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

Adding more info to obrms manpage, obtained by executing obrms without command line parameters.

66ac7b732fafdb4a27f089a814c010dea2863643 authored over 7 years ago

Adding manpage for obrms.

0bb457de5bf4f946aec6e91d46f2752dd6fba528 authored over 7 years ago

Adding manpage for obdistgen.

ac4fb70fe49f7fffc751ed324ad92dbae22b941d authored over 7 years ago

Add support for %(NNN) notation for SMILES ring closures and tighten up handling of other notations

f3418254c3e602be54db34aeee9939717f34735e authored over 7 years ago

Merge pull request #1675 from openbabel/baoilleach-patch-2

Fix MSVC warning about unused variable

fe9885896f9755149f8455411287d3a8d869a06a authored over 7 years ago

Merge pull request #1674 from openbabel/baoilleach-patch-1

Fix bug found due to MSVC warning

2e28d849670e5c59d27a8b943c79cededfbd04e5 authored over 7 years ago

Fix MSVC warning about unused variable

1b53e8628284e6790731a2170efd897f86b5d470 authored over 7 years ago

Fix bug found due to MSVC warning

There was a semicolon at the end of the 'if' statement

35a664a7ba7a4f2402e858c5f95c9ef9fbadf816 authored over 7 years ago

use isinstance to test if filename is bytes

Address #1615 by testing if filename is an instance of bytes and use a
bytes suffix in that case...

3194850fc3347981f73228db5412277846dc9978 authored over 7 years ago

Merge pull request #1666 from xomachine/master

Minor fixes in the nwchem format reader

83e8716731eb10c869d96d68dc457817b09fead7 authored over 7 years ago

Merge pull request #1670 from ghutchis/wrap-getrgb-python

Add support for wrapping GetRGB() call to return r, g, b params.

758239e261c35e410f895d3edc1387bb05fda29f authored over 7 years ago

Fixed ZTS beads reading for nwchem 6.6+

31f4f701833e4e3ed4943e54cec670258df4f6bc authored over 7 years ago

ZTS calculation result should be read in both of converged and non-converged calculation cases

eede5782d59533fee4e135f93cd593d4efc3b28b authored over 7 years ago

Add pubchem JSON format test

286b3b47dfb3c9675f3375400ad1dc2dc17097cb authored over 7 years ago

Fix istream handling for multiple mols and files

71021bf2976ff6bcb88b5c8ddf39666062e8f943 authored over 7 years ago

Create CODE_OF_CONDUCT.md

Add a code of conduct - generally hasn't been a problem, but better to be up-front.

26a3ff89978fdb59528dbd5e154246f23b55dffe authored over 7 years ago

Add support for wrapping GetRGB() call to return r, g, b params.

24ce2dbf4607f70a19fc1e1df629040cc1ef3f74 authored over 7 years ago

Merge pull request #1663 from sencer/master

Fix reading atom symbols from XSF file

c70ca0d61b63f4cd3ec578ea15571ec3e25f3e1c authored over 7 years ago

Update docstring, and add tests for rxn->rinchi

4452f3051f93d321f818f34ccc7cec83846cd797 authored over 7 years ago

Add back ability to read old string format

348cb2ffff37f7b2784d5dc01f8ab12f7bfa93f9 authored over 7 years ago

added comment in the file

976936a741b42497eeaa4433a07431b83016cfe6 authored over 7 years ago

Fix pubchem JSON reading/writing stereo as ints

f9021509b570b60c6dacc20f73357c7c2117e44f authored over 7 years ago

Fix pubchem JSON reading/writing radicals as ints

9fab78e1371bced5783eb5d04cabc9b047404fc5 authored over 7 years ago

Fix pubchem JSON reading/writing bond styles as ints

c4c1c14ad39688200767bfa9211955766d884b12 authored over 7 years ago

Fix pubchem JSON reading/writing bond orders as ints

378b3457216dca14dd20f6634da184b8ac3f919b authored over 7 years ago

Fix pubchem JSON reading/writing elements as ints

aadc5900f49d091f5d5f0eb9a4532b9274fa3a57 authored over 7 years ago

Support equilibrium/reversible rxns and reactions that are empty about from non-molecules. Also start on the Description.

