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

Update ring fragment template

d515ebee4c7dd1ee3336a8a3d1c1044e7afaeee6 authored almost 6 years ago

Merge branch 'Fix310' into refactorpython

444ef56027f45f438d5604cb1b9df7e15676eb6f authored almost 6 years ago

Revert "CMakeLists.txt: Allow configuring BABEL_DATADIR"

This reverts commit 417361bb9f19c78434b067293980085464760c20.

201a7c2020b47305d4e82e7059dfa39f1a8c9177 authored almost 6 years ago

Minor fix to Eigen definition

0f14880c01b859b46ff30b5be566ec6fcb0bc60e authored almost 6 years ago

Make sure to search generic ring fragments

7c73fa163ae4fb7bc93ff2ae5ff440ed1e11810e authored almost 6 years ago

Apply PR #1942

817f7339fe0dd45ab4d1768a9807bbd2d36e118c authored almost 6 years ago

Initial changes

13fbcc822b00b97bc58ef165edc4cdce42c2671e authored almost 6 years ago

Merge pull request #1878 from baoilleach/chemdrawrxn

Update reaction support in ChemDraw

a9909edd84af4782c49f155e0b1c5b90e5404971 authored almost 6 years ago

Add test files

23d6e0f663b25285aa853c296be16fbde2e68c72 authored almost 6 years ago

Add basic tests

2bfe5daa733ecec0b1f802563e1d3ef4b685e99f authored almost 6 years ago

Support reactions. Also fix at least the basic case for implicit hydrogens

f7cdbfaaf9f7eaa67b6cee4c144f11d0c90b3613 authored almost 6 years ago

Stash

b710ec25bf167e92ee5ebf0f4dc97c432354d147 authored almost 6 years ago

Merge pull request #1939 from johnmay/patch/fix1929

Teach the isomorphism mapper to respect atom identity

0feffb617466ed59fbd04535ecfab2a1cd883806 authored almost 6 years ago

Update test to check only one bijection is found

bcc99902efc2ec8e4a295cbaf4fb632b238f7d82 authored almost 6 years ago

Merge pull request #1909 from katrinleinweber/resolve-DOIs-securely

Hyperlink DOIs to preferred resolver

eb43e63354a9fbd4902d86bed7bec5dd6aab972d authored almost 6 years ago

Fix #1929

5a2302cf2dc87e6692f1e67775ccdc8b35118ea9 authored almost 6 years ago

Merge pull request #1928 from orex/master

define isfinite removed.

cfd78460ef6476afebcb1f0b08323901f0202841 authored almost 6 years ago

define isfinite removed.

92540caa217bdee6f040902bb1c94d04938e72bb authored almost 6 years ago

Use ring fragments

4482766b0d1e094f62ed5b6fa746f6ec98f4d1e0 authored almost 6 years ago

Merge pull request #1914 from baoilleach/Fix1912

Add SetChainsPerceived() after EndModify() in formats that add residues

f18c29f935d6816ab5d3e9f33fbcdd43f7c1c10f authored about 6 years ago

Skip any initial spaces when writing out the AtomID to ensure consistent output

8cc1443082c311e99b79b6c37ac00883eef7ac4d authored about 6 years ago

Skip any space at the start of the AtomID

4aeabbce7f7993660ed107e3be1d1e5b917fc9c1 authored about 6 years ago

Only SetChainsPerceived() if we are setting residue information in mmcif.

12c8cde30d64d72d3a277c721ababd95ed68b8da authored about 6 years ago

Merge pull request #1908 from sunoru/patch-1

Fix incorrect use of `memcpy`.

722b2134e448da8c6c2cdfb9d82e934618b296ff authored about 6 years ago

Add SetChainsPerceived() after EndModify() in a variety of formats that add residues to the OBMol

14f8cd8d71a53038e2b30de6899b0f15fbf5a9f7 authored about 6 years ago

Ensure that the PDB reader marks chains as perceived after EndModify()

6308d87e6a29dc91d56e38571a568aab3fd0da42 authored about 6 years ago

Hyperlink DOIs to preferred resolver

7dcfd2de6626d1c11871ec948bd690a93cc1f83b authored about 6 years ago

Fix incorrect use of `memcpy`.

c699bf074e207a474face6da274a186a7c26baaa authored about 6 years ago

build properly when boost is in nonstandard place

67e8347cda4ceb2db34c67f4e322bbab4baad65e authored about 6 years ago

Merge pull request #1894 from bbucior/cygwin-xdr

Compile project in Cygwin without xtcformat

6843ffe6e9ab67748b6fb5f9a58b00338663d593 authored about 6 years ago

Updated the coordinate generation from templates. Should fix #1900 while keeping #1851 running. A bit hacky though since the mcdlutil routines are hard to penetrate...

