def make_prematrixlist(pdbid,chainid): #makes a matrix given the pdb id and cahin id for now after removing simplicies i do not update data ,i assume that its very unlikly that a residue will have no simplcies with lengths less than 10 a
pdbstruct = (parse_pdb_file(download_pdb_file(pdbid),['ATOM'],[] ))
a = filter_target(pdbstruct['ATOM'], name = ['CA'], chain = [chainid])
a = filter_target(a, name = ['CA'], span=find_optimal_span(a))
simplexlist = [[ (a[x]['resseq'], a[x]['res'], a[x]['coord'] ) for x in y] for y in tessellate(a).vertices]#gives grouping in terms of four(one simplex)
data = ([(x['resseq'],x['res']) for x in a])
simplexlist = filter_simplicies(10,simplexlist)#integer sets cutoff
return (neighborlist(data,simplexlist),simplexlist,dict(data))
List of sequence numbers and the sequence itself, both trimmed.
"""
return zip(*[(i,y) for i,x,y in zip(seq_numbers, orig_seq, mut_seq) if x != '-'])
def number_sequence(seq):
""" Numbers a sequence (as in, doesn't number the gaps).
Arguments:
seq -- Sequence to be numbered.
Returns:
List of numbers corresponding to each index of the MSA.
"""
numbers = []
count = 1
for x in seq:
if x != '-':
numbers+=[count]
count+=1
else:
numbers+=['-']
return numbers
# main code below here
if __name__ == '__main__':
a = parse_pdb_file(open_pdb_file(sys.argv[1]), ['ATOM', 'DBREF', 'REMARK'], [465])
a['ATOM'] = filter_target(a, name=['CA'])
b = parse_fasta_file(open_fasta_file(sys.argv[2]))
print(b)
print(thread_sequence(b[0][1], a))
max_l = cur_l+1
end_index = y
cur_l = 0
if max_l < cur_l+1:
max_l = cur_l+1
end_index = len(res_seq_numbers)
return res_seq_numbers[end_index-max_l:end_index]
def calculate_edge_lengths(atoms, simplexlist):
""" Calculates the edge lengths of every simplex.
Arguments:
atoms -- List of atoms from the pdb structure.
simplexlist -- List of simplices.
Returns:
A 6-tuple of edge lengths for given simplices.
"""
return [ [norm(y[0]-y[1]) for y in combinations([atoms[z]['coord'] for z in x], 2) ] for x in simplexlist]
# test code below here
if __name__ == '__main__':
a = filter_target(parse_pdb_file(open_pdb_file(sys.argv[1]), ['ATOM', 'REMARK'], [465]), chain=['A'], name=['CA'])
b = tessellate(a).vertices
c = [[a[x]['res'] for x in y] for y in b]
d = simplex_potential(c)
# [print(x['resseq'],x['res'],y) for x,y in zip(a,residue_potential(a, b, d))]