6e6efde6965305aea47a1e51487c0ef4e595d83f authored over 7 years ago

Add support for 'no-structure'

5dba085ef887719290a207e9109cb9f4f7b05242 authored over 7 years ago

Ensure support for partial reactions, the empty rxn and where reactant and product are equal

31bf9e6ba881ce121b76745b963fe2bcb672520a authored over 7 years ago

Initial support for RInChI

03c0b779d38106e047df33c1bcd43ad934395ee0 authored over 7 years ago

Bump for 2.5-beta (2.4.90) version numbering.

19b8b26aaa100ca24e7fb5cd57cd5a852f8ea460 authored over 7 years ago

Fix reading atom symbols from XSF file

This is from the [official definition of XSF format](http://www.xcrysden.org/doc/XSF.html#__toc_...

1ce7159e1d7b5e6a3c7fcd18748d9d19b3b28d65 authored over 7 years ago

Merge pull request #1661 from baoilleach/reapply_rxn_agents

Add support for agents to RXN file format (Take 2)

c6643feb3d0d71ca94f28fc5abf878e725b422c6 authored over 7 years ago

Activate additional test cases based on partial reactions, and get them to pass.

3576e7b36b1d31ddcba10a341c7c6c99b8625f95 authored over 7 years ago

Update to handle multiple agents in reactions

9e66f6939d9b3f5862507fd45f7e8f95c0a9112e authored over 7 years ago

Revert "Revert "When reading RXN, add support for an optional agent""

This reverts commit 00618bfc5128a151ef1ce93cf5dd800cdd17f919.

8a3cf87ef3d6e98fa06bc57c7a2322a41d66e570 authored over 7 years ago

Revert "Revert "Add write support for agents in RXN format, and add tests for roundtrip.""

This reverts commit 02d1740622abbc3375aace82b7955336e69402e0.

306295c3bdf7c9b20fad1e343118c2d7a33198c5 authored over 7 years ago

Merge pull request #1660 from baoilleach/newrsmicomps

Allow RSMI format to read partial reactions (Take 2)

fd90dac0652238b95a27de9fb4d8448bc10ba549 authored over 7 years ago

Remove the rxn roundtrip test code which I have somehow added by accident

8e2c03e42625b2a1625dc895ed132a575b1c2771 authored over 7 years ago

Allow RSMI format to read partial reactions, i.e. without any reactants or product

45b26e5622b39d8fcc9fd4cfb4160936e5bed03e authored over 7 years ago

Revert "Add write support for agents in RXN format, and add tests for roundtrip."

This reverts commit 0a50a34e709a5247ff5381ff171415ab15bf082a.

02d1740622abbc3375aace82b7955336e69402e0 authored over 7 years ago

Revert "When reading RXN, add support for an optional agent"

This reverts commit 1edbd9e04039b4cdf1ed23d66cfb701b0ef179f7.

00618bfc5128a151ef1ce93cf5dd800cdd17f919 authored over 7 years ago

Merge pull request #1656 from nextmovesoftware/rxn_agents

Add support for agents to RXN file format

e632e9acd4facac87152f08ea05e8325f31d4c4b authored over 7 years ago

Merge pull request #1640 from baoilleach/moreagents

Allow multiple agents in OBReaction

bc35f46bee258a497125dcb2a49cbeace9f7852c authored over 7 years ago

Fix "folding" for fingerprints to larger bit sizes - #1654.

If "folding" is requested for fingerprints from smaller to larger
bit sizes, simply extend the v...

4a8b8a9e64bffc40589a3484de5d64de06c01f76 authored over 7 years ago

Merge pull request #1653 from johnmay/patch/ecfp

ECFP Fixup

b55fb088ed52b52204f5ff21d78484aaf01e77c4 authored over 7 years ago

Merge pull request #1657 from theavey/master

Clarify python examples

2a01417ebbf93c7911ab9ca9eaad5e66b589cd45 authored over 7 years ago

clarified required use of OBMol object

While running the code as given originally would work, the re`import` of openbabel made it seem ...

5830d0c2f15009b18862a45517d76d8fc695c07a authored over 7 years ago

Minor tweak to comment

5f35b00deab744ebf9c1d62951c04a835fee59d1 authored over 7 years ago

Add write support for agents in RXN format, and add tests for roundtrip.

0a50a34e709a5247ff5381ff171415ab15bf082a authored over 7 years ago

When reading RXN, add support for an optional agent

1edbd9e04039b4cdf1ed23d66cfb701b0ef179f7 authored over 7 years ago

Update download link

5b94344f240c95d210adbb86ac24c050181ed388 authored over 7 years ago

Default length for ECFP fingerprint.

e3759922ed56c7fa9a4642097cc8c0f6e2bd1f55 authored over 7 years ago

The std::vector<int> passed in is meant to be used as bit set.

