Merge pull request #1171 from haddocking/main

Merging main into CG-HADDOCK

.github/dependabot.yml

@@ -8,4 +8,4 @@ updates:
   - package-ecosystem: "pip" # See documentation for possible values
     directory: "/" # Location of package manifests
     schedule:
-      interval: "weekly"
+      interval: "monthly"

.github/workflows/validate_citation.yml

@@ -0,0 +1,22 @@
+on:
+  push:
+    branches: [main]
+    paths:
+      - CITATION.cff
+  pull_request:
+  workflow_dispatch:
+
+name: CITATION.cff
+jobs:
+  Validate-CITATION-cff:
+    runs-on: ubuntu-latest
+    name: Validate CITATION.cff
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Validate CITATION.cff
+        uses: dieghernan/cff-validator@v3

CITATION.cff

@@ -1,13 +1,13 @@
 # YAML 1.2
 # Metadata for citation of this software according to the CFF format (https://citation-file-format.github.io/)
-cff-version: 1.0.3
-message: If you use this software, please cite it using these metadata.
+cff-version: 1.2.0
+message: "If you use this software, please cite it using these metadata."
 # FIXME title as repository name might not be the best name, please make human readable
-title: 'haddocking/haddock3: v3.0.0-beta.5'
+title: 'HADDOCK3 - modular integrative modelling software'
 doi: 10.5281/zenodo.10527751
 # FIXME splitting of full names is error prone, please check if given/family name are correct
 authors:
-- given-names: João
+- given-names: Joao
   family-names: Teixeira
   name-particle: M.C.
   affiliation: Zymvol
@@ -21,8 +21,8 @@ authors:
 - given-names: Alexandre
   family-names: Bonvin
   affiliation: '@UtrechtUniversity'
-- given-names: SarahAlidoost
-  family-names: ''
+- given-names: Sarah
+  family-names: Alidoost
   affiliation: Netherlands eScience center
 - given-names: Victor
   family-names: Reys
@@ -41,14 +41,10 @@ authors:
   affiliation: Netherlands eScience Center
 - given-names: Barbara
   family-names: Vreede
-  affiliation:
 - given-names: SSchott
-  family-names: ''
-  affiliation:
 - given-names: Regen
   family-names: Tsai
-  affiliation:
-version: 3.0.0-beta.5
+version: "2024.10.0b6"
 date-released: 2024-01-18
 repository-code: https://github.com/haddocking/haddock3
-license: cc-by-4.0
+license: CC-BY-4.0

README.md

@@ -23,30 +23,21 @@ HADDOCK, standing for **H**igh **A**mbiguity **D**riven protein-protein **DOCK**
 
 ## Installation
 
+Simple installation of the [latest release](https://pypi.org/project/haddock3/) of HADDOCK3. 
+
 ```bash
 pip install haddock3
 ```
 
-Execute:
+In case you rather install the latest unreleased version use instead:
 
 ```bash
-$ haddock3 -h
-usage: haddock3 [-h] [--restart RESTART] [--extend-run EXTEND_RUN] [--setup] [--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [-v] recipe
-
-positional arguments:
-  recipe                The input recipe file path
-
-optional arguments:
-  -h, --help            show this help message and exit
-  --restart RESTART     Restart the run from a given step. Previous folders from the selected step onwards will be deleted.
-  --extend-run EXTEND_RUN
-                        Start a run from a run directory previously prepared with the `haddock3-copy` CLI. Provide the run directory created with `haddock3-copy` CLI.
-  --setup               Only setup the run, do not execute
-  --log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
-  -v, --version         show version
+git clone https://github.com/haddocking/haddock3.git
+cd haddock3
+pip install .
 ```
 
-For the installation of third-party additional software, please check the [INSTALL](docs/INSTALL.md).
+For detailed instructions and installation of third-party software, please check [INSTALL.md](docs/INSTALL.md) 
 
 You might also want to check the following utilities:
 
