def long_fixed_variable(in_dir, out_dir, ip_dist_cutoff, backbone=False, filter_sidechains=True, correct=False, verbose=True):
out = os.path.join(out_dir,'long_range_fixed-variable')
if not os.path.exists(out):
os.mkdir(out)
for i in range(20):
aa = AAint2char(i)
files.append(open(os.path.join(out, aa + '.dists'), 'w'))
pdb = setup(in_dir, correct, backbone, filter_sidechains)
pdbSize = len(pdb)
(distance_matrix, use_indices) = get_dist_and_IPs(pdb, ip_dist_cutoff)
for (p1,p2) in use_indices:
aa1 = pdb[p1].int_name
aa2 = pdb[p2].int_name
if pdb[p2].stubIntact:
p2_base_chain = ['CA', 'CB']
dists = filter_sc_dists(pdb[p1].atom_names, p2_base_chain, distance_matrix[p1][p2-p1-1], True)
files[aa1].write("".join([round(val, 2) for val in dists.values()])[1:-1] + ';' + str(aa2) + '\n')
if pdb[p1].stubIntact:
p1_base_chain = ['CA', 'CB']
dists = filter_sc_dists(p1_base_chain, pdb[p2].atom_names, distance_matrix[p1][p2-p1-1], False)
files[aa2].write("".join([round(val, 2) for val in dists.values()])[1:-1] + ';' + str(aa1) + '\n')
for f in files: f.close()
def short_fixed_variable(in_dir, out_dir, ip_dist_cutoff, backbone=False, filter_sidechains=True, correct=False, verbose=True):
out = os.path.join(out_dir,'short_range_fixed-variable')
if not os.path.exists(out):
os.mkdir(out)
files = list()
for i in range(20):
files.append([])
for j in range(1,5):
files[i].append([])
for k in ['rev', 'for']: #why do we need to seperate out the 'rev' and 'for' dists?
aa = AAint2char(i)
files[i][j].append(open(os.path.join(out, aa + '_' + j + '_' + k + '.dists'), 'w'))
pdb = setup(in_dir, correct, backbone, filter_sidechains)
pdbSize = len(pdb)
(distance_matrix, use_indices) = get_dist_and_IPs_intra_full(pdb, ip_dist_cutoff)
for (p1,p2) in use_indices:
aa1 = pdb[p1].int_name
aa2 = pdb[p2].int_name
if pdb[p2].stubIntact: #need to check whether both stubs are intact?
p2_base_chain = ['CA', 'CB']
dists = filter_sc_dists(pdb[p1].atom_names, p2_base_chain, distance_matrix[p1][p2-p1-1], True)
files[aa1][p2-p1-1][0].write("".join([round(val, 2) for val in dists.values()])[1:-1] + ';' + str(aa2) + '\n')
if pdb[p1].stubIntact:
p1_base_chain = ['CA', 'CB']
dists = filter_sc_dists(p1_base_chain, pdb[p2].atom_names, distance_matrix[p1][p2-p1-1], False)
files[aa2][p2-p1-1][1].write("".join([round(val, 2) for val in dists.values()])[1:-1] + ';' + str(aa1) + '\n')
for i in range(20):
for j in range(1,5):
for k in ['rev', 'for']:
files[i][j][k].close()
def long_variable_variable(in_dir, out_dir, ip_dist_cutoff, backbone=False, filter_sidechains=True, correct=False, verbose=True): outfile = open(os.path.join(out_dir, 'short_range_fixed-variable.dists'), 'w') pdb = setup(in_dir, correct, backbone, filter_sidechains) pdbSize = len(pdb) (distance_matrix, use_indices) = get_dist_and_IPs(pdb, ip_dist_cutoff) for (p1,p2) in use_indices: aa1 = pdb[p1].int_name aa2 = pdb[p2].int_name if pdb[p2].stubIntact and pdb[p2].stubIntact: dists = filter_sc_dists(['CA', 'CB'], ['CA', 'CB'], distance_matrix[p1][p2-p1-1], True) outfile.write(str([round(val, 2) for val in dists.values()])[1:-1] + ';' + str(aa1) + ';' + str(aa2) + '\n') outfile.close()
def short_variable_variable(in_dir, out_dir, ip_dist_cutoff, backbone=False, filter_sidechains=True, correct=False, verbose=True):
out = os.path.join(out_dir,'short_range_variable-variable')
for i in range(1,5):
files.append(open(os.path.join(out, i + '.dists'), 'w'))
pdb = setup(in_dir, correct, backbone, filter_sidechains)
pdbSize = len(pdb)
(distance_matrix, use_indices) = get_dist_and_IPs_intra_CACBOnly(pdb, ip_dist_cutoff)
for (p1,p2) in use_indices:
aa1 = pdb[p1].int_name
aa2 = pdb[p2].int_name
if pdb[p2].stubIntact and pdb[p2].stubIntact:
dists = filter_sc_dists(['CA', 'CB'], ['CA', 'CB'], distance_matrix[p1][p2-p1-1], True)
files[p2-p1-1].write("".join([round(val, 2) for val in dists.values()])[1:-1] + ';' + str(aa1) + ';' + str(aa2) + '\n')
for f in files: f.close()
