11 Commits

Author SHA1 Message Date
Greg Landrum
1a3ce773cf Molecule metadata in PNGs (#3316)
* reader stub. Navigates the file successfullly

* works

* works

* read out all metadata, not just ours

* first pass at reading out molecules

* support mol blocks too

* add python wrapper for parser

* add direct writer

* get rid of multiple definitions in PNParser.h

* update from code review

* robustification

* handle reading compressed metadata

* support compressing metadata too

* reorder arguments to make this more consistent

* add writers to python wrappers

* forgotten file

* add pickle support

* explicit zlib dependency

* get windows builds working
at least with conda boost+zlib

* switch to using boost::iostreams to do the compression/decompression

* switch to using a vector of string pairs to store the metadata

need this so that we can contain "duplicate" keys

* add metadata output to MolDraw2DCairo
still need python test

* add a python test

* initial work at reading/writing reactions from PNGs

refactor the ReactionParser.h header a bit

* cleanup debug messages

* reaction PNG support -> python

* ReactionPickler no longer includes all ProductTemplate props

* handle metadata at the MolDraw2D level
Currently only supported by MolDraw2DCairo, it's worth extending this to SVG too

* support reading multiple molecules from a png

* support multiple molecules from files and in python

* stop duplicating tags with multiple molecules

* update to get windll builds working
this change should be propagated to more cmakelists.txt files

* make sure the metadata ends up in the notebook

* make sure PNGs in the notebook also have metadata

efficiency improvements for some notebook bits (i.e stop going PNG->Image->PNG)

* no need to pretend that we might be using PIL anymore

* documentation

* update docs to show new functionality

* not sure why the doctests failed on linux

* still trying to diagnose those failures

* protect doctests in case python interpreters are being re-used

* switch tags

* the wrapped functions to read png data from files weren't working

* <sigh>... windows dlls
2020-08-25 07:51:18 +02:00
Eisuke Kawashima
75f03412ef Modernize deprecated header inclusion (#3137) 2020-05-04 10:40:57 +02:00
Greg Landrum
7c0bb0b743 clang-tidy output 2017-04-22 17:09:24 +02:00
Greg Landrum
e08e0d16d8 first pass, using google style 2015-11-14 14:58:11 +01:00
Greg Landrum
e71c0a2d2d Fixes #167
I am not completely comfortable with the fact that one reference energy in testDistGeom.py
  had to be changed. This is worth looking into some more
2013-11-27 07:26:05 +01:00
Greg Landrum
3b3d44db16 remove exe property from source files 2011-01-13 04:22:56 +00:00
Greg Landrum
f3fbef45c5 update copyright statements 2010-09-26 17:04:37 +00:00
Greg Landrum
90ff1bf2db oops, checked in with a mistake 2009-08-22 05:35:18 +00:00
Greg Landrum
0de804e645 initial pass at fixes and a test for issue 2840217 2009-08-21 18:51:40 +00:00
Greg Landrum
5d03333c22 setup svn keywords (should have done this before import... grn) 2006-05-06 22:54:39 +00:00
Greg Landrum
75a79b6327 initial import 2006-05-06 22:20:08 +00:00