github.com/openbabel/openbabel commits | Ecosyste.ms: OpenCollective

[WIP] Fix MSVS 2015

d9dc1356d0c99846f1d501336dcf8d3b36f798e9 authored over 8 years ago

Fix comment symbol in swig interfaces

a170a4e5ad07d4d78b183c0e8564a4e20faf8156 authored over 8 years ago

Merge pull request #312 from baoilleach/deprecateBabel

Add deprecation warning for babel

479dab26cc7a5086c600a6b77cf820320a00b13b authored over 8 years ago

Get CSharp build back into shape.

73b73f6fb87fd961cd3f309749b7eedf7065df24 authored over 8 years ago

Remove OBBond::IsAmidine and IsImide from public API

98d21675b5e2797c6c6682052da6b360cac1a2e0 authored over 8 years ago

Minor correction

195703fdd89af27fbf29dc180c9812ac985d80d0 authored over 8 years ago

Remove IsThiocarboxylSulfur from the public API, and put as helper function in mol2

b540b8e31679d0848606acd4bd92037e583be5f2 authored over 8 years ago

Remove OBAtom::IsSulfoneOxygen from the public API

c7e19d93dc58870764a0996bf11b1b0dc70488d6 authored over 8 years ago

Correct the URL

04e6abe5f8b1367151b723e77e18506b2372dacf authored over 8 years ago

Merge pull request #309 from baoilleach/updatedocs_merged

Doc string updates mainly for a variety of new formats

03fa0761dbd3b10a6d31036753faf8dddeda7ac5 authored over 8 years ago

Add deprecation warning to top of help text and to usage information

6c7d1d450274fa51b5a014de24692252c9526ec5 authored over 8 years ago

Merge pull request #311 from orex/master

VASP Write. Split the original "w" option into "w" and "z" options.

775734037ad0aa9b960feff84ade058aa1127a9d authored over 8 years ago

VASP Write. "w" and "z" options.

https://github.com/openbabel/openbabel/pull/188

2a2a97fa74f7f40453f4b3ae25ce396e3fc642e8 authored over 8 years ago

Doc string updates for a variety of new formats, plus a few for older formats to fix formatting.

11b98e375e9952b19c6af77ec9969f85a2752f09 authored over 8 years ago

Merge pull request #308 from baoilleach/Fix305

Fix #305 - logic error for non-ring bonds introduced into NumRotors() during distgeom updates

4336ad1650200bf6675205fb27e5a10b2e0418a7 authored over 8 years ago

Add the missing test file

f07ee189d879310a19a987c9912e7a5ea305b062 authored over 8 years ago

Minor fix to test

62c9e436b2bf1a4c7f97e7cdfe408d65526ec4f8 authored over 8 years ago

Fix logic error in recent changes to NumRotor() that caused a regression #305

dd8de8c502a433e2cea47098a11e379c4e5e2ac7 authored over 8 years ago

Merge pull request #307 from ghutchis/print-partial-charges

Add a --print option to the partial charge methods

7bac8592ae71487f2899290c16f09bfbd4a9fe85 authored over 8 years ago

Add a --print option to the partial charge methods

Prints atomic partial charges on standard output after calculating them

6de703b6a57bb8edff7a5a31cfb33cc84a6bb4b2 authored over 8 years ago

Add element abbreviations and names for 113, 115, 117, 118

From http://iupac.org/elements.html

bb634e9388ebc5642a5c7fa7e5dbd947c2c418c4 authored over 8 years ago

Don't add an "uninstall" target if Open Babel is embedded (e.g., Avogadro)

d0d8d533f756e3dfbc9c9bf39fd3bdf779cbc808 authored over 8 years ago

Merge pull request #304 from psavery/master

Changes for MSVC2010 compilation.

95145b799214cb3060d71bf5098aeb48e03a02d0 authored over 8 years ago

Merge pull request #306 from lenkd/devOpenbabel

read additional geometry optimization data

a35cd1016294196ae4ed0f4f8616e50ecb0beb08 authored over 8 years ago

read additional geometry optimization data

f90b89c8fdb60304ba010a8b0e4940698d9e3598 authored over 8 years ago

Changes for MSVC2010 compilation.

cf1bd467d918eab8cded4ebca2c502d57b0e8fff authored over 8 years ago

Merge pull request #303 from aandi/patch-uff

UFF forcefield: fix missing SetupPointers()

