Welcome to worms’s documentation!¶
Contents:
worms¶
Protein assembly design without protein interface design.
- Free software: Apache Software License 2.0
- Documentation: https://worms.readthedocs.io.
Features¶
please send angry emails to willsheffler@gmail.com until there are docs here.
Credits¶
This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.
Installation¶
Stable release¶
To install worms, run this command in your terminal:
$ pip install worms
This is the preferred method to install worms, as it will always install the most recent stable release.
If you don’t have pip installed, this Python installation guide can guide you through the process.
From sources¶
The sources for worms can be downloaded from the Github repo.
You can either clone the public repository:
$ git clone git://github.com/willsheffler/worms
Or download the tarball:
$ curl -OL https://github.com/willsheffler/worms/tarball/master
Once you have a copy of the source, you can install it with:
$ python setup.py install
worms¶
worms package¶
Subpackages¶
worms.criteria package¶
Submodules¶
worms.criteria.base module¶
TODO: Summary
-
worms.criteria.base.Ux¶ TYPE – Description
-
worms.criteria.base.Uy¶ TYPE – Description
-
worms.criteria.base.Uz¶ TYPE – Description
-
class
worms.criteria.base.CriteriaList(children)[source]¶ Bases:
worms.criteria.base.WormCriteriaTODO: Summary
-
children¶ TYPE – Description
-
-
class
worms.criteria.base.NullCriteria(from_seg=0, to_seg=-1, origin_seg=None)[source]¶ Bases:
worms.criteria.base.WormCriteriaTODO: Summary
-
from_seg¶ TYPE – Description
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to_seg¶ TYPE – Description
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worms.criteria.bounded module¶
-
class
worms.criteria.bounded.AxesIntersect(symname, tgtaxis1, tgtaxis2, from_seg, *, tol=1.0, lever=50, to_seg=-1, distinct_axes=False)[source]¶ Bases:
worms.criteria.base.WormCriteriaTODO: Summary
-
angle¶ TYPE – Description
-
distinct_axes¶ TYPE – Description
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from_seg¶ TYPE – Description
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lever¶ TYPE – Description
-
rot_tol¶ TYPE – Description
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sym_axes¶ TYPE – Description
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symname¶ TYPE – Description
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tgtaxis1¶ TYPE – Description
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tgtaxis2¶ TYPE – Description
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to_seg¶ TYPE – Description
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tol¶ TYPE – Description
-
-
worms.criteria.bounded.D2(c2=0, c2b=-1, **kw)[source]¶ TODO: Summary
Parameters: - c2 (int, optional) – Description
- c2b (TYPE, optional) – Description
- kw – passthru args
Returns: Description
Return type: TYPE
-
worms.criteria.bounded.D3(c3=0, c2=-1, **kw)[source]¶ TODO: Summary
Parameters: - c3 (int, optional) – Description
- c2 (TYPE, optional) – Description
- kw – passthru args
Returns: Description
Return type: TYPE
-
worms.criteria.bounded.D4(c4=0, c2=-1, **kw)[source]¶ TODO: Summary
Parameters: - c4 (int, optional) – Description
- c2 (TYPE, optional) – Description
- kw – passthru args
Returns: Description
Return type: TYPE
-
worms.criteria.bounded.D5(c5=0, c2=-1, **kw)[source]¶ TODO: Summary
Parameters: - c5 (int, optional) – Description
- c2 (TYPE, optional) – Description
- kw – passthru args
Returns: Description
Return type: TYPE
-
worms.criteria.bounded.D6(c6=0, c2=-1, **kw)[source]¶ TODO: Summary
Parameters: - c6 (int, optional) – Description
- c2 (TYPE, optional) – Description
- kw – passthru args
Returns: Description
Return type: TYPE
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worms.criteria.bounded.Icosahedral(c5=None, c3=None, c2=None, **kw)[source]¶ TODO: Summary
Parameters: - c5 (None, optional) – Description
- c3 (None, optional) – Description
- c2 (None, optional) – Description
- kw – passthru args
Returns: Description
Return type: TYPE
Raises: ValueError– Description
worms.criteria.cyclic module¶
worms.criteria.unbounded module¶
-
class
worms.criteria.unbounded.AxesAngle(symname, tgtaxis1, tgtaxis2, from_seg, *, tol=1.0, lever=50, to_seg=-1, space_group_str=None)[source]¶ Bases:
worms.criteria.base.WormCriteria-
alignment(segpos, out_cell_spacing=False, **kw)[source]¶ Alignment to move stuff to be in line with symdef file
Parameters: - segpos (lst) – List of segment positions / coordinates.
