Parallel task execution and updates for new Schrodinger

• Execute tasks in stage in parallel. Issue #202
• Use absolute path for custom celpp weeks. Issue #204
• Check that Schrodinger env variable is set before using. Issue #205
• Capture Schrodinger version in weekly outputs. Issue #206
• Save number of submitted targets for each participant to REST API. Issue #207
• Handle and prevent empty PDB files created by Schrodinger. Issue #208

Fix for ftp connection refused.

• Additional fix for ftp connection refused. Issue #181

Fix for failed test in 1.11.1

v1.11.2

Fix for failed test in 1.11.1

Email participant when submission is empty

• Email participant when submission is empty. Issue #197

• Allow spaces in passwords in ftp config file. Issue #198

Support added to POST to website REST service

• Fixed minor bug where unit tests for molfilevalidator.py failed when valid
  openeye license was available. Issue #177

• Added retry to external submission download to prevent complete failure of
  download in event of network hiccup. Issue #181

• Fixed bug where median value incorrectly calculated in evaluate.py. Instead
  of averaging middle two values for case of even number of elements, the old
  code just chose the latter value. Issue #183

• Fixed bug where median value incorrectly calculated in post_evaluation.py.
  Instead of averaging middle two values, the old code just chose the latter
  value. Issue #184

• Updated BlastNFilterSummary class (used by celppreports.py) to calculate
  number of targets found by counting target .txt files if value is not in
  summary.txt file. Issue #187

• Added call to website REST service in EvaluationTask and PostEvaluationTask
  to persist evaluation results to website. This change added a new flag
  --websiteserviceconfig that requires a configuration file. Issue #188

• Fixed bug in evaluate.py wait_and_check() function which caused it to
  prematurely give up on an alignment. Issue #189

• Changed evaluate.py so it now writes final.log directly to output directory.
  Issue #190

• Moved code under if main into main() function to facilitate testing.
  Issue #191

Enabled custom smtp configuration

• Breaking change Added new flag to celpprunner.py --smtpconfig
  that lets a user specify smtp configuration information.
  At the same time removed --replyto --smtp, and --smtpport since
  those options would be confusing to have also in place. Issue #166

• molfilevalidator.py has new command line option --excludedir to
  let caller ignore directories when looking for mol files. Issue #167

• Fixed bug where a network hiccup raised an exception during
  DataImportTask causing celpprunner.py to exit prematurely. Issue #168

• Improved error message output when a participant uploads a
  malformed challenge data package. Issue #169

• Version of D3R is now output in post evaluation summary email. Issue #172

• Fixed bug where celpprunner.py was not sending an email to
  people in --summaryemail list if a task fails. Issue #171

• Post evaluation summary email now outputs lines with NA
  values for any submissions that failed. Issue #130

molfilevalidator added and blastnfilter memory fix

• Added molfilevalidator.py to validate D3R submission tarfiles. Issue #165

• evaluation.py now generates RMSD.json which is a JSON version of
  RMSD files. Issue #143

• Added a fix to deal with out of memory errors encountered in
  blastnfilter stage. Issue #5

Evaluation fixes

• Fixed bug where Apo targets not getting pocket center correctly defined. Issue #151

Symmetry filter

• EvaluationTask now records evaluate.py task exit code in a file. Issue #134

• Symmetry filter added to blastnfilter.py. Issue #145

• In RMSD.txt,RMSD.csv renamed Medium to Median and swapped values
  for Maximum and Minimum. Issue #144

• Added note about new values in parenthesis in individual results
  email. Issue #142

Evaluation Improvements

• EvaluationTask modified to pass path to blastnfilter task to evaluate.py. Issue #139

• Median RMSD added to post_evaluation.py outputs. Issue #136

• Added histogram of RMSD scores to post_evaluation.py outputs. Issue #137

• Continuously output the analysis result into the pickle csv and txt files. Issue #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