821e5207e9ed6cc5e8560ceb929bd42722b4facf authored almost 9 years ago

UFF forcefield: fix missing SetupPointers()

ed174006e88c1cd4ca725bf421eb6447ff2bf8aa authored almost 9 years ago

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

a74f02c4bf8613f414dd3987cd56c031d7e07b5a authored almost 9 years ago

Add support for GEOMETRIES sections

7eac555b56f172b907c25ee76bb9150792d077eb authored almost 9 years ago

Merge pull request #299 from serval2412/master

cppcheck: fix some reports

bb0681ddfdef4d3f8456b0d461ecd28f9269567a authored almost 9 years ago

Merge pull request #297 from jeffjanes/taut_exit_status

Make obtautomer exit with status 0 on success

bbdaca6878b34cf895a0d199a66921ecc4586874 authored almost 9 years ago

Add a "make uninstall" target - fixes #300.

d34e692ac8de021aaa04405260ec7210587bbaf8 authored almost 9 years ago

Fix crash when reading NWChem vibrations #301.

NWChem reading still seems confused - format has likely changed.

36755a972bc5b7a42f95d643951443ac9b418841 authored almost 9 years ago

Merge pull request #302 from psavery/master

Fixed a problem with reading POSCARs.

0b6939067148fba68fdc02a3c0d39c31784bc25b authored almost 9 years ago

Fixed a problem with reading POSCARs.

According to the POSCAR file description at http://cms.mpi.univie.ac.at/vasp/vasp/POSCAR_file.ht...

f533e9f4275526fbca3ce508b48eb47e57785b2b authored almost 9 years ago

cppcheck: fix some reports

[src/data.cpp:108]: (error) Width 4 given in format string (no. 2) is larger than destination bu...

584b3f5ce75d80f718c92f4e2cf1f95aab0907a1 authored almost 9 years ago

Make sure to set default parameters for superheavy atoms

Solves Avogadro bug report #741 - crash with superheavy optimizations.

77e1e5ef5af31f2553c8f04df608249532a94685 authored almost 9 years ago

Merge remote branch 'upstream/master' into taut_exit_status

87aed52f483ba8dc552b8ebe001d970d74fc6401 authored almost 9 years ago

Make all tools exit with status 0 on success

Make all tools follow the convention of having an exit
status of 0 upon successful completion

ca99257a99929638925fd129a99727e520933618 authored almost 9 years ago

Merge pull request #296 from anishp/clang-warnings

fixed most of the clang warnings

7a47d759e88793821f14f79e67edd620cf04a790 authored almost 9 years ago

Make obtautomer exit with status 0 on success

Well-behaved programs are supposed to exit with status 0 upon
successful completion. Make obtaut...

1613b64f0353401844e714fef4098c63c6222344 authored almost 9 years ago

fixed most of the clang warnings

77bc3114d2367b5c0a9a9dd1523ba0533fed61e3 authored almost 9 years ago

generally better to edit .i swig file than generated .cpp

seed is defined in cx11 and polluted by perl

ee0918dad849c81af4a75ecf4ad4993c765a5d37 authored almost 9 years ago

generally better to edit .i swig file than generated .cpp

seed is defined in cx11 and polluted by perl

9e90af4dfdd27a90181fb585da1bb228f15ed793 authored almost 9 years ago

fix problem with swig bindings

I wasn't building with RUN_SWIG on, now have proper includes to resovle
types in mol.h

090b6227fdfec3056c2e71fc1e58427ff707f3c6 authored almost 9 years ago

fix problem with swig bindings

I wasn't building with RUN_SWIG on, now have proper includes to resovle
types in mol.h

dab2c81548cf59255756a50a123d0bff587eda5b authored almost 9 years ago

thread_local storge for global variables with state so things don't

crash on multithreaded programs

2f8847b6a4370a76b995f015f08bccfb0cf7cd58 authored almost 9 years ago

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

7ba32c5d6cfe80ef3581a7b3e3eb15396310a8b0 authored almost 9 years ago

thread_local storge for global variables with state so things don't

crash on multithreaded programs

8120d5c014e4c6b68734ed2244fbddde6152009b authored almost 9 years ago

Protect iterator from decrementing past .begin()

Causes issues with Clang, as discussed in #203.

d56a5d6012b1436578cb1472b5cb41ba3dffd0a5 authored almost 9 years ago

Remove debugging statements.

effc2cb792ba89506009001bd1ad157eebadf329 authored almost 9 years ago

Fix Gaussian FChk orbital energies for closed-shell files.

These files only have alpha orbital energies.

