonded - 1313
1-3 system - 1868
Same ring system - 35
Side-chain restricted 1-4 - 116
Omega 1-4 - 540
Tight phi/psi 1-4 - 692
Loose phi/psi 1-4 - 157
Other phi/psi 1-4 - 195
Other 1-4 - 589
Secondary structure - 3684
Salt bridge - 42
H bond - 230
Tight hydrophobic - 817
Loose hydrophobic - 878
Other pairs - 835795
Found distance constraints from single structure
Found interactions:
Covalently bonded - 1313
1-3 system - 1868
Same ring system - 35
Side-chain restricted 1-4 - 116
Omega 1-4 - 540
Tight phi/psi 1-4 - 540
Loose phi/psi 1-4 - 206
Other phi/psi 1-4 - 298
Other 1-4 - 589
Secondary structure - 2544
Salt bridge - 63
H bond - 233
Tight hydrophobic - 773
Loose hydrophobic - 1055
Other pairs - 836778
Found distance constraints from single structure
Found combined distance constraints from two structures
Will generate 6 structures and keep best-scoring 4
Progress: 17%|████████▍ | ETA: 0:00:37
Progress: 33%|████████████████▋ | ETA: 0:00:27
Progress: 50%|█████████████████████████ | ETA: 0:00:20
Progress: 67%|█████████████████████████████████▍ | ETA: 0:00:13
Progress: 83%|█████████████████████████████████████████▋ | ETA: 0:00:06
Progress: 100%|██████████████████████████████████████████████████| Time: 0:00:38Kept lowest scoring 4 out of
6 structures
Scores range from 1.4 to 14.0
Aligned ensemble to itself after 8 iteration(s)
Projections written to file "/tmp/exprose_out/pcs/pcs.tsv"
Projections written to file "/tmp/exprose_out/pcs/pcs_input_1.tsv"
Projections written to file "/tmp/exprose_out/pcs/pcs_input_2.tsv"
Wrote ensemble to PDB file(s) with prefix "/tmp/exprose_out/pdbs/out.pdb"
Wrote ensemble scores to file "/tmp/exprose_out/spe_scores.tsv"
Read 2634 atoms from PDB file
Projections written to file "/tmp/exprose_out/pcs/pcs_ex_1.tsv"
Read 2634 atoms from PDB file
Projections written to file "/tmp/exprose_out/pcs/pcs_ex_2.tsv"
WARNING: Cairo._jl_libpango is deprecated, use Cairo.libpango instead.
likely near /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_pipeline.jl:19
WARNING: Cairo._jl_libpango is deprecated, use Cairo.libpango instead.
likely near /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_pipeline.jl:19
WARNING: Cairo._jl_libpango is deprecated, use Cairo.libpango instead.
likely near /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_pipeline.jl:19
in apply_property at /root/.julia/packages/Compose/UIDMc/src/cairo_backends.jl
WARNING: Cairo._jl_libpango is deprecated, use Cairo.libpango instead.
likely near /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_pipeline.jl:19
in apply_property at /root/.julia/packages/Compose/UIDMc/src/cairo_backends.jl
WARNING: Cairo._jl_libpango is deprecated, use Cairo.libpango instead.
likely near /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_pipeline.jl:19
WARNING: Cairo._jl_libpango is deprecated, use Cairo.libpango instead.
likely near /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_pipeline.jl:19
WARNING: Cairo._jl_libpango is deprecated, use Cairo.libpango instead.
likely near /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_pipeline.jl:19
in apply_property at /root/.julia/packages/Compose/UIDMc/src/cairo_backends.jl
WARNING: Cairo._jl_libpango is deprecated, use Cairo.libpango instead.
likely near /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_pipeline.jl:19
in apply_property at /root/.julia/packages/Compose/UIDMc/src/cairo_backends.jl
Plotted principal components to file(s) "/tmp/exprose_out/pcs/pc_x_y.png"
Plotted RMSFs to file "/tmp/exprose_out/rmsfs.png"
n_to_write is larger than the number of eigenvectors - proceeding with all possible eigenvectors
PyMol script to view principal components written to file(s) "/tmp/exprose_out/pymol/view_pc_x.pml"
Done
-- ExProSE --
Arguments:
i1 - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CLL_H.pdb
d1 - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CLL.dssp
i2 - nothing
d2 - nothing
out_dir - /tmp/exprose_out
n_strucs - 4
tolerance_weight - 0.3
other_ratio - 20.0
extra_pdbs - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CFF_1.pdb, /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CFF_2.pdb
mod_path - nothing
n_mods - 0
Making output directory "/tmp/exprose_out"
Proceeding with one structure
Read 1367 atoms from PDB file
Read 144 residues from DSSP file
Found interactions:
Covalently bonded - 1379
1-3 system - 1966
Same ring system - 35
Side-chain restricted 1-4 - 116
Omega 1-4 - 568
Tight phi/psi 1-4 - 744
Loose phi/psi 1-4 - 157
Other phi/psi 1-4 - 195
Other 1-4 - 626
Secondary structure - 4160
Salt bridge - 42
H bond - 244
Tight hydrophobic - 865
Loose hydrophobic - 931
Other pairs - 921633
Found distance constraints from single structure
Will generate 6 structures and keep best-scoring 4
Progress: 17%|████████▍ | ETA: 0:00:29
Progress: 33%|████████████████▋ | ETA: 0:00:24
Progress: 50%|█████████████████████████ | ETA: 0:00:19
Progress: 67%|█████████████████████████████████▍ | ETA: 0:00:12
Progress: 83%|█████████████████████████████████████████▋ | ETA: 0:00:07
Progress: 100%|██████████████████████████████████████████████████| Time: 0:00:41
Kept lowest scoring 4 out of 6 structures
Scores range from 2.5 to 8.0
Aligned ensemble to itself after 3 iteration(s)
Projections written to file "/tmp/exprose_out/pcs/pcs.tsv"
Projections written to file "/tmp/exprose_out/pcs/pcs_input.tsv"
Wrote ensemble to PDB file(s) with prefix "/tmp/exprose_out/pdbs/out.pdb"
Wrote ensemble scores to file "/tmp/exprose_out/spe_scores.tsv"
Read 2634 atoms from PDB file
Projections written to file "/tmp/exprose_out/pcs/pcs_ex_1.tsv"
Read 2634 atoms from PDB file
Projections written to file "/tmp/exprose_out/pcs/pcs_ex_2.tsv"
Plotted principal components to file(s) "/tmp/exprose_out/pcs/pc_x_y.png"
Plotted RMSFs to file "/tmp/exprose_out/rmsfs.png"
n_to_write is larger than the number of eigenvectors - proceeding with all possible eigenvectors
PyMol script to view principal components written to file(s) "/tmp/exprose_out/pymol/view_pc_x.pml"
Done
-- ExProSE --
Arguments:
i1 - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CLL_H.pdb
d1 - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CLL.dssp
i2 - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CTR_H.pdb
d2 - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CTR.dssp
out_dir - /tmp/exprose_out
n_strucs - 4
tolerance_weight - 0.3
other_ratio - 20.0
extra_pdbs - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CFF_1.pdb, /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CFF_2.pdb
mod_path - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CTR_pocket_points.pdb
n_mods - 1
Making output directory "/tmp/exprose_out"
Proceeding with two structures
Read 1367 atoms from PDB file
Read 1336 atoms from PDB file
Read 144 residues from DSSP file
Read 141 residues from DSSP file
Found interactions:
Covalently bonded - 1313
1-3 system - 1868
Same ring system - 35
Side-chain restricted 1-4 - 116
Omega 1-4 - 540
Tight phi/psi 1-4 - 692
Loose phi/psi 1-4 - 157
Other phi/psi 1-4 - 195
Other 1-4 - 589
Secondary structure - 3684
Salt bridge - 42
H bond - 230
Tight hydrophobic - 817
Loose hydrophobic - 878
Other pairs - 835795
Found distance constraints from single structure
Found interactions:
Covalently bonded - 1313
1-3 system - 1868
Same ring system - 35
Side-chain restricted 1-4 - 116
Omega 1-4 - 540
Tight phi/psi 1-4 - 540
Loose phi/psi 1-4 - 206
Other phi/psi 1-4 - 298
Other 1-4 - 589
Secondary structure - 2544
Salt bridge - 63
H bond - 233
Tight hydrophobic - 773
Loose hydrophobic - 1055
Other pairs - 836778
Found distance constraints from single structure
Found combined distance constraints from two structures
Will generate 6 structures and keep best-scoring 4
Progress: 17%|████████▍ | ETA: 0:00:33
Progress: 33%|████████████████▋ | ETA: 0:00:25