- I'll accept any "non-positional" argument as name = value, and store in a dictionary (**kw) –
-
Module contents¶
Submodules¶
worms.bblock module¶
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worms.bblock.bblock_components(bblock)[source]¶ TODO: Summary
Parameters: bblock (TYPE) – Description Returns: Description Return type: TYPE
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worms.bblock.bblock_dump_pdb(out, bblock, dirn, splice, join=True, pos=array([[1., 0., 0., 0.], [0., 1., 0., 0.], [0., 0., 1., 0.], [0., 0., 0., 1.]]), chain=0, anum=1, rnum=1)[source]¶
worms.database module¶
TODO: Summary
-
class
worms.database.BBlockDB(cachedir=None, bakerdb_files=[], load_poses=False, nprocs=1, lazy=True, read_new_pdbs=False, verbosity=0)[source]¶ Bases:
objectstores Poses and BBlocks in a disk cache
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query(query, *, useclass=True, max_bblocks=150, shuffle=True)[source]¶ match name, _type, _class if one match, use it if _type and _class match, check useclass option Het:NNCx/y require exact number or require extra
Parameters: - query (TYPE) – Description
- useclass (bool, optional) – Description
Returns: Description
Return type: TYPE
-
worms.edge module¶
worms.jitsearch module¶
worms.pose_contortions module¶
TODO: Summary
-
class
worms.pose_contortions.AnnoPose(pose, iseg, srcpose, src_lb, src_ub, cyclic_entry)[source]¶ Bases:
objectTODO: Summary
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cyclic_entry¶ TYPE – Description
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iseg¶ TYPE – Description
-
pose¶ TYPE – Description
-
src_lb¶ TYPE – Description
-
src_ub¶ TYPE – Description
-
srcpose¶ TYPE – Description
-
-
class
worms.pose_contortions.CyclicTrim(sym_seg_from, sym_seg_to)¶ Bases:
tuple-
sym_seg_from¶ Alias for field number 0
-
sym_seg_to¶ Alias for field number 1
-
-
worms.pose_contortions.contort_pose_chains(pose, chains, nseg, ir_en, ir_ex, pl_en, pl_ex, chain_start, chain_end, position=None, pad=(0, 0), iseg=None, cyclictrim=None, last_seg_entrypol=None, first_seg_exitpol=None, sym_ir=None, sym_pol=None)[source]¶ make pose chains from ‘segment’ info
what a monster this has become. returns (segchains, rest) segchains elems are [enterexitchain] or, [enterchain, …, exitchain] rest holds other chains IFF enter and exit in same chain each element is a pair [pose, source] where source is (origin_pose, start_res, stop_res) cyclictrim specifies segments which are spliced across the symmetric interface. segments only needed if cyclictrim==True if cyclictrim, last segment will only be a single entry residue
Args: No
worms.segments module¶
TODO: Summary
-
class
worms.segments.Segment(spliceables, entry=None, exit=None, expert=False)[source]¶ Bases:
objectTODO: Summary
-
bodyid¶ TYPE – Description
-
entrypol¶ TYPE – Description
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entryresid¶ TYPE – Description
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entrysiteid¶ TYPE – Description
-
exitpol¶ TYPE – Description
-
exitresid¶ TYPE – Description
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exitsiteid¶ TYPE – Description
-
expert¶ TYPE – Description
-
max_sites¶ TYPE – Description
-
min_sites¶ TYPE – Description
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nchains¶ TYPE – Description
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spliceables¶ TYPE – Description
-
x2exit¶ TYPE – Description
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x2orgn¶ TYPE – Description
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make_pose_chains(indices, position=None, pad=(0, 0), iseg=None, segments=None, cyclictrim=None)[source]¶ what a monster this has become. returns (segchains, rest) segchains elems are [enterexitchain] or, [enterchain, …, exitchain] rest holds other chains IFF enter and exit in same chain each element is a pair [pose, source] where source is (origin_pose, start_res, stop_res) cyclictrim specifies segments which are spliced across the symmetric interface. segments only needed if cyclictrim==True if cyclictrim, last segment will only be a single entry residue
Parameters: - indices (TYPE) – Description