13fc168395656554bac47c8a42eb7bc2347f7389 authored almost 9 years ago

Fix crash with new fchk support for orbital energies.

fe37a6f3b5578f97a1481afd4d1b6811cb766136 authored almost 9 years ago

Merge pull request #291 from ghutchis/ENH_add_orbital_energies_fchk

Add alpha and beta orbital energies to Gaussian fchk parsing.

a7c6ab2efaeaf2ace6d61547b2b6f5e25aebec57 authored almost 9 years ago

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

5e6c4f00c5f818df59cb788f8d30bfa9e2814e9e authored almost 9 years ago

Add dative NO2 fragment

f96de61a04ef4d0565b232135dd01272e880d153 authored almost 9 years ago

Merge pull request #287 from arkose/patch-1

CMakeLists.txt fix for wrongly hard-coded path

bdcf6a0ec29226e5a100f0b20a0987f6fcf6d89d authored almost 9 years ago

Merge pull request #289 from dspoel/master

Added support for As, Ge and Se in obthermo.

641694d3b4bcc13c4ec7c1335dca7c95f484f17c authored almost 9 years ago

Merge pull request #290 from cstein/dalton-format-update

Overhaul of the DALTON format

a46b23305ee033d276d6aedef86a93509b7fccf9 authored almost 9 years ago

Add alpha and beta orbital energies to fchk parsing.

17feba9a2771eb1813d3a596a7e250aa58f140bb authored almost 9 years ago

Overhaul of the DALTON format

* Adds basic support for ATOMBASIS format
in both reading and writing

* make the plugin...

348351e5722c636d13349604dc14a7627f90b27b authored almost 9 years ago

Added support for As, Ge and Se in obthermo.

In addition updated the reference for the other values.

0aaba2477c20543caf695d7d76890b8602311e5d authored almost 9 years ago

CMakeLists.txt fix for wrongly hard-coded path

The main improvement is getting rid of the hard-coded path by using the already-existing variabl...

0691a09af6273db624d02b1ee42fbc9c77b97bb1 authored almost 9 years ago

Move ORCA format to conditional compile on regex.h. Fixes #282

7d621d9c9f2f07a1f105896a765bf2afa22e6028 authored almost 9 years ago

Merge pull request #285 from ghutchis/FIX_static_ecfp_fingerprints

Fix static ecfp fingerprints

a93281eb0ca84ce547d28aed0aaae622a0631cb1 authored almost 9 years ago

Use conditional instead of "test"

7e083b38331e51e12c0667c7526cb6ee96f26b6d authored almost 9 years ago

Fix invalid .travis.yml

0765ab752140b7bf420e922a77cc362b23ae21b4 authored almost 9 years ago

Use Travis build matrix - no Clang static builds.

24526e2f6d89a3c9e0fd3acfda4ab14f96e567ce authored almost 9 years ago

Only run ctest for dynamic builds.

eb05690b3179a8618c4ade77980cfac6ba17f077 authored almost 9 years ago

Define the ECFP fingerprints

52ca5462eded9612ef5e3be1ec023ca0e8df1fcc authored almost 9 years ago

Merge branch 'master' of github.com:openbabel/openbabel into FIX_static_ecfp_fingerprints

076e84388eee19a1e970584c53df9ae43d15267d authored almost 9 years ago

Merge pull request #284 from ghutchis/ENH_travis_static_build

Add a static build with both GCC and Clang to Travis CI.

953d22dce7ca0b5565d67b38580f28de64da2c00 authored almost 9 years ago

Merge branch 'master' of github.com:openbabel/openbabel into FIX_static_ecfp_fingerprints

0a572e40f5152bcb5917da44eaa7971bd1cefbb5 authored almost 9 years ago

Add ECFP0 and static build versions for the ECFP fingerprints.

e1dddf48a47bf4187928dbc98fc4676fffd85c98 authored almost 9 years ago

Merge pull request #283 from torcolvin/static

Allow compilation as static binaries

aaa36b6a52bfc75ef519e6e00954086f7445c20d authored almost 9 years ago

Add a static build with both GCC and Clang to Travis CI.

118e94a301f6c262642d11f60735c776aa7c0134 authored almost 9 years ago

Merge pull request #281 from openbabel/ENH_ecfp_fingerprints

Initial implementation of ECFP fingerprints.

