openbabel commits | Ecosyste.ms: OpenCollective

A better hvector fix

If there isn't a reasonable bond vector, simply don't add a hydrogen at
all.

github.com/openbabel/openbabel - 1b57a5a5c9043ea219c07c8f16f4ecbcc69fd3f0 authored over 5 years ago

Merge remote-tracking branch 'upstream/master' into some_tests

github.com/openbabel/openbabel - a718bfa4b6b4dc7a93280ecd54b1e1f533e8cd9d authored over 5 years ago

Merge branch 'master' into some_tests

github.com/openbabel/openbabel - 20a47d77c123525011aa5bc2feac48599b594d38 authored over 5 years ago

Merge pull request #1981 from dkoes/h_vector_fix

avoid non-finite bond vectors

github.com/openbabel/openbabel - 0808607d3554f27b080da86537c8bba5e61edbdc authored over 5 years ago

Merge branch 'some_tests' of github.com:dkoes/openbabel into some_tests

github.com/openbabel/openbabel - 373c035b2c952eecc7e54c51a1706623d571e0c0 authored over 5 years ago

Fix some broken structures

Apparently the intial download had some issues - wonder if there are
more?

github.com/openbabel/openbabel - 5c7f9c4ec1076207ccfb5593ac0436e82d420de2 authored over 5 years ago

Merge branch 'h_vector_fix' into some_tests

github.com/openbabel/openbabel - f8a826bec12e26b2c294a3811ef74d37b9fbb304 authored over 5 years ago

Add test for adding hydrogen

This is extensible and I will be extending it in my other pull request
(including fixing the val...

github.com/openbabel/openbabel - 4eb87ae18ca27e476ccec883a15ed73d305c041a authored over 5 years ago

Merge remote-tracking branch 'openbabel/master' into h_vector_fix

github.com/openbabel/openbabel - 359c35d67bbb788600de3d1b08579dbf65ffa7ac authored over 5 years ago

Prune redundant files

github.com/openbabel/openbabel - 8438ca8b37b89e3db64de36fca26ad1b1afaa9bb authored over 5 years ago

Change inputs to use wildcard aliases

SDFs from the PDB use the alias feature to describe atom types.
Treating aliases as functional g...

github.com/openbabel/openbabel - 481912c89da7f1659eeb576388dcbf671c3e0088 authored over 5 years ago

Fix reference pdbqt

We now do a better job of preserving atom names and residue information

github.com/openbabel/openbabel - 5423b31a946e041a16fd3f3e3f50d009d2ccb1c5 authored over 5 years ago

update reference tests

We now include formal charges in mol2

github.com/openbabel/openbabel - d81cc9a69c731d986a1612c9f00ef71a966ba080 authored over 5 years ago

Merge pull request #1985 from dkoes/include_fix

include babelconfig in vector3.h

github.com/openbabel/openbabel - 26fb24548e84135ce5a076bcc60c228b689eb269 authored over 5 years ago

Better handling of empty PDBs

github.com/openbabel/openbabel - c53f0f6a2d59f01c40a306e3d34facb003537cdb authored over 5 years ago

Move UNIT_ATOM record location

Put it between atom and bonds so we don't have to read (potentially)
past end of molecule to rea...

github.com/openbabel/openbabel - c828be5d561b3dc628dd58e70f53055afff917bf authored over 5 years ago

Fix mol2 gzip problem

Don't read past the end of the molecule looking for UNITY atom type
information.

github.com/openbabel/openbabel - df016ace26587b3554e9ecfa6834bcb36a00efdd authored over 5 years ago

Add testroundtrip.py to tests

github.com/openbabel/openbabel - af0d9e2bc01d36457528d46d7cc06ccc58fe1a36 authored over 5 years ago

Refine empty PDB molecule handling

gzip implementation depended on return false

github.com/openbabel/openbabel - 810e9d7a67ac628769fd78e3bb654c662cb97dd8 authored over 5 years ago

Large amount of test cases from pdb

github.com/openbabel/openbabel - 70d6eda7de2e3df0bfb923acb682de7c10b1eb8e authored over 5 years ago

Check validity of bonds before updating

This currently has a particularly specific check, but I expect other
checks will be needed at so...

github.com/openbabel/openbabel - 939978e185d411c89d5a9150bb7b8c0d70b10307 authored over 5 years ago