- position (None, optional) – Description
- pad (tuple, optional) – Description
- iseg (None, optional) – Description
- segments (None, optional) – Description
- cyclictrim (None, optional) – Description
Returns: Description
Return type: TYPE
-
merge_idx(head, head_idx, tail, tail_idx)[source]¶ TODO: Summary
Parameters: - head (TYPE) – Description
- head_idx (TYPE) – Description
- tail (TYPE) – Description
- tail_idx (TYPE) – Description
Returns: Description
Return type: TYPE
-
merge_idx_slow(head, head_idx, tail, tail_idx)[source]¶ TODO: Summary
Parameters: - head (TYPE) – Description
- head_idx (TYPE) – Description
- tail (TYPE) – Description
- tail_idx (TYPE) – Description
Returns: return joint index, -1 if head/tail pairing is invalid
Return type: TYPE
-
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class
worms.segments.Segments(segments)[source]¶ Bases:
objectlight wrapper around list of Segments
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segments¶ TYPE – Description
-
-
class
worms.segments.SpliceSite(sele, polarity, chain=None)[source]¶ Bases:
objectTODO: Summary
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chain¶ TYPE – Description
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polarity¶ TYPE – Description
-
selections¶ TYPE – Description
-
-
class
worms.segments.Spliceable(body, sites, *, bodyid=None, min_seg_len=1, allowed_pairs=None)[source]¶ Bases:
objectTODO: Summary
-
allowed_pairs¶ TYPE – Description
-
body¶ TYPE – Description
-
bodyid¶ TYPE – Description
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chains¶ TYPE – Description
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end_of_chain¶ TYPE – Description
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min_seg_len¶ TYPE – Description
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nsite¶ TYPE – Description
-
sites¶ TYPE – Description
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start_of_chain¶ TYPE – Description
-
is_compatible(isite, ires, jsite, jres)[source]¶ TODO: Summary
Parameters: - isite (TYPE) – Description
- ires (TYPE) – Description
- jsite (TYPE) – Description
- jres (TYPE) – Description
Returns: Description
Return type: TYPE
-
resids(isite)[source]¶ TODO: Summary
Parameters: isite (TYPE) – Description Returns: Description Return type: TYPE
-
-
class
worms.segments.Worms(segments, scores, indices, positions, criteria, detail)[source]¶ Bases:
objectTODO: Summary
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criteria¶ TYPE – Description
-
detail¶ TYPE – Description
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indices¶ TYPE – Description
-
positions¶ TYPE – Description
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score0¶ TYPE – Description
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score0sym¶ TYPE – Description
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scores¶ TYPE – Description
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segments¶ TYPE – Description
-
splicepoint_cache¶ dict – Description
-
pose(which, *, align=True, end=None, only_connected='auto', join=True, cyclic_permute=None, cyclictrim=None, provenance=False, make_chain_list=False, **kw)[source]¶ makes a pose for the ith worm
-
splicepoints(which)[source]¶ TODO: Summary
Parameters: which (TYPE) – Description Returns: Description Return type: TYPE
-
splices(which)[source]¶ TODO: Summary
Parameters: which (TYPE) – Description Returns: Description Return type: TYPE
-
sympose(which, score=False, provenance=False, fullatom=False, asym_score_thresh=50, min_cell_spacing=130, *, parallel=False)[source]¶ TODO: Summary
Parameters: - which (TYPE) – Description
- score (bool, optional) – Description
- provenance (bool, optional) – Description
- fullatom (bool, optional) – Description
- parallel (bool, optional) – Description
- asym_score_thresh (int, optional) – Description
Returns: Description
Return type: TYPE
Raises: IndexError– Description
-
worms.util module¶
TODO: Summary
-
class
worms.util.InProcessExecutor(*args, **kw)[source]¶ Bases:
objectTODO: Summary
-
class
worms.util.MultiRange(nside)[source]¶ Bases:
objectTODO: Summary
-
len¶ TYPE – Description
