Jan Holst Jensen
5616dc2597
Add support for dative bonds. ( #1190 )
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* Add support for dative bonds to molfile reader plus writer and to SMILES reader (SMILES writer already supports it).
Initial V3000 molfile reader and writer dative bond support by Esben Jannik Bjerrum.
* first pass at adding -> as dative bond in smiles/smarts
more testing required
* all tests pass
* update .cmake files for lex
2016-12-14 09:44:18 +01:00
Greg Landrum
f4a02f5f13
Expanded sequence support ( #1140 )
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* patch from Roger Sayle to support nucleic acids as well as amino acids
* add some tests which do not yet pass
* fix a bug I introduced in residue name parsing
* basic sequence testing
* add some more tests
2016-11-04 04:29:26 +01:00
Greg Landrum
9f9f2cd2d2
support additional trans-uranic elements ( #1134 )
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* support additional trans-uranic elements
- update the atomic data and isotope lists
- update the SMILES and SMARTS parsers
* rebreak an input file
2016-11-03 11:48:31 -04:00
Greg Landrum
f0bb85dfdb
Fixes #1049 ( #1050 )
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* fixes #1049
That was almost too easy
* elaborate the test a bit
2016-09-01 09:22:17 +02:00
Greg Landrum
8009b867b5
Fixes #1034 : squiggle bonds are now preserved if no sanitization is done ( #1043 )
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* backup commit
* typo
* forgot the test file
* also test that atom chirality is handled properly
2016-08-30 16:02:31 +02:00
Greg Landrum
7a49dd3bb9
fixes #1023 ( #1027 )
2016-08-18 16:29:29 -04:00
Brian Kelley
ddf7c73b50
Adds Atom atom map and rlabel apis ( #1004 )
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* Adds Atom atom map and rlabel apis
* Moves RLabels to their own namespace, adds other properties.
* Removes namespaces, liberally adds Atom to function names.
* move detail::computedPropName to RDKit::detail::computedPropName
2016-08-11 04:46:41 +02:00
Brian Kelley
900fc391aa
Fixes middle-justified symbols in sd files, adds M_CHG tests ( #1002 )
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* Adds boost::trim, M CHG tests
* stoi is a c++11 feature
* Actually test charges
2016-08-02 14:41:08 +02:00
Paolo Tosco
63b6bdef46
- RCSB SDF files which feature right-justified element names can now be parsed ( #994 )
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- added a relevant test
2016-07-27 14:49:52 +02:00
Greg Landrum
339fa081e5
Merge fix/github908 branch
2016-07-27 04:49:55 +02:00
Greg Landrum
d30bf4a6df
the fix for #188 also
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fixes #192
2016-03-29 13:19:10 +02:00
Greg Landrum
53b6e52765
ok, this time it is a proper fix
2016-03-29 13:09:22 +02:00
Greg Landrum
9a13afba24
Fixes #188
2016-03-29 10:58:56 +02:00
Greg Landrum
added01998
Prefer wedging bonds to Hs when possible
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Fixes #772
2016-02-15 14:32:30 +01:00
Greg Landrum
2ca85c775f
Fixes #741
2016-02-13 05:38:03 +01:00
Brian Kelley
6d5b7a0305
Adds more extensive tests (recursion, multithreading)
2016-01-20 17:09:58 -05:00
Brian Kelley
ae13f0a93a
Adds tests for locale switching
2016-01-20 17:09:58 -05:00
Greg Landrum
e08e0d16d8
first pass, using google style
2015-11-14 14:58:11 +01:00
Brian Kelley
210f2951e0
Silences warnings in tests
2015-10-18 21:20:11 -04:00
Brian Kelley
54311dff9c
Suppresses warnings in tests
2015-10-18 16:09:58 -04:00
Brian Kelley
95a92282d1
Dictionary access is saniztized and optimized.
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o rdkit gains a RDKit::common_properties namespace that contains common string value properties
o Dict.h and below gain getPropIfPresent that attempts to retrieve a property and returns
true/false on success or failure. This is used to optimize access.
o rdkit learns how to pass property keys by reference, not value.