Type carbonyl only for neutral oxygen

github.com/openbabel/openbabel - 07024bc00bfc13a1eae56c50d3bd6e63313451ad authored over 5 years ago

Further refinements of bond typing

Make rules more conservative. Don't adjust bonds in cases where
alternative charges could equal...

github.com/openbabel/openbabel - 81605a30aa51a97628b9f3a8af01db3ee0e5b155 authored over 5 years ago

Make bondtype more specific

Fix problem with pdb_ligands_sdf/3dcv_55e.sdf (and many other structures
I've noticed)

github.com/openbabel/openbabel - 24c926c918a3b34b07a8727a07e699126270d911 authored over 5 years ago

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

github.com/openbabel/openbabel - 22359e9fc2589b721a72f9f738f8f267c9a30df1 authored over 5 years ago

typo fix

github.com/openbabel/openbabel - 2a333f90aba2747af4514373dd20ffbbfa421759 authored over 5 years ago

update the docstring, remove old properties

old properties will raise the error

github.com/openbabel/openbabel - 4d312ea42b9444c5890bcf5acd734e7ae8054b9c authored over 5 years ago

Make pybel compatible with #1975

github.com/openbabel/openbabel - a3700549adb6e2122d2e0c324ae42f5b150daa75 authored over 5 years ago

Merge pull request #1997 from nextmovesoftware/rogersmi

Add SMILES support for elements specified by 3-digit number, e.g. [#101]

github.com/openbabel/openbabel - 5530553439401becf58554869a43a89398bef4b4 authored over 5 years ago

Don't report failure on a legitimately empty mol

github.com/openbabel/openbabel - 09e2192e50bbd6c872426539ac112423b30358e7 authored over 5 years ago

Make typing more specific to get coproporphyrinogen correct

github.com/openbabel/openbabel - 02695ab2a41aa6bd5ba2d6c508c9438156fcca7c authored over 5 years ago

Only support three digits for this extension.

github.com/openbabel/openbabel - d91583e70e1357317ee799f5a417ccb37bfe26e8 authored over 5 years ago

Add tests. Tighten up handling of boundaries.

github.com/openbabel/openbabel - 46ddafb733073cb51f301d0672b25e77cde8e6c4 authored over 5 years ago

Fix file format options

github.com/openbabel/openbabel - c3e2e58269037ef9de006c69bf10c8e41c1d8df8 authored over 5 years ago

Better (?) bond typing rule

See pdb_ligands_sdf/5jzn_gui.sdf for an example where the old rule fails
if you don't punt on ar...

github.com/openbabel/openbabel - 42a3520c7cbddde1872e4c34845fd4b91d46ffd6 authored over 5 years ago

When writing SMILES for an element without a symbol, use"[#elementno]"

github.com/openbabel/openbabel - 8e8a8777c03706261ab9f530351f79e6143cdab5 authored over 5 years ago

Increase buffer size to ensure support for isotopes of heavy elements

github.com/openbabel/openbabel - 4b4718b735fa59934eb00a2825f868af90530b46 authored over 5 years ago

Parse elements described via their atomic symbol, e.g. [#6].

github.com/openbabel/openbabel - 0ffed63d23a595ec360efc00d9ebb8a9fd89183c authored over 5 years ago

Fix segfault

Coordinate vector needs to exist when expanding aliases

github.com/openbabel/openbabel - a6646b85b89e91d88ae69eaee493f759c15d2297 authored over 5 years ago

Fix mol2 kekulization w/charges

Need to parse the charges out of the file before Kekulizing or it
doesn't have the right atomic ...

github.com/openbabel/openbabel - 9d077df7857184fab01280b47b6f04b75449c43a authored over 5 years ago

Fix mol2 typing

Just because an N is bonded to an O doesn't mean it should be positively
charged (N.4). See the...

github.com/openbabel/openbabel - d0fbb97b0d1e99c87a91d8e648f1cf70ab24002d authored over 5 years ago

Only build maeparser if boost is present

Confirmed code and tests only build if Boost is present, and it can also
be disabled with explic...

github.com/openbabel/openbabel - 3eb99e6a1a28e585077ed70a2c8504f75a9dea5a authored over 5 years ago

Support for formal charges in mol2

This outputs and reads UNITY_ATOM_ATTR records so formal charges can be
roundtripped between mol...

