Rnapolis

Latest version: v0.6.2

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0.6.0

This version introduces two new scripts: aligner and unifier.

The aligner script uses PyMOL’s built-in align command with CLUSTAL format export. It takes two paths to PDB or mmCIF files, aligns them, and writes only the aligned residues to the specified output directory.

The unifier script processes a list of PDB or mmCIF files, aiming to unify their content. If the residue count or sequence differs between structures, the program halts, requiring prior use of the aligner. Otherwise, the unifier removes residues with differing atom counts across structures, reorders atoms consistently, and unifies residue naming. The output files will have identical atom counts, orders, and residue identifiers.

What's Changed
* feat: implement structure unifier by tzok in https://github.com/tzok/rnapolis-py/pull/322

**Full Changelog**: https://github.com/tzok/rnapolis-py/compare/0.5.0...0.6.0

0.5.0

What's Changed

* feat: fill BPSEQ with gaps by tzok in https://github.com/tzok/rnapolis-py/pull/229
* fix: dot-bracket encoding with gaps by tzok in https://github.com/tzok/rnapolis-py/pull/230
* fix: incorrect strand sequence by tzok in https://github.com/tzok/rnapolis-py/pull/231
* feat: support alternate locations by tzok in https://github.com/tzok/rnapolis-py/pull/243
* feat: resolve occupancy related clashes by tzok in https://github.com/tzok/rnapolis-py/pull/244
* feat: improve nucleotide detection heuristic by tzok in https://github.com/tzok/rnapolis-py/pull/260
* feat: use highs solver if available by tzok in https://github.com/tzok/rnapolis-py/pull/261
* fix: JSON export in annotator by tzok in https://github.com/tzok/rnapolis-py/pull/262
* feat: improve motif extraction by tzok in https://github.com/tzok/rnapolis-py/pull/263
* feat: improve mmcif transformer by tzok in https://github.com/tzok/rnapolis-py/pull/270
* feat: improve molecule filtering by tzok in https://github.com/tzok/rnapolis-py/pull/271
* fix: add missing entity category by tzok in https://github.com/tzok/rnapolis-py/pull/272
* feat: add retain category functionality by tzok in https://github.com/tzok/rnapolis-py/pull/273
* fix: one letter name for long cif inputs by tzok in https://github.com/tzok/rnapolis-py/pull/291
* feat: improve molecule filter by tzok in https://github.com/tzok/rnapolis-py/pull/290
* fix: add missing mmcif dictionary file by tzok in https://github.com/tzok/rnapolis-py/pull/301
* feat: implement parsing to DataFrames by tzok in https://github.com/tzok/rnapolis-py/pull/316

Dependencies updated regularly thanks to dependabot.

**Full Changelog**: https://github.com/tzok/rnapolis-py/compare/0.4.0...0.5.0

0.1.0

Main changes
- Determines structural elements (stems, single strands, hairpins and loops)
- Solves pseudoknot order assignment (POA) problem optimally using the MILP model

**Full Changelog**: https://github.com/tzok/rnapolis-py/compare/0.0.2...0.1.0

0.0.5

What's Changed
* feat: release 0.0.5 by tzok in https://github.com/tzok/rnapolis-py/pull/6


**Full Changelog**: https://github.com/tzok/rnapolis-py/compare/0.0.2...0.0.5

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