Progress: 50%|█████████████████████████ | ETA: 0:00:19
Progress: 67%|█████████████████████████████████▍ | ETA: 0:00:13
Progress: 83%|█████████████████████████████████████████▋ | ETA: 0:00:06Kept lowest scoring 4 out of 6 structures
Scores range from 0.3 to 8.3
Progress: 100%|██████████████████████████████████████████████████| Time: 0:00:37
Read 1111 pocket points from pocket points PDB file
Generating ensemble with modulator 1 of 1
Found 2934 interactions between the modulator and the protein
Will generate 6 structures and keep best-scoring 4
Progress: 17%|████████▍ | ETA: 0:00:32
Progress: 33%|████████████████▋ | ETA: 0:00:26
Progress: 50%|█████████████████████████ | ETA: 0:00:20
Progress: 67%|█████████████████████████████████▍ | ETA: 0:00:14
Progress: 83%|█████████████████████████████████████████▋ | ETA: 0:00:07Kept lowest scoring 4 out of 6 structures
Scores range from 3.6 to 57.9
Progress: 100%|██████████████████████████████████████████████████| Time: 0:00:44
Aligned ensemble to itself after 3 iteration(s)
Projections written to file "/tmp/exprose_out/pcs/pcs.tsv"
Projections written to file "/tmp/exprose_out/pcs/pcs_input_1.tsv"
Projections written to file "/tmp/exprose_out/pcs/pcs_input_2.tsv"
Wrote ensemble to PDB file(s) with prefix "/tmp/exprose_out/pdbs/out.pdb"
Wrote ensemble scores to file "/tmp/exprose_out/spe_scores.tsv"
Read 2634 atoms from PDB file
Projections written to file "/tmp/exprose_out/pcs/pcs_ex_1.tsv"
Read 2634 atoms from PDB file
Projections written to file "/tmp/exprose_out/pcs/pcs_ex_2.tsv"
Plotted principal components to file(s) "/tmp/exprose_out/pcs/pc_x_y.png"
Plotted RMSFs to file "/tmp/exprose_out/rmsfs.png"
Wrote ensemble to PDB file(s) with prefix "/tmp/exprose_out/pdbs_mod_1/out.pdb"
Projections written to file "/tmp/exprose_out/mod_1/pcs.tsv"
Wrote ensemble scores to file "/tmp/exprose_out/mod_1/spe_scores.tsv"
Plotted principal components to file(s) "/tmp/exprose_out/mod_1/pc_x_y.png"
Aligned ensemble to itself after 2 iteration(s)
Plotted RMSFs to file "/tmp/exprose_out/mod_1/rmsfs.png"
n_to_write is larger than the number of eigenvectors - proceeding with all possible eigenvectors
PyMol script to view principal components written to file(s) "/tmp/exprose_out/pymol/view_pc_x.pml"
Done
-- ExProSE --
Arguments:
i1 - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CTR_H.pdb
d1 - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CTR.dssp
i2 - nothing
d2 - nothing
out_dir - /tmp/exprose_out
n_strucs - 4
tolerance_weight - 0.3
other_ratio - 20.0
extra_pdbs - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CFF_1.pdb, /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CFF_2.pdb
mod_path - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CTR_pocket_points.pdb
n_mods - 1
Making output directory "/tmp/exprose_out"
Proceeding with one structure
Read 1336 atoms from PDB file
Read 141 residues from DSSP file
Found interactions:
Covalently bonded - 1347
1-3 system - 1919
Same ring system - 35
Side-chain restricted 1-4 - 120
Omega 1-4 - 552
Tight phi/psi 1-4 - 540
Loose phi/psi 1-4 - 232
Other phi/psi 1-4 - 298
Other 1-4 - 608
Secondary structure - 2544
Salt bridge - 84
H bond - 239
Tight hydrophobic - 789
Loose hydrophobic - 1084
Other pairs - 881389
Found distance constraints from single structure
Will generate 6 structures and keep best-scoring 4
Progress: 17%|████████▍ | ETA: 0:00:29
Progress: 33%|████████████████▋ | ETA: 0:00:24
Progress: 50%|█████████████████████████ | ETA: 0:00:18
Progress: 67%|█████████████████████████████████▍ | ETA: 0:00:13
Progress: 83%|█████████████████████████████████████████▋ | ETA: 0:00:06
Progress: 100%|██████████████████████████████████████████████████| Time: 0:00:37
Kept lowest scoring 4 out of 6 structures
Scores range from 0.5 to 3.4
Read 1111 pocket points from pocket points PDB file
Generating ensemble with modulator 1 of 1
Found 2891 interactions between the modulator and the protein
Will generate 6 structures and keep best-scoring 4
Progress: 17%|████████▍ | ETA: 0:00:37
Progress: 33%|████████████████▋ | ETA: 0:00:28
Progress: 50%|█████████████████████████ | ETA: 0:00:20
Progress: 67%|█████████████████████████████████▍ | ETA: 0:00:13
Progress: 83%|█████████████████████████████████████████▋ | ETA: 0:00:07
Progress: 100%|██████████████████████████████████████████████████| Time: 0:00:40
Kept lowest scoring 4 out of 6 structures
Scores range from 0.0 to 6.3
Aligned ensemble to itself after 2 iteration(s)
Projections written to file "/tmp/exprose_out/pcs/pcs.tsv"
Projections written to file "/tmp/exprose_out/pcs/pcs_input.tsv"
Wrote ensemble to PDB file(s) with prefix "/tmp/exprose_out/pdbs/out.pdb"
Wrote ensemble scores to file "/tmp/exprose_out/spe_scores.tsv"
Read 2634 atoms from PDB file
Projections written to file "/tmp/exprose_out/pcs/pcs_ex_1.tsv"
Read 2634 atoms from PDB file
Projections written to file "/tmp/exprose_out/pcs/pcs_ex_2.tsv"
Plotted principal components to file(s) "/tmp/exprose_out/pcs/pc_x_y.png"
Plotted RMSFs to file "/tmp/exprose_out/rmsfs.png"
Wrote ensemble to PDB file(s) with prefix "/tmp/exprose_out/pdbs_mod_1/out.pdb"
Projections written to file "/tmp/exprose_out/mod_1/pcs.tsv"
Wrote ensemble scores to file "/tmp/exprose_out/mod_1/spe_scores.tsv"
Plotted principal components to file(s) "/tmp/exprose_out/mod_1/pc_x_y.png"
Aligned ensemble to itself after 2 iteration(s)
Plotted RMSFs to file "/tmp/exprose_out/mod_1/rmsfs.png"
n_to_write is larger than the number of eigenvectors - proceeding with all possible eigenvectors
PyMol script to view principal components written to file(s) "/tmp/exprose_out/pymol/view_pc_x.pml"
Done
Test Summary: | Pass Total
Pipeline | 5 5
Parameterisation tests not run; to run these, set run_param_test to true in runtests.jl
Testing ProteinEnsembles tests passed
Results with Julia v1.3.0
Testing was successful .
Last evaluation was ago and took 13 minutes, 33 seconds.
Click here to download the log file.
Click here to show the log contents.
Resolving package versions...
Installed Ratios ───────────────── v0.3.1
Installed KernelDensity ────────── v0.5.1
Installed SortingAlgorithms ────── v0.3.1
Installed DiffResults ──────────── v0.0.4
Installed Arpack ───────────────── v0.3.1
Installed Cairo ────────────────── v0.8.0
Installed DataStructures ───────── v0.15.0
Installed ProteinEnsembles ─────── v0.3.0
Installed AxisAlgorithms ───────── v1.0.0
Installed Juno ─────────────────── v0.7.2
Installed StaticArrays ─────────── v0.12.1
Installed QuadGK ───────────────── v2.1.1
Installed Compat ───────────────── v2.2.0
Installed FFTW ─────────────────── v1.1.0
Installed Compose ──────────────── v0.7.4
Installed CategoricalArrays ────── v0.5.5
Installed StatsFuns ────────────── v0.8.0
Installed BinaryProvider ───────── v0.5.8
Installed LineSearches ─────────── v7.0.1
Installed Hexagons ─────────────── v0.2.0
Installed DocStringExtensions ──── v0.7.0
Installed NLSolversBase ────────── v7.5.0
Installed Missings ─────────────── v0.4.3
Installed ProgressMeter ────────── v1.2.0
Installed IterTools ────────────── v1.3.0
Installed MacroTools ───────────── v0.5.1
Installed Loess ────────────────── v0.5.0
Installed Distributions ────────── v0.19.2
Installed FixedPointNumbers ────── v0.6.1
Installed OrderedCollections ───── v1.1.0
Installed Rmath ────────────────── v0.6.0
Installed Parameters ───────────── v0.12.0
Installed SpecialFunctions ─────── v0.9.0
Installed PositiveFactorizations ─ v0.2.3
Installed IndirectArrays ───────── v0.5.0
Installed Showoff ──────────────── v0.3.1
Installed JSON ─────────────────── v0.20.0
Installed CommonSubexpressions ─── v0.2.0
Installed ColorTypes ───────────── v0.8.0
Installed Distances ────────────── v0.8.2
Installed DataAPI ──────────────── v1.1.0
Installed NaNMath ──────────────── v0.3.3
Installed Gadfly ───────────────── v1.1.0
Installed ForwardDiff ──────────── v0.10.7
