duello 0.1.0__tar.gz

duello-0.1.0/.cargo/config.toml

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+[env]
+CMAKE_POLICY_VERSION_MINIMUM="3.16"

duello-0.1.0/.github/dependabot.yml

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+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  - package-ecosystem: "cargo" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "monthly"

duello-0.1.0/.github/workflows/rust.yml

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+name: Rust
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+env:
+  CARGO_TERM_COLOR: always
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Build
+      run: cargo build --verbose
+    - name: Run tests
+      run: cargo test --verbose
+    - name: Run clippy
+      run: cargo clippy --no-deps
+    - name: Run clippy on tests
+      run: cargo clippy --tests --no-deps

duello-0.1.0/.gitignore

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+# Generated by Cargo
+# will have compiled files and executables
+debug/
+target/
+*.vmd
+*.json
+log
+*.tga
+
+# Remove Cargo.lock from gitignore if creating an executable, leave it for libraries
+# More information here https://doc.rust-lang.org/cargo/guide/cargo-toml-vs-cargo-lock.html
+Cargo.lock
+
+# These are backup files generated by rustfmt
+**/*.rs.bk
+
+*.pdb
+*.xtc
+*.pdf
+potential.pqr
+potential_angles.pqr
+
+*~
+*.dat
+*.dat.gz
+*.xyz
+scene.vmd
+output.*
+.DS_Store
+.mypy*
+.ipynb_checkpoints

duello-0.1.0/.vscode/extensions.json

@@ -0,0 +1,3 @@
+{
+      "recommendations": ["rust-lang.rust-analyzer", "tamasfe.even-better-toml"]
+}

duello-0.1.0/.vscode/launch.json

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+{
+    // Use IntelliSense to learn about possible attributes.
+    // Hover to view descriptions of existing attributes.
+    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "type": "lldb",
+            "request": "launch",
+            "name": "Cargo test",
+            "cargo": {
+                "args": [
+                    "test",
+                    "--no-run",
+                    "--lib"
+                ]
+            },
+            "args": []
+        }
+    ]
+}

duello-0.1.0/.vscode/settings.json

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+{
+    "rust-analyzer.diagnostics.disabled": [
+        "unresolved-proc-macro"
+    ],
+    "rust-analyzer.checkOnSave.command": "check",
+    "editor.formatOnSave": true,
+    "editor.defaultFormatter": "rust-lang.rust-analyzer",
+    "rust-analyzer.rustfmt.extraArgs": [
+        "+stable"
+    ],
+    "file_scan_exclusions": [
+        "**/.git",
+        "**/.svn",
+        "**/.hg",
+        "**/CVS",
+        "**/.DS_Store",
+        "**/Thumbs.db",
+        "**/.classpath",
+        "**/.settings",
+        "**/~"
+    ],
+    "files.associations": {
+        "__bit_reference": "cpp",
+        "__bits": "cpp",
+        "__config": "cpp",
+        "__debug": "cpp",
+        "__locale": "cpp",
+        "__split_buffer": "cpp",
+        "__string": "cpp",
+        "__tuple": "cpp",
+        "array": "cpp",
+        "atomic": "cpp",
+        "bit": "cpp",
+        "bitset": "cpp",
+        "cctype": "cpp",
+        "chrono": "cpp",
+        "cmath": "cpp",
+        "compare": "cpp",
+        "cstddef": "cpp",
+        "cstdint": "cpp",
+        "cstdio": "cpp",
+        "cstdlib": "cpp",
+        "cstring": "cpp",
+        "cwchar": "cpp",
+        "cwctype": "cpp",
+        "exception": "cpp",
+        "initializer_list": "cpp",
+        "ios": "cpp",
+        "iosfwd": "cpp",
+        "iostream": "cpp",
+        "istream": "cpp",
+        "limits": "cpp",
+        "locale": "cpp",
+        "memory": "cpp",
+        "new": "cpp",
+        "ostream": "cpp",
+        "stdexcept": "cpp",
+        "streambuf": "cpp",
+        "string": "cpp",
+        "string_view": "cpp",
+        "system_error": "cpp",
+        "tuple": "cpp",
+        "type_traits": "cpp",
+        "typeinfo": "cpp",
+        "unordered_map": "cpp",
+        "vector": "cpp",
+        "algorithm": "cpp",
+        "__errc": "cpp",
+        "__hash_table": "cpp",
+        "__mutex_base": "cpp",
+        "__node_handle": "cpp",
+        "__threading_support": "cpp",
+        "__verbose_abort": "cpp",
+        "clocale": "cpp",
+        "cstdarg": "cpp",
+        "ctime": "cpp",
+        "mutex": "cpp",
+        "optional": "cpp",
+        "ratio": "cpp",
+        "variant": "cpp",
+        "*.tcc": "cpp",
+        "concepts": "cpp",
+        "functional": "cpp",
+        "iterator": "cpp",
+        "memory_resource": "cpp",
+        "random": "cpp",
+        "utility": "cpp"
+    },
+    "rust-analyzer.showUnlinkedFileNotification": false,
+    "rust-analyzer.cargo.noDefaultFeatures": false,
+    "rust-analyzer.checkOnSave": true,
+    "editor.tabCompletion": "on",
+    "python.languageServer": "Pylance",  // or "Default"
+    "python.autoComplete.addBrackets": true,
+    "editor.quickSuggestions": {
+        "other": true,
+        "comments": false,
+        "strings": true
+    }
+}

duello-0.1.0/.zed/settings.json

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+// Folder-specific settings
+//
+// For a full list of overridable settings, and general information on folder-specific settings,
+// see the documentation: https://zed.dev/docs/configuring-zed#folder-specific-settings
+{
+  "file_scan_exclusions": [
+    "**/*~",
+    "**/.git",
+    "**/.svn",
+    "**/.hg",
+    "**/CVS",
+    "**/.DS_Store",
+    "**/Thumbs.db",
+    "**/.classpath",
+    "**/.settings"
+  ]
+}

duello-0.1.0/.zenodo.json

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+{
+    "title": "Duello - Virial Coefficient and Dissociation Constant Estimation for Rigid Macromolecules",
+    "description": "Duello is a tool to evaluate the two-body partition function between rigid bodies, performing a statistical mechanical average over inter-molecular orientations using subdivided icosahedrons. The osmotic second virial coefficient; binary dissociation constant; and the potential of mean force is calculated.",
+    "creators": [
+        {
+            "name": "Mikael Lund",
+            "affiliation": "Division of Theoretical Chemistry, Department of Chemistry, Lund University, Sweden",
+            "orcid": "0000-0001-8178-8175"
+        }
+    ],
+    "contributors": [
+        {"type": "Researcher", "name": "Isabel Vinterbladh", "orcid": "0009-0007-0801-2611"}
+    ],
+    "keywords": [
+        "statistical thermodynamics",
+        "virial coefficient",
+        "intermolecular interactions",
+        "molecular simulation",
+        "docking"
+    ],
+    "related_identifiers": [
+        {
+            "scheme": "url",
+            "identifier": "https://github.com/mlund/duello",
+            "relation": "isSupplementTo"
+        }
+    ],
+    "access_right": "open",
+    "upload_type": "software"
+}