D3r

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* Added molfilevalidator.py to validate D3R submission tarfiles.
`Issue 165 <https://github.com/drugdata/D3R/issues/165>`_

* evaluation.py now generates RMSD.json which is a JSON version of
RMSD files. `Issue 143 <https://github.com/drugdata/D3R/issues/143>`_

* Added a fix to deal with out of memory errors encountered in
blastnfilter stage. `Issue 5 <https://github.com/drugdata/D3R/issues/5>`_

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* Fixed bug where Apo targets not getting pocket center correctly defined
`Issue 151 <https://github.com/drugdata/D3R/issues/151>`_

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* EvaluationTask now records evaluate.py task exit code in a file
`Issue 134 <https://github.com/drugdata/D3R/issues/134>`_

* Symmetry filter added to blastnfilter.py
`Issue 145 <https://github.com/drugdata/D3R/issues/145>`_

* In RMSD.txt,RMSD.csv renamed Medium to Median and swapped values
for Maximum and Minimum
`Issue 144 <https://github.com/drugdata/D3R/issues/144>`_

* Added note about new values in parenthesis in individual results
email
`Issue 142 <https://github.com/drugdata/D3R/issues/142>`_

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* EvaluationTask modified to pass path to blastnfilter task to evaluate.py
`Issue 139 <https://github.com/drugdata/D3R/issues/139>`_

* Median RMSD added to post_evaluation.py outputs
`Issue 136 <https://github.com/drugdata/D3R/issues/136>`_

* Added histogram of RMSD scores to post_evaluation.py outputs
`Issue 137 <https://github.com/drugdata/D3R/issues/137>`_

* Continuously output the analysis result into the pickle csv and txt files
`Issue 133 <https://github.com/drugdata/D3R/issues/133>`_

* Align the docked complex using the binding site alignment for each of the crystal template and calculate the RMSD, if the binding site alignment failed, then the whole protein alignment will be applied

* Improve the extraction step in the evaluate.py to ensure the RMSD calculating was only applied to the docked ligand but not all others ligand like solvents or co-factors

* Add the ligand center calculation step in the evaluate.py to output the distance of the docked ligand with the crystal ligand. Also calculate the distance between the original LMCSS ligand center with the crystal ligand center

* Update the genchallengedata.py to extract Apo chain which is closed to the LMCSS ligand `Issue 135 <https://github.com/drugdata/D3R/issues/135>`_

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* requirements.txt and setup.py modified to require biopython
v1.6.8, which is the last version compatible with python2.6

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* Bug fix, evaluation of a submission will not fail if one
candidate in that submission fails.