Feat: sym_redock_exlude_motifs feat added

ipd/sym/sym_util.py

@@ -16,10 +16,11 @@ def get_sym_frames(symid, opt, cenvec):
     frames, _ = get_nneigh(allframes, min(len(allframes), opt.max_nsub))
     return allframes, frames
 
-def sym_redock(xyz, Lasu, frames, opt, **_):
+def sym_redock(xyz, Lasu, frames, opt, mask=None, **_):
     # resolve clashes in placed subunits
     # could probably use this to optimize the radius as well
-    def clash_error_comp(R0, T0, xyz, fit_tscale):
+    # mask: 1d th.Tensor or list
+    def clash_error_comp(R0, T0, xyz, fit_tscale, mask=None):            
         xyz0 = xyz[:Lasu]
         xyz0_corr = xyz0.reshape(-1, 3) @ R0.T
         xyz0_corr = xyz0_corr.reshape(xyz0.shape) + fit_tscale*T0
@@ -35,9 +36,18 @@ def clash_error_comp(R0, T0, xyz, fit_tscale):
         Xsymmall = Xsymmall[:, 0, :]
         dsymm = th.cdist(Xsymmall, Xsymmall, p=2)
         dsymm_2 = dsymm.clone()
+        if mask is not None: 
+            mask0 = mask[:Lasu.item()] if isinstance(Lasu, th.Tensor) else th.tensor(mask[:Lasu])
+            mask_dsymm = ~(mask0[None, :].expand(Lasu, Lasu))
+            mask_dsymm = mask_dsymm | mask_dsymm.T
         # dsymm_2 = dsymm.clone().fill_diagonal_(9999) # avoid in-place operation
-        for i in range(0, len(Xsymmall), Lasu):
-            dsymm_2[i:i + Lasu, i:i + Lasu] = 9999
+        for i in range(0, len(Xsymmall), Lasu): # loop over rows
+            dsymm_2[i:i + Lasu, i:i + Lasu] = 9999 # masking intra-contact
+            if mask is not None: 
+                for j in range(0, len(Xsymmall), Lasu): # loop over cols
+                    if j == i: continue
+                    # masking inter-contacts involving masked residues
+                    dsymm_2[i:i + Lasu, j:j + Lasu][mask_dsymm] = 9999
         clash = th.clamp(opt.fit_wclash - dsymm_2, min=0)
         loss = th.sum(clash) / Lasu
         return loss
@@ -54,7 +64,7 @@ def Q2R(Q):
 
         def closure():
             lbfgs.zero_grad()
-            loss = clash_error_comp(Q2R(Q0), T0, xyz, opt.fit_tscale)
+            loss = clash_error_comp(Q2R(Q0), T0, xyz, opt.fit_tscale, mask=mask)
             loss.backward()  #retain_graph=True)
             return loss
 

lib/evn/.clang-format

@@ -0,0 +1,17 @@
+BasedOnStyle:  LLVM
+Standard:        Cpp11
+IndentWidth:     4
+TabWidth:        4
+UseTab:          Never
+ColumnLimit: 90
+AllowShortIfStatementsOnASingleLine: true
+AllowShortCaseLabelsOnASingleLine: true
+AlignConsecutiveShortCaseStatements:
+  Enabled: true
+  AcrossEmptyLines: true
+  AcrossComments: true
+AllowShortBlocksOnASingleLine: true
+AllowShortEnumsOnASingleLine: true
+AllowShortFunctionsOnASingleLine: true
+AllowShortLambdasOnASingleLine: true
+AllowShortLoopsOnASingleLine: true

lib/evn/.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,64 @@
+## 🚀 Summary
+
+<!--
+Explain what this PR does and why it matters.
+Keep it short and focused.
+-->
+
+Closes #...
+
+---
+
+## 🔧 Type of change
+
+<!-- Check the relevant boxes and update your PR title to follow Conventional Commits -->
+
+- [ ] **feat**: A new feature
+- [ ] **fix**: A bug fix
+- [ ] **docs**: Documentation only changes
+- [ ] **style**: Formatting, missing semi colons, etc
+- [ ] **refactor**: Refactoring (no functional changes)
+- [ ] **perf**: A code change that improves performance
+- [ ] **test**: Adding or fixing tests
+- [ ] **chore**: Maintenance and tooling
+- [ ] **ci**: Changes to CI/CD configuration
+
+---
+
+## ✅ Checklist
+
+- [ ] PR title uses [Conventional Commits](https://www.conventionalcommits.org/)
+- [ ] Tests added or updated (if applicable)
+- [ ] Documentation updated (if applicable)
+- [ ] I have verified this builds and works as intended
+- [ ] I’m ready for review!
+
+---
+
+## 🧪 Testing
+
+<!--
+Explain how you tested your changes.
+List commands, CI results, or screenshots if helpful.
+-->
+
+---
+
+## 📦 Release impact
+
+> semantic-release will determine version bump automatically.
+
+- [ ] BREAKING CHANGE (explain in footer below)
+- [ ] This should trigger a **patch** release
+- [ ] This should trigger a **minor** release
+- [ ] This is internal only — no release needed
+
+If this is a breaking change, explain why below.
+
+---
+
+## 📓 Notes for reviewer
+
+<!--
+Optional: anything you'd like the reviewer to focus on, be aware of, or follow up later.
+-->

