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github.com/openbabel/openbabel

Open Babel is a chemical toolbox designed to speak the many languages of chemical data.
https://github.com/openbabel/openbabel

Merge branch 'master' of https://github.com/dspoel/openbabel

bc5985fe9d12a7dcd6b198fb2c879ea469426ec8 authored over 9 years ago
added C indicator in header file

7b24906579ded4d2bbc23a1ab56f83d946587147 authored over 9 years ago
Merge pull request #201 from dkoes/addH_multiconformer_fix

do not blow away multiple conformers when adding hydrogens

3dda99492fb2a3a02cc374bb49684c2094d71348 authored over 9 years ago
Ensure we don't double-free _c array.

929b095db4f8a8205fcc3cc56739f8bad4e48582 authored over 9 years ago
restore correct fix, just set conformer instead of begin/endmodify

c952658896cf4b886e9ab0bab640c1d7735f00ac authored over 9 years ago
single space added to comment

f6f0ca5122581202155b4687c772fdd4331b13a7 authored over 9 years ago
trying to fix autovalidator failure

377b9b6229cd9cd116371a70e032c4f70065f15e authored over 9 years ago
added C indicator in header file

8fde66fc6d448d4ccc3308eb187fe4c8988bb194 authored over 9 years ago
Merge branch 'master' of https://github.com/dspoel/openbabel

bd4374d781e21aca5d721d81fdded446e8e68b3f authored over 9 years ago
splitted new functions out in separate C++ file data_utilities.cpp

b7fd6b28bee9c2292327473c856cbf661078a9f0 authored over 9 years ago
splitted new functions out in separate C++ file data_utilities.cpp

8b587b1d881863cf2155c7e2c9041af80ecb4e99 authored over 9 years ago
removed std:: and reordered order of includes

a2d890db9ebc1d56d788d2d6b6afbc22c7618c57 authored over 9 years ago
separated variable to make compiler happy

4b4d8fdc85ccc62c6a6c0cd7262ec7a1d091c2da authored over 9 years ago
Merge branch 'master' of github.com:dkoes/openbabel

3f2bf42b971f29b473ab416fe2c56dd971fe01f9 authored over 9 years ago
fix mc hydrogens

7bfeb0969ae01ec620f531477e811dc6e112ddde authored over 9 years ago
Merge branch 'addH_multiconformer_fix'

e0399414eac0a32cdb36d7cb7f539c6078a300cb authored over 9 years ago
Merge branch 'obconv-rewrite'

3777f7717786c8ce23fa35ab38e274e6f10906d9 authored over 9 years ago
fix debug compile

abe2f03e2852329435be1c0f5aa83911eb6ad236 authored over 9 years ago
made functions extern

1a87a81a7f15e0b98b086f55c77605a4082675a4 authored over 9 years ago
moved functions outside openbabel namespace

79de2d3591ad53ff3281ebbd9ebea0ee462d81df authored over 9 years ago
added include file and removed unused vars

871f7edd794c69717c836bc34a4f301ca19265bb authored over 9 years ago
add missing files

35383e9528e5ae2f72e659df292d9b3eefec3451 authored over 9 years ago
New obthermo tool with correspoding data

09b6ba806bfc6e02476786a85034eea316d5072e authored over 9 years ago
Merge pull request #199 from BALL-Contrib/obconv_patch

Added further checks for zlib availability in OBConversion

ece8406842f48bce62a12281c70fb5d4f347089a authored over 9 years ago
If the atom type is Du or Xx, check the atom id for an element name, e.g. D2

Also check for possible isotopes (e.g., using D or T instead of H).

e10387cf43a46beaefccd2caef422c337d0787d3 authored over 9 years ago
Added further checks for zlib availability

More checks were necessary to make all occurrences
of zlib-dependent code build conditional.