Although the raw fingerprint hashes are useful, they cannot be
provided back through this existin...

a5978e1fe095abc884d3b42bbf59e92e732a50e7 authored over 7 years ago

Merge pull request #1652 from baoilleach/fixinchistereeo

Correct handling of stereo when writing InChIs

406dce3decd643f4bebf443555acc01e209c3fdf authored over 7 years ago

Merge pull request #1638 from baoilleach/daylightarom

Implement the Daylight aromaticity model as described by John Mayfield

1991439efd920f27cd9755fe8abf5c18699d4a58 authored over 7 years ago

Merge pull request #1631 from cowsandmilk/pdbelementcase

Lowercase second element letter in PDB and test

a06e271b3a2b5173a2290cf99aabe6fa3ae4310f authored over 7 years ago

Merge pull request #1645 from wojdyr/patch-1

space-groups.txt: correct Hall symbol for C -4 2 b

1a5308cf20df9875fc600158900410f517188575 authored over 7 years ago

Merge pull request #1650 from baoilleach/kekulize_fix

Reset path to empty in kekulization code (potential segfault)

d9ef2be70686554c560f4b1b58bca8994c2a3324 authored over 7 years ago

Fix segfault in new kekulization code as the path-so-far was not being reset to empty

4d860e26d469828b3e3ab00ec5c1489c57982bf1 authored over 7 years ago

InChI stereo code assumes that AtomIds are simply AtomIdxs-1, but this may not be true. The fix is to properly convert from AtomIds to AtomIdxs.

fa82fff9678a46e51ddcd2a9a5887d4a2cb29eb4 authored over 7 years ago

More thoroughly test PDB element typing

Fixes: lowercase second element letter when ATOM record without element
columns
Fixes: CL1 inter...

7a007dd7f9e07077b50cfbb22fcf82f738ce3c4f authored over 7 years ago

space-groups.txt: correct Hall symbol for C -4 2 b

338c88ac753d2b464e0910520b01cb36f5c8615a authored over 7 years ago

Add arsenic aromatic atoms

d78062b160b9e4ed30a06cf38eba68c67ddd9f82 authored over 7 years ago

Remove final reference to original _agent

bb1e05e06f28a22415678d6735aaee085f1721bd authored over 7 years ago

Change OBReaction to support multiple agents instead of just one

d6e3b329153a0fd659e3fe6cb4ed1d50455c2521 authored over 7 years ago

Update the canonstable.can file as the aromaticity model has changed. The changes look legit.

ebd75c069b33e0a19520de88d5db2d543a900602 authored over 7 years ago

Remove test cases that are no longer aromatic

6dc9f644f192b8918adbc90e4e5213dbc30d99e3 authored over 7 years ago

Correct test cases in aromatics.smi that were failing kekulization and causing test failures as 'n' was used instead of [nH].

911cf5305e36cb913fde8efce85c34637fc4c29c authored over 7 years ago

Update Kekule test

85f83342282fa9e2cb079118144c4ec3e3cf1760 authored over 7 years ago

Implement the Daylight aromaticity model as described by John Mayfield

7bd42366b6d5b6c5cb9ea30ca5a80956b3d6a5af authored over 7 years ago

Merge pull request #1637 from oititov/master

Added fix for OBMolAtomBFSIter in Python3

4438fd40f0ebfd715c29a3225a210ce173d16449 authored over 7 years ago

Added fix for OBMolAtomBFSIter in Python3

6c9d2af092306456819dddb8a0fc8aa9f4e85db9 authored over 7 years ago

Merge pull request #1622 from psavery/add-missing-formats-static

Added some missing formats to the static build

6bfa4234df4e6744fec858b9e562d419848e6985 authored over 7 years ago

Merge pull request #1626 from baoilleach/radicals

Handle undervalent atoms and radicals in Mol files and Smiles

62c45ec1f50d201c23eb3b34c35264dfc2788ead authored over 7 years ago

Merge pull request #1634 from ghutchis/mopac-handle-charges

Make sure to handle molecular total charge by default for keywords

f59d8afc8151f82b7477d3287e7eda3b054d517f authored over 7 years ago

Make sure to handle molecular total charge by default for keywords

3bdb2c9365dc7db9502d04d092e7c0c7de398ab1 authored over 7 years ago

Remove extra OBBond::GetPeriodicDirection method

Avoid cluttering the Open Babel API, now that earlier research code
has been refactored.

d76d9f293a6c61de52db2a80f7bc0d1d33d6ae03 authored over 7 years ago

Clean up API for minimum image convention

Adopt MinimumImageFractional and MinimumImageCartesian notation from
Giovanni Garberoglio's impl...

