diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index e69f75d..7a496dd 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -19,4 +19,4 @@ ] } } -} \ No newline at end of file +} diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 133e214..038a803 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -3,7 +3,6 @@ name: ci on: push: - jobs: test: runs-on: ubuntu-latest diff --git a/INSTALLATION.md b/INSTALLATION.md index 37c6135..0b0c57c 100644 --- a/INSTALLATION.md +++ b/INSTALLATION.md @@ -19,9 +19,9 @@ To install Whiscy, follow these steps: - Clone the repository: - ```bash - git clone https://github.com/haddocking/whiscy && cd whiscy - ``` + ```bash + git clone https://github.com/haddocking/whiscy && cd whiscy + ``` - Install the scripts @@ -33,23 +33,23 @@ To install Whiscy, follow these steps: - Check the installation - ```text - $ whiscy -h - usage: whiscy [-h] [-o output_file] [--version] - surface_list conversion_table alignment_file distance_file - - positional arguments: - surface_list Surface list - conversion_table Conversion table - alignment_file Alignment file - distance_file Distance file - - options: - -h, --help show this help message and exit - -o output_file, --output output_file - If set, output prediction to this file - --version show program's version number and exit - ``` + ```text + $ whiscy -h + usage: whiscy [-h] [-o output_file] [--version] + surface_list conversion_table alignment_file distance_file + + positional arguments: + surface_list Surface list + conversion_table Conversion table + alignment_file Alignment file + distance_file Distance file + + options: + -h, --help show this help message and exit + -o output_file, --output output_file + If set, output prediction to this file + --version show program's version number and exit + ``` ### Troubleshooting diff --git a/USAGE.md b/USAGE.md index 5aa75af..d36783f 100644 --- a/USAGE.md +++ b/USAGE.md @@ -10,9 +10,9 @@ Below we will give an example of how to use WHISCY to predict the binding site o Download the PDB file of the protein 1PPE from the [RCSB PDB](https://www.rcsb.org/structure/1PPE) website. - ```bash - wget https://files.rcsb.org/download/1PPE.pdb - ``` +```bash +wget https://files.rcsb.org/download/1PPE.pdb +``` ### Setup the prediction @@ -32,26 +32,26 @@ $ whiscy_setup 1PPE.pdb E 2024-04-22 11:44:44,046 cli_setup:319 INFO - Protdist calculated 2024-04-22 11:44:44,054 cli_setup:326 INFO - Conversion table file generated 2024-04-22 11:44:44,054 cli_setup:328 INFO - Whiscy setup finished - ``` +``` This script will generate a set of files needed for the prediction step with `whiscy`. Here it is a list of the generated files in our 1PPE complex. > Follow the links to see a set of pre-generated files for the 1PPE protein. -| File name | Explanation | -| ----------------------------------------- |----------------------------------------------------------------| -| [1ppe.hssp](example/1ppe.hssp) | Multiple sequence alignment download from the HSSP database | -| [1ppe.hssp.bz2](example/1ppe.hssp.bz2) | HSSP MSA file compressed | -| [1ppe.pdb](example/1ppe.pdb) | PDB file download from the Protein Data Bank | -| [1ppe_E.pdb](example/1ppe_E.pdb) | 1ppe.pdb parsed to select only the given `chain_id` | -| [1ppe_E.rsa](example/1ppe_E.rsa) | SASA output of `freesasa` in `NACCESS` format of `1ppe_E.pdb` file| -| [1ppe_E.fasta](example/1ppe_E.fasta) | Sequence of 1ppe_E.pdb. Alternative residues have been removed | -| [1ppe_E.phylseq](example/1ppe_E.phylseq) | MSA file translated from