@@ -62,6 +53,25 @@ The most basic usage is:
 haddock3 <configuration-file.toml>
 ```
 
+For help on haddock3 usage:
+
+```bash
+$ haddock3 -h
+usage: haddock3 [-h] [--restart RESTART] [--extend-run EXTEND_RUN] [--setup] [--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [-v] recipe
+
+positional arguments:
+  recipe                The input recipe file path
+
+optional arguments:
+  -h, --help            show this help message and exit
+  --restart RESTART     Restart the run from a given step. Previous folders from the selected step onwards will be deleted.
+  --extend-run EXTEND_RUN
+                        Start a run from a run directory previously prepared with the `haddock3-copy` CLI. Provide the run directory created with `haddock3-copy` CLI.
+  --setup               Only setup the run, do not execute
+  --log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
+  -v, --version         show version
+```
+
 Check the [EXAMPLES](https://github.com/haddocking/haddock3/blob/main/examples/README.md) page for more some usage examples and the [MANUAL]() (_coming soon!_) for a more detailed explanation of the configuration file.
 
 ## Support

pyproject.toml

@@ -48,15 +48,15 @@ dependencies = [
 
 [project.optional-dependencies]
 dev = [
-  "coverage==7.6.7",
+  "coverage==7.6.8",
   "pytest==8.3.3",
   "pytest-cov==6.0.0",
-  "hypothesis==6.119.3",
+  "hypothesis==6.122.0",
   "pytest-mock==3.14.0",
   "fastapi==0.115.5",
-  "httpx==0.27.2",
+  "httpx==0.28.0",
   "mpi4py==4.0.1",
-  "kaleido==0.2.1",
+  "kaleido==0.4.1",
   "pytest-random-order==1.1.1",
 
 ]

src/haddock/cns/toppar/carbohydrate.param

@@ -57,6 +57,7 @@ BOND CCA  NH1    1000.0    1.45   !as extended atom carbon-N
 BOND CCS  C      1000.0    1.52   !"    "       "     "   -C
 BOND CCE  C      1000.0    1.52
 BOND CCA  C      1000.0    1.52
+BOND CC6  OC     1000.0    1.25   ! standard CO bond (parm10)
 
 
 ANGLe H    OH1  CCS   500.0   109.35
@@ -148,6 +149,10 @@ ANGLe C    CCE  OES   500.0   107.24
 ANGLe C    CCA  OES   500.0   107.24
 ANGLe C    CCE  CCS   500.0   108.72
 ANGLe C    CCA  CCS   500.0   108.72
+! other angles
+ANGLe OC   CC6  OC    500.00  123.3548
+ANGLe CCS  CC6  OC    500.0   109.70 ! guess from CCS-CC6-OAS (to check: experimental structures have 112-113)
+
 
 
 DIHEdral  X    CCS   CCS   X      2.0  3   0.0
@@ -174,6 +179,7 @@ DIHEdral  X    C     CCA   X      2.0  3   0.0
 DIHEdral  X    C     CCS   X      2.0  3   0.0 ! N-acetyl in NAG, 8/30/93
 DIHEdral  CCS  NH1   C     CCS    2.0  2   0.0 ! peptide plane in NAG
                                                !   guess - PDA 8/99
+DIHEdral  CCS  OES   CCE   CCS    2.0  2   0.0 ! guessing for BDP
 
 IMPRoper  CCS X    X    CCS    500.0     0  35.26439 
 IMPRoper  CCE X    X    CCS    500.0     0  35.26439 
@@ -205,6 +211,7 @@ IMPRoper  HAS CCE  OAS  CCS    500.00    0  66.8
 IMPRoper  HAS HAS  CCE  CCS    500.00    0  70.3 !SIA C3
 IMPRoper  HAS HAS  CCS  CCE    500.00    0  70.3 !SIA C3
 IMPRoper  HAS HAS  CCA  CCS    500.00    0  70.3
+IMPRoper  HAS HAS  CCS  CCS    500.00    0  70.3 !ABE C3
 IMPRoper  HAS OH1  CCS  CCS    500.00    0  66.9 !MAN,GLC,GLA,NAG,FCA,XYP C3 - A2G,FCA,SIA C4 - SIA C7,C8
 IMPRoper  HAS OAS  CCS  CCS    500.00    0  66.9
 IMPRoper  HAS CCS  OH1  CCS    500.00    0  66.8 !FUC C3 MAN,GLC,GLA,NAG,FUC,XYP C4
@@ -231,6 +238,8 @@ IMPRoper  HAS OES  OAS  CCS    500.00    0  67.6 !A12,A13,A14,A16,B12L,B14L alph
 IMPRoper  C   CCS  NH1  O      500.00    0   0.0 !NAG,SIA planar
 IMPRoper  NH1 C    CCS  H      500.00    0   0.0 !NAG,SIA planar
 IMPRoper  CCS NH1  C    CCS    500.00    0 180.0 !NAG,SIA trans peptide
+! new impropers
+IMPRoper  CC6 CCS  OC   OC     500.00    0   0.0 !BDP, angle taken from charmm
 
 
 {Asn-NAG}