5aae885738d4aada51b0870da42c62f450655cec authored over 7 years ago

Merge pull request #1632 from baoilleach/FixForCPP17

Remove erroneous -1 in switch statement

53ff1358b933cc77636eae179e210a74c8e9b44c authored over 7 years ago

Remove erroneous -1 in switch statement

48ea604f653bc70a0238aeb0ec96e214bb835900 authored over 7 years ago

Merge pull request #1630 from cowsandmilk/patch1624

Compiler version parsing and comparison from CMake 2.8

3b6a9f8ddd181f0802e26ebb25299ac615e014c3 authored over 7 years ago

Lowercase second element letter in PDB and test

Fix for #1628 by lowercasing second letter of element. Begin testing
reading PDB file format.

0391b5952549bf0be67f9ea2f3ccce07e67fbb1e authored over 7 years ago

Compiler version parsing and comparison from CMake 2.8

Fix for #1624 by using CMake's version parsing. Also move to using
CMake's internal version comp...

00120f89cf62b121c30d0b2a891b159e19b53624 authored over 7 years ago

Implement periodic boundary conditions

Used `git apply` to apply relevant code for periodic boundary
conditions from an ongoing researc...

68abae0834cb5bb4b5caa15bb1a0a6d48074451f authored over 7 years ago

Merge pull request #1629 from nextmovesoftware/frerejacque

Correct the spelling of the Frerejacque number in a comment

383c31bdcdf4b8738dbe153716db503b95331487 authored over 7 years ago

Correct the spelling of the Frerejacque number.

78effccd9e10e05d056f22402f1f4a18769b2f1b authored over 7 years ago

Move all formats to formats.cmake and use that for both static and shared builds

74da7dbf42cb14ef511715106a30495c548d08b6 authored over 7 years ago

Merge pull request #1627 from psavery/siesta-use-obErrorLog

For SIESTA format, use obErrorLog instead of cerr

41e4509565c6dbf0a9f11b1726a24e250028f967 authored over 7 years ago

For SIESTA format, use obErrorLog instead of cerr

607f1c36112897699d469ae079f622732390ebc9 authored over 7 years ago

Merge pull request #1599 from keipertk/master

Correct MM3 carboxyl oxygen atom type definition

a3cb8b7a78ffc03d3459fa620e41afd1fad19fc1 authored over 7 years ago

Merge pull request #1608 from cmanion/csharp-bindings

Fix some small misspellings in the csharp bindings

78f0ebee5a7b61b2e5d55033255572e43e184659 authored over 7 years ago

Merge pull request #1623 from psavery/siesta-warnings-cerr

In SiestaFormat, print warnings to cerr

3f244ca984febd14e9af945a5894a81149e71b5b authored over 7 years ago

In SiestaFormat, print warnings to cerr

babe799be56088e38720ce3d75fa7fa703fcfef1 authored over 7 years ago

Merge pull request #1619 from arkose/master

Changes needed to compile with C++17

9ea5983e4c81bbd4d93b3f6d03c59c5a4816b875 authored over 7 years ago

Changes needed to compile with C++17

Two changes are made: register keywords are removed
and an implicit cast in a switch is made exp...

58caefa85a6428a3fa4ba0696980008b41553fbc authored over 7 years ago

Merge pull request #1617 from bbucior/make-install-elements

Fix install regression with element data

13451978d8e24b492e19b410707108a9978c226a authored over 7 years ago

Fix `make install` regression with element data

a3db1249f70074e1364d6d27decdfd1c5bbc8a06 authored over 7 years ago

Remove not-longer-needed comment, and some blank lines.

c76269e38f741d04de7628d4314a41cbf2038c9e authored over 7 years ago

Update depiction to handle drawing radical dots based on the spin setting, or (if

spin is zero) degree of undervalence. Note that only one or two dots are drawn.

4199ee24f59906aae934602541383d875698b6b3 authored over 7 years ago