HSSP to PHYLIP format | -| [1ppe_E.conv](example/1ppe_E.conv) | PDB residue numeration to FASTA sequence numeration | -| [1ppe_E.out](example/1ppe_E.out) | Output of the `protdist` software on 1ppe_E.pdb | -| [1ppe_E.sur](example/1ppe_E.sur) | >15 % surface residue list according to `sa_pred_cutoff` cutoff | -| [1ppe_E.suract](example/1ppe_E.suract) | >40 % surface residue list according to `sa_act_cutoff` cutoff | -| [1ppe_E.lac](example/1ppe_E.lac) | 0-15 % accessible residue list | +| File name | Explanation | +| ---------------------------------------- | ------------------------------------------------------------------ | +| [1ppe.hssp](example/1ppe.hssp) | Multiple sequence alignment download from the HSSP database | +| [1ppe.hssp.bz2](example/1ppe.hssp.bz2) | HSSP MSA file compressed | +| [1ppe.pdb](example/1ppe.pdb) | PDB file download from the Protein Data Bank | +| [1ppe_E.pdb](example/1ppe_E.pdb) | 1ppe.pdb parsed to select only the given `chain_id` | +| [1ppe_E.rsa](example/1ppe_E.rsa) | SASA output of `freesasa` in `NACCESS` format of `1ppe_E.pdb` file | +| [1ppe_E.fasta](example/1ppe_E.fasta) | Sequence of 1ppe_E.pdb. Alternative residues have been removed | +| [1ppe_E.phylseq](example/1ppe_E.phylseq) | MSA file translated from HSSP to PHYLIP format | +| [1ppe_E.conv](example/1ppe_E.conv) | PDB residue numeration to FASTA sequence numeration | +| [1ppe_E.out](example/1ppe_E.out) | Output of the `protdist` software on 1ppe_E.pdb | +| [1ppe_E.sur](example/1ppe_E.sur) | >15 % surface residue list according to `sa_pred_cutoff` cutoff | +| [1ppe_E.suract](example/1ppe_E.suract) | >40 % surface residue list according to `sa_act_cutoff` cutoff | +| [1ppe_E.lac](example/1ppe_E.lac) | 0-15 % accessible residue list | ### Make the interface prediction diff --git a/media/1ppe_whiscy.png b/media/1ppe_whiscy.png index be94248..32f8b8c 100644 Binary files a/media/1ppe_whiscy.png and b/media/1ppe_whiscy.png differ diff --git a/media/loch_haddock.png b/media/loch_haddock.png index 270547a..124f6b1 100644 Binary files a/media/loch_haddock.png and b/media/loch_haddock.png differ diff --git a/media/whiscy_logo.png b/media/whiscy_logo.png index 858c191..b872b8c 100644 Binary files a/media/whiscy_logo.png and b/media/whiscy_logo.png differ diff --git a/media/whiscy_logo.svg b/media/whiscy_logo.svg index 7692ee7..24c0894 100644 --- a/media/whiscy_logo.svg +++ b/media/whiscy_logo.svg @@ -1,125 +1 @@ - - - - - - image/svg+xml - - - - - - - - - - - - - - - WHISCY - +WHISCY \ No newline at end of file diff --git a/src/whiscy/cli_consadjust.py b/src/whiscy/cli_consadjust.py index 21706e5..6df7817 100755 --- a/src/whiscy/cli_consadjust.py +++ b/src/whiscy/cli_consadjust.py @@ -84,7 +84,7 @@ def main(): neg = True index = np.argmax(z_values < currz) - upperz = z_values[index] + z_values[index] if index >= 24999: pscore = 0.5 diff --git a/src/whiscy/cli_setup.py b/src/whiscy/cli_setup.py index 5d0bf9c..d49046a 100755 --- a/src/whiscy/cli_setup.py +++ b/src/whiscy/cli_setup.py @@ -226,7 +226,7 @@ def main(): hssp_file = hssp_file.replace("hssp", "hssp3") hssp.decompress_bz2(compressed_hssp_file, hssp_file) logger.info("HSSP alignment stored to {0}".format(hssp_file)) - except Exception as err: + except Exception: logger.warning("HSSP file could not be downloaded") try: if "hssp3" in hssp_file: diff --git a/src/whiscy/modules/pam_data.py b/src/whiscy/modules/pam_data.py index 61ec698..6cf97a7 100644 --- a/src/whiscy/modules/pam_data.py +++ b/src/whiscy/modules/pam_data.py @@ -1,208 +1,1171 @@ """Data used in the PAM calc module""" +code = [ + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + 0, + -1, + 4, + 3, + 6, + 13, + 7, + 8, + 9, + -1, + 11, + 10, + 12, + 2, + -1, + 14, + 5, + 1, + 15, + 16, + -1, + 19, + 17, + -1, + 18, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + 0, + -1, + 4, + 3, + 6, + 13, + 7, + 8, + 9, + -1, + 11, + 10, + 12, + 2, + -1, + 14, + 5, + 1, + 15, + 16, + -1, + 19, + 17, + -1, + 18, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, +] -code = [-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, - -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, - -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, - -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 0, -1, - 4, 3, 6, 13, 7, 8, 9, -1, 11, 10, 12, 2, -1, 14, 5, 1, 15, 16, -1, 19, - 17, -1, 18, -1, -1, -1, -1, -1, -1, -1, 0, -1, 4, 3, 6, 13, 7, 8, 9, - -1, 11, 10, 12, 2, -1, 14, 5, 1, 15, 16, -1, 19, 17, -1, 18, -1, -1, - -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, - -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, - -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, - -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, - -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, - -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, - -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, - -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1] +logpameigval = [ + -0.022091252, + -0.019297602, + 0.000004760, + -0.017477817, + -0.016575549, + -0.015504543, + -0.002112213, + -0.002685727, + -0.002976402, + -0.013440755, + -0.012926992, + -0.004293227, + -0.005356688, + -0.011064786, + -0.010480731, + -0.008760449, + -0.007142318, + -0.007381851, + -0.007806557, + -0.008127024, +] -logpameigval = [-0.022091252,-0.019297602, 0.000004760,-0.017477817, - -0.016575549,-0.015504543,-0.002112213,-0.002685727, - -0.002976402,-0.013440755,-0.012926992,-0.004293227, - -0.005356688,-0.011064786,-0.010480731,-0.008760449, - -0.007142318,-0.007381851,-0.007806557,-0.008127024] +pameigvec = [ + [ + -0.173697, + -0.885673, + -1.0049, + 0.286697, + 1.88382, + 1.83495, + -0.198369, + 0.197182, + -0.328623, + 0.46536, + -0.29925, + -0.0965166, + -0.74739, + -0.854738, + 0.678401, + -0.183266, + 0.192614, + -0.482818, + 0.146535, + 0.0798611, + ], + [ + -0.184354, + -0.175916, + -1.0076, + -0.142763, + -0.0628839, + 0.0139009, + 0.141204, + 0.331822, + -0.539164, + -0.708375, + 0.0817457, + -0.37228, + 2.4085, + -2.80149, + -2.21178, + 1.28384, + 1.42798, + 0.0188545, + -0.4161, + -0.332652, + ], + [ + -3.40863, + -0.900981, + -0.994619, + 2.41327, + -0.811826, + -0.630945, + -0.174313, + 0.293746, + -0.383093, + -1.26984, + 0.89058, + -0.481288, + 0.12826, + 0.0590369, + 0.799897, + -0.296714, + -0.552095, + 0.384358, + 0.177192, + 0.169113, + ], + [ + 2.46339, + -1.69023, + -0.992457, + 0.277099, + -0.415795, + -0.0669855, + -0.230705, + 0.389199, + -0.543538, + -1.76778, + 0.892756, + -0.58089, + -0.185477, + -0.168277, + -0.685745, + -1.4301, + -1.48203, + 0.838871, + 0.35372, + 0.654423, + ], + [ + -0.0653222, + -0.142554, + -1.00875, + -0.0956775, + 0.00982116, + 0.0114652, + -0.267974, + -5.26286, + -1.24758, + 0.00651089, + -0.0117717, + 0.384433, + 0.233031, + 0.151659, + -0.112617, + -0.07216, + -0.130136, + 0.277631, + -0.271657, + 0.0955676, + ], + [ + 0.411745, + -1.0016, + -0.993702, + 1.55374, + -0.744468, + -0.843633, + -0.175287, + 0.385097, + -0.406764, + 3.44619, + -1.97631, + -0.351715, + 0.735297, + 0.188087, + -0.904437, + 