def __init__(self, pastafile, reffile, seqfile, verbose=False):
"""
Constructor
@param pastafile: filename for residue list
@type pastafile: string
@param reffile: filename for reference list (eg. BMRB ASCII file)
@type reffile: string
@param seqfile: filename for FASTA sequence file
@type seqfile: string
"""
fh = FileHandler()
## list of Residue.PastaResidue objects
self.residues = fh.read_pasta(pastafile, reffile)
## list of Residue.AminoAcid objects
self.amino_acids = fh.read_preset(reffile)
## list of Residue.AminoAcid objects
self.seq = fh.read_seq(seqfile, reffile)
self.P = None ## numpy.ndarray for typing posterior probabilities
self.L = None ## numpy.ndarray for linking constraints
self.S = None ## numpy.ndarray for aa type in sequence
self.A = None ## list of assignments and respective similarity score
## ILP STUFF
self.B = None ## list of assignments and respective costs
self.C = None ## cost matrix ILP
self.Xs = None ## assignment matrices from solution pool,
self.ILP_L = None ## Linking Matrix of ILP
self.typing_elapsed = 0
self.linking_elapsed = 0
self.mapping_elapsed = 0
self.full_running_time = 0
from Mapping import Mapping
from Mapping2 import AbstractMapping
from Definitions import three2One
from MaxLikelihood import Likelihood
from numpy import array,mean, max
import pylab as pl
fh = FileHandler()
pairs = 'tests/residue_lists/all_pairs.pasta'
singles = 'tests/residue_lists/all_singles.pasta'
seqfile_pairs = 'tests/sequences/all_pairs.fasta'
seqfile_singles = 'tests/sequences/all_singles.fasta'
statsfile = 'tests/reference_lists/bmrb.shift'
single_residues = fh.read_pasta(singles, statsfile)
amino_acids = fh.read_seq(seqfile_singles, statsfile)
atoms = {'CO' :0, 'CA' :1,
'CB' :2, 'CG' :3,
'CG1':4, 'CG2':5,
'CD' :6, 'CD1':7,
'CD2':8, 'CE' :9,
'CE1':10, 'CE2':11,
'CE3':12, 'CZ':13, 'CZ2':14,
'CZ3':15, "CH2":16}
aa_names = ''.join([aa.one_let for aa in amino_acids])
# k = aa_names.index("F")
# print "Residue: ",res.name_im1, res.get_carbons(previous=True)
# print "Amino Acid: ",aa.three_let, aa.get_carbons()
mapper1 = Mapping(aa_mapping=True)
L = Likelihood()