lib/evn/.github/workflows/build_publish.yml

@@ -0,0 +1,102 @@
+name: Build and upload to PyPI
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    # branches:
+      # - main
+  release:
+    types:
+      - published
+
+jobs:
+  build_wheels:
+    name: Build wheels for ${{ matrix.os }}
+    runs-on: ${{ matrix.runs-on }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ linux-intel, linux-arm, macOS-intel, macOS-arm ]
+        # os: [ linux-intel, linux-arm, windows, macOS-intel, macOS-arm ]
+        include:
+          - archs: auto
+            platform: auto
+          - os: linux-intel
+            runs-on: ubuntu-latest
+          - os: linux-arm
+            runs-on: ubuntu-24.04-arm
+          # - os: windows
+            # runs-on: windows-latest
+          - os: macos-intel
+            # macos-13 was the last x86_64 runner
+            runs-on: macos-13
+          - os: macos-arm
+            # macos-14+ (including latest) are ARM64 runners
+            runs-on: macos-latest
+            archs: auto,universal2
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v2.23.1
+        env:
+          CIBW_PLATFORM: ${{ matrix.platform }}
+          CIBW_ARCHS: ${{ matrix.archs }}
+        # Can also be configured directly, using `with:`
+        # with:
+        #   package-dir: .
+        #   output-dir: wheelhouse
+        #   config-file: "{package}/pyproject.toml"
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          version: "0.6.8"
+          enable-cache: true
+
+      - name: Test wheels
+        run: |
+          echo "Testing wheels with nox"
+          uv run --extra dev nox
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
+          path: ./wheelhouse/*.whl
+
+  build_sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Build sdist
+        run: pipx run build --sdist
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-sdist
+          path: dist/*.tar.gz
+
+  upload_pypi:
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write
+    # if: github.event_name == 'release' && github.event.action == 'published'
+    # or, alternatively, upload to PyPI on every tag starting with 'v' (remove on: release above to use this)
+    # if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          # unpacks all CIBW artifacts into dist/
+          pattern: cibw-*
+          path: dist
+          merge-multiple: true
+
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        # with:
+          # To test: repository-url: https://test.pypi.org/legacy/

lib/evn/.github/workflows/codecov.yaml

@@ -0,0 +1,30 @@
+name: codecov
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.13'
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+
+      - name: Run tests with coverage
+        run: |
+            uv run --extra all pytest --cov --cov-branch --cov-report=xml
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v5
+        with:
+            token: ${{ secrets.CODECOV_TOKEN }}

lib/evn/.github/workflows/semantic-release.yaml

@@ -0,0 +1,31 @@
+# .github/workflows/semantic-release.yaml
+
+name: Semantic Release
+
+on:
+  push:
+    branches: [main]
+
+jobs:
+  release:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write      # for tag, changelog commit, release
+      issues: write        # optional if you want to use release notes
+      pull-requests: write # optional
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Lint commit messages
+        uses: wagoid/commitlint-github-action@v5
+
+      - name: Semantic Release
+        uses: cycjimmy/semantic-release-action@v4
+        with:
+          extra_plugins: |
+            @semantic-release/changelog
+            @semantic-release/git
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}

lib/evn/.gitignore

@@ -0,0 +1,47 @@
+sublime_build.log*
+wheelhouse
+__pycache__
+*.egg-info
+*.egg
+*.pyc
+evn/_build
+__pycache__
+# Prerequisites
+*.d
+
+# Compiled Object files
+*.slo
+*.lo
+*.o
+*.obj
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Compiled Dynamic libraries
+*.so
+*.dylib
+*.dll
+
+# Fortran module files
+*.mod
+*.smod
+
+# Compiled Static libraries
+*.lai
+*.la
+*.a
+*.lib
+
+# Executables
+*.exe
+*.out
+*.app
+
+.doit.*
+_build
+*.sublime-workspace
+/test-logs
+.test*
+*.orig

lib/evn/.pre-commit-config.yaml

@@ -0,0 +1,50 @@
+# .pre-commit-config.yaml
+repos:
+  # ✅ Ruff: linter, formatter, isort
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.3.3
+    hooks:
+      - id: ruff
+        args: [--fix, evn]
+
+  # ✅ Validate pyproject.toml metadata and structure
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: v0.24.1
+    hooks:
+      - id: validate-pyproject
+        # Optional extra validations from SchemaStore:
+        additional_dependencies: ["validate-pyproject-schema-store[all]"]
+
+  # ✅ Check for trailing whitespace, tabs, EOFs
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+
+  # ✅ Detect merge conflict markers
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: check-merge-conflict
+
+  # ✅ Commitizen: Conventional Commit linter (Python-native)
+  - repo: https://github.com/commitizen-tools/commitizen
+    rev: v3.21.0
+    hooks:
+      - id: commitizen
+        stages: [commit-msg]
+        language_version: python3.12
+
+  - repo: https://github.com/christophmeissner/pytest-pre-commit
+    rev: 1.0.0
+    hooks:
+      - id: pytest
+        args: [--ignore,evn/format,--ignore,evn/tests/format]
+        additional_dependencies: ['assertpy', 'click', 'icecream', 'multipledispatch',
+          'PrettyPrintTree', 'pyyaml', 'rapidfuzz', 'rich', 'ruff',
+          'typing_extensions; python_version < "3.10"', 'wrapt','hypothesis', 'ninja_import', 'tomli']
+        pass_filenames: false
+        always_run: true

lib/evn/.python-version

@@ -0,0 +1 @@
+3.13