github.com/openbabel/openbabel - 9a8b16615211c5bf23a1f3c51adf0a7e9f709561 authored over 5 years ago

Add maeparser support to openbabel (#2)

Add fully functional maeparser support for both reading and writing mae/maegz format. Also adde...

github.com/openbabel/openbabel - 99dfb0b649bb817a118adb34e00c05f33e40723e authored over 5 years ago

Merge pull request #1992 from dkoes/python_installdir_fix

Address Ubuntu bug in defining python install dir

github.com/openbabel/openbabel - 528f73fe64376ce8922897748e2879a6d599e7ed authored over 5 years ago

Add support for reading insertion codes for pdbqt

github.com/openbabel/openbabel - ad17efb07932095c9ad9ca5e1e0b68439144e289 authored over 5 years ago

Add support to insertion codes to pdbqt output

github.com/openbabel/openbabel - 9bcc398c824f83dfd2215b0a841b3f332ebb36a2 authored over 5 years ago

Fix bug with chain perception

Copying a molecule shouldn't trigger chain perception if the src
molecule already has perceived ...

github.com/openbabel/openbabel - d1f809cee64639438b27175ee5574a5b136b7718 authored over 5 years ago

Insertion code fix and tests

Provide regression test

github.com/openbabel/openbabel - 4c418f9a0cba7dc5e768763954beb3625d6f2b78 authored over 5 years ago

Fix copying of residue information

The OBResidue copy constructor was not being used in the OBMol copy
constructor and components o...

github.com/openbabel/openbabel - 418f9198eca52ac0026c8d6ea63f8aeb063414cb authored over 5 years ago

Fix hyb state after addh

Reset the hybridization perceived flags since hyb is no longer correct
after adding hydrogens

github.com/openbabel/openbabel - 0c9ecd2f8961fe2206ed124968a98e17c3b13301 authored over 5 years ago

Address Ubuntu bug in defining python install dir

See https://bugs.launchpad.net/ubuntu/+source/python3-defaults/+bug/1814653
Fix might be slightl...

github.com/openbabel/openbabel - 30fcd3163e11a572f85064f3a53be83e98b32363 authored over 5 years ago

Merge pull request #1991 from orex/master

fpsformat.cpp: compile bugfix header added.

github.com/openbabel/openbabel - d3497529fc68d837fc5063061326c1e837b12c9e authored over 5 years ago

fpsformat.cpp: compile bugfix header added.

github.com/openbabel/openbabel - 77c8c88a510a1445ae4e4832944555a622be8c73 authored over 5 years ago

Merge branch 'openbabel_master'

github.com/openbabel/openbabel - 5a69f384dbd12a355287d0e3c827d987b7e1698c authored over 5 years ago

include babelconfig in vector3.h since in includes no other openbabel

headers and so OBAPI is not defined

github.com/openbabel/openbabel - e61d1d17a4eab4e6362b9ba71e42ab922192d029 authored over 5 years ago

Merge pull request #1975 from baoilleach/valencedegree

Rename/add valence and degree methods

github.com/openbabel/openbabel - 90739b4c5caf8f1af41c968354a5bfbb1f3aa630 authored over 5 years ago

Merge pull request #1973 from e-kwsm/fix-exit-code

Exit with non-zero if an error occurs

github.com/openbabel/openbabel - 8c50db57fb7017dec49c7a99a520a9d9e4c6634b authored over 5 years ago

Merge pull request #1965 from baoilleach/MoreSetUnset

Move to a single function for setting/unsetting bond and atom flags

github.com/openbabel/openbabel - fb3abd63ec9b5bf422016ae9228d5b1366c00ae6 authored over 5 years ago

deal with swig and thread local

github.com/openbabel/openbabel - cd1438c46414f6d5f8455de6bbb207859c78193d authored over 5 years ago

deal wit hswig

github.com/openbabel/openbabel - 90efb4e0e461439ea7dd25b9a92d174806870fe5 authored over 5 years ago

avoid non-finite bond vectors

github.com/openbabel/openbabel - 59cf6e084af997a5f688439a86d08c089cfab80a authored over 5 years ago

Merge remote-tracking branch 'openbabel/master'

github.com/openbabel/openbabel - f69ef5444118cd2f0f785fd18a56b85577ab0ac5 authored over 5 years ago

fix cmake build

github.com/openbabel/openbabel - aa6e027f33230abb3a1b33c9f76f06cd0004bc47 authored over 5 years ago