773da85e12f69168fb65337e4a56edd8004438f1 authored almost 9 years ago

Allow compilation as static binaries

183879562e44e02f71ba4523f1aa327999d769b5 authored almost 9 years ago

Merge pull request #280 from cryos/optimize-native-default

Default OPTIMIZE_NATIVE to OFF, fixes #279

9fdccbaf4789e829fef303315af8fea2b7f708f7 authored almost 9 years ago

Match radii and diameters properly (i.e., ECFP2 => radius = 1)

943e3ab119bb5056fb3113c8c63d9bf151e93673 authored almost 9 years ago

Initial implementation of ECFP fingerprints.

Donated by Noel O'Boyle and Roger Sayle of NextMove.

1a469807501697d33edad7270522cb5ae3541a65 authored almost 9 years ago

Default OPTIMIZE_NATIVE to OFF, fixes #279

Default the OPTIMIZE_NATIVE option to OFF, and update the documentation
to more accurately refle...

e35ade6e69db6a99bc817f555fa66ddb8c456e0d authored almost 9 years ago

Merge pull request #277 from ktns/sharedptr_config

Select which shared pointer implementation to be used at configure time

76420f4d4c6bf786a5a0671f7c9b169718257121 authored almost 9 years ago

Merge pull request #278 from mmghahremanpour/master

Improved GAFF atom types

204f9dcabceeaf29bc9e4edc9a74b9a339529ec8 authored almost 9 years ago

Merge pull request #275 from ntropia2/master

Modified phmodel.txt to fix azide transformation

43a7618fa2eb35453d806722b9d6fd22549f4e22 authored almost 9 years ago

Merge pull request #1 from openbabel/master

GAFF atom types

06cbe24051897e579aca7d0f7f95ecabf91735cc authored almost 9 years ago

gaff.prm and bondtyp.txt are updated in order to reproduce the atom types based on the Wang et al. Vol. 25, No. 9 . Journal of computational Chemistry. 2004

4182dcb8f0be77129c07c71c0f494c4b54be10f4 authored almost 9 years ago

Use babelconfig.h to choose shared pointer

Uses template alias if available, or #define directive otherwise.

Closes #268.

92477289b5fbcab7f7a1ff5f36889434426de9d7 authored almost 9 years ago

Check which implementation of shared_ptr is available

1bbd2102b5109f8dd23172c34753feb858136d7d authored almost 9 years ago

Merge pull request #276 from psavery/master

Added an extra line to the end of space-groups.txt which allows the p…

5e7120a5435f2b1ad29b35077837acfdfda1ed34 authored almost 9 years ago

Added an extra line to the end of space-groups.txt which allows the parser to find the last spacegroup. Also added a little more needed flexibility when identifying a spacegroup via a string in spacegroup.cpp

fdbfd042b6d4b2f44842565627d11bd8dc2da482 authored almost 9 years ago

Modified to recognize both azide ion and group

Added pattern to catch inorganic azide ([N-]=[N+]=[N-]).
Added patterns to recognize several (...

d768dd5b94202a2662add168d8c71ef8b7014a5a authored almost 9 years ago

Further modified azide models, preventing detaching

The transformation:

[ND2:1]=[ND2:2]=N-A >> [N-1]=[N+:2]=N-A

has been removed to preven...

161ea9cb4d3c7f5b9485594a304b81e3e98a3c36 authored almost 9 years ago

Updated azide entry to fix fragmentation

The old azide entry misses a nitrogen, and with the second pattern it results in a fragmentatio...

a18dc6dde40f981a7eb5ad6a5907390e9aca4195 authored almost 9 years ago

Merge pull request #273 from cryos/unix-dynamic-loading

The findFiles member should return 0 for error

250f272c10ef165915598bc89b3632e8e08e46cf authored almost 9 years ago

The findFiles member should return 0 for error

The Windows equivalent returns 0 for error/no files, this variant should
do the same. This membe...

5572aa4d60e7d3a57b742249fa696cb571195049 authored almost 9 years ago

Merge pull request #271 from openbabel/FIX_dg_build_error

Only use distance geometry method if EIGEN is available. Fixes #270.

a09028185ee433b0c2af0ecb947aeaac4cb1c06c authored almost 9 years ago

Only use distance geometry method if EIGEN is available. Fixes #270.

b91b11c073b00bd3e355ea8d3288b5a3d5f4cd2b authored almost 9 years ago

Merge pull request #253 from ghutchis/dist-geom-fixes

Improve distance geometry coordinate generation methods.

200ebd0320579adc4d4cbea2c856c2fde6d18b55 authored almost 9 years ago