2abe078bfe14b3150c7e29ad92c2f2ea692588f1 authored over 6 years ago

Add code of fragment index generator

9dc17134d350360fd80c156e56b4aa6e5a972bdf authored over 6 years ago

Merge pull request #1896 from baoilleach/obchemtsfm

Fix OBChemTsfm wrapping of implicit H counts. As reported with test case by @bbucior.

101b67db0e999756c5f5f137d8971f04efb3d9a6 authored over 6 years ago

Fix OBChemTsfm handling where the implicit H count was going below 0 and wrapping.

8e1e563f5fc701b7a207984d9641412822390525 authored over 6 years ago

Compile project in Cygwin without xtcformat

1778d4de4de43aad405a31bd0451c126268220a2 authored over 6 years ago

Merge pull request #1892 from baoilleach/Fix1866

Avoid out-of-range access in OBMolBondBFSIter

39e4596d99ccb55b775a032303aa5338f130ca84 authored over 6 years ago

Merge pull request #1885 from baoilleach/Fix1830

Support lone pair stereo on nitrogen as well as sulfur

cd3966da6b40b50035980a51e8657890dcaf79ae authored over 6 years ago

Merge pull request #1890 from fredrikw/issue_1889

Changed indexing of fragments, should fix #1889

1b5affab95985589ab369183dd9b833199a9bf69 authored over 6 years ago

Added test for #1889

12669bdf078e7f71a6b789f1cd4778e82a288003 authored over 6 years ago

Changed indexing of fragments, should fix #1889

9e17a2960b6fc460f885bc0e73896b7fec4a39d5 authored over 6 years ago

Merge pull request #1888 from psavery/adf-dftb-2018-add-detection-string

ADF DFTB: Add new detection string for ADF 2018

73ddeb3449c90fbaa99245d57e4b0bd43d045369 authored over 6 years ago

ADF DFTB: Allow for energy reading for ADF 2018

For DFTB output in ADF 2018, the energy line was changed
from "Energies" to "Energy Decompositio...

2c2d1b264705986c4a51a4f6d1920e9f7a16a0b5 authored over 6 years ago

ADF DFTB: Add new detection string for ADF 2018

For ADF 2018 (which has not yet been released), the string
"| D F T B |" is no longer pr...

30fd00e8c2a663e2aa9f0cba4a9e8ee8cfb4934e authored over 6 years ago

Avoid calling GetBond() when there are no bonds present. Also, reuse numbonds instead of multiple calls to NumBonds().

9d1b6feb38dc8ef52c28beeab433deb7e262d55f authored over 6 years ago

Support lone pair stereo on nitrogen as well as sulfur

290833ef07409698043681867d0618ce07bcdcdb authored over 6 years ago

Merge pull request #1882 from mkrykunov/patch-1

Update qeq.txt

081cdd8391555cdd81c5979d76a62569b91ea424 authored over 6 years ago

Update qeq.txt

I think that Pb3 (lead) was a typo in the qeq.txt file. So it should be just Pb.

161021f17941a4d0f0ea46b2b880dcf817a58e52 authored over 6 years ago

Merge pull request #1880 from openbabel/revert-1870-FirstLast

Revert "Updates to SMILES options to specify first and last atoms when writing"

fa34a74781e36751a15354eaae50e3ca8e836807 authored over 6 years ago

Revert "Updates to SMILES options to specify first and last atoms when writing"

181b1ba84662d165d6a70e013752a3a03ce35513 authored over 6 years ago

add cross options to obrms

a7a3a5f9f04846e0ad6003f35c53a82f6ef5b9c9 authored over 6 years ago

Use standardized -xk and -xf flags for handling program keywords

c9c500388dac1469364f778f4f4aa3a6ff7cc7c5 authored over 6 years ago

Merge pull request #1873 from ghutchis/build-obmm

Rebuild OBMM tool for interactive MM optimization

7fa98cb153c6e087bdfc85c45f28854a62dbf961 authored over 6 years ago

Merge pull request #1870 from baoilleach/FirstLast

Updates to SMILES options to specify first and last atoms when writing

a8a1e583619672a6ceff3d136507d523b0fead81 authored over 6 years ago

Rebuild OBMM tool for interactive MM optimization

(Useful for Avogadro2 and Jupyter energies, etc.)

f42eef57bb0d0a6b5b1e294c6e30dd15cac1894d authored over 6 years ago

Avoid changing const of OBBond::GetLength

Restored const to OBBond::GetLength. Avoided changes to existing API
by dereferencing the `this...

