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progress.log
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RELEASE - OASA 0.13.1
----------------------------------------
* fixes - cairo_out - use cached version of ring searching - significantly speeds
up exports of larger molecules (10x or even more)
- fix disconnected molecules crashing cairo_out
- graph - fix rare lockups in SSSR algorithm
- __init__ - make name_database import conditional
* enhancements - molfile - parse charge information from property line in molfiles
* acknowledgments - thanks to István Vágó for several useful bug reports
RELEASE - OASA 0.13.0
----------------------------------------
* enhancements - cairo_out - double bonds in 3D rotated molecules look much better
(z-coordinate is taken into account when the bond is drawn)
* fixes - smiles - smiles encoder did not prefix two digit ring numbers with "%"
- graph - SSSR code did not find really smallest rings in case no vertices with
degree 2 were present in the initial drawing (fullerene and such)
- molecule - aromatic bond detection uses SSSR instead of all possible rings
when there are more then 10 smallest rings - fixes lockup for fullerene
- cairo_out - when scaling != 1 the resulting image was improperly cropped
RELEASE - OASA 0.12.7
----------------------------------------
* enhancements - cairo_out - mols_to_cairo and mol_to_cairo convenience functions added
* fixes - cairo_out - background was not properly painted (thanks to Noel O'Boyle for reporting this)
RELEASE - OASA 0.12.6
----------------------------------------
* enhancements - cairo_out - more than one molecule can be placed onto a canvas
(use method mols_to_cairo())
- cairo_out - support for PDF and SVG export added
(use format argument to mols_to_cairo() or mol_to_png())
- inchi_key - code updated to reflect 1.02 final of InChI
- subprocess is used instead of deprecated popen
- molfile - SDFiles are now supported using a new class based interface
and generators for file reading
* fixes - pybel_bridge - charge is properly copied between OASA and pybel
RELEASE - OASA 0.12.5
----------------------------------------
* enhancements - cairo_out - default color scheme was changed to a slightly modified version of
http://bodr.svn.sourceforge.net/viewvc/*checkout*/bodr/trunk/bodr/elements/elements.xml?revision=34&content-type=text%2Fplain (old scheme is still available)
- cairo_out - carbon atom in methane is always visible
- cairo_out - it is possible to change symbol and hydrogen display on per-atom
basis by setting atom.properties_['show_hydrogens'] == True
and/or atom.properties_['show_symbol]
- cairo_out - function mol_to_png now passes all keyword arguments to cairo_out
constructor
- cairo_out - more tuning of double bond centering
- monoisotopic mass was added to the periodic_table and formula dict
can thus compute exact (monoisotopic) mass
- molfile - RAD property is properly parsed
* changes - several changes to make OASA compatible with Python 2.6 were made which break
backwards compatibility with Python 2.3
* info - this version of OASA corresponds to that of BKChem-0.12.5
RELEASE - OASA 0.12.1
----------------------------------------
* bugfixes - coords_generator - coordinate generation obeys E/Z stereochemistry
even for branched structures
- cairo_out - charges should no longer shift placement of atom symbols
- H2N (hydrogen before atom symbol) should be placed properly
- bonds that have exactly 45 degree angle should no longer disappear
* enhancements - cairo_out - more elaborate algorithm is used to decide
about centering of a double bond
* acknowledgments - Noel O'Boyle - for merciless bug hunting
RELEASE - OASA 0.12.0
----------------------------------------
* first public release