Merge devel with master branch #49
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…ly applies to a this place at DockFlow: "Continue [y/n]".
… was a huge bottleneck for large libraries. The ineficiency came from .mol2 file checking AND "grep" the same file over and over, a huge problem especially over Network file systems (clusters and HPC). In my desktop it took: ~800 ligands - 1m 30s to compute ~30000 took > 5 minutes @mazinger it took: ~800 ligands - 5m 30s to compute ~30000 took > 15 minutes This new implementation is orders of magnitude faster for two reasons: 1 - ChemBase and previous computed are stored in arrays. No more "grep". 2 - "for loops" were replaced by single line "case", which was amazingly faster.
…ces. It's LigFlow folder is already named "resp" (bcc, gas, original..) to simplify the naming schema.
…mol2" already existed. Now if it's there already we delete it first.
…f it wasn't asked to This is noticeable when running --resp and --bcc at the same time, meaning that the file "LigFlow.xargs" or "LigFlow_bcc.xargs" may exist
… to "16" (NC_CHANGED) everytime "-nc" was evoked.
…ion was incorrect. I forgot to list ONLY ".mol2" files in the output folder
…umber of poses/ligand "-n".
…" instead of "SCORE_PROGRAM"
…ing SOLVATED complexes.
Also a bugFix for LigFlow when running on SLURM Gaussian, now each ligand will run on it's temporary folder. The code may be clarifyed if we replace all the "mkdir -p blabla ; cd /tmp/blabla ; antechamber... " by a function.
… useless for this version.
Fixed a -pf y, missing @LigFlow_functions.bash
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I'll update and run the tests before merging |
bounding_size.py was returning HALF the boxsize.
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