-
nside¶ TYPE – Description
-
psum¶ TYPE – Description
-
-
worms.util.bigprod(iterable)[source]¶ TODO: Summary
Parameters: iterable (TYPE) – Description Returns: Description Return type: TYPE
-
worms.util.dicts_to_items(inp)[source]¶ TODO: Summary
Parameters: inp (TYPE) – Description Returns: Description Return type: TYPE
-
worms.util.first_duplicate(segs)[source]¶ TODO: Summary
Parameters: segs (TYPE) – Description Returns: Description Return type: TYPE
-
worms.util.get_bb_coords(pose, which_resi=None)[source]¶ extract rif style stubs from rosetta pose
Parameters: - pose (TYPE) – Description
- which_resi (None, optional) – Description
Returns: Description
Return type: TYPE
Raises: ValueError– Description
-
worms.util.get_bb_stubs(pose, which_resi=None)[source]¶ extract rif style stubs from rosetta pose
Parameters: - pose (TYPE) – Description
- which_resi (None, optional) – Description
Returns: Description
Return type: TYPE
Raises: ValueError– Description
-
worms.util.get_chain_bounds(pose)[source]¶ TODO: Summary
Parameters: pose (TYPE) – Description Returns: Description Return type: TYPE
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worms.util.get_symdata[source]¶ TODO – Summary
Parameters: name (TYPE) – Description Returns: Description Return type: TYPE
-
worms.util.get_symdata_modified(name, string_substitutions=None, scale_positions=None)[source]¶ TODO: Summary
Parameters: - name (TYPE) – Description
- string_substitutions (None, optional) – Description
- scale_positions (None, optional) – Description
Returns: Description
Return type: TYPE
-
worms.util.get_symfile_contents[source]¶ TODO – Summary
Parameters: name (TYPE) – Description Returns: Description Return type: TYPE
-
worms.util.infer_cyclic_symmetry(pose)[source]¶ TODO: Summary
Parameters: pose (TYPE) – Description Raises: NotImplementedError– Description
-
worms.util.items_to_dicts(inp)[source]¶ TODO: Summary
Parameters: inp (TYPE) – Description Returns: Description Return type: TYPE
-
worms.util.no_overlapping_adjacent_residues(p)[source]¶ TODO: Summary
Parameters: p (TYPE) – Description Returns: Description Return type: TYPE
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worms.util.no_overlapping_residues(p)[source]¶ TODO: Summary
Parameters: p (TYPE) – Description Returns: Description Return type: TYPE
-
worms.util.numpy_stub_from_rosetta_stub(rosstub)[source]¶ TODO: Summary
Parameters: rosstub (TYPE) – Description Returns: Description Return type: TYPE
-
worms.util.parallel_batch_map(pool, function, accumulator, batch_size, map_func_args, **kw)[source]¶ TODO: Summary
Parameters: - pool (TYPE) – Description
- function (TYPE) – Description
- accumulator (TYPE) – Description
- batch_size (TYPE) – Description
- map_func_args (TYPE) – Description
- kw – passthru args
Yields: TYPE – Description
-
worms.util.parallel_nobatch_map(pool, function, accumulator, batch_size, map_func_args, **kw)[source]¶ TODO: Summary
Parameters: - pool (TYPE) – Description
- function (TYPE) – Description
- accumulator (TYPE) – Description
- batch_size (TYPE) – Description
- map_func_args (TYPE) – Description
- kw – passthru args
Yields: TYPE – Description
-
worms.util.pose_bounds(pose, lb, ub)[source]¶ TODO: Summary
Parameters: - pose (TYPE) – Description
- lb (TYPE) – Description
- ub (TYPE) – Description
Returns: Description
Return type: TYPE
Raises: ValueError– Description
-
worms.util.rosetta_stub_from_numpy_stub(npstub)[source]¶ TODO: Summary
Parameters: npstub (TYPE) – Description Returns: Description Return type: TYPE
-
worms.util.subpose(pose, lb, ub=-1)[source]¶ TODO: Summary
Parameters: - pose (TYPE) – Description
- lb (TYPE) – Description
- ub (TYPE, optional) – Description
Returns: Description
Return type: TYPE
-
worms.util.symfile_path(name)[source]¶ TODO: Summary
Parameters: name (TYPE) – Description Returns: Description Return type: TYPE
-
worms.util.tqdm_parallel_map(pool, function, accumulator, map_func_args, batch_size, **kw)[source]¶ TODO: Summary
Parameters: - pool (TYPE) – Description
- function (TYPE) – Description
- accumulator (TYPE) – Description
- map_func_args (TYPE) – Description
- batch_size (TYPE) – Description
