Python dict2ter Examples

Example #1

File: pdb.py Project: chungtseng/pycogent

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

Example #2

File: pdb.py Project: yatisht/pycogent

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

Example #3

File: pdb.py Project: blankenberg/pycogent

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

Example #4

File: test_pdb.py Project: GavinHuttley/pycogent

 def test_dict2ter(self):
     d = {'ser_num': 1, 'chain_id': 'A', 'res_name': 'MET', 'res_ic': ' ', \
           'res_id': 1,}
     assert dict2ter(d) == 'TER       2      MET A   1 \n'

Example #5

 def test_dict2ter(self):
     d = {'ser_num': 1, 'chain_id': 'A', 'res_name': 'MET', 'res_ic': ' ', \
           'res_id': 1,}
     assert dict2ter(d) == 'TER       2      MET A   1 \n'

Example #6

File: test_pdb.py Project: yesimon/pycogent

 def test_dict2ter(self):
     d = {"ser_num": 1, "chain_id": "A", "res_name": "MET", "res_ic": " ", "res_id": 1}
     assert dict2ter(d) == "TER       2      MET A   1 \n"