45b5777251fa0e4c70f65427fc647c13ac6c7402 authored over 6 years ago

Merge branch 'origin/master' into periodic-boundaries

Resolved remaining merge conflicts in mol.h and mol.cpp

4cc2543c389d844fbdc013b4b98b6898d0462315 authored over 6 years ago

Merge pull request #1836 from baoilleach/smilesrxn

Implement reaction handling as part of OBMol

76d983243990f22c59935dd9463ac5be2a1d343f authored over 6 years ago

Fixes #1851: check some limits when converting smi to sdf using --gen2D (#1852)

See bts:
https://github.com/openbabel/openbabel/files/2081924/bt.txt
https://github.com/openba...

eeca1427135316c22dee3733a4da44ea19d0a052 authored over 6 years ago

Fragment-based coordinate generation (#1850)

* Initial implementation for fragment based builder
* Implement table of contents for speed up
...

540fd561fe6525deeed44b9e05d7894d82403e9f authored over 6 years ago

Merge branch 'master' into smilesrxn

5937140d083b7caf24d0f5e4632f8ae7776c0996 authored over 6 years ago

Merge branch 'master' of github.com:openbabel/openbabel into fix-dg-stereo

d95d6e371520f721711763323dc278f0895b7445 authored over 6 years ago

Fix compiler warnings

f0b277dd3dd8eaf5e4e617a0df8fa8c1be15c3b1 authored over 6 years ago

Merge pull request #1849 from baoilleach/OBAtomGetResidue

Simplify/fix behavior of OBAtom::GetResidue so that it behaves like other lazy properties

99ce72863cef2949f108c4fd686ded6ae350ccf5 authored over 6 years ago

Update test case

2457ba9bda82f6dfa60da4a1d79d19cf3e7d2793 authored over 6 years ago

On second thoughts - don't add 'm' option - it doesn't make any sense. Also add tests

aee9367e99e31e9e81fdf25a3b9058bad1fbb274 authored over 6 years ago

Merge pull request #1864 from ghutchis/skip-inchi-warnings

Ignore compile warnings on inchi directory.

699a54e1f904ab936f7c09af3f8ade5bddfda793 authored over 6 years ago

Add new option 'g' and 'm' as mirrors of 'f' (first) and 'l' (last) except that they do not adjust the hydrogen count

656e56438cd8cc1db6b0afa6a1e56b80e3452ac1 authored over 6 years ago

Ignore compile warnings on inchi directory.

857ec067a33b2015315a3631fe599c7d84a8caab authored over 6 years ago

Merge pull request #1847 from baoilleach/KeepAromaticity

Keep aromaticity in EndModify()

8bb9ee46d5d11ccc665fc5352bbe80b651b4e6f0 authored over 6 years ago

add --separate option to obrms to deal with multiple ligand reference

fiels

09329515052563a3d5070c3120c7ab2d8bf184bb authored over 6 years ago

Fix#192: parse and use '-a' flag for obrotate (#1835)

* Fix#192: parse and use '-a' flag for obrotate

Only command-line parsing was missing

e6e22dd18209073f9c9d408b09370a39daf62778 authored over 6 years ago

Fix an issue where ring membership of atoms and bonds was not being reset by the perception routine. (#1856)

a2ef24d68f060e7dbe03ad7582b6fa21ef057b5e authored over 6 years ago

Ensure that the check for OBBond::IsInRing obeys the OBMol perception flags (#1848)

* Ensure that the check for OBBond::IsInRing obeys the OBMol perception flags rather than first ...

dcee817b932b25f6cede2e6d25c9dcda6b7d9175 authored over 6 years ago

Modify cleaning blank line behaviors (#1855)

* Modify cleaning blank line behaviors, with avoiding peek() and tellg() bugs.

