Crosslinking and Energy Minimize improvements#1324
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…unctions such as angle and bond distributions, as well as freud rdf
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## develop #1324 +/- ##
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+ Coverage 77.03% 77.16% +0.12%
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Files 62 64 +2
Lines 6736 7816 +1080
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+ Hits 5189 6031 +842
- Misses 1547 1785 +238 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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…rate multi-site crosslinks. Adjust some of the args in relax_path, add utility functions that helps to optimally place new sites into current path
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| return crosslink2( | ||
| self, | ||
| crosslinker=crosslinker, | ||
| bead_name=bead_name, | ||
| backbone_name=backbone_name, | ||
| radius=radius, | ||
| excluded_bond_depth=excluded_bond_depth, | ||
| n_connection_sites=n_connection_sites, | ||
| volume_constraint=volume_constraint, | ||
| initial_point=initial_point, | ||
| seed=seed, | ||
| chunk_size=chunk_size, | ||
| run_on_gpu=run_on_gpu, | ||
| n_rotation_samples=n_rotation_samples, | ||
| overlap_radius=overlap_radius, | ||
| ) |
| from mbuild.path.path_utils import calculate_sq_distances | ||
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| class CrosslinkerGeometry(Path): |
| # Center positions at origin | ||
| if len(self.coordinates) > 0: | ||
| centroid = np.mean(self.coordinates, axis=0) | ||
| self.coordinates = (self.coordinates - centroid).astype(np.float32) |
| Path | ||
| self (modified in place). | ||
| """ | ||
| from mbuild.path.crosslink import replace_sites |
| overlap_radius=None, | ||
| ): | ||
| """Add a crosslink to this path. See module-level crosslink() for details.""" | ||
| from mbuild.path.crosslink import crosslink as crosslink2 |
| import numpy as np | ||
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| from mbuild.exceptions import PathConvergenceError | ||
| from mbuild.path.build import Path |
| if n <= 1: | ||
| return True, [0] if n == 1 else [] | ||
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| abs_tol = bond_length * tolerance |
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PR Summary:
Update crosslinking path functions
Added Uutilities for:
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