id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 9170 SMILES needs escape-sequence insertion Tristan Croll Eric Pettersen "{{{ The following bug report has been submitted: Platform: Linux-5.19.0-43-generic-x86_64-with-glibc2.35 ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC) Description Trying to create a molecule from a SMILES string with explicit hydrogens didn't go so well, due to mis-parsing of the string at the command-line stage. Trying to fetch it via the `smiles.fetch_smiles` API also failed at first, with the string being rejected by the server. Entering the string directly at https://cactus.nci.nih.gov/translate/ worked, and inspection of the result showed it expected most of the symbols to be escaped. This works: {{{ def escape_for_html(string): string = string.replace('[','%5B') string = string.replace(']','%5D') string = string.replace('(','%28') string = string.replace(')','%29') string = string.replace('@','%40') string = string.replace('+','%2B') return string smiles = '[H:10][C:1]1([C:2]([C:4]([C:7]([C:5]([C:3]1([H:14])[H:15])([H:18])[H:19])([H:23])[C@:8]([H:24])([C:6]([H:20])([H:21])[H:22])[N+:9]([H:25])([H:26])[H:27])([H:16])[H:17])([H:12])[H:13])[H:11]' from chimerax.smiles.smiles import fetch_smiles m = fetch_smiles(session, escape_for_html(smiles))[0] }}} ... although I'm not sure this example contains *every* character that needs to be escaped. Log: > isolde shorthand Initialising ISOLDE-specific command aliases: Alias Equivalent full command ------------------------------------------------- st isolde step {arguments} aw isolde add water {arguments} awsf isolde add water {arguments} sim false al isolde add ligand {arguments} aa isolde add aa $1 sel {arguments} ht isolde mod his sel {arguments} so setattr sel atoms occupancy {arguments} ab isolde adjust bfactors {arguments} ss isolde sim start sel rt isolde release torsions sel {arguments} rd isolde release distances sel {arguments} ra rd; rt pf isolde pepflip sel cf isolde cisflip sel cbb color bfactor {arguments} cbo color byattr occupancy {arguments} cbc color {arguments} bychain; color {arguments} byhet cs clipper set contourSensitivity {arguments} UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > ui tool show Shell > usage smiles ""smiles"" is not a command name > open > b'[H:10][C:1]1([C:2]([C:4]([C:7]([C:5]([C:3]1([H:14])[H:15])([H:18])[H:19])([H:23])[C@:8]([H:24])([C:6]([H:20])([H:21])[H:22])[N+:9]([H:25])([H:26])[H:27])([H:16])[H:17])([H:12])[H:13])[H:11]' > format smiles > open > [H:10][C:1]1([C:2]([C:4]([C:7]([C:5]([C:3]1([H:14])[H:15])([H:18])[H:19])([H:23])[C@:8]([H:24])([C:6]([H:20])([H:21])[H:22])[N+:9]([H:25])([H:26])[H:27])([H:16])[H:17])([H:12])[H:13])[H:11] > format smiles [Repeated 1 time(s)] > usage open format smiles 'smiles' is a database format type; use the command 'usage open database' with the corresponding database type instead > open > [H:10][C:1]1([C:2]([C:4]([C:7]([C:5]([C:3]1([H:14])[H:15])([H:18])[H:19])([H:23])[C@:8]([H:24])([C:6]([H:20])([H:21])[H:22])[N+:9]([H:25])([H:26])[H:27])([H:16])[H:17])([H:12])[H:13])[H:11] > from smiles > usage open database Missing or invalid ""database"" argument: Expected one of 'alphafold', 'ccd', 'cellpack', 'cod', 'eds', 'edsdiff', 'emdb', 'emdb_china', 'emdb_europe', 'emdb_japan', 'emdb_us', 'esmfold', 'ftp', 'help', 'http', 'https', 'pcod', 'pdb', 'pdbdev', 'pdbe', 'pdbe_bio', 'pdbj', 'pubchem', 'rcsb_bio', 'smiles', 'tcia', or 'uniprot' > usage open smiles Expected fewer arguments > usage open open names [format format] [fromDatabase fromDatabase] [name a text string] [format/database-specific arguments] — read and display data names: file names to open; a name of 'browse' will bring up a file browser format: one of aln, amber, amira, apbs, bild, brix, ccd, ccp4, cellpack, clustal, cmap, cmd, cod, collada, com, compiled python, coords, corecif, cube, dat, dcd, defattr, delphi, dicom, dock, dsn6, dv, dynamo, emanhdf, fasta, fchk, fsc, generic_particles, geomodel, gltf, gopenmol, gro, hdf, hssp, html, ihm, images, imagic, imod, imodmap, ims, log, macmolplt, markers, mmcif, mmtf, model2point, mol2, mole, motivelist, motl, mrc, msf, mtz, nbo31, nbo47, netcdfmap, nifti, nrrd, obj, out, pcod, pdb, pdbqt, peet, pfam, photo, pif, pir, positions, priism, profec, pseudobonds, psf, python, qout, relion, rmf, rsf, schrodinger maestro, sdf, segger, session, sff, situs, smallcif, smiles, spider, sqmout, star, stl, stockholm, storm, swc, swissdock, tbl, tom_em, trr, uhbd, uniprot, viperdb, vtk, web fetch, xplor, xtc, xyz, or