Installed OpenSpecFun_jll ──────── v0.5.3+1
Installed CSTParser ────────────── v1.1.0
Installed DiffEqDiffTools ──────── v1.5.0
Installed DiffRules ────────────── v0.1.0
Installed Interpolations ───────── v0.12.5
Installed Optim ────────────────── v0.19.5
Installed Calculus ─────────────── v0.5.1
Installed ArrayInterface ───────── v2.0.0
Installed Conda ────────────────── v1.3.0
Installed VersionParsing ───────── v1.1.3
Installed Requires ─────────────── v0.5.2
Installed Colors ───────────────── v0.9.6
Installed Graphics ─────────────── v0.4.0
Installed Measures ─────────────── v0.3.0
Installed Contour ──────────────── v0.5.1
Installed ArgParse ─────────────── v0.6.2
Installed Media ────────────────── v0.5.0
Installed OffsetArrays ─────────── v0.11.2
Installed TextWrap ─────────────── v0.3.0
Installed PDMats ───────────────── v0.9.10
Installed Reexport ─────────────── v0.2.0
Installed FillArrays ───────────── v0.8.2
Installed WoodburyMatrices ─────── v0.4.1
Installed Tokenize ─────────────── v0.5.7
Installed StatsBase ────────────── v0.32.0
Installed CoupledFields ────────── v0.1.0
Installed AbstractFFTs ─────────── v0.5.0
Updating `~/.julia/environments/v1.3/Project.toml`
[186d2b2d] + ProteinEnsembles v0.3.0
Updating `~/.julia/environments/v1.3/Manifest.toml`
[621f4979] + AbstractFFTs v0.5.0
[c7e460c6] + ArgParse v0.6.2
[7d9fca2a] + Arpack v0.3.1
[4fba245c] + ArrayInterface v2.0.0
[13072b0f] + AxisAlgorithms v1.0.0
[b99e7846] + BinaryProvider v0.5.8
[00ebfdb7] + CSTParser v1.1.0
[159f3aea] + Cairo v0.8.0
[49dc2e85] + Calculus v0.5.1
[324d7699] + CategoricalArrays v0.5.5
[3da002f7] + ColorTypes v0.8.0
[5ae59095] + Colors v0.9.6
[bbf7d656] + CommonSubexpressions v0.2.0
[34da2185] + Compat v2.2.0
[a81c6b42] + Compose v0.7.4
[8f4d0f93] + Conda v1.3.0
[d38c429a] + Contour v0.5.1
[7ad07ef1] + CoupledFields v0.1.0
[9a962f9c] + DataAPI v1.1.0
[864edb3b] + DataStructures v0.15.0
[01453d9d] + DiffEqDiffTools v1.5.0
[163ba53b] + DiffResults v0.0.4
[b552c78f] + DiffRules v0.1.0
[b4f34e82] + Distances v0.8.2
[31c24e10] + Distributions v0.19.2
[ffbed154] + DocStringExtensions v0.7.0
[7a1cc6ca] + FFTW v1.1.0
[1a297f60] + FillArrays v0.8.2
[53c48c17] + FixedPointNumbers v0.6.1
[f6369f11] + ForwardDiff v0.10.7
[c91e804a] + Gadfly v1.1.0
[a2bd30eb] + Graphics v0.4.0
[a1b4810d] + Hexagons v0.2.0
[9b13fd28] + IndirectArrays v0.5.0
[a98d9a8b] + Interpolations v0.12.5
[c8e1da08] + IterTools v1.3.0
[682c06a0] + JSON v0.20.0
[e5e0dc1b] + Juno v0.7.2
[5ab0869b] + KernelDensity v0.5.1
[d3d80556] + LineSearches v7.0.1
[4345ca2d] + Loess v0.5.0
[1914dd2f] + MacroTools v0.5.1
[442fdcdd] + Measures v0.3.0
[e89f7d12] + Media v0.5.0
[e1d29d7a] + Missings v0.4.3
[d41bc354] + NLSolversBase v7.5.0
[77ba4419] + NaNMath v0.3.3
[6fe1bfb0] + OffsetArrays v0.11.2
[efe28fd5] + OpenSpecFun_jll v0.5.3+1
[429524aa] + Optim v0.19.5
[bac558e1] + OrderedCollections v1.1.0
[90014a1f] + PDMats v0.9.10
[d96e819e] + Parameters v0.12.0
[85a6dd25] + PositiveFactorizations v0.2.3
[92933f4c] + ProgressMeter v1.2.0
[186d2b2d] + ProteinEnsembles v0.3.0
[1fd47b50] + QuadGK v2.1.1
[c84ed2f1] + Ratios v0.3.1
[189a3867] + Reexport v0.2.0
[ae029012] + Requires v0.5.2
[79098fc4] + Rmath v0.6.0
[992d4aef] + Showoff v0.3.1
[a2af1166] + SortingAlgorithms v0.3.1
[276daf66] + SpecialFunctions v0.9.0
[90137ffa] + StaticArrays v0.12.1
[2913bbd2] + StatsBase v0.32.0
[4c63d2b9] + StatsFuns v0.8.0
[b718987f] + TextWrap v0.3.0
[0796e94c] + Tokenize v0.5.7
[81def892] + VersionParsing v1.1.3
[efce3f68] + WoodburyMatrices v0.4.1
[2a0f44e3] + Base64
[ade2ca70] + Dates
[8bb1440f] + DelimitedFiles
[8ba89e20] + Distributed
[9fa8497b] + Future
[b77e0a4c] + InteractiveUtils
[76f85450] + LibGit2
[8f399da3] + Libdl
[37e2e46d] + LinearAlgebra
[56ddb016] + Logging
[d6f4376e] + Markdown
[a63ad114] + Mmap
[44cfe95a] + Pkg
[de0858da] + Printf
[9abbd945] + Profile
[3fa0cd96] + REPL
[9a3f8284] + Random
[ea8e919c] + SHA
[9e88b42a] + Serialization
[1a1011a3] + SharedArrays
[6462fe0b] + Sockets
[2f01184e] + SparseArrays
[10745b16] + Statistics
[4607b0f0] + SuiteSparse
[8dfed614] + Test
[cf7118a7] + UUIDs
[4ec0a83e] + Unicode
Building Arpack → `~/.julia/packages/Arpack/cu5By/deps/build.log`
Building Cairo ─→ `~/.julia/packages/Cairo/ZbzIH/deps/build.log`
Building Conda ─→ `~/.julia/packages/Conda/kLXeC/deps/build.log`
Building FFTW ──→ `~/.julia/packages/FFTW/loJ3F/deps/build.log`
Building Rmath ─→ `~/.julia/packages/Rmath/BoBag/deps/build.log`
Testing ProteinEnsembles
Resolving package versions...
Status `/tmp/jl_bJnLGx/Manifest.toml`
[621f4979] AbstractFFTs v0.5.0
[c7e460c6] ArgParse v0.6.2
[7d9fca2a] Arpack v0.3.1
[4fba245c] ArrayInterface v2.0.0
[13072b0f] AxisAlgorithms v1.0.0
[b99e7846] BinaryProvider v0.5.8
[00ebfdb7] CSTParser v1.1.0
[159f3aea] Cairo v0.8.0
[49dc2e85] Calculus v0.5.1
[324d7699] CategoricalArrays v0.5.5
[3da002f7] ColorTypes v0.8.0
[5ae59095] Colors v0.9.6
[bbf7d656] CommonSubexpressions v0.2.0
[34da2185] Compat v2.2.0
[a81c6b42] Compose v0.7.4
[8f4d0f93] Conda v1.3.0
[d38c429a] Contour v0.5.1
[7ad07ef1] CoupledFields v0.1.0
[9a962f9c] DataAPI v1.1.0
[864edb3b] DataStructures v0.15.0
[01453d9d] DiffEqDiffTools v1.5.0
[163ba53b] DiffResults v0.0.4
[b552c78f] DiffRules v0.1.0
[b4f34e82] Distances v0.8.2
[31c24e10] Distributions v0.19.2
[ffbed154] DocStringExtensions v0.7.0
[7a1cc6ca] FFTW v1.1.0
[1a297f60] FillArrays v0.8.2
[53c48c17] FixedPointNumbers v0.6.1
[f6369f11] ForwardDiff v0.10.7
[c91e804a] Gadfly v1.1.0
[a2bd30eb] Graphics v0.4.0
[a1b4810d] Hexagons v0.2.0
[9b13fd28] IndirectArrays v0.5.0
[a98d9a8b] Interpolations v0.12.5
[c8e1da08] IterTools v1.3.0
[682c06a0] JSON v0.20.0
[e5e0dc1b] Juno v0.7.2
[5ab0869b] KernelDensity v0.5.1
[d3d80556] LineSearches v7.0.1
[4345ca2d] Loess v0.5.0
[1914dd2f] MacroTools v0.5.1
[442fdcdd] Measures v0.3.0
[e89f7d12] Media v0.5.0
[e1d29d7a] Missings v0.4.3
[d41bc354] NLSolversBase v7.5.0
[77ba4419] NaNMath v0.3.3
[6fe1bfb0] OffsetArrays v0.11.2
[efe28fd5] OpenSpecFun_jll v0.5.3+1
[429524aa] Optim v0.19.5
[bac558e1] OrderedCollections v1.1.0
[90014a1f] PDMats v0.9.10
[d96e819e] Parameters v0.12.0
[85a6dd25] PositiveFactorizations v0.2.3
[92933f4c] ProgressMeter v1.2.0
[186d2b2d] ProteinEnsembles v0.3.0
[1fd47b50] QuadGK v2.1.1
[c84ed2f1] Ratios v0.3.1
[189a3867] Reexport v0.2.0
[ae029012] Requires v0.5.2
[79098fc4] Rmath v0.6.0
[992d4aef] Showoff v0.3.1
[a2af1166] SortingAlgorithms v0.3.1
[276daf66] SpecialFunctions v0.9.0
[90137ffa] StaticArrays v0.12.1
[2913bbd2] StatsBase v0.32.0
[4c63d2b9] StatsFuns v0.8.0
[b718987f] TextWrap v0.3.0
[0796e94c] Tokenize v0.5.7
[81def892] VersionParsing v1.1.3
[efce3f68] WoodburyMatrices v0.4.1
[2a0f44e3] Base64 [`@stdlib/Base64`]
[ade2ca70] Dates [`@stdlib/Dates`]
[8bb1440f] DelimitedFiles [`@stdlib/DelimitedFiles`]
[8ba89e20] Distributed [`@stdlib/Distributed`]
[9fa8497b] Future [`@stdlib/Future`]
[b77e0a4c] InteractiveUtils [`@stdlib/InteractiveUtils`]
[76f85450] LibGit2 [`@stdlib/LibGit2`]
[8f399da3] Libdl [`@stdlib/Libdl`]
[37e2e46d] LinearAlgebra [`@stdlib/LinearAlgebra`]
[56ddb016] Logging [`@stdlib/Logging`]
[d6f4376e] Markdown [`@stdlib/Markdown`]
[a63ad114] Mmap [`@stdlib/Mmap`]
[44cfe95a] Pkg [`@stdlib/Pkg`]
[de0858da] Printf [`@stdlib/Printf`]
[9abbd945] Profile [`@stdlib/Profile`]
[3fa0cd96] REPL [`@stdlib/REPL`]
[9a3f8284] Random [`@stdlib/Random`]
[ea8e919c] SHA [`@stdlib/SHA`]
[9e88b42a] Serialization [`@stdlib/Serialization`]
[1a1011a3] SharedArrays [`@stdlib/SharedArrays`]
[6462fe0b] Sockets [`@stdlib/Sockets`]
[2f01184e] SparseArrays [`@stdlib/SparseArrays`]
[10745b16] Statistics [`@stdlib/Statistics`]
[4607b0f0] SuiteSparse [`@stdlib/SuiteSparse`]
[8dfed614] Test [`@stdlib/Test`]
[cf7118a7] UUIDs [`@stdlib/UUIDs`]
[4ec0a83e] Unicode [`@stdlib/Unicode`]
┌ Warning: `lgamma(x::Real)` is deprecated, use `(logabsgamma(x))[1]` instead.
