Symmetric Modeling Utilities

get axes and align at stuff

sym_util.get_xforms_by_chain(sele='all', verbose=False, userms=False)

sym_util.find_symelems(sele_or_xforms='all', verbose=False)

sym_util.guessdxaxes(sele='all', verbose=False)

sym_util.aligndx(sele='all', verbose=False)

sym_util.guesscxaxis(sele, nfold=None, chains0=[], extrasel='name CA')

sym_util.aligncx(sele, nfold, alignsele=None, tgtaxis=Vec( 0.000000, 0.000000, 1.000000 ), chains=[], extrasel='name CA')

sym_util.align_helix(sele, nrepeat, tgt_axis=Vec( 1.000000, 0.000000, 0.000000 ))

sym_util.symmetrize(sele='not symmetrized_*', alignsele=None, chains=[], delete=True)

sym_util.showcxaxis(sele, nfold=None, chains=[], length=30, col=(1, 1, 1), lbl='Cx Axis')

sym_util.myint(s)

sym_util.selbycomp(trn=0)

sym_util.rechain(sel, nres)

sym_util.makekinwire(sel, movres, fixres)

sym_util.get_contigs(x, n=7)

>>> test = list(range(1,8)) + list(range(20,33)) + list(range(40,44)) + list(range(49,50))+ list(range(0,8))
>>> print test
[1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 49, 0, 1, 2, 3, 4, 5, 6, 7]

>>> print get_contigs( test )
[[1, 2, 3, 4, 5, 6, 7], [20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32], [0, 1, 2, 3, 4, 5, 6, 7]]

sym_util.get_fixed_size_contigs(x, n=7)

>>> test = list(range(1,8)) + list(range(20,33)) + list(range(40,44)) + list(range(49,50))+ list(range(0,8))
>>> print test
[1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 49, 0, 1, 2, 3, 4, 5, 6, 7]

>>> for f in get_fixed_size_contigs(test,7): print f
[1, 2, 3, 4, 5, 6, 7]
[20, 21, 22, 23, 24, 25, 26]
[21, 22, 23, 24, 25, 26, 27]
[22, 23, 24, 25, 26, 27, 28]
[23, 24, 25, 26, 27, 28, 29]
[24, 25, 26, 27, 28, 29, 30]
[25, 26, 27, 28, 29, 30, 31]
[26, 27, 28, 29, 30, 31, 32]
[0, 1, 2, 3, 4, 5, 6]
[1, 2, 3, 4, 5, 6, 7]

>>> for f in get_fixed_size_contigs(test,9): print f
[20, 21, 22, 23, 24, 25, 26, 27, 28]
[21, 22, 23, 24, 25, 26, 27, 28, 29]
[22, 23, 24, 25, 26, 27, 28, 29, 30]
[23, 24, 25, 26, 27, 28, 29, 30, 31]
[24, 25, 26, 27, 28, 29, 30, 31, 32]

>>> print len(get_fixed_size_contigs(test,1))
28

>>> for f in get_fixed_size_contigs(test,4): print f
[1, 2, 3, 4]
[2, 3, 4, 5]
[3, 4, 5, 6]
[4, 5, 6, 7]
[20, 21, 22, 23]
[21, 22, 23, 24]
[22, 23, 24, 25]
[23, 24, 25, 26]
[24, 25, 26, 27]
[25, 26, 27, 28]
[26, 27, 28, 29]
[27, 28, 29, 30]
[28, 29, 30, 31]
[29, 30, 31, 32]
[0, 1, 2, 3]
[1, 2, 3, 4]
[2, 3, 4, 5]
[3, 4, 5, 6]
[4, 5, 6, 7]

sym_util.tmpname()

sym_util.gen_helical_alignments(sele1, sele2, pref='HALN')

sym_util.colorI53(sel='visible')

sym_util.alignsym(sel='all', arch='I32', ax1=Vec( 0.000000, 0.000000, 1.000000 ), ax2=Vec( 0.356825, 0.000002, 0.934171 ))

sym_util.xtal_frames(tgt=None, skip=(), r=100)

sym_util.make_helix_old(sele='vis', n=30, nfold=1)

sym_util.color_by_2component(col1='green', col2='cyan')

sym_util.make_ab_components(dir)

sym_util.trim_sym(sel='all', na=1, nb=1)

sym_util.nulltest()

>>> print "foo"
foo

sym_util.load_tests(loader, tests, ignore)