Example #1
0
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)
Example #2
0
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)