│ caller = lstirling_asym(::BigFloat) at misc.jl:56
└ @ StatsFuns ~/.julia/packages/StatsFuns/2QE7p/src/misc.jl:56
Test Summary: | Pass Total
Types | 8 8
Could not find element for atom with name X
Test Summary: | Pass Total
Atoms | 26 26
Read 214 residues from DSSP file
Read 1336 atoms from PDB file
Read 141 residues from DSSP file
Read 3312 atoms from PDB file
Read 3804 atoms from PDB file
Read 3312 atoms from PDB file
Read 3312 atoms from PDB file
Read 476 pocket points from pocket points PDB file
Read 43 pocket centres from LIGSITEcs output PDB file
Test Summary: | Pass Total
IO | 31 31
Read 2035 atoms from PDB file
Read 214 residues from DSSP file
Found distance constraints from single structure
Found combined distance constraints from two structures
Test Summary: | Pass Total
Interactions | 41 41
Kept lowest scoring 2 out of 4 structures
Scores range from 10.0 to 20.0
Test Summary: | Pass Total
Generate | 12 12
Test Summary: | Pass Total
Align | 11 11
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read in protein ensemble
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read in protein ensemble
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read in protein ensemble
Test Summary: | Pass Total
PCA | 10 10
Found 2 interactions between the modulator and the protein
Read 395 pocket points from LIGSITEcs pocket points PDB file
Read 43 pocket centres from LIGSITEcs output PDB file
Assigned all points
Wrote pocket number assignments to file "/tmp/jl_ZvnHbJ"
Test Summary: | Pass Total
Perturb | 9 9
-- ExProSE --
Arguments:
i1 - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CLL_H.pdb
d1 - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CLL.dssp
i2 - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CTR_H.pdb
d2 - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CTR.dssp
out_dir - /tmp/exprose_out
n_strucs - 4
tolerance_weight - 0.3
other_ratio - 20.0
extra_pdbs - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CFF_1.pdb, /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CFF_2.pdb
mod_path - nothing
n_mods - 0
Making output directory "/tmp/exprose_out"
Proceeding with two structures
Read 1367 atoms from PDB file
Read 1336 atoms from PDB file
Read 144 residues from DSSP file
Read 141 residues from DSSP file
Found interactions:
Covalently bonded - 1313
1-3 system - 1868
Same ring system - 35
Side-chain restricted 1-4 - 116
Omega 1-4 - 540
Tight phi/psi 1-4 - 692
Loose phi/psi 1-4 - 157
Other phi/psi 1-4 - 195
Other 1-4 - 589
Secondary structure - 3684
Salt bridge - 42
H bond - 230
Tight hydrophobic - 817
Loose hydrophobic - 878
Other pairs - 835795
Found distance constraints from single structure
Found interactions:
Covalently bonded - 1313
1-3 system - 1868
Same ring system - 35
Side-chain restricted 1-4 - 116
Omega 1-4 - 540
Tight phi/psi 1-4 - 540
Loose phi/psi 1-4 - 206
Other phi/psi 1-4 - 298
Other 1-4 - 589
Secondary structure - 2544
Salt bridge - 63
H bond - 233
Tight hydrophobic - 773
Loose hydrophobic - 1055
Other pairs - 836778
Found distance constraints from single structure
Found combined distance constraints from two structures
Will generate 6 structures and keep best-scoring 4
Progress: 17%|████████▍ | ETA: 0:00:34
Progress: 33%|████████████████▋ | ETA: 0:00:26
Progress: 50%|█████████████████████████ | ETA: 0:00:19
Progress: 67%|█████████████████████████████████▍ | ETA: 0:00:13
Progress: 83%|█████████████████████████████████████████▋ | ETA: 0:00:06
Progress: 100%|██████████████████████████████████████████████████| Time: 0:00:37
Kept lowest scoring 4 out of 6 structures
Scores range from 0.4 to 16.3
Aligned ensemble to itself after 3 iteration(s)
Projections written to file "/tmp/exprose_out/pcs/pcs.tsv"
Projections written to file "/tmp/exprose_out/pcs/pcs_input_1.tsv"
Projections written to file "/tmp/exprose_out/pcs/pcs_input_2.tsv"
Wrote ensemble to PDB file(s) with prefix "/tmp/exprose_out/pdbs/out.pdb"
Wrote ensemble scores to file "/tmp/exprose_out/spe_scores.tsv"
Read 2634 atoms from PDB file
Projections written to file "/tmp/exprose_out/pcs/pcs_ex_1.tsv"
Read 2634 atoms from PDB file
Projections written to file "/tmp/exprose_out/pcs/pcs_ex_2.tsv"
WARNING: Cairo._jl_libpango is deprecated, use Cairo.libpango instead.
likely near /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_pipeline.jl:19
WARNING: Cairo._jl_libpango is deprecated, use Cairo.libpango instead.
likely near /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_pipeline.jl:19
WARNING: Cairo._jl_libpango is deprecated, use Cairo.libpango instead.
likely near /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_pipeline.jl:19
in apply_property at /root/.julia/packages/Compose/UIDMc/src/cairo_backends.jl
WARNING: Cairo._jl_libpango is deprecated, use Cairo.libpango instead.
likely near /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_pipeline.jl:19
in apply_property at /root/.julia/packages/Compose/UIDMc/src/cairo_backends.jl
WARNING: Cairo._jl_libpango is deprecated, use Cairo.libpango instead.
likely near /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_pipeline.jl:19
WARNING: Cairo._jl_libpango is deprecated, use Cairo.libpango instead.
likely near /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_pipeline.jl:19
WARNING: Cairo._jl_libpango is deprecated, use Cairo.libpango instead.
likely near /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_pipeline.jl:19
in apply_property at /root/.julia/packages/Compose/UIDMc/src/cairo_backends.jl
WARNING: Cairo._jl_libpango is deprecated, use Cairo.libpango instead.
likely near /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_pipeline.jl:19
in apply_property at /root/.julia/packages/Compose/UIDMc/src/cairo_backends.jl
Plotted principal components to file(s) "/tmp/exprose_out/pcs/pc_x_y.png"
Plotted RMSFs to file "/tmp/exprose_out/rmsfs.png"
n_to_write is larger than the number of eigenvectors - proceeding with all possible eigenvectors
PyMol script to view principal components written to file(s) "/tmp/exprose_out/pymol/view_pc_x.pml"
Done
-- ExProSE --
Arguments:
i1 - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CLL_H.pdb
d1 - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CLL.dssp
i2 - nothing
d2 - nothing
out_dir - /tmp/exprose_out
n_strucs - 4
tolerance_weight - 0.3
other_ratio - 20.0
extra_pdbs - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CFF_1.pdb, /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CFF_2.pdb
mod_path - nothing
n_mods - 0
Making output directory "/tmp/exprose_out"
Proceeding with one structure
Read 1367 atoms from PDB file
Read 144 residues from DSSP file
Found interactions:
Covalently bonded - 1379
1-3 system - 1966
Same ring system - 35
Side-chain restricted 1-4 - 116
Omega 1-4 - 568
Tight phi/psi 1-4 - 744
Loose phi/psi 1-4 - 157
Other phi/psi 1-4 - 195
Other 1-4 - 626
Secondary structure - 4160
Salt bridge - 42
H bond - 244
Tight hydrophobic - 865
Loose hydrophobic - 931
Other pairs - 921633
Found distance constraints from single structure
Will generate 6 structures and keep best-scoring 4
Progress: 17%|████████▍ | ETA: 0:00:40
Progress: 33%|████████████████▋ | ETA: 0:00:28
Progress: 50%|█████████████████████████ | ETA: 0:00:22
Progress: 67%|█████████████████████████████████▍ | ETA: 0:00:15
Progress: 83%|█████████████████████████████████████████▋ | ETA: 0:00:08
Progress: 100%|██████████████████████████████████████████████████| Time: 0:00:46
Kept lowest scoring 4 out of 6 structures
Scores range from 1.7 to 14958.0
Aligned ensemble to itself after 2 iteration(s)
Projections written to file "/tmp/exprose_out/pcs/pcs.tsv"
Projections written to file "/tmp/exprose_out/pcs/pcs_input.tsv"
Wrote ensemble to PDB file(s) with prefix "/tmp/exprose_out/pdbs/out.pdb"
Wrote ensemble scores to file "/tmp/exprose_out/spe_scores.tsv"
Read 2634 atoms from PDB file
Projections written to file "/tmp/exprose_out/pcs/pcs_ex_1.tsv"
Read 2634 atoms from PDB file
Projections written to file "/tmp/exprose_out/pcs/pcs_ex_2.tsv"
Plotted principal components to file(s) "/tmp/exprose_out/pcs/pc_x_y.png"