267608224a87d38df6366c4a772053f3cbef49a7 authored over 9 years ago
Fix minor whitespae issue

ac2a135eb8560d5d8246eee2abdb5d266ad9ab17 authored over 9 years ago
Merge branch 'master' of github.com:openbabel/openbabel

ecaf777e1cdd7fa1bb2a22cf956e69fc1a21d460 authored over 9 years ago
Make sure aromatic 6-membered ring analysis doesn't trigger for fused rings.

Caused problems with substituted purine bases.

63ed4c16b1a438ff03d4f5cbd69c43c95cc2cb79 authored over 9 years ago
Merge pull request #197 from kartlee/master

Fixed the (HM: 63 m c) to (HM: P 63 m c) in space group data file.

d876faf55128d04c23da614cec546c0666b50f2c authored over 9 years ago
Fixed the (HM: 63 m c) to (HM: P 63 m c) in space group data file.

19552d7308720915d12b00fe0c4efdebe312a3a0 authored over 9 years ago
Merge pull request #191 from dkoes/obconv-rewrite

OBConversion improvements

f6133205062d09179581e587ffa930ce98b19ebb authored over 9 years ago
Merge branch 'master' of github.com:dkoes/openbabel

078223a1854394c333506d04b1895deb6b94f0fc authored over 9 years ago
do the right thing when the output file ends in .gz

the is new behavior taking advantage of the improved gzip support

8342a8146afa197458d1e93f7828369159c2acf6 authored over 9 years ago
put auto-gzip check for ReadFile in correct place

9065c661c798e5def031aec2cbe5fd9b5199a944 authored over 9 years ago
Merge branch 'obconv-rewrite'

734db12fb3d0dade8e8700989d51841b220d029f authored over 9 years ago
improve backwards compat support for auto-detecting gzip instreams

b82d8f49d934ae6c3e4808683a11b8dff667ea8f authored over 9 years ago
Merge branch 'obconv-rewrite'

1d808ac230803e1746edde02e3755015e0bcc255 authored over 9 years ago
Fix compiler warnings in obconversion

f643c92945182cfa60e9a69ae49f0ad86671f6e1 authored over 9 years ago
wow, serious errors that the compiler didn't catch

60c1e3b383bb915555b29dcd2a61cfb154b093e0 authored over 9 years ago
Merge branch 'master' of github.com:dkoes/openbabel

53faa3ac037a6ac5bf7a054608ec922ff15b043f authored over 9 years ago
Merge branch 'master' of github.com:dkoes/openbabel

Conflicts:
src/obconversion.cpp

d1db70cd8fe18c9fb3d632194188dd7c98a9c1f3 authored over 9 years ago
Merge branch 'obconv-rewrite'

Conflicts:
src/obconversion.cpp

6a5b57038a2d87382f355242ddcaa1228ea0435d authored over 9 years ago
Merge branch 'obconv-rewrite'

25d96906a64c2155816c93bd4efd447573ed765a authored over 9 years ago
forgot to remove boost includes

6ee3ef66c88c5257aa25b74e1a6ed5479ca9568a authored over 9 years ago
Merge branch 'obconv-rewrite'

89ec5fd439e8d1e7b5f797c96dce7965ea81466e authored over 9 years ago
modified 1ubq

86867f8e7147dfa32c6731ac34cf4d1e9eef2d8e authored over 9 years ago
Merge branch 'obconv-rewrite'

156c3a1ed18b100e6e284120d0bdb8d1f2417eb6 authored over 9 years ago
fix for multifile zip support

4b16912df8e591f5deadd76b3af75bfd11453547 authored over 9 years ago
Merge branch 'obconv-rewrite'

e8fcdf3af7767e4103652e003291eb327d8d7d47 authored over 9 years ago
Merge branch 'obconv-rewrite'

a1f304327bcf47cc8594a8f8e49210a40f4c4bc2 authored over 9 years ago
add test cases

d34579511061a09ac7ea873294fa85c3eaff875e authored over 9 years ago
fix xml reading at end

698c1ba30c041a0a45b43d3c4216261d789ebb14 authored over 9 years ago
testing gzip support

