-
Notifications
You must be signed in to change notification settings - Fork 0
/
Changes
191 lines (130 loc) · 5.7 KB
/
Changes
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
0.9.2 2024-11-26
- Fix a pair of bugs in valence calculation.
0.9.1 2024-11-26
- Handling trigonal bipyramidal centers.
- Exporting all Chemistry::OpenSMILES::is_chiral_*() subroutines.
- Fixing a bug where H atom counts of 0 given in square brackets were
not preserved.
0.9.0 2023-10-25
- Handling square planar chirality.
0.8.6 2023-06-19
- Implementing is_ring_atom().
- No longer removing chiral centers from atoms in rings.
- Accepting coloring subroutine references in
is_unimportant_double_bond() and mark_all_double_bonds().
- Returning false instead of undefined value.
- Exporting %bond_order_to_symbol and %bond_symbol_to_order to simplify
conversion between bond symbols and orders.
0.8.5 2023-01-26
- Fixing incorrect chirality handling code as it did not consider all
ring bonds up to now.
0.8.4 2022-11-29
- Ceasing to mark unimportant double bonds in
Chemistry::OpenSMILES::Stereo.
0.8.3 2022-11-03
- Exporting %Chemistry::OpenSMILES::normal_valence.
0.8.2 2022-09-20
- Adding Chemistry::OpenSMILES::Aromaticity and
Chemistry::OpenSMILES::Stereo from smiles-scripts project v0.2.0.
- Fixing prototypes of recently added functions.
- Introducing Chemistry::OpenSMILES::is_double_bond().
- Introducing Chemistry::OpenSMILES::is_ring_bond().
0.8.1 2022-05-11
- Fixing a bug with incomplete cis/trans markers on ring bonds.
- Introducing Chemistry::OpenSMILES::toggle_cistrans().
- Introducing two functions for bond type determination.
0.8.0 2022-05-05
- Implementing support for tetrahedral chiral centers having lone
pairs.
- Safeguarding against infinite cycles in
Chemistry::OpenSMILES::Writer::_permutation_order().
- Fixing mistake in Chemistry::OpenSMILES::Parser::parse()
documentation.
0.7.0 2021-10-30
- Fixing important issue with representing tetrahedral chiral centers
by introducing 'chirality_neighbours' key to atom hashes.
0.6.0 2021-10-18
- Allowing multi-digit hydrogen counts if enabled via parser option.
- Standardizing chiral markers for allenal carbons.
- Not standardizing chiral markers in raw output.
- Reporting '@' and '@@' chiralities with other than 4 neighbours as
they cannot be processed right now.
0.5.2 2021-10-11
- Creating explicitly refvertexed Graph objects to get around all the
problems caused by interpreting them as scalar values.
0.5.1 2021-08-29
- Working around an incompatibility with Graph v0.9721.
0.5.0 2021-08-26
- Handling raw parsing output in
Chemistry::OpenSMILES::clean_chiral_centers().
- Fixing a bug in position counting due to $1 pollution.
- Detecting and reporting disconnected parts of moieties.
- Introducing Chemistry::OpenSMILES::is_chiral() to detect both chiral
atoms and moieties.
- Fixing bug in Chemistry::OpenSMILES::clean_chiral_centers() which
caused removal of all chiral centers, not just tetrahedral.
- Introducing Chemistry::OpenSMILES::mirror() to invert chiral centers,
currently only tetrahedral.
- Fixing bug in printing of chiral centers, previously only tetrahedral
centers were printed.
0.4.6 2021-04-14
- Fixing reading/writing of cis/trans ring bonds.
0.4.5 2021-03-25
- Fixing a bug in aromatic bond detection.
0.4.4 2021-03-09
- Introducing Chemistry::OpenSMILES::clean_chiral_centers() to remove
unnecessary tetrahedral chiral settings.
0.4.3 2021-01-25
- Supporting tetrahedral chirality in
Chemistry::OpenSMILES::Writer::write_SMILES().
- Chiralities @TH1 and @TH2 are the same as @ and @@, respectively.
- Specifying the requirement of Graph v0.97 or later.
- Fixing issue with homepage.
0.4.2 2021-01-20
- Exporting Chemistry::OpenSMILES::Writer::write_SMILES().
- Removing chirality information from written SMILES, as code to
write this reliably is not yet available.
- Fixing writing of cis/trans bonds.
0.4.1 2021-01-12
- Fixing an issue with 'scalar %hash' in t/01_atoms.t.
- Listing a dependency on Graph::Traversal::DFS.
0.4.0 2021-01-11
- Adding Chemistry::OpenSMILES::Writer, implementing a SMILES writer
for the data structures built by Chemistry::OpenSMILES::Parser.
- Converting 'charge' atom field to integer.
- Exporting Chemistry::OpenSMILES::is_aromatic().
0.3.2 2020-10-05
- Explicitly setting bond order to ':' on bonds between aromatic
atoms.
0.3.1 2020-09-17
- Establishing deterministic order while generating graph vertices
for implicit hydrogen atoms.
0.3.0 2020-09-16
- Deriving counts of implicit hydrogen atoms.
- Default number of attached hydrogen atoms for atoms in square
brackets is 0.
- Supporting bracketless '*' atom.
0.2.1 2020-08-13
- Adding 'number' atom field to store atom positions in the initial
SMILES string.
- Making 'class' atom field mandatory.
- Making 'isotope' atom field an integer.
0.2.0 2020-05-20
- Fixing an issue with graph merging.
- Unifying the representation of single bonds.
- Extending POD documentation.
0.1.3 2020-05-19
- Detecting and reporting unbalanced parentheses.
- Detecting and reporting unclosed ring bonds.
- Fixing position pointers in error messages, removing line numbers.
- Adding versioned dependency on Module::Build::Parse::Yapp v0.1.2.
- Declaring minimum Perl version.
- Fixing the POD.
0.1.2 2020-05-17
- Turning hydrogen counts into real vertices. If 'raw' option is
present, hydrogen counts are left as integers instead.
0.1.1 2020-05-14
- Adding missing dependency on Graph::Undirected.
- Adding POD.
0.1.0 2020-05-13
- Initial release.