Plotted RMSFs to file "/tmp/exprose_out/rmsfs.png"
n_to_write is larger than the number of eigenvectors - proceeding with all possible eigenvectors
PyMol script to view principal components written to file(s) "/tmp/exprose_out/pymol/view_pc_x.pml"
Done
-- ExProSE --
Arguments:
i1 - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CLL_H.pdb
d1 - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CLL.dssp
i2 - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CTR_H.pdb
d2 - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CTR.dssp
out_dir - /tmp/exprose_out
n_strucs - 4
tolerance_weight - 0.3
other_ratio - 20.0
extra_pdbs - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CFF_1.pdb, /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CFF_2.pdb
mod_path - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CTR_pocket_points.pdb
n_mods - 1
Making output directory "/tmp/exprose_out"
Proceeding with two structures
Read 1367 atoms from PDB file
Read 1336 atoms from PDB file
Read 144 residues from DSSP file
Read 141 residues from DSSP file
Found interactions:
Covalently bonded - 1313
1-3 system - 1868
Same ring system - 35
Side-chain restricted 1-4 - 116
Omega 1-4 - 540
Tight phi/psi 1-4 - 692
Loose phi/psi 1-4 - 157
Other phi/psi 1-4 - 195
Other 1-4 - 589
Secondary structure - 3684
Salt bridge - 42
H bond - 230
Tight hydrophobic - 817
Loose hydrophobic - 878
Other pairs - 835795
Found distance constraints from single structure
Found interactions:
Covalently bonded - 1313
1-3 system - 1868
Same ring system - 35
Side-chain restricted 1-4 - 116
Omega 1-4 - 540
Tight phi/psi 1-4 - 540
Loose phi/psi 1-4 - 206
Other phi/psi 1-4 - 298
Other 1-4 - 589
Secondary structure - 2544
Salt bridge - 63
H bond - 233
Tight hydrophobic - 773
Loose hydrophobic - 1055
Other pairs - 836778
Found distance constraints from single structure
Found combined distance constraints from two structures
Will generate 6 structures and keep best-scoring 4
Progress: 17%|████████▍ | ETA: 0:00:31
Progress: 33%|████████████████▋ | ETA: 0:00:25
Progress: 50%|█████████████████████████ | ETA: 0:00:18
Progress: 67%|█████████████████████████████████▍ | ETA: 0:00:12
Progress: 83%|█████████████████████████████████████████▋ | ETA: 0:00:06
Progress: 100%|██████████████████████████████████████████████████| Time: 0:00:37
Kept lowest scoring 4 out of 6 structures
Scores range from 0.5 to 101.0
Read 1111 pocket points from pocket points PDB file
Generating ensemble with modulator 1 of 1
Found 3193 interactions between the modulator and the protein
Will generate 6 structures and keep best-scoring 4
Progress: 17%|████████▍ | ETA: 0:00:41
Progress: 33%|████████████████▋ | ETA: 0:00:29
Progress: 50%|█████████████████████████ | ETA: 0:00:21
Progress: 67%|█████████████████████████████████▍ | ETA: 0:00:14
Progress: 83%|█████████████████████████████████████████▋ | ETA: 0:00:07
Progress: 100%|██████████████████████████████████████████████████| Time: 0:00:43
Kept lowest scoring 4 out of 6 structures
Scores range from 1.5 to 3.9
Aligned ensemble to itself after 5 iteration(s)
Projections written to file "/tmp/exprose_out/pcs/pcs.tsv"
Projections written to file "/tmp/exprose_out/pcs/pcs_input_1.tsv"
Projections written to file "/tmp/exprose_out/pcs/pcs_input_2.tsv"
Wrote ensemble to PDB file(s) with prefix "/tmp/exprose_out/pdbs/out.pdb"
Wrote ensemble scores to file "/tmp/exprose_out/spe_scores.tsv"
Read 2634 atoms from PDB file
Projections written to file "/tmp/exprose_out/pcs/pcs_ex_1.tsv"
Read 2634 atoms from PDB file
Projections written to file "/tmp/exprose_out/pcs/pcs_ex_2.tsv"
Plotted principal components to file(s) "/tmp/exprose_out/pcs/pc_x_y.png"
Plotted RMSFs to file "/tmp/exprose_out/rmsfs.png"
Wrote ensemble to PDB file(s) with prefix "/tmp/exprose_out/pdbs_mod_1/out.pdb"
Projections written to file "/tmp/exprose_out/mod_1/pcs.tsv"
Wrote ensemble scores to file "/tmp/exprose_out/mod_1/spe_scores.tsv"
Plotted principal components to file(s) "/tmp/exprose_out/mod_1/pc_x_y.png"
Aligned ensemble to itself after 2 iteration(s)
Plotted RMSFs to file "/tmp/exprose_out/mod_1/rmsfs.png"
n_to_write is larger than the number of eigenvectors - proceeding with all possible eigenvectors
PyMol script to view principal components written to file(s) "/tmp/exprose_out/pymol/view_pc_x.pml"
Done
-- ExProSE --
Arguments:
i1 - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CTR_H.pdb
d1 - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CTR.dssp
i2 - nothing
d2 - nothing
out_dir - /tmp/exprose_out
n_strucs - 4
tolerance_weight - 0.3
other_ratio - 20.0
extra_pdbs - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CFF_1.pdb, /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CFF_2.pdb
mod_path - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CTR_pocket_points.pdb
n_mods - 1
Making output directory "/tmp/exprose_out"
Proceeding with one structure
Read 1336 atoms from PDB file
Read 141 residues from DSSP file
Found interactions:
Covalently bonded - 1347
1-3 system - 1919
Same ring system - 35
Side-chain restricted 1-4 - 120
Omega 1-4 - 552
Tight phi/psi 1-4 - 540
Loose phi/psi 1-4 - 232
Other phi/psi 1-4 - 298
Other 1-4 - 608
Secondary structure - 2544
Salt bridge - 84
H bond - 239
Tight hydrophobic - 789
Loose hydrophobic - 1084
Other pairs - 881389
Found distance constraints from single structure
Will generate 6 structures and keep best-scoring 4
Progress: 17%|████████▍ | ETA: 0:00:29
Progress: 33%|████████████████▋ | ETA: 0:00:25
Progress: 50%|█████████████████████████ | ETA: 0:00:18
Progress: 67%|█████████████████████████████████▍ | ETA: 0:00:12
Progress: 83%|█████████████████████████████████████████▋ | ETA: 0:00:06
Progress: 100%|██████████████████████████████████████████████████| Time: 0:00:36
Kept lowest scoring 4 out of 6 structures
Scores range from 0.0 to 0.0
Read 1111 pocket points from pocket points PDB file
Generating ensemble with modulator 1 of 1
Found 2951 interactions between the modulator and the protein
Will generate 6 structures and keep best-scoring 4
Progress: 17%|████████▍ | ETA: 0:00:33
Progress: 33%|████████████████▋ | ETA: 0:00:26
Progress: 50%|█████████████████████████ | ETA: 0:00:19
Progress: 67%|█████████████████████████████████▍ | ETA: 0:00:13
Progress: 83%|█████████████████████████████████████████▋ | ETA: 0:00:07
Progress: 100%|██████████████████████████████████████████████████| Time: 0:00:39
Kept lowest scoring 4 out of 6 structures
Scores range from 0.0 to 15.3
Aligned ensemble to itself after 2 iteration(s)
Projections written to file "/tmp/exprose_out/pcs/pcs.tsv"
Projections written to file "/tmp/exprose_out/pcs/pcs_input.tsv"
Wrote ensemble to PDB file(s) with prefix "/tmp/exprose_out/pdbs/out.pdb"
Wrote ensemble scores to file "/tmp/exprose_out/spe_scores.tsv"
Read 2634 atoms from PDB file
Projections written to file "/tmp/exprose_out/pcs/pcs_ex_1.tsv"
Read 2634 atoms from PDB file
Projections written to file "/tmp/exprose_out/pcs/pcs_ex_2.tsv"
Plotted principal components to file(s) "/tmp/exprose_out/pcs/pc_x_y.png"
Plotted RMSFs to file "/tmp/exprose_out/rmsfs.png"
Wrote ensemble to PDB file(s) with prefix "/tmp/exprose_out/pdbs_mod_1/out.pdb"
Projections written to file "/tmp/exprose_out/mod_1/pcs.tsv"
Wrote ensemble scores to file "/tmp/exprose_out/mod_1/spe_scores.tsv"
Plotted principal components to file(s) "/tmp/exprose_out/mod_1/pc_x_y.png"
Aligned ensemble to itself after 2 iteration(s)
Plotted RMSFs to file "/tmp/exprose_out/mod_1/rmsfs.png"
n_to_write is larger than the number of eigenvectors - proceeding with all possible eigenvectors
PyMol script to view principal components written to file(s) "/tmp/exprose_out/pymol/view_pc_x.pml"
Done
Test Summary: | Pass Total
Pipeline | 5 5
Parameterisation tests not run; to run these, set run_param_test to true in runtests.jl
Testing ProteinEnsembles tests passed
Results with Julia v1.3.1-pre-7704df0a5a
Testing was successful .
Last evaluation was ago and took 13 minutes, 12 seconds.
Click here to download the log file.
Click here to show the log contents.
Resolving package versions...
