def test_dict2pdb(self):
"""testing pdb dict round-trip.
"""
line = 'ATOM 1 N MET A 1 53.045 42.225 33.724 1.00 2.75 N\n'
d = pdb2dict(line)
line2 = dict2pdb(d)
assert line == line2
d.pop('coords')
assert d == {
'ser_num': 1,
'res_long_id': ('MET', 1, ' '),
'h_flag': ' ',
'at_name': ' N ',
'at_long_id': ('N', ' '),
'bfactor': 2.75,
'chain_id': 'A',
'occupancy': 1.0,
'element': ' N',
'res_name': 'MET',
'seg_id': ' ',
'at_id': 'N',
'alt_loc': ' ',
'res_ic': ' ',
'res_id': 1,
'at_type': 'ATOM '
}
def test_dict2pdb(self):
"""testing pdb dict round-trip.
"""
line = "ATOM 1 N MET A 1 53.045 42.225 33.724 1.00 2.75 N\n"
d = pdb2dict(line)
line2 = dict2pdb(d)
assert line == line2
d.pop("coords")
assert d == {
"ser_num": 1,
"res_long_id": ("MET", 1, " "),
"h_flag": " ",
"at_name": " N ",
"at_long_id": ("N", " "),
"bfactor": 2.75,
"chain_id": "A",
"occupancy": 1.0,
"element": " N",
"res_name": "MET",
"seg_id": " ",
"at_id": "N",
"alt_loc": " ",
"res_ic": " ",
"res_id": 1,
"at_type": "ATOM ",
}
def write_coords(atoms):
old_fields = defaultdict(str)
coords = ['MODEL 1\n']
for atom in atoms.sortedvalues():
fields = atom.getDict()
if (old_fields['chain_id'] != fields['chain_id']) and old_fields['chain_id'] and old_fields['res_name'] in AA_NAMES:
coords.append(dict2ter(old_fields))
if (old_fields['model'] != fields['model']) and old_fields['model'] != '': # model can be 0 :)
if old_fields['chain_id'] and old_fields['res_name'] in AA_NAMES:
coords.append(dict2ter(old_fields))
coords.append('ENDMDL\n')
coords.append('MODEL %4i\n' % (fields['model'] + 1))
coords.append(dict2pdb(fields))
old_fields = fields
if fields['res_name'] in AA_NAMES:
coords.append(dict2ter(fields))
coords.append('ENDMDL\n')
coords.append('END \n')
return coords
def write_coords(atoms):
old_fields = defaultdict(str)
coords = ['MODEL 1\n']
for atom in atoms.sortedvalues():
fields = atom.getDict()
if (old_fields['chain_id'] != fields['chain_id']) and old_fields['chain_id'] and old_fields['res_name'] in AA_NAMES:
coords.append(dict2ter(old_fields))
if (old_fields['model'] != fields['model']) and old_fields['model'] != '': # model can be 0 :)
if old_fields['chain_id'] and old_fields['res_name'] in AA_NAMES:
coords.append(dict2ter(old_fields))
coords.append('ENDMDL\n')
coords.append('MODEL %4i\n' % (fields['model'] + 1))
coords.append(dict2pdb(fields))
old_fields = fields
if fields['res_name'] in AA_NAMES:
coords.append(dict2ter(fields))
coords.append('ENDMDL\n')
coords.append('END \n')
return coords
def test_dict2pdb(self):
"""testing pdb dict round-trip.
"""
line = 'ATOM 1 N MET A 1 53.045 42.225 33.724 1.00 2.75 N\n'
d = pdb2dict(line)
line2 = dict2pdb(d)
assert line == line2
d.pop('coords')
assert d == {'ser_num': 1, 'res_long_id': ('MET', 1, ' '),
'h_flag': ' ',
'at_name': ' N ',
'at_long_id': ('N', ' '),
'bfactor': 2.75, 'chain_id': 'A',
'occupancy': 1.0, 'element': ' N',
'res_name': 'MET',
'seg_id': ' ', 'at_id': 'N',
'alt_loc': ' ',
'res_ic': ' ',
'res_id': 1,
'at_type': 'ATOM '}
def write_coords(atoms):
old_fields = defaultdict(str)
coords = ["MODEL 1\n"]
for atom in atoms.sortedvalues():
fields = atom.getDict()
if (
(old_fields["chain_id"] != fields["chain_id"])
and old_fields["chain_id"]
and old_fields["res_name"] in AA_NAMES
):
coords.append(dict2ter(old_fields))
if (old_fields["model"] != fields["model"]) and old_fields["model"] != "": # model can be 0 :)
if old_fields["chain_id"] and old_fields["res_name"] in AA_NAMES:
coords.append(dict2ter(old_fields))
coords.append("ENDMDL\n")
coords.append("MODEL %4i\n" % (fields["model"] + 1))
coords.append(dict2pdb(fields))
old_fields = fields
if fields["res_name"] in AA_NAMES:
coords.append(dict2ter(fields))
coords.append("ENDMDL\n")
coords.append("END \n")
return coords
