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6b6921d45f
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work from thinkpad
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2021-02-09 16:03:02 +00:00 |
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534a6754cd
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add foldx5 wrapper
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2021-02-09 15:45:21 +00:00 |
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4163ede798
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dont break when the pdb file is in a weird place with a weird name
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2021-02-09 15:20:55 +00:00 |
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8302d01867
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check to handle missing I/O/P dirs if drug unset
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2021-02-09 15:00:03 +00:00 |
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725e9b53ca
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test2 runfoldx symlink
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2021-02-09 14:43:03 +00:00 |
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56150ae3c8
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various changes
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2021-02-09 14:42:44 +00:00 |
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ca68996264
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renamed file runFoldx.py in test2/ to reflect this
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2021-02-09 10:54:35 +00:00 |
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86670bbac3
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remove shell scripts run with subprocess() and launch foldx directly from python
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2021-02-08 18:06:02 +00:00 |
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9df3913a84
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modifying script to avoid invoking bash as a subprocess
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2021-02-08 16:59:42 +00:00 |
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99b77434b5
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more debug
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2021-02-08 16:16:53 +00:00 |
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fa25a30dcf
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fixup broken shell scripts
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2021-02-08 15:44:21 +00:00 |
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1f8cfc2403
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test2 bugfixes
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2021-02-08 15:24:22 +00:00 |
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7a9b16255a
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added user defined option for processing dir to allow me to specify external storage device for running it
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2020-12-02 11:26:26 +00:00 |
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08ad16adbb
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added chain_extract.py and pdb_chain_extract.py
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2020-11-30 14:11:46 +00:00 |
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fc4313045f
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adding options to specify files by user
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2020-11-27 13:02:15 +00:00 |
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20bba2ad70
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added my_pdbtools containing pdbtools cloned from a git repo
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2020-11-17 13:56:23 +00:00 |
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802522d1c6
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updating notes to running_scripts.py as running for another drug-target
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2020-11-17 13:55:16 +00:00 |
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ac5b86a9cd
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modified running script to mention chain info for foldx
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2020-11-16 16:16:24 +00:00 |
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2ac4ea8f5c
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added script to interrogate pdb files mainly for res numbers
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2020-11-16 16:01:31 +00:00 |
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ccdd6029be
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updated results summary in the data_extraction.py
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2020-11-12 17:05:29 +00:00 |
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f9fd74812a
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handling missing dir for data_extraction.py
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2020-11-12 13:21:06 +00:00 |
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b0b9e91af7
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added what is required as a minimum to run data_extraction
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2020-11-06 19:04:27 +00:00 |
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b2284f7216
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added base histogram script for af and or
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2020-10-13 13:38:17 +01:00 |
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1f9ea3f789
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added ns prefix to SNPs for unambiguity
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2020-10-13 13:37:22 +01:00 |
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59911687c8
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changing labels in graphs for frontiers journal
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2020-10-09 13:10:08 +01:00 |
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2f1f02e1de
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renamed other_plots.R to other_plots_combined.R and changing labels to capital letters for journal
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2020-10-09 12:17:24 +01:00 |
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667804ad83
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saving work minor changes perhaps
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2020-10-08 16:03:12 +01:00 |
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7f5ca7f5a4
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added af and OR columns in the data
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2020-10-06 19:39:59 +01:00 |
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69f3629cc0
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indicated hardcoded active site residues for pnca
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2020-10-06 19:12:32 +01:00 |
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be50636b15
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script to subset data for dnds cals
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2020-10-06 19:11:34 +01:00 |
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4285bbd59f
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added barplot_subcolours_aa_combined.R to combine and label these plots
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2020-10-06 18:43:20 +01:00 |
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18b6407539
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adjusted x axis position label for barplot_subcols_aa_LIG.R
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2020-10-06 18:42:24 +01:00 |
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9784cba232
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generated labelled ps_plots_combined.R and capital "P" for position in barplots coloured aa for Lig
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2020-10-06 18:15:50 +01:00 |
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e60b4c5492
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output corr plots with coloured dots
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2020-10-06 17:47:24 +01:00 |
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9d2d6cfd84
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updated TASK in hist_af_or_combined.R
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2020-10-06 16:43:59 +01:00 |
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a549e52825
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renamed dist_plots.R to dist_plots_check.R as its exploratory
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2020-10-06 16:39:24 +01:00 |
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5f441d09d9
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added hist_af_or_combined.R to generate plots for output and moved previosu run to scratch_plots/
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2020-10-06 16:33:25 +01:00 |
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f240c969ec
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added hist_af.R
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2020-10-06 15:07:42 +01:00 |
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07104a8c8e
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updated .gitignore
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2020-10-06 09:55:19 +01:00 |
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74c4ef16ae
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added basic_barplots_foldx.R for supp figure
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2020-10-06 09:53:34 +01:00 |
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4c345ea9f4
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moved not required plots to scratch
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2020-10-06 09:52:54 +01:00 |
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9597997741
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saving predictions script
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2020-09-30 14:09:08 +01:00 |
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8a6c7968f5
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added predictions for ps and lig and output to results
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2020-09-30 13:12:05 +01:00 |
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a77b472dfa
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added prediction.R to do logistic regression
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2020-09-30 10:04:49 +01:00 |
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d2093e7a4c
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added ../data_extraction_epistasis.py for getting list for epistasis work
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2020-09-29 16:09:54 +01:00 |
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81796df71a
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added corr_data.R corr_PS_LIG_all.R corr_PS_LIG_v2.R
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2020-09-29 16:08:25 +01:00 |
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c58fa8cd4d
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added dist_plot.R to generate plots for writing results
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2020-09-23 19:24:42 +01:00 |
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48050752db
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added more analysis in extreme_muts.R to be tidied later
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2020-09-23 19:23:34 +01:00 |
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a3aab4556a
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added fold and duet agreement to extreme_muts.R
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2020-09-23 11:20:22 +01:00 |
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6d08b646fc
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added foldx scaled and foldx outcome to plotting_data.R
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2020-09-23 11:12:41 +01:00 |
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