Hi all, I am unable to see an inline structure depiction in the Jupyter notebook, nor in the JupyterLab notebook, tested with both the Python 2 and Python 3 kernels, and rdkit.__version__ '2018.03.1'.
I installed miniconda and RDKit on my Mac using: curl -O 'https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh' bash Miniconda3-latest-MacOSX-x86_64.sh conda install conda-build conda install -c conda-forge jupyterlab conda install -c rdkit rdkit My test code is: from rdkit import Chem from rdkit.Chem.Draw import IPythonConsole mol = Chem.MolFromSmiles("c1ccccc1O") mol It gives a broken image link, the contents of which are: data:image/png;base64, There is no message in the console log reporting a problem. My assumption is that I am missing a library which is needed for the PNG generation step. I have put the output of "conda list" at the end of this email. Can someone suggest what to do next? I did not see a discussion of this problem on the recent mailing list nor in the issue tracker. As a backup, I saw that IPythonConsole supports SVG mode. I enabled it using: IPythonConsole.ipython_useSVG = True This gave me another broken image icon. I tracked it down to incorrect handling of the "svg" namespace. A fix was for this was made on 14 May 2018, and will be part of the fall release. (See https://github.com/rdkit/rdkit/pull/1866 ). For now I can monkey-patch the run-time using: === from rdkit.Chem import Draw original_moltoSVG = Draw._moltoSVG def new_moltoSVG(*args, **kwargs): s = original_moltoSVG(*args, **kwargs) return s.replace("xmlns:svg='http://www.w3.org/2000/svg'", "xmlns='http://www.w3.org/2000/svg'") Draw._moltoSVG = new_moltoSVG === However, I would like to get the regular PNG output to work. Cheers, Andrew [email protected] # packages in environment at /Users/dalke/miniconda3: # # Name Version Build Channel appdirs 1.4.3 py_1 conda-forge appnope 0.1.0 py36_0 conda-forge asn1crypto 0.24.0 py36_0 attrs 18.1.0 py_1 conda-forge automat 0.7.0 py_1 conda-forge backcall 0.1.0 py_0 conda-forge beautifulsoup4 4.6.3 py36_0 blas 1.0 mkl bleach 2.1.4 py_1 conda-forge bzip2 1.0.6 h1de35cc_5 ca-certificates 2018.8.24 ha4d7672_0 conda-forge cairo 1.14.12 hc4e6be7_4 certifi 2018.8.24 py36_1 cffi 1.11.5 py36h342bebf_0 chardet 3.0.4 py36h96c241c_1 conda 4.5.11 py36_0 conda-forge conda-build 3.13.0 py36_0 conda-env 2.6.0 h36134e3_0 constantly 15.1.0 py_0 conda-forge cryptography 2.2.2 py36h1de35cc_0 decorator 4.3.0 py_0 conda-forge entrypoints 0.2.3 py36_2 conda-forge filelock 3.0.6 py36_0 fontconfig 2.13.0 h5d5b041_1 freetype 2.9.1 hb4e5f40_0 gettext 0.19.8.1 h15daf44_3 glib 2.56.2 hd9629dc_0 glob2 0.6 py36_0 html5lib 1.0.1 py_0 conda-forge hyperlink 17.3.1 py_0 conda-forge icu 58.2 h4b95b61_1 idna 2.6 py36h8628d0a_1 incremental 17.5.0 py_0 conda-forge