Installed Ratios ───────────────── v0.3.1
Installed IndirectArrays ───────── v0.5.0
Installed ColorTypes ───────────── v0.8.0
Installed Conda ────────────────── v1.3.0
Installed ProteinEnsembles ─────── v0.3.0
Installed Colors ───────────────── v0.9.6
Installed Gadfly ───────────────── v1.1.0
Installed Optim ────────────────── v0.19.5
Installed Graphics ─────────────── v0.4.0
Installed OpenSpecFun_jll ──────── v0.5.3+1
Installed NaNMath ──────────────── v0.3.3
Installed QuadGK ───────────────── v2.1.1
Installed Hexagons ─────────────── v0.2.0
Installed DataStructures ───────── v0.15.0
Installed SpecialFunctions ─────── v0.9.0
Installed Compat ───────────────── v2.2.0
Installed Compose ──────────────── v0.7.4
Installed DiffResults ──────────── v0.0.4
Installed StaticArrays ─────────── v0.12.1
Installed IterTools ────────────── v1.3.0
Installed MacroTools ───────────── v0.5.1
Installed Showoff ──────────────── v0.3.1
Installed FixedPointNumbers ────── v0.6.1
Installed StatsBase ────────────── v0.32.0
Installed FillArrays ───────────── v0.8.2
Installed Cairo ────────────────── v0.8.0
Installed OffsetArrays ─────────── v0.11.2
Installed AxisAlgorithms ───────── v1.0.0
Installed ForwardDiff ──────────── v0.10.7
Installed Arpack ───────────────── v0.3.1
Installed LineSearches ─────────── v7.0.1
Installed Calculus ─────────────── v0.5.1
Installed CSTParser ────────────── v1.1.0
Installed FFTW ─────────────────── v1.1.0
Installed ArgParse ─────────────── v0.6.2
Installed CommonSubexpressions ─── v0.2.0
Installed Missings ─────────────── v0.4.3
Installed BinaryProvider ───────── v0.5.8
Installed StatsFuns ────────────── v0.8.0
Installed ProgressMeter ────────── v1.2.0
Installed DocStringExtensions ──── v0.7.0
Installed Measures ─────────────── v0.3.0
Installed NLSolversBase ────────── v7.5.0
Installed Parameters ───────────── v0.12.0
Installed Rmath ────────────────── v0.6.0
Installed Media ────────────────── v0.5.0
Installed DiffRules ────────────── v0.1.0
Installed Requires ─────────────── v0.5.2
Installed ArrayInterface ───────── v2.0.0
Installed AbstractFFTs ─────────── v0.5.0
Installed Distances ────────────── v0.8.2
Installed Tokenize ─────────────── v0.5.7
Installed Interpolations ───────── v0.12.5
Installed CoupledFields ────────── v0.1.0
Installed KernelDensity ────────── v0.5.1
Installed TextWrap ─────────────── v0.3.0
Installed PositiveFactorizations ─ v0.2.3
Installed Reexport ─────────────── v0.2.0
Installed Distributions ────────── v0.19.2
Installed WoodburyMatrices ─────── v0.4.1
Installed CategoricalArrays ────── v0.5.5
Installed OrderedCollections ───── v1.1.0
Installed JSON ─────────────────── v0.20.0
Installed DataAPI ──────────────── v1.1.0
Installed Loess ────────────────── v0.5.0
Installed PDMats ───────────────── v0.9.10
Installed Contour ──────────────── v0.5.1
Installed VersionParsing ───────── v1.1.3
Installed SortingAlgorithms ────── v0.3.1
Installed DiffEqDiffTools ──────── v1.5.0
Installed Juno ─────────────────── v0.7.2
Updating `~/.julia/environments/v1.3/Project.toml`
[186d2b2d] + ProteinEnsembles v0.3.0
Updating `~/.julia/environments/v1.3/Manifest.toml`
[621f4979] + AbstractFFTs v0.5.0
[c7e460c6] + ArgParse v0.6.2
[7d9fca2a] + Arpack v0.3.1
[4fba245c] + ArrayInterface v2.0.0
[13072b0f] + AxisAlgorithms v1.0.0
[b99e7846] + BinaryProvider v0.5.8
[00ebfdb7] + CSTParser v1.1.0
[159f3aea] + Cairo v0.8.0
[49dc2e85] + Calculus v0.5.1
[324d7699] + CategoricalArrays v0.5.5
[3da002f7] + ColorTypes v0.8.0
[5ae59095] + Colors v0.9.6
[bbf7d656] + CommonSubexpressions v0.2.0
[34da2185] + Compat v2.2.0
[a81c6b42] + Compose v0.7.4
[8f4d0f93] + Conda v1.3.0
[d38c429a] + Contour v0.5.1
[7ad07ef1] + CoupledFields v0.1.0
[9a962f9c] + DataAPI v1.1.0
[864edb3b] + DataStructures v0.15.0
[01453d9d] + DiffEqDiffTools v1.5.0
[163ba53b] + DiffResults v0.0.4
[b552c78f] + DiffRules v0.1.0
[b4f34e82] + Distances v0.8.2
[31c24e10] + Distributions v0.19.2
[ffbed154] + DocStringExtensions v0.7.0
[7a1cc6ca] + FFTW v1.1.0
[1a297f60] + FillArrays v0.8.2
[53c48c17] + FixedPointNumbers v0.6.1
[f6369f11] + ForwardDiff v0.10.7
[c91e804a] + Gadfly v1.1.0
[a2bd30eb] + Graphics v0.4.0
[a1b4810d] + Hexagons v0.2.0
[9b13fd28] + IndirectArrays v0.5.0
[a98d9a8b] + Interpolations v0.12.5
[c8e1da08] + IterTools v1.3.0
[682c06a0] + JSON v0.20.0
[e5e0dc1b] + Juno v0.7.2
[5ab0869b] + KernelDensity v0.5.1
[d3d80556] + LineSearches v7.0.1
[4345ca2d] + Loess v0.5.0
[1914dd2f] + MacroTools v0.5.1
[442fdcdd] + Measures v0.3.0
[e89f7d12] + Media v0.5.0
[e1d29d7a] + Missings v0.4.3
[d41bc354] + NLSolversBase v7.5.0
[77ba4419] + NaNMath v0.3.3
[6fe1bfb0] + OffsetArrays v0.11.2
[efe28fd5] + OpenSpecFun_jll v0.5.3+1
[429524aa] + Optim v0.19.5
[bac558e1] + OrderedCollections v1.1.0
[90014a1f] + PDMats v0.9.10
[d96e819e] + Parameters v0.12.0
[85a6dd25] + PositiveFactorizations v0.2.3
[92933f4c] + ProgressMeter v1.2.0
[186d2b2d] + ProteinEnsembles v0.3.0
[1fd47b50] + QuadGK v2.1.1
[c84ed2f1] + Ratios v0.3.1
[189a3867] + Reexport v0.2.0
[ae029012] + Requires v0.5.2
[79098fc4] + Rmath v0.6.0
[992d4aef] + Showoff v0.3.1
[a2af1166] + SortingAlgorithms v0.3.1
[276daf66] + SpecialFunctions v0.9.0
[90137ffa] + StaticArrays v0.12.1
[2913bbd2] + StatsBase v0.32.0
[4c63d2b9] + StatsFuns v0.8.0
[b718987f] + TextWrap v0.3.0
[0796e94c] + Tokenize v0.5.7
[81def892] + VersionParsing v1.1.3
[efce3f68] + WoodburyMatrices v0.4.1
[2a0f44e3] + Base64
[ade2ca70] + Dates
[8bb1440f] + DelimitedFiles
[8ba89e20] + Distributed
[9fa8497b] + Future
[b77e0a4c] + InteractiveUtils
[76f85450] + LibGit2
[8f399da3] + Libdl
[37e2e46d] + LinearAlgebra
[56ddb016] + Logging
[d6f4376e] + Markdown
[a63ad114] + Mmap
[44cfe95a] + Pkg
[de0858da] + Printf
[9abbd945] + Profile
[3fa0cd96] + REPL
[9a3f8284] + Random
[ea8e919c] + SHA
[9e88b42a] + Serialization
[1a1011a3] + SharedArrays
[6462fe0b] + Sockets
[2f01184e] + SparseArrays
[10745b16] + Statistics
[4607b0f0] + SuiteSparse
[8dfed614] + Test
[cf7118a7] + UUIDs
[4ec0a83e] + Unicode
Building Conda ─→ `~/.julia/packages/Conda/kLXeC/deps/build.log`
Building Cairo ─→ `~/.julia/packages/Cairo/ZbzIH/deps/build.log`
Building Arpack → `~/.julia/packages/Arpack/cu5By/deps/build.log`
Building FFTW ──→ `~/.julia/packages/FFTW/loJ3F/deps/build.log`
Building Rmath ─→ `~/.julia/packages/Rmath/BoBag/deps/build.log`
Testing ProteinEnsembles
Resolving package versions...
Status `/tmp/jl_cz0BEz/Manifest.toml`
[621f4979] AbstractFFTs v0.5.0
[c7e460c6] ArgParse v0.6.2
[7d9fca2a] Arpack v0.3.1
[4fba245c] ArrayInterface v2.0.0
[13072b0f] AxisAlgorithms v1.0.0
[b99e7846] BinaryProvider v0.5.8
[00ebfdb7] CSTParser v1.1.0
[159f3aea] Cairo v0.8.0
[49dc2e85] Calculus v0.5.1
[324d7699] CategoricalArrays v0.5.5
[3da002f7] ColorTypes v0.8.0
[5ae59095] Colors v0.9.6
[bbf7d656] CommonSubexpressions v0.2.0
[34da2185] Compat v2.2.0
[a81c6b42] Compose v0.7.4
[8f4d0f93] Conda v1.3.0
[d38c429a] Contour v0.5.1
[7ad07ef1] CoupledFields v0.1.0
[9a962f9c] DataAPI v1.1.0
[864edb3b] DataStructures v0.15.0
[01453d9d] DiffEqDiffTools v1.5.0
[163ba53b] DiffResults v0.0.4
[b552c78f] DiffRules v0.1.0
[b4f34e82] Distances v0.8.2
[31c24e10] Distributions v0.19.2
[ffbed154] DocStringExtensions v0.7.0
[7a1cc6ca] FFTW v1.1.0
[1a297f60] FillArrays v0.8.2
[53c48c17] FixedPointNumbers v0.6.1
[f6369f11] ForwardDiff v0.10.7
[c91e804a] Gadfly v1.1.0
[a2bd30eb] Graphics v0.4.0
[a1b4810d] Hexagons v0.2.0
[9b13fd28] IndirectArrays v0.5.0
[a98d9a8b] Interpolations v0.12.5
[c8e1da08] IterTools v1.3.0
[682c06a0] JSON v0.20.0
[e5e0dc1b] Juno v0.7.2
[5ab0869b] KernelDensity v0.5.1
[d3d80556] LineSearches v7.0.1
[4345ca2d] Loess v0.5.0
[1914dd2f] MacroTools v0.5.1
[442fdcdd] Measures v0.3.0
[e89f7d12] Media v0.5.0
[e1d29d7a] Missings v0.4.3
[d41bc354] NLSolversBase v7.5.0
[77ba4419] NaNMath v0.3.3
[6fe1bfb0] OffsetArrays v0.11.2
[efe28fd5] OpenSpecFun_jll v0.5.3+1
[429524aa] Optim v0.19.5
[bac558e1] OrderedCollections v1.1.0
[90014a1f] PDMats v0.9.10
[d96e819e] Parameters v0.12.0
[85a6dd25] PositiveFactorizations v0.2.3
[92933f4c] ProgressMeter v1.2.0
[186d2b2d] ProteinEnsembles v0.3.0
[1fd47b50] QuadGK v2.1.1
[c84ed2f1] Ratios v0.3.1
[189a3867] Reexport v0.2.0
[ae029012] Requires v0.5.2
[79098fc4] Rmath v0.6.0
[992d4aef] Showoff v0.3.1
[a2af1166] SortingAlgorithms v0.3.1
[276daf66] SpecialFunctions v0.9.0
[90137ffa] StaticArrays v0.12.1
[2913bbd2] StatsBase v0.32.0
[4c63d2b9] StatsFuns v0.8.0
[b718987f] TextWrap v0.3.0
[0796e94c] Tokenize v0.5.7
[81def892] VersionParsing v1.1.3
[efce3f68] WoodburyMatrices v0.4.1
[2a0f44e3] Base64 [`@stdlib/Base64`]
[ade2ca70] Dates [`@stdlib/Dates`]
[8bb1440f] DelimitedFiles [`@stdlib/DelimitedFiles`]
[8ba89e20] Distributed [`@stdlib/Distributed`]
[9fa8497b] Future [`@stdlib/Future`]
[b77e0a4c] InteractiveUtils [`@stdlib/InteractiveUtils`]
[76f85450] LibGit2 [`@stdlib/LibGit2`]
[8f399da3] Libdl [`@stdlib/Libdl`]
[37e2e46d] LinearAlgebra [`@stdlib/LinearAlgebra`]
[56ddb016] Logging [`@stdlib/Logging`]
[d6f4376e] Markdown [`@stdlib/Markdown`]
[a63ad114] Mmap [`@stdlib/Mmap`]
[44cfe95a] Pkg [`@stdlib/Pkg`]
[de0858da] Printf [`@stdlib/Printf`]
[9abbd945] Profile [`@stdlib/Profile`]
[3fa0cd96] REPL [`@stdlib/REPL`]
[9a3f8284] Random [`@stdlib/Random`]
[ea8e919c] SHA [`@stdlib/SHA`]
[9e88b42a] Serialization [`@stdlib/Serialization`]
[1a1011a3] SharedArrays [`@stdlib/SharedArrays`]
[6462fe0b] Sockets [`@stdlib/Sockets`]
[2f01184e] SparseArrays [`@stdlib/SparseArrays`]
[10745b16] Statistics [`@stdlib/Statistics`]
[4607b0f0] SuiteSparse [`@stdlib/SuiteSparse`]
[8dfed614] Test [`@stdlib/Test`]
[cf7118a7] UUIDs [`@stdlib/UUIDs`]
[4ec0a83e] Unicode [`@stdlib/Unicode`]
┌ Warning: `lgamma(x::Real)` is deprecated, use `(logabsgamma(x))[1]` instead.
