molscope 0.6.0__tar.gz → 0.6.2__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {molscope-0.6.0 → molscope-0.6.2}/PKG-INFO +2 -2
- {molscope-0.6.0 → molscope-0.6.2}/README.md +1 -1
- molscope-0.6.2/molscope/__init__.py +90 -0
- {molscope-0.6.0 → molscope-0.6.2}/molscope.egg-info/PKG-INFO +2 -2
- {molscope-0.6.0 → molscope-0.6.2}/pyproject.toml +1 -1
- molscope-0.6.0/molscope/__init__.py +0 -53
- {molscope-0.6.0 → molscope-0.6.2}/LICENSE +0 -0
- {molscope-0.6.0 → molscope-0.6.2}/molscope/__main__.py +0 -0
- {molscope-0.6.0 → molscope-0.6.2}/molscope/cli.py +0 -0
- {molscope-0.6.0 → molscope-0.6.2}/molscope/coarsegrain.py +0 -0
- {molscope-0.6.0 → molscope-0.6.2}/molscope/contactmap.py +0 -0
- {molscope-0.6.0 → molscope-0.6.2}/molscope/descriptors.py +0 -0
- {molscope-0.6.0 → molscope-0.6.2}/molscope/elements.py +0 -0
- {molscope-0.6.0 → molscope-0.6.2}/molscope/ensemble.py +0 -0
- {molscope-0.6.0 → molscope-0.6.2}/molscope/graph.py +0 -0
- {molscope-0.6.0 → molscope-0.6.2}/molscope/io.py +0 -0
- {molscope-0.6.0 → molscope-0.6.2}/molscope/molecule.py +0 -0
- {molscope-0.6.0 → molscope-0.6.2}/molscope/plotting.py +0 -0
- {molscope-0.6.0 → molscope-0.6.2}/molscope.egg-info/SOURCES.txt +0 -0
- {molscope-0.6.0 → molscope-0.6.2}/molscope.egg-info/dependency_links.txt +0 -0
- {molscope-0.6.0 → molscope-0.6.2}/molscope.egg-info/entry_points.txt +0 -0
- {molscope-0.6.0 → molscope-0.6.2}/molscope.egg-info/requires.txt +0 -0
- {molscope-0.6.0 → molscope-0.6.2}/molscope.egg-info/top_level.txt +0 -0
- {molscope-0.6.0 → molscope-0.6.2}/setup.cfg +0 -0
- {molscope-0.6.0 → molscope-0.6.2}/tests/test_clustering.py +0 -0
- {molscope-0.6.0 → molscope-0.6.2}/tests/test_coarsegrain.py +0 -0
- {molscope-0.6.0 → molscope-0.6.2}/tests/test_contactmap.py +0 -0
- {molscope-0.6.0 → molscope-0.6.2}/tests/test_descriptors.py +0 -0
- {molscope-0.6.0 → molscope-0.6.2}/tests/test_features.py +0 -0
- {molscope-0.6.0 → molscope-0.6.2}/tests/test_graph.py +0 -0
- {molscope-0.6.0 → molscope-0.6.2}/tests/test_io.py +0 -0
- {molscope-0.6.0 → molscope-0.6.2}/tests/test_molecule.py +0 -0
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Metadata-Version: 2.4
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Name: molscope
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Version: 0.6.
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Version: 0.6.2
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Summary: Lightweight molecular structure analysis, visualisation, graph export, and coarse-graining in Python.
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Author-email: Roshan Shrestha <roshanpra@gmail.com>
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License-Expression: MIT
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| 3D structure rendering | Residue contact map | Coarse-grained beads |
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## What it does
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| 3D structure rendering | Residue contact map | Coarse-grained beads |
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| --- | --- | --- |
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## What it does
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"""Lightweight molecular structure analysis, visualisation, graph export, and coarse-graining.
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molscope reads ``.xyz``, ``.pdb``, ``.cif`` and ``.sdf`` files (optionally
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gzip-compressed), lets you select and measure atoms, analyse structures and
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ensembles, export molecular graphs for machine learning, coarse-grain onto
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beads, and visualise everything in 3D.
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What it does
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------------
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- **Read and write** XYZ, PDB, mmCIF and SDF; fetch by id from RCSB; load
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multi-model NMR ensembles (:func:`read`, :func:`fetch`, :func:`read_pdb_models`).
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- **Select and measure** by chain, element or residue; distances, angles,
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dihedrals and Kabsch-aligned RMSD (:class:`Molecule`).
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- **Analyse** centroids, radius of gyration, inertia tensor, bonds and contacts.
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- **Contact maps** at atom or residue level (:class:`ContactMap`).