- kw – passthru args
-
worms.util.trim_pose(pose, resid, direction, pad=0)[source]¶ trim end of pose from direction, leaving <=pad residues beyond resid
Parameters: - pose (TYPE) – Description
- resid (TYPE) – Description
- direction (TYPE) – Description
- pad (int, optional) – Description
Returns: Description
Return type: TYPE
Raises: ValueError– Description
worms.vertex module¶
TODO: Summary
worms.vis module¶
TODO: Summary
-
worms.vis.numcom¶ int – Description
-
worms.vis.numline¶ int – Description
-
worms.vis.numray¶ int – Description
-
worms.vis.numseg¶ int – Description
-
worms.vis.numvec¶ int – Description
-
worms.vis.showme_state¶ TYPE – Description
-
worms.vis.cgo_cyl(c1, c2, r, col=(1, 1, 1), col2=None)[source]¶ TODO: Summary
Parameters: - c1 (TYPE) – Description
- c2 (TYPE) – Description
- r (TYPE) – Description
- col (tuple, optional) – Description
- col2 (None, optional) – Description
Returns: Description
Return type: TYPE
-
worms.vis.cgo_lineabs(a, c, col=(1, 1, 1))[source]¶ TODO: Summary
Parameters: - a (TYPE) – Description
- c (TYPE) – Description
- col (tuple, optional) – Description
Returns: Description
Return type: TYPE
-
worms.vis.cgo_segment(c1, c2, col=(1, 1, 1))[source]¶ TODO: Summary
Parameters: - c1 (TYPE) – Description
- c2 (TYPE) – Description
- col (tuple, optional) – Description
Returns: Description
Return type: TYPE
-
worms.vis.cgo_sphere(c, r=1, col=(1, 1, 1))[source]¶ TODO: Summary
Parameters: - c (TYPE) – Description
- r (int, optional) – Description
- col (tuple, optional) – Description
Returns: Description
Return type: TYPE
-
worms.vis.format_atom(atomi=0, atomn='ATOM', idx=' ', resn='RES', chain='A', resi=0, insert=' ', x=0, y=0, z=0, occ=0, b=0)[source]¶
-
worms.vis.show_with_axis(worms, idx=0)[source]¶ TODO: Summary
Parameters: - worms (TYPE) – Description
- idx (int, optional) – Description
-
worms.vis.show_with_z_axes(worms, idx=0, only_connected=0, **kw)[source]¶ TODO: Summary
Parameters: - worms (TYPE) – Description
- idx (int, optional) – Description
- only_connected (int, optional) – Description
- kw – passthru args
-
worms.vis.showcyl(c1, c2, r, col=(1, 1, 1), col2=None, lbl='')[source]¶ TODO: Summary
Parameters: - c1 (TYPE) – Description
- c2 (TYPE) – Description
- r (TYPE) – Description
- col (tuple, optional) – Description
- col2 (None, optional) – Description
- lbl (str, optional) – Description
-
worms.vis.showline(a, c, col=(1, 1, 1), lbl='')[source]¶ TODO: Summary
Parameters: - a (TYPE) – Description
- c (TYPE) – Description
- col (tuple, optional) – Description
- lbl (str, optional) – Description
-
worms.vis.showlineabs(a, c, col=(1, 1, 1), lbl='')[source]¶ TODO: Summary
Parameters: - a (TYPE) – Description
- c (TYPE) – Description
- col (tuple, optional) – Description
- lbl (str, optional) – Description
-
worms.vis.showme(*args, how='pymol', **kw)[source]¶ TODO: Summary
Parameters: - args – passthru args
- how (str, optional) – Description
- kw – passthru args
Returns: Description
Return type: TYPE
Raises: NotImplementedError– Description
-
worms.vis.showme_pymol(what, headless=False, block=False, **kw)[source]¶ TODO: Summary
Parameters: - what (TYPE) – Description
- headless (bool, optional) – Description
- block (bool, optional) – Description
- kw – passthru args
Returns: Description
Return type: TYPE
-
worms.vis.showsegment(c1, c2, col=(1, 1, 1), lbl='')[source]¶ TODO: Summary
Parameters: - c1 (TYPE) – Description
- c2 (TYPE) – Description
- col (tuple, optional) – Description
- lbl (str, optional) – Description
Module contents¶
Top-level package for worms.
Contributing¶
Contributions are welcome, and they are greatly appreciated! Every little bit helps, and credit will always be given.
You can contribute in many ways:
Types of Contributions¶
Report Bugs¶
Report bugs at https://github.com/willsheffler/worms/issues.
If you are reporting a bug, please include:
- Your operating system name and version.
- Any details about your local setup that might be helpful in troubleshooting.
- Detailed steps to reproduce the bug.
Fix Bugs¶
Look through the GitHub issues for bugs. Anything tagged with “bug” and “help wanted” is open to whoever wants to implement it.
