Bugfixes, a few extra features

README.md

@@ -5,7 +5,13 @@
 
 ## Installation
 
-Clone the repository, then install the necessary libraries with `pip`:
+With `pip`:
+
+```
+pip install DockQ
+```
+
+Or, if you want the latest commit: clone the repository and run `pip` within the repo directory:
 
 ```
 git clone https://github.com/bjornwallner/DockQ/
@@ -47,44 +53,47 @@ Total DockQ over 3 native interfaces: 0.653 with BAC:ABC model:native mapping
 Native chains: A, B
 	Model chains: B, A
 	DockQ: 0.994
-	irms: 0.000
-	Lrms: 0.000
+	iRMSD: 0.000
+	LRMSD: 0.000
 	fnat: 0.983
 	fnonnat: 0.008
-	clashes: 0.000
 	F1: 0.987
-	DockQ_F1: 0.996
+	clashes: 0
 Native chains: A, C
 	Model chains: B, C
 	DockQ: 0.511
-	irms: 1.237
-	Lrms: 6.864
+	iRMSD: 1.237
+	LRMSD: 6.864
 	fnat: 0.333
 	fnonnat: 0.000
-	clashes: 0.000
 	F1: 0.500
-	DockQ_F1: 0.567
+	clashes: 0
 Native chains: B, C
 	Model chains: A, C
 	DockQ: 0.453
-	irms: 2.104
-	Lrms: 8.131
+	iRMSD: 2.104
+	LRMSD: 8.131
 	fnat: 0.500
 	fnonnat: 0.107
-	clashes: 0.000
-	F1: 0.641
-	DockQ_F1: 0.500
+    F1: 0.641
+	clashes: 0
 ```
 
 A more compact output option is available with the flag `--short`:
 
 ```
 $ DockQ examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb --short
 
-DockQ 0.994 DockQ_F1 0.996 Fnat 0.983 iRMS 0.000 LRMS 0.000 Fnonnat 0.008 clashes 0 mapping BA:AB examples/1A2K_r_l_b.model.pdb B A -> examples/1A2K_r_l_b.pdb A B
-DockQ 0.511 DockQ_F1 0.567 Fnat 0.333 iRMS 1.237 LRMS 6.864 Fnonnat 0.000 clashes 0 mapping BC:AC examples/1A2K_r_l_b.model.pdb B C -> examples/1A2K_r_l_b.pdb A C
-DockQ 0.453 DockQ_F1 0.500 Fnat 0.500 iRMS 2.104 LRMS 8.131 Fnonnat 0.107 clashes 0 mapping AC:BC examples/1A2K_r_l_b.model.pdb A C -> examples/1A2K_r_l_b.pdb B C
+Total DockQ over 3 native interfaces: 0.653 with BAC:ABC model:native mapping
+DockQ 0.994 iRMSD 0.000 LRMSD 0.000 fnat 0.983 fnonnat 0.008 F1 0.987 clashes 0 mapping BA:AB examples/1A2K_r_l_b.model.pdb B A -> examples/1A2K_r_l_b.pdb A B
+DockQ 0.511 iRMSD 1.237 LRMSD 6.864 fnat 0.333 fnonnat 0.000 F1 0.500 clashes 0 mapping BC:AC examples/1A2K_r_l_b.model.pdb B C -> examples/1A2K_r_l_b.pdb A C
+DockQ 0.453 iRMSD 2.104 LRMSD 8.131 fnat 0.500 fnonnat 0.107 F1 0.641 clashes 0 mapping AC:BC examples/1A2K_r_l_b.model.pdb A C -> examples/1A2K_r_l_b.pdb B C
+```
+
+A dictionary containing the complete results data can be dumped in JSON format with the `--json filename.json` flag:
 
+```
+$ DockQ examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb --json filename.json
 ```
 
 ## Model/Native chain mapping
@@ -156,10 +165,10 @@ Small molecules in PDB or mmCIF files can be scored and the mapping optimized in
 $ DockQ examples/1HHO_hem.cif examples/2HHB_hem.cif --small_molecule --mapping :ABEFG --short
 