│ caller = lstirling_asym(::BigFloat) at misc.jl:56
└ @ StatsFuns ~/.julia/packages/StatsFuns/2QE7p/src/misc.jl:56
Test Summary: | Pass Total
Types | 8 8
Could not find element for atom with name X
Test Summary: | Pass Total
Atoms | 26 26
Read 214 residues from DSSP file
Read 1336 atoms from PDB file
Read 141 residues from DSSP file
Read 3312 atoms from PDB file
Read 3804 atoms from PDB file
Read 3312 atoms from PDB file
Read 3312 atoms from PDB file
Read 476 pocket points from pocket points PDB file
Read 43 pocket centres from LIGSITEcs output PDB file
Test Summary: | Pass Total
IO | 31 31
Read 2035 atoms from PDB file
Read 214 residues from DSSP file
Found distance constraints from single structure
Found combined distance constraints from two structures
Test Summary: | Pass Total
Interactions | 41 41
Kept lowest scoring 2 out of 4 structures
Scores range from 10.0 to 20.0
Test Summary: | Pass Total
Generate | 12 12
Test Summary: | Pass Total
Align | 11 11
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read in protein ensemble
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read in protein ensemble
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read in protein ensemble
Test Summary: | Pass Total
PCA | 10 10
Found 2 interactions between the modulator and the protein
Read 395 pocket points from LIGSITEcs pocket points PDB file
Read 43 pocket centres from LIGSITEcs output PDB file
Assigned all points
Wrote pocket number assignments to file "/tmp/jl_YvADKU"
Test Summary: | Pass Total
Perturb | 9 9
-- ExProSE --
Arguments:
i1 - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CLL_H.pdb
d1 - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CLL.dssp
i2 - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CTR_H.pdb
d2 - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CTR.dssp
out_dir - /tmp/exprose_out
n_strucs - 4
tolerance_weight - 0.3
other_ratio - 20.0
extra_pdbs - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CFF_1.pdb, /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CFF_2.pdb
mod_path - nothing
n_mods - 0
Making output directory "/tmp/exprose_out"
Proceeding with two structures
Read 1367 atoms from PDB file
Read 1336 atoms from PDB file
Read 144 residues from DSSP file
Read 141 residues from DSSP file
Found interactions:
Covalently bonded - 1313
1-3 system - 1868
Same ring system - 35
Side-chain restricted 1-4 - 116
Omega 1-4 - 540
Tight phi/psi 1-4 - 692
Loose phi/psi 1-4 - 157
Other phi/psi 1-4 - 195
Other 1-4 - 589
Secondary structure - 3684
Salt bridge - 42
H bond - 230
Tight hydrophobic - 817
Loose hydrophobic - 878
Other pairs - 835795
Found distance constraints from single structure
Found interactions:
Covalently bonded - 1313
1-3 system - 1868
Same ring system - 35
Side-chain restricted 1-4 - 116
Omega 1-4 - 540
Tight phi/psi 1-4 - 540
Loose phi/psi 1-4 - 206
Other phi/psi 1-4 - 298
Other 1-4 - 589
Secondary structure - 2544
Salt bridge - 63
H bond - 233
Tight hydrophobic - 773
Loose hydrophobic - 1055
Other pairs - 836778
Found distance constraints from single structure
Found combined distance constraints from two structures
Will generate 6 structures and keep best-scoring 4
Progress: 17%|████████▍ | ETA: 0:00:36
Progress: 33%|████████████████▋ | ETA: 0:00:27
Progress: 50%|█████████████████████████ | ETA: 0:00:20
Progress: 67%|█████████████████████████████████▍ | ETA: 0:00:13
Progress: 83%|█████████████████████████████████████████▋ | ETA: 0:00:06
Progress: 100%|██████████████████████████████████████████████████| Time: 0:00:38Kept lowest scoring 4 out of 6 structures
Scores range from 12.1 to 174.6
Aligned ensemble to itself after 6 iteration(s)
Projections written to file "/tmp/exprose_out/pcs/pcs.tsv"
Projections written to file "/tmp/exprose_out/pcs/pcs_input_1.tsv"
Projections written to file "/tmp/exprose_out/pcs/pcs_input_2.tsv"
Wrote ensemble to PDB file(s) with prefix "/tmp/exprose_out/pdbs/out.pdb"
Wrote ensemble scores to file "/tmp/exprose_out/spe_scores.tsv"
Read 2634 atoms from PDB file
Projections written to file "/tmp/exprose_out/pcs/pcs_ex_1.tsv"
Read 2634 atoms from PDB file
Projections written to file "/tmp/exprose_out/pcs/pcs_ex_2.tsv"
WARNING: Cairo._jl_libpango is deprecated, use Cairo.libpango instead.
likely near /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_pipeline.jl:19
WARNING: Cairo._jl_libpango is deprecated, use Cairo.libpango instead.
likely near /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_pipeline.jl:19
WARNING: Cairo._jl_libpango is deprecated, use Cairo.libpango instead.
likely near /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_pipeline.jl:19
in apply_property at /root/.julia/packages/Compose/UIDMc/src/cairo_backends.jl
WARNING: Cairo._jl_libpango is deprecated, use Cairo.libpango instead.
likely near /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_pipeline.jl:19
in apply_property at /root/.julia/packages/Compose/UIDMc/src/cairo_backends.jl
WARNING: Cairo._jl_libpango is deprecated, use Cairo.libpango instead.
likely near /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_pipeline.jl:19
WARNING: Cairo._jl_libpango is deprecated, use Cairo.libpango instead.
likely near /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_pipeline.jl:19
WARNING: Cairo._jl_libpango is deprecated, use Cairo.libpango instead.
likely near /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_pipeline.jl:19
in apply_property at /root/.julia/packages/Compose/UIDMc/src/cairo_backends.jl
WARNING: Cairo._jl_libpango is deprecated, use Cairo.libpango instead.