67616b937dfefe82de1d60bb4c3e33093afa9a7e authored over 9 years ago
another fix

clear status on original stream before seeking

fe28546be44205b375f905bee5087d3f07b90933 authored over 9 years ago
fix xml problem

need to set auxconv in assignment, this is _not_ a good design pattern

ccec4db7d5be1ef4920f72e8e4d908d7c0ffa1a3 authored over 9 years ago
fix bug with xmlconversion

implement assignment operator so ownership of allocated streams remains with one obconversion

5c9cadb858c40e4f637639ae5244b5f197508690 authored over 9 years ago
switch lineend stream to work on stream, not streambuf

this way we are not retaining a pointer to the underlying streambuf, just the user provided stream

f93ea8817a4ae34e15c9e3de8b6801812a5e408d authored over 9 years ago
"fix" eof/bad iostream behavior

2c90acb23082426105d93665ac9522585bc4a50f authored over 9 years ago
bug fixes

bd7719c5a123a6ac6d934572f3086e5b7835512e authored over 9 years ago
slight reworking of gzip state, babel fix

04bbfab75a5e0e6fc6e2cb50183f7955c570b111 authored over 9 years ago
this is intensely frustrating

b7793d06c8c7b3d49736a12ec3ae2f9626693e49 authored over 9 years ago
checkpoint work on obconversion fix

still broken

da0215dacf10d534947e5dcbfc41236ed9dceb3b authored over 9 years ago
brms

e864e619f3dba2572170e3c330b09fde9eff7a5d authored over 9 years ago
Merge branch 'master' of github.com:dkoes/openbabel

8f62b25d39c32b91958367ac1d4335fd04a74562 authored over 9 years ago
Merge branch 'master' of git://github.com/openbabel/openbabel

7df763046aa71e9335c9c7fa8f804244d217db7b authored over 9 years ago
Merge pull request #189 from orex/mmcif

mmcifformat plugin now support atoms occupancy and atom_type category

40bc0f105c3d3dc7f189cd6d54ddfef6f5452dbf authored over 9 years ago
mmcifformat plugin now support atoms occupancy and atom_type category (oxidation implemented).

140439d8a77fe0d50d058599e63f54ee5aec66aa authored over 9 years ago
obfitall

aef88f293ab9c57a1a08f772aa6fde531807d7b8 authored over 9 years ago
Merge pull request #188 from orex/VASPimpr

New option in VASP format. Custom atom sorting.

6557fdf79a2ad0fd510aea7ce3665c2873390e6d authored over 9 years ago
Merge pull request #187 from jeffjanes/precision

Don't set precision to 0 when reporting time estimate

f340bd57b3d983a803f023d6d4e21857d124b48a authored over 9 years ago
New option in VASP format. Custom atom sorting.

8ee8ac9c2ca14a02c1073f7188f5eeba0be8e3ca authored over 9 years ago
Merge pull request #185 from patrickfuller/eqeq-fix

Fix for #173

3462e3692c760241f3281a4a4d8030924a6fa528 authored over 9 years ago
Merge pull request #186 from baoilleach/popcnt

Add support for hardware popcount

4f2fb78494b101c0a72c6e7df996892c3dffe6af authored over 9 years ago
Don't set precision to 0 when reporting time estimate

Changing the stream precision to 0 seems like a bad idea.

I'd rather see a reported time of 90....

80cb185c3c14cd955fc6a9ff8e6c5aae3d4cd1b9 authored over 9 years ago
Add Susi Lehtola's patch (SF BUG 945) to use modulo 360 testing for angles, e.g. so that -179.8 is close to +180. This fixes the rotor test failure.

eeee1d1996c2a605d3f3cc5759474c14af1d39ae authored over 9 years ago
Move the setting of CXX flags to before the various include statements...otherwise it has no effect

23c20908cbb0e8d6fd0008f46b0d2077d2216a88 authored over 9 years ago
As suggested by jeffjanes, I'm enabling the hardware support for pop count on systems that support it. It can be turned off if need be.