72c8e9841782c5cfcfdeec73113b453dbd09ea2c authored over 6 years ago

Merge pull request #1826 from dkoes/pluginfix

Generate useful error messages if plugins can't be found.

635140c7a43b0eab31dc3a88ca6fa391d11b363a authored over 6 years ago

Merge pull request #2 from baoilleach/pluginfix

Add a Python test

a4fbc8eaa94a45153dc1da8a17448061f7d1dc0f authored over 6 years ago

Minor fix so that the remaining tests keep working

17b1cc01adf84b762d5c52f83cb0b1737df4da07 authored over 6 years ago

Based on code from @afonari, incorporate @dkoes' test case.

e1ab50d2e0f040498203dad08cbb4e10dc1f33df authored over 6 years ago

Merge branch 'origin/master' into periodic-boundaries

Updated mmcifformat.cpp, mol.cpp, and CMakeLists.txt to resolve
remaining merge conflicts.

3212f6fa80aa7ab0b7c24bcf450a3bdf31957b45 authored over 6 years ago

Attempt to manually resolve merge conflicts for PBC

Periodic boundary code is based on an old version of Open Babel, so I
attempted to manually reso...

4b342993a09e82a64417535d160920b9693674ac authored over 6 years ago

Simplify/fix behavior of OBAtom::GetResidue so that it behaves like the other lazily evaluated functions.

8940c9af51650b188185b05652d334d6a52827ca authored over 6 years ago

Merge pull request #1846 from ghutchis/add-rotors-filter

Added rotors as a descriptor/filter.

484b29dcaadfb76d0cef79454e5fd5eea9e581c5 authored over 6 years ago

Merge pull request #1845 from ghutchis/check-180-carbonyl

Ensure carbonyl groups are checked at both 0 and 180.

8a06e39268c85048fc399d95302704a7ec97618c authored over 6 years ago

Add test to ensure that aromaticity is preserved on atom deletion

9e3c495ae42d335129705ab5da1581fbafc8bc1e authored over 6 years ago

Preserve aromaticity in EndModify. Also remove workaround for bug now fixed correctly in #1724.

793de2d822d7c74822bc8cd7db4060a2e85f7982 authored over 6 years ago

Write unit tests

These cases cover periodic boundaries and bond output for CIFs

aa8c81accaba173a0ea511eb4dda2c0598a74677 authored over 6 years ago

Added rotors as a descriptor/filter.

Ran through clang-format, so some unrelated whitespace changes

06ddeb5f0577c0d2f056f4dd9778edc4223c7912 authored over 6 years ago

Ensure carbonyl groups are checked at both 0 and 180.

Bug discovered by Karl Johnson group at Pitt.

110c1033647479a2ec75ce321e89449a329eb38f authored over 6 years ago

transform CDXML coordinate

ffc45644803b977919a86bfc34a8e429c1da8bec authored over 6 years ago

add mol to cdxml test

c329280f703aa263e71708fdce2c3b515fdd4531 authored over 6 years ago

fix cdxml wedge/hash bond assignment

bac3943e2b8900f5fbef4af5ebbc8246138e3aac authored over 6 years ago

Use the pImpl idiom (d pointer) to hide the implementation details

943aaac7ecfb5f388e9121058237eb61e2132eaf authored over 6 years ago

Merge pull request #1818 from serval2412/Fix1282

Fixes #1282: check format input is provided

124d99c191493c376fa71daee0395d7a4b81be36 authored over 6 years ago

Add docs

f404923e09f6b3e828c05d91fdcd60230db36c7a authored over 6 years ago

Add test for invalid rxn

623d6c977fc7fe5e5d618f86aeec6051d3302292 authored over 6 years ago

Add more reaction validity tests

65b48f13224de66d5e66283a597857ffa953ce1e authored over 6 years ago

Add a QA test for #1282

a1593df4eb96140d99d4dac8f3ff5b81bf13a99d authored over 6 years ago

Update testbindings for recent API change

99518fb29420f01d60ef69c4728376efd3d434db authored over 6 years ago

Minor updates to RInChI to get RXN tests to pass

f9ac4852d54f2dbc40ab622671869a40eb82cbca authored over 6 years ago

Port RXN format over to new system

aa11361721f18a87803d1b3155a3c022f342e9a6 authored over 6 years ago