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- **Ensembles**: pairwise RMSD, RMSF, averaging, conformer clustering
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(:mod:`molscope.ensemble`, :func:`cluster`, :func:`rmsd_matrix`).
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- **Export for ML**: structural descriptors and molecular graphs for NetworkX,
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PyTorch Geometric and DGL (:func:`descriptors`, :class:`MolecularGraph`).
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- **Coarse-grain** onto residue, Martini-style or custom bead mappings
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(:mod:`molscope.coarsegrain`).
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- **Visualise** with 3D matplotlib plots, an interactive py3Dmol viewer, and
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spin GIFs.
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Examples
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--------
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>>> import molscope as ms
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>>> mol = ms.read("1fqy.pdb") # parser chosen from the extension
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>>> mol = ms.fetch("1fqy") # ...or download straight from RCSB by id
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>>> print(mol.summary()) # atoms, formula, chains, bounding box
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>>> ca = mol.alpha_carbons() # select the C-alpha atoms
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>>> mol.plot(color_by="chain") # render in 3D
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>>> g = mol.to_graph() # molecular graph for ML, no extra deps
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>>> cg = mol.coarse_grain("residue_com") # one bead per residue
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See https://github.com/roshan2004/molscope for the full documentation.
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"""
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from . import coarsegrain, ensemble
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from .coarsegrain import BeadMapping, BondMapping, CoarseGrainReport, DroppedAtom
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from .contactmap import ContactMap
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from .descriptors import descriptors, featurize_many
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from .ensemble import Clustering, cluster, rmsd_matrix
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from .ensemble import contact_frequency as ensemble_contact_frequency
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from .graph import MolecularGraph
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from .io import (
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fetch,
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read,
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read_cif,
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read_pdb,
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read_pdb_models,
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read_sdf,
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read_xyz,
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read_xyz_frames,
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write_pdb,
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write_xyz,
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)
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from .molecule import Molecule
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from .plotting import plot_rmsd_heatmap
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__all__ = [
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"Clustering",
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"BeadMapping",
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"BondMapping",
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"CoarseGrainReport",
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"ContactMap",
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"DroppedAtom",
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"Molecule",
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"MolecularGraph",
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"cluster",
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"coarsegrain",
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"descriptors",
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"ensemble",
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"ensemble_contact_frequency",
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"featurize_many",
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"fetch",
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"plot_rmsd_heatmap",
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"read",
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"read_cif",
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"read_pdb",
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"read_pdb_models",
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"read_sdf",
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"read_xyz",
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"read_xyz_frames",
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"rmsd_matrix",
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"write_pdb",
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"write_xyz",
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]
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__version__ = "0.6.2"
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Metadata-Version: 2.4
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Name: molscope
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Version: 0.6.
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Version: 0.6.2
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Summary: Lightweight molecular structure analysis, visualisation, graph export, and coarse-graining in Python.
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Author-email: Roshan Shrestha <roshanpra@gmail.com>
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License-Expression: MIT
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| 3D structure rendering | Residue contact map | Coarse-grained beads |
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## What it does
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[project]
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name = "molscope"
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version = "0.6.
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version = "0.6.2"
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description = "Lightweight molecular structure analysis, visualisation, graph export, and coarse-graining in Python."
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readme = "README.md"
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requires-python = ">=3.9"
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"""molscope: read, analyse, and plot molecular structures in 3D."""
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from . import coarsegrain, ensemble
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from .coarsegrain import BeadMapping, BondMapping, CoarseGrainReport, DroppedAtom
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from .contactmap import ContactMap
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from .descriptors import descriptors, featurize_many
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from .ensemble import Clustering, cluster, rmsd_matrix
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from .ensemble import contact_frequency as ensemble_contact_frequency
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from .graph import MolecularGraph
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from .io import (
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fetch,
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read,
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read_cif,
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read_pdb,
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read_pdb_models,
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read_sdf,
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read_xyz,
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read_xyz_frames,
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write_pdb,
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write_xyz,
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)
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from .molecule import Molecule
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from .plotting import plot_rmsd_heatmap
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__all__ = [
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"Clustering",
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"BeadMapping",
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"BondMapping",
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"CoarseGrainReport",
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"ContactMap",
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"DroppedAtom",
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"Molecule",
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"MolecularGraph",
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"cluster",
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"coarsegrain",
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"descriptors",
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"ensemble",
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"ensemble_contact_frequency",
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"featurize_many",
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"fetch",
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"plot_rmsd_heatmap",
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"read",
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"read_cif",
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"read_pdb",
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"read_pdb_models",
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"read_sdf",
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"read_xyz",
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"read_xyz_frames",
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"rmsd_matrix",
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"write_pdb",
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"write_xyz",
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]
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__version__ = "0.6.0"
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