0.289089, + -1.65422, + 0.177167, + -0.146884, + 0.250162, + ], + [ + -1.46727, + 2.10777, + -0.9997, + -1.83253, + 0.527169, + 0.327848, + -0.228532, + 0.39569, + -0.510345, + 0.172614, + -0.202514, + -0.508889, + -0.0845795, + -0.16422, + -1.27133, + -1.46079, + -1.68406, + 0.685183, + 0.331996, + 0.684302, + ], + [ + -0.0358926, + -0.101557, + -1.0116, + -0.332503, + -0.196083, + -0.33719, + -0.250326, + 0.316732, + -0.566645, + 0.055228, + -0.0474809, + -0.496718, + -1.85709, + 0.644994, + -0.657107, + 0.980698, + 0.993692, + 1.38279, + -0.619067, + -0.747332, + ], + [ + 0.418693, + 0.437099, + -0.995008, + -0.951753, + 0.506729, + 0.416234, + -0.116331, + 0.255448, + -0.181811, + -0.851382, + 0.440693, + -0.67166, + 1.20247, + 0.832078, + 1.74873, + 3.77201, + -2.59574, + -0.020501, + -0.294246, + -0.0926676, + ], + [ + 0.125546, + -0.0372708, + -0.995249, + 0.281829, + 2.9408, + -3.14634, + -0.100311, + 0.0550663, + 0.61025, + -0.178163, + 0.40751, + 1.30446, + -0.137214, + 0.576156, + -0.721845, + 0.624154, + 0.424991, + -0.423803, + 1.73362, + 1.19383, + ], + [ + 0.0180848, + 0.0195127, + -0.986272, + -0.0422427, + -0.0639326, + 0.0913046, + -0.0163454, + 0.163283, + 1.15374, + 0.263141, + 0.678789, + 2.26955, + 0.201714, + -0.32496, + 0.14775, + -0.423257, + -0.587479, + 0.62248, + -1.06261, + -1.22256, + ], + [ + 0.254528, + 0.0789705, + -1.00771, + -0.252216, + 0.231033, + 0.338253, + -0.122814, + 0.41346, + -0.510865, + 0.460223, + 0.425877, + -0.347116, + 1.89864, + 1.78614, + 0.739422, + -0.88218, + 1.38203, + 0.548471, + 0.111328, + -0.142583, + ], + [ + -0.106978, + -0.00225986, + -1.01125, + 0.0638037, + -0.139527, + 0.163789, + -0.0895913, + 0.233315, + 0.587038, + -3.85451, + -6.80573, + 1.53798, + 0.593227, + 1.02989, + 0.45206, + -0.415565, + 0.350157, + 0.343607, + 0.0730036, + -0.369488, + ], + [ + -0.0168964, + 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There are only some whiskeys that aren’t as good as others.", - "Winston Churchill": "The water was not fit to drink. To make it palatable, we had to add whisky. By diligent effort, I learned to like it.", - "Tommy Cooper": "I’m on a whisky diet. I’ve lost three days already.", - "Humphrey Bogart": "I should never have switched from Scotch to Martinis.", - "Johnny Carson": "Happiness is having a rare steak, a bottle of whisky, and a dog to eat the rare steak.", - "Abraham Lincoln": "Tell me what brand of whiskey that Grant drinks. I would like to send a barrel of it to my other generals.", - "Alexander Fleming": "A good gulp of hot whiskey at bedtime—it’s not very scientific, but it helps.", - "W.C. Fields": "Always carry a flagon of whiskey in case of snakebite and furthermore always carry a small snake.", - "James Joyce": "The light music of whiskey falling into a glass—an agreeable interlude.", - "Igor Stravinsky": "My God, so much I like to drink Scotch that sometimes I think my name is Igor Stra-whiskey.", - "Haruki Murakami": "The second whiskey is always my favorite. From the third on, it no longer has any taste. It's just something to pour into your stomach.", - "Mikael Trellet": "Whiscy, to use without moderation.", - "Jorge Roel": "Coffee keeps me going until it's acceptable to drink Whiskey" - } +_quotes = { + "Mark Twain": "Too much of anything is bad, but too much good whiskey is barely enough.", + "Raymond Chandler": "There is no bad whiskey. There are only some whiskeys that aren’t as good as others.", + "Winston Churchill": "The water was not fit to drink. To make it