Implement Features¶
Look through the GitHub issues for features. Anything tagged with “enhancement” and “help wanted” is open to whoever wants to implement it.
Write Documentation¶
worms could always use more documentation, whether as part of the official worms docs, in docstrings, or even on the web in blog posts, articles, and such.
Submit Feedback¶
The best way to send feedback is to file an issue at https://github.com/willsheffler/worms/issues.
If you are proposing a feature:
- Explain in detail how it would work.
- Keep the scope as narrow as possible, to make it easier to implement.
- Remember that this is a volunteer-driven project, and that contributions are welcome :)
Get Started!¶
Ready to contribute? Here’s how to set up worms for local development.
Fork the worms repo on GitHub.
Clone your fork locally:
$ git clone git@github.com:your_name_here/worms.git
Install your local copy into a conda environment
$ conda env update
Create a branch for local development:
$ git checkout -b name-of-your-bugfix-or-feature
Now you can make your changes locally.
When you’re done making changes, check that your changes pass the tests:
$ pytest
To get flake8 and tox, just pip install them into your virtualenv.
Commit your changes and push your branch to GitHub:
$ git add . $ git commit -m "Your detailed description of your changes." $ git push origin name-of-your-bugfix-or-featureSubmit a pull request through the GitHub website.
Pull Request Guidelines¶
Before you submit a pull request, check that it meets these guidelines:
- The pull request should include tests.
- If the pull request adds functionality, the docs should be updated. Put your new functionality into a function with a docstring, and add the feature to the list in README.rst.
- The pull request should work for Python 2.6, 2.7, 3.3, 3.4 and 3.5, and for PyPy. Check https://travis-ci.org/willsheffler/worms/pull_requests and make sure that the tests pass for all supported Python versions.
Tips¶
Hook up your editor to run this (see your editor’s docs…):
$ python util/runtests.py CURRENT_FILE
Credits —-~~~~~ - Will Sheffler - Ivan Vulovic - Una Natterman - David Baker - Yang Hisa - Rubal Mout
History¶
0.1.24 (2018-04-25)¶
- change two-stage xindex thershold multiplier for 1st stage from 1.25 to 2.0
0.1.23 (2018-04-24)¶
- add initial draft of Una’s criteria for P213 xtal
0.1.22 (2018-04-20)¶
- add initial draft of Una’s criteria for P3, P4 and P6 layers
0.1.21 (2018-04-19)¶
- peace sign heterotrimer site compatibility bug fix
- xindex search now stores lists instead of one-per-bin
0.1.20 (2018-04-16)¶
- add more dihedral sym files
0.1.19 (2018-04-6)¶
- minor performance impovements in hash-index based search
0.1.17 (2018-04-4)¶
- hash-index based search for Cyclic(…, origin_seg=…)
0.1.16 (2018-03-15)¶
- I52 symmetry bug fix
0.1.15 (2018-03.05)¶
- add NullCriteria that always returns 0 err
0.1.14 (2018-02-28)¶
- fix provenance bug in ‘cyclic entry’ cases
- try to make serialization of Segments more efficient
0.1.13 (2018-02-16)¶
- raise exception if system too large
0.1.12 (2018-02-16)¶
- partial bignum fix
0.1.11 (2018-02-15)¶
- fix memory bug
- make distribution work better
- maybe fix pose bug, still some logic err, but maybe ok
0.1.10 (2018-02-15)¶
- add max_results option to grow
- fix C2 sym bug
- fix xform axis cen bug
- fix memory “bug” with batch parallel processing
0.1.9 (2018-02-08)¶
- add max_samples option to grow
0.1.8 (2018-02-07)¶
- origin_seg bug fix
0.1.6 (2018-02-01)¶
- middle-to-end cyclic fusions working
- add pretty logo of mid-to-end C3 fusion
0.1.6 (2018-02-01)¶
- bug fix in fullatom option
0.1.5 (2018-02-01)¶
- add fullatom option to Worms.sympose
- cyclic premutation working for simple beginning-to-end case
0.1.4 (2018-02-01)¶
- pypi deplolment derp
0.1.3 (2018-02-01)¶
- pypi deplolment derp
0.1.2 (2018-01-23)¶
- Add __main__ for module to run tests
- move worms.pdb to worms.data because pdb is kinda reserved
- move utility stuff to util.py
- add some interactive visualization utils for debugging
0.1.1 (2018-01-23)¶
- First release on PyPI.