[Rdkit-discuss] Help building the RDKit cookbook
Yo Folks, I need some help building the RDKit documentation (how meta, I need documentation on the documentation). I go in $RDBASE/Docs/Book and I 'make html' which barfs the following: mkdir -p _build/html/api mkdir -p _build/html/cppapi cp /opt/RDKit_master/rdkit/docs/* _build/html/api cp: cannot stat ‘/opt/RDKit_master/rdkit/docs/*’: No such file or directory make: *** [apidocs] Error 1 This is obvious why ($RDBASE/rdkit/docs/ has nothing in it! - but the dir exists). I also did a find $RDBASE -name docs but this returns only one directory which I created myself. I guess my question has two parts to it. The first is what is the make process trying to copy (what are the correct values for APIDOCSHOME and CPPAPIDOCSHOME)? And the second is should this work out of the box (why don't the defaults of 'make html' just work) ? Thank you! - Jean-Paul Ebejer Early Stage Researcher -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Help building the RDKit cookbook
hmm, interesting problem. By default the make html target will also build the API documentation. You don't need this. Please try: make singlehtml and see if that works. Worst case you can just edit the Makefile by hand and remove the apidocs dependency from the html target. i.e. replace this: html: apidocs $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html @echo @echo Build finished. The HTML pages are in $(BUILDDIR)/html. with this: html: $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html @echo @echo Build finished. The HTML pages are in $(BUILDDIR)/html. Best, -greg On Thu, Apr 30, 2015 at 8:51 AM, JP jeanpaul.ebe...@inhibox.com wrote: Yo Folks, I need some help building the RDKit documentation (how meta, I need documentation on the documentation). I go in $RDBASE/Docs/Book and I 'make html' which barfs the following: mkdir -p _build/html/api mkdir -p _build/html/cppapi cp /opt/RDKit_master/rdkit/docs/* _build/html/api cp: cannot stat ‘/opt/RDKit_master/rdkit/docs/*’: No such file or directory make: *** [apidocs] Error 1 This is obvious why ($RDBASE/rdkit/docs/ has nothing in it! - but the dir exists). I also did a find $RDBASE -name docs but this returns only one directory which I created myself. I guess my question has two parts to it. The first is what is the make process trying to copy (what are the correct values for APIDOCSHOME and CPPAPIDOCSHOME)? And the second is should this work out of the box (why don't the defaults of 'make html' just work) ? Thank you! - Jean-Paul Ebejer Early Stage Researcher -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] SDF tags and -
On 2015-04-29 23:08, Greg Landrum wrote: Here are my thoughts on this: The RDKit is usually strict while parsing molecules from SDF, SMILES, or other formats. My point was that given ''' my_property2 1234 my_property3 ''' a lexer shouldn't have a problem recognizing the 2 tags. A leninent parser would return stuff in between as value: 1234\n\n There are exceptions to this: the RDKit ignores the limit on line length while reading SDFs: there's no chance of confusion here, so I believe it's safe to do so. Similarly, a lenient parser could ignore the line length and value length limits. I still need to put some thought into patching the SDWriter so that it can recognize things like consecutive line endings in property values. The big question is what it should do when it encounters such a case. Is that an error? Should it just write the output up to the blank line? A conservative writer should never write out 1234\n\n. Squash the multiple newlines. And/or give it a strict flag that makes it error out instead. I'm sure Andrew's seen a lot of badly broken SDFs. It doesn't mean you can't handle the ones you can unambiguously parse. Dimitri -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] SDF properties in case of error
Hi all, I am currently working on a program which needs to process libraries of large SDF files. One requirement is to always produce a valid output including the molecule title/name or a specified property for referencing. With specifying sanitize=False with ForwardSDMolSupplier and using Chem.Sanitize afterwards with an appropriate Exception handling helps in most cases to get the SD file properties and still detect errors in the molecules to avoid importing rubbish. However, in some cases this does not help. E.g. when an unknown atom (most of the time this is X) is found in the MolBlock the import fails with an Post-condition Violation and None is yielded. This is fine to detect the problem BUT it is impossible to get any information about the molecule which failed. My question is if there is a way to get to the data even for those cases? The files tend to be very big so accessing the molecule re-parsing it line-by-line in python to get the name for a specific molecule number (found by enumerating the supplier) is not really an option. What would be a good solution in my opinion is to create an empty molecule with all sd properties, including _Name, in case of an error instead of None. The actual error could then also be communicated into python via an '_Error' property. With this it would still be possible to continue processing of the file in a for loop, in contrast to raising an Exception, and it is easy to check if the molecule is empty. Maybe this behaviour could be activated via an option and the default would be to return None, to not break any existing code. I am very keen on getting your view on this issue. Best regards, Michael -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
