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[PyPLIF] Analisis paska PyPLIF – Post PyPLIF Analysis

Januari 21, 2013

Paska running PyPLIF untuk postdocking analysis guna penapisan virtual diperlukan langkah-langkah khusus meliputi (Catatan: ~10500 senyawa; penambatan molekul ~ 60 jam; PyPLIF ~ 6 jam):

Post PyPLIF runs after an SBVS campaign still need several analysis steps:

  1. Mengumpulkan hasil pada satu file | Collecting results in one file
  2. Pengurutan untuk menentukan yang terbaik tiap entry | Sorting for each entry to find the best PyPLIF score
  3. Pemilihan yang terbaik tiap entri | Selecting only the best from each entry
  4. Pengurutan seluruhnya (ranking) berdasarkan PyPLIF (jika sama diurutkan khusus yang PyPLIFnya sama dengan nilai ChemPLP) | Ranking based on PyPLIF (if PyPLIF exactly the same, the ChemPLP score will also be considered)
  5. Perhitungan EF | EF calculation

 

  • for i in $(cat ../testset.list); do cat ../$i.pyplif.csv >> all.pyplif.csv; done
  • sed “s/_conf_/    conf_/g” all.pyplif.csv > mod_all.pyplif.csv
  • sort -k 1,1 -k 4r,4n -k 3,3n mod_all.pyplif.csv > sorted-by-entry_all.pyplif.csv
  • awk ‘{if(old[$1]!=1){{old[$1]=1}{print}}}’ sorted-by-entry_all.pyplif.csv > sorted-by-entry_uniq-best.pyplif.csv
  • sort -k 4r,4n -k 2,2n sorted-by-entry_uniq-best.pyplif.csv >  sorted-by-pyplif-chemplp_uniq-best.pyplif.csv
  • grep -Ev TYR sorted-by-pyplif-chemplp_uniq-best.pyplif.csv > sorted-by-pyplif-chemplp-with-ref_uniq-best.pyplif.csv
  • grep -Ev LLX sorted-by-pyplif-chemplp-with-ref_uniq-best.pyplif.csv > sorted-by-pyplif-chemplp-no-ref_uniq-best.pyplif.csv
  • /mod_EF_calc.sh 185 10300 sorted-by-pyplif-chemplp-no-ref_uniq-best.pyplif.csv

Pogung 21 Januari 2013 07.30 am

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