likely near /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_pipeline.jl:19
in apply_property at /root/.julia/packages/Compose/UIDMc/src/cairo_backends.jl
Plotted principal components to file(s) "/tmp/exprose_out/pcs/pc_x_y.png"
Plotted RMSFs to file "/tmp/exprose_out/rmsfs.png"
n_to_write is larger than the number of eigenvectors - proceeding with all possible eigenvectors
PyMol script to view principal components written to file(s) "/tmp/exprose_out/pymol/view_pc_x.pml"
Done
-- ExProSE --
Arguments:
i1 - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CLL_H.pdb
d1 - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CLL.dssp
i2 - nothing
d2 - nothing
out_dir - /tmp/exprose_out
n_strucs - 4
tolerance_weight - 0.3
other_ratio - 20.0
extra_pdbs - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CFF_1.pdb, /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CFF_2.pdb
mod_path - nothing
n_mods - 0
Making output directory "/tmp/exprose_out"
Proceeding with one structure
Read 1367 atoms from PDB file
Read 144 residues from DSSP file
Found interactions:
Covalently bonded - 1379
1-3 system - 1966
Same ring system - 35
Side-chain restricted 1-4 - 116
Omega 1-4 - 568
Tight phi/psi 1-4 - 744
Loose phi/psi 1-4 - 157
Other phi/psi 1-4 - 195
Other 1-4 - 626
Secondary structure - 4160
Salt bridge - 42
H bond - 244
Tight hydrophobic - 865
Loose hydrophobic - 931
Other pairs - 921633
Found distance constraints from single structure
Will generate 6 structures and keep best-scoring 4
Progress: 17%|████████▍ | ETA: 0:00:41
Progress: 33%|████████████████▋ | ETA: 0:00:29
Progress: 50%|█████████████████████████ | ETA: 0:00:23
Progress: 67%|█████████████████████████████████▍ | ETA: 0:00:16
Progress: 83%|█████████████████████████████████████████▋ | ETA: 0:00:08
Kept lowest scoring 4 out of 6Progress: 100%|██████████████████████████████████████████████████| Time: 0:00:45
structures
Scores range from 0.3 to 15100.3
Aligned ensemble to itself after 5 iteration(s)
Projections written to file "/tmp/exprose_out/pcs/pcs.tsv"
Projections written to file "/tmp/exprose_out/pcs/pcs_input.tsv"
Wrote ensemble to PDB file(s) with prefix "/tmp/exprose_out/pdbs/out.pdb"
Wrote ensemble scores to file "/tmp/exprose_out/spe_scores.tsv"
Read 2634 atoms from PDB file
Projections written to file "/tmp/exprose_out/pcs/pcs_ex_1.tsv"
Read 2634 atoms from PDB file
Projections written to file "/tmp/exprose_out/pcs/pcs_ex_2.tsv"
Plotted principal components to file(s) "/tmp/exprose_out/pcs/pc_x_y.png"
Plotted RMSFs to file "/tmp/exprose_out/rmsfs.png"
n_to_write is larger than the number of eigenvectors - proceeding with all possible eigenvectors
PyMol script to view principal components written to file(s) "/tmp/exprose_out/pymol/view_pc_x.pml"
Done
-- ExProSE --
Arguments:
i1 - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CLL_H.pdb
d1 - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CLL.dssp
i2 - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CTR_H.pdb
d2 - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CTR.dssp
out_dir - /tmp/exprose_out
n_strucs - 4
tolerance_weight - 0.3
other_ratio - 20.0
extra_pdbs - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CFF_1.pdb, /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CFF_2.pdb
mod_path - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CTR_pocket_points.pdb
n_mods - 1
Making output directory "/tmp/exprose_out"
Proceeding with two structures
Read 1367 atoms from PDB file
Read 1336 atoms from PDB file
Read 144 residues from DSSP file
Read 141 residues from DSSP file
Found interactions:
Covalently bonded - 1313
1-3 system - 1868
Same ring system - 35
Side-chain restricted 1-4 - 116
Omega 1-4 - 540
Tight phi/psi 1-4 - 692
Loose phi/psi 1-4 - 157
Other phi/psi 1-4 - 195
Other 1-4 - 589
Secondary structure - 3684
Salt bridge - 42
H bond - 230
Tight hydrophobic - 817
Loose hydrophobic - 878
Other pairs - 835795
Found distance constraints from single structure
Found interactions:
Covalently bonded - 1313
1-3 system - 1868
Same ring system - 35
Side-chain restricted 1-4 - 116
Omega 1-4 - 540
Tight phi/psi 1-4 - 540
Loose phi/psi 1-4 - 206
Other phi/psi 1-4 - 298
Other 1-4 - 589
Secondary structure - 2544
Salt bridge - 63
H bond - 233
Tight hydrophobic - 773
Loose hydrophobic - 1055
Other pairs - 836778
Found distance constraints from single structure
Found combined distance constraints from two structures
Will generate 6 structures and keep best-scoring 4
Progress: 17%|████████▍ | ETA: 0:00:30
Progress: 33%|████████████████▋ | ETA: 0:00:25
Progress: 50%|█████████████████████████ | ETA: 0:00:18
Progress: 67%|█████████████████████████████████▍ | ETA: 0:00:12
Progress: 83%|█████████████████████████████████████████▋ | ETA: 0:00:06
Progress: 100%|██████████████████████████████████████████████████| Time: 0:00:36
Kept lowest scoring 4 out of 6 structures
Scores range from 3.8 to 35.0
Read 1111 pocket points from pocket points PDB file
Generating ensemble with modulator 1 of 1
Found 2963 interactions between the modulator and the protein
Will generate 6 structures and keep best-scoring 4
Progress: 17%|████████▍ | ETA: 0:00:32
Progress: 33%|████████████████▋ | ETA: 0:00:29
Progress: 50%|█████████████████████████ | ETA: 0:00:21
Progress: 67%|█████████████████████████████████▍ | ETA: 0:00:14
Progress: 83%|█████████████████████████████████████████▋ | ETA: 0:00:07
Progress: 100%|██████████████████████████████████████████████████| Time: 0:00:42
Kept lowest scoring 4 out of 6 structures
Scores range from 1.1 to 36.2
Aligned ensemble to itself after 3 iteration(s)
Projections written to file "/tmp/exprose_out/pcs/pcs.tsv"
Projections written to file "/tmp/exprose_out/pcs/pcs_input_1.tsv"
Projections written to file "/tmp/exprose_out/pcs/pcs_input_2.tsv"
Wrote ensemble to PDB file(s) with prefix "/tmp/exprose_out/pdbs/out.pdb"
Wrote ensemble scores to file "/tmp/exprose_out/spe_scores.tsv"
Read 2634 atoms from PDB file
Projections written to file "/tmp/exprose_out/pcs/pcs_ex_1.tsv"
Read 2634 atoms from PDB file
Projections written to file "/tmp/exprose_out/pcs/pcs_ex_2.tsv"
Plotted principal components to file(s) "/tmp/exprose_out/pcs/pc_x_y.png"
Plotted RMSFs to file "/tmp/exprose_out/rmsfs.png"
Wrote ensemble to PDB file(s) with prefix "/tmp/exprose_out/pdbs_mod_1/out.pdb"
Projections written to file "/tmp/exprose_out/mod_1/pcs.tsv"
Wrote ensemble scores to file "/tmp/exprose_out/mod_1/spe_scores.tsv"
Plotted principal components to file(s) "/tmp/exprose_out/mod_1/pc_x_y.png"
Aligned ensemble to itself after 2 iteration(s)
Plotted RMSFs to file "/tmp/exprose_out/mod_1/rmsfs.png"
n_to_write is larger than the number of eigenvectors - proceeding with all possible eigenvectors
PyMol script to view principal components written to file(s) "/tmp/exprose_out/pymol/view_pc_x.pml"
Done
-- ExProSE --
Arguments:
i1 - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CTR_H.pdb
d1 - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CTR.dssp
i2 - nothing
d2 - nothing
out_dir - /tmp/exprose_out
n_strucs - 4
tolerance_weight - 0.3
other_ratio - 20.0
extra_pdbs - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CFF_1.pdb, /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CFF_2.pdb
mod_path - /root/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CTR_pocket_points.pdb
n_mods - 1
Making output directory "/tmp/exprose_out"
Proceeding with one structure
Read 1336 atoms from PDB file
Read 141 residues from DSSP file
Found interactions:
Covalently bonded - 1347
1-3 system - 1919
Same ring system - 35
Side-chain restricted 1-4 - 120
Omega 1-4 - 552
Tight phi/psi 1-4 - 540
Loose phi/psi 1-4 - 232
Other phi/psi 1-4 - 298
Other 1-4 - 608
Secondary structure - 2544
Salt bridge - 84
H bond - 239
Tight hydrophobic - 789
Loose hydrophobic - 1084
Other pairs - 881389
Found distance constraints from single structure
Will generate 6 structures and keep best-scoring 4
Progress: 17%|████████▍ | ETA: 0:00:31
Progress: 33%|████████████████▋ | ETA: 0:00:24
Progress: 50%|█████████████████████████ | ETA: 0:00:18
Progress: 67%|█████████████████████████████████▍ | ETA: 0:00:12
Progress: 83%|█████████████████████████████████████████▋ | ETA: 0:00:06
Progress: 100%|██████████████████████████████████████████████████| Time: 0:00:36
Kept lowest scoring 4 out of 6 structures
Scores range from 0.0 to 0.7
Read 1111 pocket points from pocket points PDB file
Generating ensemble with modulator 1 of 1
Found 3171 interactions between the modulator and the protein
Will generate 6 structures and keep best-scoring 4
Progress: 17%|████████▍ | ETA: 0:00:32
Progress: 33%|████████████████▋ | ETA: 0:00:27
Progress: 50%|█████████████████████████ | ETA: 0:00:20
Progress: 67%|█████████████████████████████████▍ | ETA: 0:00:13
Progress: 83%|█████████████████████████████████████████▋ | ETA: 0:00:07Kept lowest scoring 4 out of 6 structures
Scores range from 1.0 to 17.3
Progress: 100%|██████████████████████████████████████████████████| Time: 0:00:39
Aligned ensemble to itself after 2 iteration(s)
Projections written to file "/tmp/exprose_out/pcs/pcs.tsv"
Projections written to file "/tmp/exprose_out/pcs/pcs_input.tsv"
Wrote ensemble to PDB file(s) with prefix "/tmp/exprose_out/pdbs/out.pdb"
Wrote ensemble scores to file "/tmp/exprose_out/spe_scores.tsv"
Read 2634 atoms from PDB file
Projections written to file "/tmp/exprose_out/pcs/pcs_ex_1.tsv"
Read 2634 atoms from PDB file
Projections written to file "/tmp/exprose_out/pcs/pcs_ex_2.tsv"
Plotted principal components to file(s) "/tmp/exprose_out/pcs/pc_x_y.png"
Plotted RMSFs to file "/tmp/exprose_out/rmsfs.png"
Wrote ensemble to PDB file(s) with prefix "/tmp/exprose_out/pdbs_mod_1/out.pdb"
Projections written to file "/tmp/exprose_out/mod_1/pcs.tsv"
Wrote ensemble scores to file "/tmp/exprose_out/mod_1/spe_scores.tsv"
Plotted principal components to file(s) "/tmp/exprose_out/mod_1/pc_x_y.png"
Aligned ensemble to itself after 2 iteration(s)
Plotted RMSFs to file "/tmp/exprose_out/mod_1/rmsfs.png"
n_to_write is larger than the number of eigenvectors - proceeding with all possible eigenvectors
PyMol script to view principal components written to file(s) "/tmp/exprose_out/pymol/view_pc_x.pml"
Done
Test Summary: | Pass Total
Pipeline | 5 5
Parameterisation tests not run; to run these, set run_param_test to true in runtests.jl
Testing ProteinEnsembles tests passed