A new namespace has been added to RDKit, common_properties
that contains the std::string values for commonly used
properties. This helps to avoid typos in string values
but also avoids a creation of std::strings from character
values. All accessors (has/get/clear and getPropIfPresent) now pass
the key by reference.
Additionally, getPropIfPresent removes the double lookup
of hasProp/getProp which can be a significant speedup
in the smiles and smarts parsers (10-20%)
2015-01-15 12:23:29 -05:00
Greg Landrum
c6dd83a47c
Fixes #360
2014-10-25 12:13:01 +02:00
Greg Landrum
cd03d877fb
Fixes #337
2014-10-04 14:44:42 +02:00
Greg Landrum
2d8500b407
Fixes #314
2014-08-21 07:29:09 +02:00
Greg Landrum
6b26036f6a
Fixes #269
2014-05-23 08:26:26 +02:00
Greg Landrum
e4cfc340a4
support white and black lists for getMolFragsWithQuery
2014-03-25 08:18:30 -04:00
Greg Landrum
fe07610683
copy over conformers too. Part of #234
2014-03-18 06:06:24 +01:00
Greg Landrum
196c2278fb
Fixes #234
2014-03-17 08:33:07 +01:00
Greg Landrum
601c21f19d
Fixes #189
2014-03-13 05:23:56 +01:00
Greg Landrum
75be63fd6b
merge with trunk
2014-02-09 05:00:18 +01:00
Greg Landrum
0839cf41ad
Fixes #210
2014-02-03 05:25:27 +01:00
Greg Landrum
deed4a9acf
Merge branch 'Issue194_V3000MolWriter'
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Conflicts:
Code/GraphMol/Chirality.cpp
Code/GraphMol/FileParsers/test1.cpp
2014-01-22 07:07:27 +01:00
Greg Landrum
aab11535e8
Fixes #196
2014-01-16 02:07:03 -05:00
Greg Landrum
53a2937eb6
Fixes #194
2014-01-15 03:19:26 -05:00
Greg Landrum
c13a643e06
Fixes #191
2014-01-12 05:42:50 +01:00
Greg Landrum
0ce8f23c6e
further R group handling
2014-01-10 04:24:22 +01:00
Greg Landrum
f653e9e961
more isotope fixing
2014-01-08 06:51:48 +01:00
Greg Landrum
4b72d1b153
add (non-standard) handling of R groups to v3k mol parser
2014-01-08 05:22:15 +01:00
Greg Landrum
3f90cecd9c
Fixes #164
2013-12-31 08:27:09 +01:00
Greg Landrum
355556b7de
get atom lists working
2013-12-29 07:05:25 +01:00
Greg Landrum
0b8bd3079d
fix isotope handling in V3K
2013-12-28 07:37:52 +01:00
Greg Landrum
d280c90117
a few more tests and a fix to not print empty bond blocks
2013-12-26 07:40:16 +01:00
Greg Landrum
9e91538d64
get rgroups working
2013-12-25 08:18:44 +01:00
Greg Landrum
329841d9ba
add some tests; add radicals to output
2013-12-24 06:56:12 +01:00
Greg Landrum
ae14fa3bd9
add support for the ZCH and HYD elements in mol files
2013-12-07 17:40:04 +01:00
Greg Landrum
0f92877061
stop messing up aromaticity and hybridization;
...
all tests pass, but this is definitely not the most efficient thing.
2013-11-30 08:07:09 +01:00
Greg Landrum
3b0c72c4bf
initial pass at ZBO support.
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does not yet handle the HYD and ZCH lines
2013-11-30 06:58:03 +01:00
Greg Landrum
f6517b572e
Fixes #166
2013-11-25 05:36:45 +01:00
Greg Landrum
1501af51a5
PDB reader/writer fixes;
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add MolToMolFile() to python API
2013-10-25 05:02:09 +02:00
Greg Landrum
e0e741bd49
very minimal testing of pdb reading/writing
2013-10-11 16:58:20 +02:00