intel-openmp 2018.0.3 0 ipykernel 4.9.0 py36_0 conda-forge ipython 6.5.0 py36_0 conda-forge ipython_genutils 0.2.0 py_1 conda-forge jedi 0.12.1 py36_0 conda-forge jinja2 2.10 py36_0 jpeg 9b he5867d9_2 jsonschema 2.6.0 py36_2 conda-forge jupyter_client 5.2.3 py_1 conda-forge jupyter_core 4.4.0 py_0 conda-forge jupyterlab 0.34.6 py36_0 conda-forge jupyterlab_launcher 0.13.1 py_2 conda-forge libboost 1.65.1 hcc95346_4 libcxx 4.0.1 h579ed51_0 libcxxabi 4.0.1 hebd6815_0 libedit 3.1.20170329 hb402a30_2 libffi 3.2.1 h475c297_4 libgfortran 3.0.1 h93005f0_2 libiconv 1.15 hdd342a3_7 libpng 1.6.34 he12f830_0 libsodium 1.0.16 0 conda-forge libtiff 4.0.9 hcb84e12_2 libxml2 2.9.8 hab757c2_1 markupsafe 1.0 py36h1de35cc_1 mistune 0.8.3 py36h470a237_2 conda-forge mkl 2018.0.3 1 mkl_fft 1.0.4 py36h5d10147_1 mkl_random 1.0.1 py36h5d10147_1 nbconvert 5.3.1 py_1 conda-forge nbformat 4.4.0 py_1 conda-forge ncurses 6.1 h0a44026_0 notebook 5.6.0 py36_1 conda-forge numpy 1.15.1 py36h6a91979_0 numpy-base 1.15.1 py36h8a80b8c_0 olefile 0.45.1 py36_0 openssl 1.0.2p h470a237_0 conda-forge pandas 0.23.4 py36h6440ff4_0 pandoc 2.2.2 hde52d81_1 conda-forge pandocfilters 1.4.2 py_1 conda-forge parso 0.3.1 py_0 conda-forge pcre 8.42 h378b8a2_0 pexpect 4.6.0 py36_0 conda-forge pickleshare 0.7.4 py36_0 conda-forge pillow 5.2.0 py36hb68e598_0 pip 10.0.1 py36_0 pixman 0.34.0 hca0a616_3 pkginfo 1.4.2 py36_1 prometheus_client 0.3.0 py_0 conda-forge prompt_toolkit 1.0.15 py_1 conda-forge psutil 5.4.7 py36h1de35cc_0 ptyprocess 0.6.0 py36_0 conda-forge py-boost 1.65.1 py36h1439ea1_4 pyasn1 0.4.4 py_0 conda-forge pyasn1-modules 0.2.1 py_0 conda-forge pycosat 0.6.3 py36hee92d8f_0 pycparser 2.18 py36h724b2fc_1 pygments 2.2.0 py_1 conda-forge pyhamcrest 1.9.0 py_2 conda-forge pyopenssl 18.0.0 py36_0 pysocks 1.6.8 py36_0 python 3.6.5 hc167b69_1 python-dateutil 2.7.3 py_0 conda-forge python.app 2 py36_8 pytz 2018.5 py36_0 pyyaml 3.13 py36h1de35cc_0 pyzmq 17.1.2 py36hae99301_0 conda-forge rdkit 2018.03.4.0 py36h6adbef8_1 rdkit readline 7.0 hc1231fa_4 requests 2.18.4 py36h4516966_1 ruamel_yaml 0.15.37 py36h1de35cc_2 send2trash 1.5.0 py_0 conda-forge service_identity 17.0.0 py_0 conda-forge setuptools 39.2.0 py36_0 simplegeneric 0.8.1 py_1 conda-forge six 1.11.0 py36h0e22d5e_1 sqlite 3.23.1 hf1716c9_0 terminado 0.8.1 py36_1 conda-forge testpath 0.3.1 py36_1 conda-forge tk 8.6.7 h35a86e2_3 tornado 5.1 py36h470a237_1 conda-forge traitlets 4.3.2 py36_0 conda-forge twisted 17.5.0 py36_0 urllib3 1.22 py36h68b9469_0 wcwidth 0.1.7 py_1 conda-forge webencodings 0.5.1 py_1 conda-forge wheel 0.31.1 py36_0 xz 5.2.4 h1de35cc_4 yaml 0.1.7 hc338f04_2 zeromq 4.2.5 hfc679d8_5 conda-forge zlib 1.2.11 hf3cbc9b_2 zope.interface 4.5.0 py36h470a237_1 conda-forge ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
