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Quote identifier-shaped numbers (e.g. PDB code 6E72) in JSON output #445

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Quote identifier-shaped numbers (e.g. PDB code 6E72) in JSON output #445

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13 changes: 13 additions & 0 deletions src/to_json.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -128,12 +128,25 @@ class JsonWriter {
else if (opt.quote_numbers < 2 && is_numb(value) &&
// exception: 012 (but not 0.12) is assumed to be a string
(value[0] != '0' || value[1] == '.' || value[1] == '\0') &&
// exception: digit-string + E + digit-string (e.g. 6E72) is
// assumed to be an identifier such as a PDB code, not a number
!looks_like_numberlike_id(value) &&
(opt.quote_numbers == 0 || value.back() != ')'))
write_as_number(value);
else
write_string(as_string(value));
}

// returns true for tokens of the form digits + E + digits (e.g. 6E72):
// valid CIF numbers but indistinguishable from alphanumeric identifiers
// such as PDB codes, which a JSON reader would parse as huge floats
static bool looks_like_numberlike_id(const std::string& v) {
size_t epos = v.find('E');
return epos != std::string::npos &&
v.find_first_not_of("0123456789") == epos &&
v.find_first_not_of("0123456789", epos + 1) == std::string::npos;
}

void open_cat(const std::string& cat, size_t* tag_pos) {
if (!cat.empty()) {
change_indent(+1);
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7 changes: 7 additions & 0 deletions tests/test_cif_json.py
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Original file line number Diff line number Diff line change
Expand Up @@ -52,6 +52,13 @@ def test_json_number_normalization(self):
self.assertEqual(parsed, {'test': {'_a': -0.99, '_b': 0.04,
'_c': -0.04, '_d': 0.5}})

def test_json_numberlike_id(self):
# 6E72 is a valid CIF number but also a PDB code - quote it (#444)
doc = cif.read_string('data_6E72 _entry.id 6E72 _a 1.2E3 _b 2e4')
parsed = json.loads(doc.as_json())
self.assertEqual(parsed, {'6e72': {'_entry.id': '6E72',
'_a': 1200.0, '_b': 20000.0}})

class TestMmjson(unittest.TestCase):
def test_read_1pfe(self):
path = full_path('1pfe.json')
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