75a03bb31c63bd34c6bdbb8312bcfafbb50fef24 authored over 9 years ago
Fix to param file parsing check

4a711e3e215acb4811cdcbf720c9552751fc7dcd authored over 9 years ago
Merge pull request #181 from baoilleach/ImproveDeleteHydrogens

Fix for DeleteHydrogens behaviour #178

f3b13e77ca16ab727c12b6b53dc281f75faa2ad6 authored over 9 years ago
Only suppress hydrogens if the atom has a charge of 0 and is not assigned an atom class.

f95e44e9f6ba36c5f6f45eb55dad5284fedddf91 authored over 9 years ago
Merge pull request #183 from jeffjanes/tanimoto_test

Add regression test for fast tanimoto search

9a9b6a11805beabc26905f0cb7e90c9e9efc0bbd authored over 9 years ago
Add regression test for fast tanimoto search

I break -at option in a local build, and make test failed to detect
the breakage. Add a regress...

bffb772094db413f600a8193757094e5bcb904d6 authored over 9 years ago
Merge pull request #182 from jeffjanes/stopwatch

Fix OBStopwatch to return fractional seconds

dbd00588cc57a8a2e4d3ceb4941713ee0adeb27a authored over 9 years ago
Fix the OBStopwatch

OBStopwatch was using integer division to arrive at a double,
and so would report only integer s...

28eea160b2761d0faec3a9b34462faae9ee87a22 authored over 9 years ago
Disable RegisterOptionParam for PointCloud and STL format.

Prevents bogus warnings about re-defined command-line options.
Fixes Issue #170.

97e3eac10bfecf36f7292044348b2cefc89b43b8 authored over 9 years ago
DeleteHydrogens() and its variants should not remove anything but non-isotopically labelled hydrogens attached to a single heavy atom nbr.

b375e8f49a58ec84d987152cbaf37e03ded15694 authored almost 10 years ago
Merge pull request #180 from baoilleach/RemoveMSVCDeps

Remove msvc deps

339f8c30d9aa10be9948dc61dc51885aac0bf6c6 authored almost 10 years ago
Remove additional MSVC specific files in windows-msvc

8e5bf94ef9348e5d83f9a04bd26fa7424392f0c1 authored almost 10 years ago
memlieak comment

ddd7455186c71537968a3d7dfafe57be54afb8bb authored almost 10 years ago
Merge branch 'master' of github.com:dkoes/openbabel

a22f8ed3a5a486eb2f3f29a6e22b619bf97b4b35 authored almost 10 years ago
Merge pull request #171 from baoilleach/Fix134

Fix for #134

6929bf5941bb02e76c72d92854a341e5aaa1a7c6 authored almost 10 years ago
Specify the XDR include location explicitly

08d840e4e89b9c6250945b3cfd9902694afa0903 authored almost 10 years ago
Merge pull request #175 from baoilleach/MSVCBuildCharges_b

Edit ifdef MSVC to be MSVC version specific

2cc2e2babcdbf35cb0a2772611ca2704cd0dd96b authored almost 10 years ago
Check that _MSC_VER is defined before checking its value

3f0ea1eb3c5bce43a6bb68423ffe1dd76485d3b4 authored almost 10 years ago
Edit ifdef MSVC to be MSVC version specific

cc37035d1420c9889868fbfdf5e7ac5fa34a9be0 authored almost 10 years ago
Remove windows-vc2008 folder

04887cbbe852b654e7a89be7d1c46f3b2487e4f9 authored almost 10 years ago
Merge pull request #174 from baoilleach/FixMSVCConformerOp

Fix for compile error with MSVC 2013.

f7b6857638f551d2dc591e13e3e05b952927c7e7 authored almost 10 years ago
Fix for compile error with MSVC 2013.

0262f465e97fe578dcfd71b3189ca4603b57b651 authored almost 10 years ago
Fix for #134

94a7595a730f00fffd90e19a76a5f763a986b2c2 authored almost 10 years ago