def model(trgt, tmpl8, od):
# open target sequence
rc('open ' + trgt)
# open template structure, and generate sequence
rc('open ' + tmpl8)
rc('sequence #0')
# MAV objects
fmav = findMAVs()
target, template = fmav
tar_seq = target.seqs[0]
temp_seq = copy(template.seqs[0])
seq_name = tmpl8.split('/')[-1]
# align sequences
# get template secondary structure matrix
nb = Pmw.NoteBook()
structPage = nb.add("From Structure")
ssParams = SSParams(structPage, template.prefs)
kw = {'ssMatrix': ssParams.getMatrix()}
# generalize these vars later. tired of hacking rn.
# match target fasta sequence to template pdb sequence
target.alignSeq(temp_seq, displayName=seq_name,
matrix=template.prefs[MATRIX], gapOpenStrand=-18.0,
scoreGap=-1, scoreGapOpen=-12, gapOpenHelix=-18.0,
gapOpenOther=-6.0, gapChar='.', guideSeqs=None,
ssFraction=0.3, **kw)
# run modeller on alignment
kw = {'licenseKey': 'MODELIRANJE'}
ModellerBase.model(target, tar_seq, openModels.list(modelTypes=[Molecule]),
'5', 1, 1, 0, veryFast=0, **kw)
def model(tmpl8, loops):
# open template structure, and generate sequence
rc('open ' + tmpl8)
rc('sequence #0; wait')
# MAV objects
fmav = findMAVs()
template = fmav[0]
temp_seq = template.seqs[0]
seq_name = tmpl8.split('/')[-1]
# run modeller on alignment
kw = {'licenseKey': 'MODELIRANJE'}
ModellerBase.model(template, temp_seq, openModels.list(modelTypes=[Molecule]),
'10', 1, 1, 0, veryFast=0, loopInfo=('', loops), **kw)
