filips filipsPL
filipsPL
/ dock_gbsa_rescore.in
Last active
September 26, 2019 10:56
— forked from bougui505/dock_gbsa_rescore.in
Template of dock6.9 for GBSA Hawkins rescore of docked molecules. Replace LIG with your mol2 file of docked ligands and REC by your mol2 file for the receptor
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| conformer_search_type flex | |
| write_fragment_libraries no | |
| user_specified_anchor no | |
| limit_max_anchors no | |
| min_anchor_size 5 | |
| pruning_use_clustering yes | |
| pruning_max_orients 1000 | |
| pruning_clustering_cutoff 100 | |
| pruning_conformer_score_cutoff 100.0 | |
| pruning_conformer_score_scaling_factor 1.0 |
filipsPL
/ process_dock6_logs.sh
Last active
September 23, 2019 09:40
For all *.logs files in the directory: extracts scores and compound names from dock6 docking logs and puts it to the simple csv file, with the name of the input file.
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| for f in *.logs; | |
| do echo $f; | |
| echo "compound,score" > `basename $f .logs`.csv; | |
| cat $f | egrep "Molecule:|Grid_Score" | tr -s " " | sed -e ':a;N;$!ba;s/\n Grid_Score: / /g' -e 's/Molecule: //g' | \ | |
| tr " " "," >> `basename $f .logs`.csv; | |
| done |
filipsPL
/ autoweka_process.sh
Created
February 28, 2019 12:06
Quick and dirty way of processing log files from autoweka to extract the best classifier found by the system. Results may still need some tuning before supplying to weka experimenter, but in many cases it works out of the box.
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| #!/bin/bash | |
| # direcotry with log files from autoweka | |
| autowekadir="./" | |
| # weka.classifiers.meta.FilteredClassifier -F "weka.filters.supervised.attribute.AttributeSelection -E \"$eval\" -S \"$selection\"" -S 1 -W $classifier | |
| # best classifier: weka.classifiers.lazy.IBk | |
| # arguments: [-K, 4, -F] | |
| # attribute search: weka.attributeSelection.GreedyStepwise | |
| # attribute search arguments: [-B, -R] |
filipsPL
/ python+tee.py
Created
November 7, 2018 20:29
Function which: 1) runs the command 2) for the specified time (duration) and 3) pipes output to the file AND to screen (live).
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| import time | |
| from time import strftime | |
| import subprocess | |
| def runForDuration(cmdline, duration, logFile): | |
| teeCommand = ['tee', '-a', logFile ] # quick and dirty hack to get log to file | |
| try: | |
| p1 = subprocess.Popen(cmdline, stdout=subprocess.PIPE, stderr=subprocess.STDOUT) | |
| p2 = subprocess.Popen(teeCommand, stdin=p1.stdout) |
filipsPL
/ list_big_files.sh
Created
December 15, 2017 08:37
List files bigger than the given size and optionally compress them
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| #!/bin/bash | |
| ### list files bigger than the given size | |
| ### and optionally compress them | |
| filesize=100M # files bigger than this will be listed; default is 100M | |
| for f in `find . -type f -size +$filesize` | |
| do |
filipsPL
/ maketoc.py
Created
September 27, 2017 13:02
Super simple TOC generator from a ready HTML file.
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| #!/usr/bin/env python | |
| # -*- coding: utf-8 -*- | |
| from re import sub | |
| fname = "FAQ.html" | |
| header="<h4>" | |
| outfile = "FAQ+TOC.html" | |
| #-----------------------------------------# |
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| #!/bin/bash | |
| for ses in `screen -r | grep "(Detached)"| cut -f 2`; do screen -r "$ses"; done |
filipsPL
/ rysuj-rrd.sh
Created
April 12, 2016 12:04
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| #!/bin/bash | |
| DATA=`date` | |
| DIR=/usr/local/bin/rrd/pi/rrd/ | |
| OUTDIR=/var/www/pi/sysinfo/img/ | |
| BAZA=$DIR/temperatura.rrd | |
| var=cisnienie |
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| #!/bin/bash | |
| rrdtool create airq.rrd --step 3600 \ | |
| DS:pm10:GAUGE:1800:0:500 \ | |
| DS:pm25:GAUGE:1800:0:500 \ | |
| RRA:AVERAGE:0.5:1:144 \ | |
| RRA:AVERAGE:0.5:3:336 \ | |
| RRA:AVERAGE:0.5:144:367 \ | |
| RRA:AVERAGE:0.5:1008:250 \ |
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| gua | |
| OpenBabel11131516582D | |
| 7 7 0 0 0 0 0 0 0 0999 V2000 | |
| -0.3090 -0.9511 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 | |
| -1.3090 -0.9511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| -1.8968 -1.7601 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 | |
| -1.6180 -0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 | |
| -0.8090 0.5878 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 | |
| -0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 |