 Total DockQ-small_molecules over 4 native interfaces: 0.659 with ABDCF:ABEFG model:native mapping
-DockQ 0.950 irms 0.455 Lrms 1.451 fnat 0.964 fnonnat 0.070 clashes 0.000 F1 0.946 DockQ_F1 0.945 mapping AB:AB examples/1HHO_hem.cif A B -> examples/2HHB_hem.cif A B
-Lrms 0.585 mapping AD:AE (HEM) examples/1HHO_hem.cif A D -> examples/2HHB_hem.cif A E
-Lrms 28.096 mapping BC:BF (PO4) examples/1HHO_hem.cif B C -> examples/2HHB_hem.cif B F
-Lrms 1.311 mapping BF:BG (HEM) examples/1HHO_hem.cif B F -> examples/2HHB_hem.cif B G
+DockQ 0.950 iRMSD 0.455 LRMSD 1.451 fnat 0.964 fnonnat 0.070 clashes 0.000 F1 0.946 DockQ_F1 0.945 mapping AB:AB examples/1HHO_hem.cif A B -> examples/2HHB_hem.cif A B
+LRMSD 0.585 mapping AD:AE (HEM) examples/1HHO_hem.cif A D -> examples/2HHB_hem.cif A E
+LRMSD 28.096 mapping BC:BF (PO4) examples/1HHO_hem.cif B C -> examples/2HHB_hem.cif B F
+LRMSD 1.311 mapping BF:BG (HEM) examples/1HHO_hem.cif B F -> examples/2HHB_hem.cif B G
 ```
 
 Only LRMSD is reported for small molecules.
@@ -170,7 +179,7 @@ Only LRMSD is reported for small molecules.
 
 Interfaces involving nucleic acids are seamlessly scored along with protein interfaces. The DockQ score is calculated for protein-NA or NA-NA interfaces in the same way as for protein-protein interfaces (two DockQ scores are reported for double helix chains).
 
-**Other uses**
+## Other uses
 
 Run DockQ with `-h/--help` to see a list of the available flags:
 
@@ -218,8 +227,8 @@ run_on_all_native_interfaces(model, native, chain_map=chain_map)
 
 ({('A', 'B'): {'DockQ_F1': 0.9437927182141027,
    'DockQ': 0.9425398964102757,
-   'irms': 0.3753064373774967,
-   'Lrms': 0.5535111803522507,
+   'iRMSD': 0.3753064373774967,
+   'LRMSD': 0.5535111803522507,
    'fnat': 0.8907563025210085,
    'nat_correct': 106,
    'nat_total': 119,
@@ -241,6 +250,16 @@ run_on_all_native_interfaces(model, native, chain_map=chain_map)
 
 See issue [#33](https://github.com/bjornwallner/DockQ/issues/33) if you want to merge multiple chains (e.g. heavy and light antibody chains) into a single receptor or ligand
 
+## Legend of outputs
+
+* `DockQ`: DockQ score as defined in the [original DockQ paper](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0161879)
+* `iRMSD`: RMSD of interfacial residues
+* `LRMSD`: Ligand RMSD
+* `fnat`: Fraction of retrieved native contacts (same as Recall or TPR)
+* `fnonnat`: Fraction of predicted contacts that are not native (same as FPR)
+* `F1`: Harmonic mean of the precision and recall in predicted interfacial contacts
+* `clashes`: number of clashing interfacial residues in model (distance between residues below 2Å)
+
 ## Citing DockQ v2
 
 If you use DockQ v2, please cite the preprint: https://doi.org/10.1101/2024.05.28.596225 

pyproject.toml

@@ -1,23 +1,23 @@
 [build-system]
-requires = ["setuptools>=68", "cython", "numpy ~= 1.21",]
+requires = ["setuptools>=68", "cython", "numpy < 2.0"]
 build-backend = "setuptools.build_meta"
 
 [project]
 name = "dockq"
-version = "2.1"
+version = "2.1.2"
 authors = [
   { name="Claudio Mirabello", email="[email protected]" },
   { name="Bjorn Wallner", email="[email protected]" },
 ]
 description = "A Quality Measure for Protein, Nucleic Acids and Small Ligand Docking Models"
 readme = "README.md"
-requires-python = ">=3.9"
+requires-python = ">=3.8"
 classifiers = [
     "Programming Language :: Python :: 3",
     "License :: OSI Approved :: MIT License",
     "Operating System :: OS Independent",
 ]
-dependencies = ["biopython >= 1.79", "networkx", "parallelbar"]
+dependencies = ["numpy < 2.0", "biopython >= 1.79", "networkx", "parallelbar"]
 
 [project.urls]
 Homepage = "https://github.com/bjornwallner/DockQ"

run_test.sh

@@ -3,10 +3,12 @@ set -euo pipefail
 
 rm -f test .coverage
 
+PYTHON=${1:-"python"}
+
 if command -v coverage &> /dev/null; then
     binary="coverage run --parallel-mode -m DockQ.DockQ "
 else
-    binary="DockQ"
+    binary="$PYTHON -m DockQ.DockQ"
 fi
 
 $binary examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb > test
@@ -49,9 +51,11 @@ diff <(grep -v "*" test) <(grep -v "*" testdata/6q2n_peptide.dockq)
 $binary examples/1HHO_hem.cif examples/2HHB_hem.cif --small_molecule --mapping :ABEFG > test
 
 # Test that cython version behaves the same as nocython
-python src/DockQ/DockQ.py examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb > test
+$PYTHON src/DockQ/DockQ.py examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb > test
 diff <(grep -v "*" test) <(grep -v "*" testdata/1A2K.dockq)
-python src/DockQ/DockQ.py examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb --no_align > test
+$PYTHON src/DockQ/DockQ.py examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb --no_align > test
 diff <(grep -v "*" test) <(grep -v "*" testdata/1A2K.dockq)
 
-coverage combine
+if command -v coverage &> /dev/null; then
+	coverage combine
+fi

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = DockQ
-version = 2.1
+version = 2.1.2
 
 [options]
 package_dir =
@@ -10,7 +10,7 @@ install_requires =
     setuptools
     cython
     parallelbar
-    numpy~=1.21
+    numpy<2.0
     biopython>=1.79
     networkx