palatable, we had to add whisky. By diligent effort, I learned to like it.", + "Tommy Cooper": "I’m on a whisky diet. I’ve lost three days already.", + "Humphrey Bogart": "I should never have switched from Scotch to Martinis.", + "Johnny Carson": "Happiness is having a rare steak, a bottle of whisky, and a dog to eat the rare steak.", + "Abraham Lincoln": "Tell me what brand of whiskey that Grant drinks. I would like to send a barrel of it to my other generals.", + "Alexander Fleming": "A good gulp of hot whiskey at bedtime—it’s not very scientific, but it helps.", + "W.C. Fields": "Always carry a flagon of whiskey in case of snakebite and furthermore always carry a small snake.", + "James Joyce": "The light music of whiskey falling into a glass—an agreeable interlude.", + "Igor Stravinsky": "My God, so much I like to drink Scotch that sometimes I think my name is Igor Stra-whiskey.", + "Haruki Murakami": "The second whiskey is always my favorite. From the third on, it no longer has any taste. It's just something to pour into your stomach.", + "Mikael Trellet": "Whiscy, to use without moderation.", + "Jorge Roel": "Coffee keeps me going until it's acceptable to drink Whiskey", +} def get_one(): one = random.choice(list(_quotes)) - return "\"{}\"\n - {}".format(_quotes[one], one) + return '"{}"\n - {}'.format(_quotes[one], one) diff --git a/tests/gold/run_parasmooth.sh b/tests/gold/run_parasmooth.sh index 924dcb3..3895352 100755 --- a/tests/gold/run_parasmooth.sh +++ b/tests/gold/run_parasmooth.sh @@ -1,3 +1,3 @@ #!/bin/bash -./parasmooth 2SNIE.acons 2SNIE.lcons 2SNIE.rd parasmooth.par > 2SNIE.parasmooth +./parasmooth 2SNIE.acons 2SNIE.lcons 2SNIE.rd parasmooth.par >2SNIE.parasmooth diff --git a/tests/gold/run_whiscy.sh b/tests/gold/run_whiscy.sh index 95de003..57922f8 100755 --- a/tests/gold/run_whiscy.sh +++ b/tests/gold/run_whiscy.sh @@ -1,4 +1,4 @@ #!/bin/bash -./whiscy 2SNIE.sur 2SNIE.conv 2SNIE.phylseq 2SNIE.out 2>&1 | awk 'NR > 8' > 2SNIE.whiscy +./whiscy 2SNIE.sur 2SNIE.conv 2SNIE.phylseq 2SNIE.out 2>&1 | awk 'NR > 8' >2SNIE.whiscy #./whiscy 2SNIE.sur 2SNIE.conv 2SNIE.phylseq 2SNIE.out diff --git a/tests/test_consadjust_regression.py b/tests/test_consadjust_regression.py index 2a734a9..60478d0 100644 --- a/tests/test_consadjust_regression.py +++ b/tests/test_consadjust_regression.py @@ -1,8 +1,8 @@ import filecmp +import os import subprocess -from pathlib import Path import sys -import os +from pathlib import Path import pytest diff --git a/tests/test_parasmooth_regression.py b/tests/test_parasmooth_regression.py index 5825d50..c35a2e9 100644 --- a/tests/test_parasmooth_regression.py +++ b/tests/test_parasmooth_regression.py @@ -1,8 +1,8 @@ import filecmp -import sys +import os import subprocess +import sys from pathlib import Path -import os import pytest diff --git a/tests/test_resdist_regression.py b/tests/test_resdist_regression.py index dbeb148..137e851 100644 --- a/tests/test_resdist_regression.py +++ b/tests/test_resdist_regression.py @@ -1,13 +1,12 @@ +import os import subprocess import sys -import os from pathlib import Path import pytest from . import GOLDEN_DATA_PATH - env = os.environ.copy() env["PYTHONPATH"] = str( Path(Path(__file__).parent.parent, "src"), diff --git a/tests/test_whiscy_regression.py b/tests/test_whiscy_regression.py index 18cbcf5..8e6ba5a 100644 --- a/tests/test_whiscy_regression.py +++ b/tests/test_whiscy_regression.py @@ -1,8 +1,6 @@ import filecmp import os -import shutil import subprocess -import os import sys from pathlib import Path