worms package¶

Subpackages¶

Submodules¶

worms.bblock module¶

worms.bblock.BBlock(entry, pdbfile, filehash, pose, ss)[source]¶

worms.bblock.bblock_components(bblock)[source]¶

TODO: Summary

Parameters:	bblock (TYPE) – Description
Returns:	Description
Return type:	TYPE

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.bblock.bblock_str(bblock)[source]¶

TODO: Summary

Parameters:	bblock (TYPE) – Description
Returns:	Description
Return type:	TYPE

worms.bblock.chain_of_ires[source]¶

Summary

Parameters:	bb (TYPE) – Description ires (TYPE) – Description
Returns:	Description
Return type:	TYPE

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: object

stores Poses and BBlocks in a disk cache

bblock(pdbkey)[source]¶

bblockfile(pdbkey)[source]¶

build_pdb_data(entry)[source]¶: return Nnew, Nmissing

check_lock_cachedir()[source]¶

islocked_cachedir()[source]¶

load_cached_bblock_into_memory(pdbkey)[source]¶

load_cached_pose_into_memory(pdbfile)[source]¶

load_from_pdbs()[source]¶

load_from_pdbs_inner(exe)[source]¶

lock_cachedir()[source]¶

pose(pdbfile)[source]¶: load pose from _bblock_cache, read from file if not in memory

posefile(pdbfile)[source]¶

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

query_names(query, *, useclass=True)[source]¶: query for names only

unlock_cachedir()[source]¶

class worms.database.SpliceDB(cachedir=None)[source]¶

Bases: object

Stores valid NC splices for bblock pairs

add(params, pdbkey0, pdbkey1, val)[source]¶

cachepath(params, pdbkey)[source]¶

partial(params, pdbkey)[source]¶

sync_to_disk()[source]¶

worms.database.flatten_path(pdbfile)[source]¶

worms.edge module¶

worms.edge.Edge(u, ublks, v, vblks, verbosity=0, **kw)[source]¶

worms.edge.get_allowed_splices(u, ublks, v, vblks, splicedb=None, max_splice_rms=0.7, ncontact_cut=10, clashd2=9.0, contactd2=100.0, rms_range=5, clash_contact_range=9, skip_on_fail=True, parallel=False, verbosity=1, sync_to_disk_every=0.001)[source]¶

worms.edge.splice_metrics_pair(blk0, blk1, max_splice_rms=0.7, clashd2=9.0, contactd2=100.0, rms_range=9, clash_contact_range=9, skip_on_fail=True)[source]¶

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: object

TODO: Summary

cyclic_entry¶: TYPE – Description

iseg¶: TYPE – Description

pose¶: TYPE – Description

src_lb¶: TYPE – Description

src_ub¶: TYPE – Description

srcpose¶: TYPE – Description

seq()[source]¶

TODO: Summary

Returns:	Description
Return type:	TYPE

srcseq()[source]¶

TODO: Summary

Returns:	Description
Return type:	TYPE

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.pose_contortions.make_contorted_pose(*, entryexits, entrypol, exitpol, indices, from_seg, to_seg, origin_seg, seg_pos, position, is_cyclic, align, cryst_info, end, iend, only_connected, join, cyclic_permute, cyclictrim, provenance, make_chain_list)[source]¶: there be dragons here

worms.pose_contortions.reorder_spliced_as_N_to_C(body_chains, polarities)[source]¶

remap chains of each body such that concatenated chains are N->C

Parameters:	body_chains (TYPE) – Description polarities (TYPE) – Description
Returns:	Description
Return type:	TYPE
Raises:	`ValueError` – Description

worms.search module¶

worms.search.random() → x in the interval [0, 1).¶

worms.segments module¶

TODO: Summary

class worms.segments.Segment(spliceables, entry=None, exit=None, expert=False)[source]¶

Bases: object

TODO: Summary

bodyid¶: TYPE – Description

entrypol¶: TYPE – Description

entryresid¶: TYPE – Description

entrysiteid¶: TYPE – Description

exitpol¶: TYPE – Description

exitresid¶: TYPE – Description

exitsiteid¶: TYPE – Description

expert¶: TYPE – Description

max_sites¶: TYPE – Description

min_sites¶: TYPE – Description

nchains¶: TYPE – Description

spliceables¶: TYPE – Description

x2exit¶: TYPE – Description

x2orgn¶: TYPE – Description

init_segment_data()[source]¶

TODO: Summary

Raises:	`ValueError` – Description

make_head()[source]¶

TODO: Summary

Returns:	Description
Return type:	TYPE

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

make_tail()[source]¶

TODO: Summary

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

same_bodies_as(other)[source]¶

TODO: Summary

Parameters:	other (TYPE) – Description
Returns:	Description
Return type:	TYPE

split_idx(idx, head, tail)[source]¶

return indices for separate head and tail segments

Parameters:	idx (TYPE) – Description head (TYPE) – Description tail (TYPE) – Description
Returns:	Description
Return type:	TYPE

class worms.segments.Segments(segments)[source]¶

Bases: object

light wrapper around list of Segments

segments¶: TYPE – Description

index(val)[source]¶

TODO: Summary

Parameters:	val (TYPE) – Description
Returns:	Description
Return type:	TYPE

split_at(idx)[source]¶

TODO: Summary

Parameters:	idx (TYPE) – Description
Returns:	Description
Return type:	TYPE

class worms.segments.SpliceSite(sele, polarity, chain=None)[source]¶

Bases: object

TODO: Summary

chain¶: TYPE – Description

polarity¶: TYPE – Description

selections¶: TYPE – Description

resid(id, pose)[source]¶

TODO: Summary

Parameters:	id (TYPE) – Description pose (TYPE) – Description
Returns:	Description
Return type:	TYPE
Raises:	`ValueError` – Description

class worms.segments.Spliceable(body, sites, *, bodyid=None, min_seg_len=1, allowed_pairs=None)[source]¶

