D3r

------------------

* Remove intermediate files with pymol prefix from challenge data
package. `Issue 73 <https://github.com/drugdata/D3R/issues/73>`_

* Place docked files in top-level target directory in submissions.
`Issue 86 <https://github.com/drugdata/D3R/issues/86>`_

* Fixed sporadically failing unit test. `Issue 104 <https://github.com/drugdata/D3R/issues/104>`_

* Add evaluation chain permuter implementation and tests. `Issue 107 <https://github.com/drugdata/D3R/issues/107>`_

-------------------

* Modified ParticipantDatabase to optionally strip off _ from guid
when doing search for Participant. This is to handle case where
single participant has multiple submissions to CELPP. `Issue 98 <https://github.com/drugdata/D3R/issues/98>`_

* Switched os.getlogin() calls to pwd.getpwuid(os.getuid())[0]
cause os.getlogin() was raising OSError on Travis. `Issue 102 <https://github.com/drugdata/D3R/issues/102>`_

* Fixed bug where evaluation task completed email had log messages
from other evaluation task emails in them. `Issue 99 <https://github.com/drugdata/D3R/issues/99>`_

* Updated readme.txt file in challenge data package to reflect
use of new_release_structure_sequence_canonical.tsv instead of
new_release_structure_sequence.tsv file. `Issue 97 <https://github.com/drugdata/D3R/issues/97>`_

-------------------

* Fixed bug where large amounts of output to standard out/err caused
celpprunner.py to exit due to an exception from smtplib due to
very large email. `Issue 95 <https://github.com/drugdata/D3R/issues/95>`_

-------------------

* Added createchallenge stage which is NOT a stage, but a fake stage
that runs the following stages: makedb,import,blast,challengedata. `Issue 92 <https://github.com/drugdata/D3R/issues/92>`_

* Moved logic to setup logging handlers to start of celpprunner.py to remove
no handlers found error for d3r.celpp.util. `Issue 91 <https://github.com/drugdata/D3R/issues/91>`_

* Fixed bug where participant_list.csv could not be parsed if file was
written with carriage return delimiters instead of newlines. `Issue 93 <https://github.com/drugdata/D3R/issues/93>`_

* Cleaned up CELPPade by updating documentation and simplifying variable names

* Version of d3r is now written to 'start' file in each stage/task. `Issue 94 <https://github.com/drugdata/D3R/issues/94>`_

-------------------

* Evaluation task now emails results of evaluation to external
submitter. Issues `49 <https://github.com/drugdata/D3R/issues/49>`_ , `81 <https://github.com/drugdata/D3R/issues/81>`_

* Adjusted files uploaded to ftp server in EvaluationTask to
reflect changes in output from genchallengedata.py script.
Issues `79 <https://github.com/drugdata/D3R/issues/79>`_ , `80 <https://github.com/drugdata/D3R/issues/80>`_

* Added WebDavFileTransfer class to enable upload & download
of files via WebDa for celppade tools. `Issue 76 <https://github.com/drugdata/D3R/issues/76>`_

* Added tsv files and Components-inchi.ich files to list of
files uploaded to ftp by DataImportTask. `Issue 78 <https://github.com/drugdata/D3R/issues/78>`_

* Updated challenge data package readme.txt to include documentation
for hiTanimoto. `Issue 75 <https://github.com/drugdata/D3R/issues/75>`_

* Added pdb_seqres.txt.gz to list of files uploaded to ftp by
MakeBlastDBTask. `Issue 77 <https://github.com/drugdata/D3R/issues/77>`_

* Download canonical tsv file in data import stage. `Issue 84 <https://github.com/drugdata/D3R/issues/84>`_

* Added --rdkitpython flag to celpprunner.py and modified
code to pass it to chimera_proteinligprep.py. `Issue 88 <https://github.com/drugdata/D3R/issues/88>`_

* Fixed bug where celpprunner would fail if evaluation
stage is rerun with completed evaluation tasks. `Issue 87 <https://github.com/drugdata/D3R/issues/87>`_

* Improved documentation in RMSD.txt. Issues `82 <https://github.com/drugdata/D3R/issues/82>`_ , `83 <https://github.com/drugdata/D3R/issues/83>`_

--------------------

* Modified blastnfilter candidate txt file by adding hiTanimoto and
adding more information to hiResHolo and SMCSS.

* Genchallengedata.py modified to keep single chains for all holo
proteins (LMCSS, SMCSS, hiResHolo, hiTanimoto)

* In blastnfilter, hiResHolo now only has top structure
reported and only one chain. Where top structure is
highest resolution hit.