zdock fromDatabase: one of alphafold, ccd, cellpack, cod, eds, edsdiff, emdb, emdb_china, emdb_europe, emdb_japan, emdb_us, esmfold, ftp, help, http, https, pcod, pdb, pdbdev, pdbe, pdbe_bio, pdbj, pubchem, rcsb_bio, smiles, tcia, or uniprot format/database-specific arguments: format- or database-specific arguments; to see their syntax use 'usage open format format' or 'usage open database database' commands respectively, where format and database are as per the above > open > [H:10][C:1]1([C:2]([C:4]([C:7]([C:5]([C:3]1([H:14])[H:15])([H:18])[H:19])([H:23])[C@:8]([H:24])([C:6]([H:20])([H:21])[H:22])[N+:9]([H:25])([H:26])[H:27])([H:16])[H:17])([H:12])[H:13])[H:11] > format smiles No such database '[h' > open > [H:10][C:1]1([C:2]([C:4]([C:7]([C:5]([C:3]1([H:14])[H:15])([H:18])[H:19])([H:23])[C@:8]([H:24])([C:6]([H:20])([H:21])[H:22])[N+:9]([H:25])([H:26])[H:27])([H:16])[H:17])([H:12])[H:13])[H:11] > format smiles No such database '[h' > usage open format smiles 'smiles' is a database format type; use the command 'usage open database' with the corresponding database type instead > usage open smiles Expected fewer arguments > usage open database smiles open names [ignoreCache true or false] [resName a text string] — read and display data names: file names to open; a name of 'browse' will bring up a file browser > open > \\[H:10\\]\\[C:1\\]1(\\[C:2\\](\\[C:4\\](\\[C:7\\](\\[C:5\\](\\[C:3\\]1(\\[H:14\\])\\[H:15\\])(\\[H:18\\])\\[H:19\\])(\\[H:23\\])\\[C@:8\\](\\[H:24\\])(\\[C:6\\](\\[H:20\\])(\\[H:21\\])\\[H:22\\])\\[N+:9\\](\\[H:25\\])(\\[H:26\\])\\[H:27\\])(\\[H:16\\])\\[H:17\\])(\\[H:12\\])\\[H:13\\])\\[H:11\\] > from smiles > open CCCC fromDatabase smiles Translated SMILES to 3D structure via NCI web service (SMILES: CCCC) > close > open > [H:10][C:1]1([C:2]([C:4]([C:7]([C:5]([C:3]1([H:14])[H:15])([H:18])[H:19])([H:23])[C@:8]([H:24])([C:6]([H:20])([H:21])[H:22])[N+:9]([H:25])([H:26])[H:27])([H:16])[H:17])([H:12])[H:13])[H:11] > from smiles No such database '[h' > open > r'[H:10][C:1]1([C:2]([C:4]([C:7]([C:5]([C:3]1([H:14])[H:15])([H:18])[H:19])([H:23])[C@:8]([H:24])([C:6]([H:20])([H:21])[H:22])[N+:9]([H:25])([H:26])[H:27])([H:16])[H:17])([H:12])[H:13])[H:11]' > from smiles No such database 'r'[h' Failed to translate SMILES to 3D structure via NCI web service(SMILES: [H:10][C:1]1([C:2]([C:4]([C:7]([C:5]([C:3]1([H:14])[H:15])([H:18])[H:19])([H:23])[C@:8]([H:24])([C:6]([H:20])([H:21])[H:22])[N+:9]([H:25])([H:26])[H:27])([H:16])[H:17])([H:12])[H:13])[H:11]) > open > %5BH:10%5D%5BC:1%5D1%28%5BC:2%5D%28%5BC:4%5D%28%5BC:7%5D%28%5BC:5%5D%28%5BC:3%5D1%28%5BH:14%5D%29%5BH:15%5D%29%28%5BH:18%5D%29%5BH:19%5D%29%28%5BH:23%5D%29%5BC%40:8%5D%28%5BH:24%5D%29%28%5BC:6%5D%28%5BH:20%5D%29%28%5BH:21%5D%29%5BH:22%5D%29%5BN%2B:9%5D%28%5BH:25%5D%29%28%5BH:26%5D%29%5BH:27%5D%29%28%5BH:16%5D%29%5BH:17%5D%29%28%5BH:12%5D%29%5BH:13%5D%29%5BH:11%5D > from smiles [Repeated 1 time(s)] OpenGL version: 3.3.0 NVIDIA 515.105.01 OpenGL renderer: NVIDIA GeForce RTX 3070/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.9.11 Locale: en_GB.UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: xcb XDG_SESSION_TYPE=x11 DESKTOP_SESSION=ubuntu XDG_SESSION_DESKTOP=ubuntu XDG_CURRENT_DESKTOP=ubuntu:GNOME DISPLAY=:1 Manufacturer: Dell Inc. Model: XPS 8950 OS: Ubuntu 22.04 Jammy Jellyfish Architecture: 64bit ELF Virtual Machine: none CPU: 20 12th Gen Intel(R) Core(TM) i7-12700 Cache Size: 25600 KB Memory: total used free shared buff/cache available Mem: 31Gi 6.0Gi 7.6Gi 225Mi 17Gi 24Gi Swap: 2.0Gi 0B 2.0Gi Graphics: 0000:01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA104 [GeForce RTX 3070 Lite Hash Rate] [10de:2488] (rev a1) Subsystem: Dell GA104 [GeForce RTX 3070 Lite Hash Rate] [1028:c903] Kernel driver in use: nvidia Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2023.5.7 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.21.0 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.1 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.6.0 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-LinuxSupport: 1.0.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-QScore: 1.0 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 distro: 1.7.0 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.9.26 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 23.1 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 rdkit-pypi: 2022.9.2 requests: 2.28.2 scipy: 1.9.3 setuptools: 67.4.0 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0 }}} " defect closed normal Input/Output fixed all ChimeraX