Bases: object

TODO: Summary

allowed_pairs¶: TYPE – Description

body¶: TYPE – Description

bodyid¶: TYPE – Description

chains¶: TYPE – Description

end_of_chain¶: TYPE – Description

min_seg_len¶: TYPE – Description

nsite¶: TYPE – Description

sites¶: TYPE – Description

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

sitepair_allowed(isite, jsite)[source]¶

TODO: Summary

Parameters:	isite (TYPE) – Description jsite (TYPE) – Description
Returns:	Description
Return type:	TYPE

spliceable_positions()[source]¶

selection of resids, and map ‘global’ index to selected index

Returns:	Description
Return type:	TYPE

class worms.segments.Worms(segments, scores, indices, positions, criteria, detail)[source]¶

Bases: object

TODO: Summary

criteria¶: TYPE – Description

detail¶: TYPE – Description

indices¶: TYPE – Description

positions¶: TYPE – Description

score0¶: TYPE – Description

score0sym¶: TYPE – Description

scores¶: TYPE – Description

segments¶: TYPE – Description

splicepoint_cache¶: dict – Description

clear_caches()[source]¶: TODO: Summary

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.segments.lineno()[source]¶

Returns the current line number in our program.

Returns:	Description
Return type:	TYPE

worms.util module¶

TODO: Summary

class worms.util.InProcessExecutor(*args, **kw)[source]¶

Bases: object

TODO: Summary

map(func, *iterables)[source]¶

TODO: Summary

Parameters:	func (TYPE) – Description iterables – Description
Returns:	Description
Return type:	TYPE

submit(fn, *args, **kw)[source]¶

TODO: Summary

Parameters:	fn (TYPE) – Description args – Description kw – passthru args
Returns:	Description
Return type:	TYPE

class worms.util.MultiRange(nside)[source]¶

Bases: object

TODO: Summary

len¶: TYPE – Description

nside¶: TYPE – Description

psum¶: TYPE – Description

class worms.util.NonFuture(result)[source]¶

Bases: object

TODO: Summary

result()[source]¶

TODO: Summary

Returns:	Description
Return type:	TYPE

worms.util.bigprod(iterable)[source]¶

TODO: Summary

Parameters:	iterable (TYPE) – Description
Returns:	Description
Return type:	TYPE

worms.util.contig_idx_breaks[source]¶

worms.util.cpu_count()[source]¶

TODO: Summary

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.expand_array_if_needed[source]¶

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

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.hash_str_to_int(s)[source]¶

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

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.residue_coords(p, ir, n=3)[source]¶

worms.util.residue_sym_err(p, ang, ir, jr, n=1, axis=[0, 0, 1], verbose=0)[source]¶

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.util.unique_key(a, b=None)[source]¶

worms.util.unique_key_int32s(a, b)[source]¶

worms.util.worst_CN_connect(p)[source]¶

TODO: Summary

Parameters:	p (TYPE) – Description
Returns:	Description
Return type:	TYPE

worms.util.xform_pose(xform, pose, lb=1, ub=-1)[source]¶

TODO: Summary

Parameters:	xform (TYPE) – Description pose (TYPE) – Description lb (int, optional) – Description ub (TYPE, optional) – Description

worms.vertex module¶

TODO: Summary

worms.vertex.Vertex(bbs, dirn, bbids=None, min_seg_len=1, verbosity=0)[source]¶

Summary

Parameters:	bbs (TYPE) – Description bbids (TYPE) – Description dirn (TYPE) – Description min_seg_len (TYPE) – Description
Returns:	Description
Return type:	TYPE

worms.vertex.vertex_single(bbstate, bbid, din, dout, min_seg_len, verbosity=0)[source]¶: build on bblock’s worth of vertex

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.is_rosetta_pose(to_show)[source]¶

worms.vis.pymol_load(to_show, state=None, name=None, **kw)[source]¶

worms.vis.pymol_load_pose(pose, name)[source]¶

worms.vis.pymol_xform(name, xform)[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.showcom(sel='all')[source]¶

TODO: Summary

Parameters:	sel (str, optional) – Description

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

worms.vis.showsphere(c, r=1, col=(1, 1, 1), lbl='')[source]¶

TODO: Summary

Parameters:	c (TYPE) – Description r (int, optional) – Description col (tuple, optional) – Description lbl (str, optional) – Description

worms.vis.showvecfrompoint(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

Module contents¶

Top-level package for worms.