Merge branch 'obrms_enhancement'

github.com/openbabel/openbabel - 59a8d6c4de3ecd22471a3a9c52a3a51b9958dedf authored over 5 years ago

Update URL of specification of MDL MOL [skip ci]

github.com/openbabel/openbabel - 9418c9d4343247bf229a30aa4781a88e8ccbac55 authored over 5 years ago

Merge pull request #1978 from dkoes/obrms_enhancement

Obrms enhancement

github.com/openbabel/openbabel - 53ce98c75a8b10bfdc37ebf8f5cbda6727208212 authored over 5 years ago

Update doc [skip ci]

- Fix "SEE ALSO"
- replace `babel` with `obabel`
- fix self-reference
- Remove leading/t...

github.com/openbabel/openbabel - 5e33a9d80b48d7db7a462d4670e6ac14ed1a96e4 authored over 5 years ago

Merge branch 'obrms_enhancement' of github.com:dkoes/openbabel into obrms_enhancement

github.com/openbabel/openbabel - b7d7a0690a2acec494a16b4b696913ea01137359 authored almost 6 years ago

fix firstonly logic and extend man page

github.com/openbabel/openbabel - 85ccd84950a8e02c7d88a3a439097c030c51fc5a authored almost 6 years ago

Move to a single function for setting/unsetting bond and atom flags

github.com/openbabel/openbabel - a503b4bef019c45d57d0373136d08d48b6c82621 authored almost 6 years ago

Merge pull request #1972 from yishutu/yishutu-gitignore

Add __init__.py to gitignore

github.com/openbabel/openbabel - 48387991b746a312dab55cd2ce34c1469ad8351c authored almost 6 years ago

Replace static methods, or in-place expressions, to calculate the total valence or total degree with calls to the new OBAtom methods.

github.com/openbabel/openbabel - 970f4e42ee87d6635611150cf706262f0f80098f authored almost 6 years ago

Rename or add Valence and Degree methods of OBAtom

github.com/openbabel/openbabel - e949134dc3851b4e2fd741695443b6bef80c2354 authored almost 6 years ago

Merge pull request #1968 from baoilleach/deprecated

Remove low-hanging deprecated methods

github.com/openbabel/openbabel - 33df57a7c0c7ef24929ea0f85240c40d05602a51 authored almost 6 years ago

Merge pull request #1974 from e-kwsm/update-gromacs-urls

Update URLs of specification of gromacs

github.com/openbabel/openbabel - 64425dcd56194e12d3a623b0a32aad79d7c9ed02 authored almost 6 years ago

Update URLs of specification of gromacs

github.com/openbabel/openbabel - 44b1ecb6a7a24a04719000c36f83b3e0e3445fb6 authored almost 6 years ago

Change EOL from CRLF to LF

tools/
- obfragment.cpp
- obsort-fragment.cpp
- obtorsion.cpp

github.com/openbabel/openbabel - b61de6c809f9154cf9ccbb4d68b7e3d56ef3e86a authored almost 6 years ago

Exit with non-zero if an error occurs

- tools/
- babel.cpp
- obabel.cpp
- obconformer.cpp
- obspectrophore.cpp
- test/...

github.com/openbabel/openbabel - 759bb19e5d82fb31295d8c305b3531c3fdae319f authored almost 6 years ago

Merge pull request #1969 from e-kwsm/gaussian

Update Gaussian format

github.com/openbabel/openbabel - 58c67b6813e761bcfc6918d5d3e257f2c6c51614 authored almost 6 years ago

Merge pull request #1970 from e-kwsm/improve-python

Improve python script

github.com/openbabel/openbabel - 532ca37c32385114212dcc9a9c50e13075e9073a authored almost 6 years ago

Merge pull request #1971 from yishutu/pybel_with

Make `pybel.Outputfile` compatible with `with` statment

github.com/openbabel/openbabel - d28440de93f3c57e375571d647cffeba24f1d525 authored almost 6 years ago

add __init__.py to .gitignore

github.com/openbabel/openbabel - 9f761c56c2190cab66381c2944f1f32963464b33 authored almost 6 years ago

Add __entry__ and __exit__ methods to pybel.Outputfile

github.com/openbabel/openbabel - 26f192587f4b2269536fe0a82d50480b987544c5 authored almost 6 years ago

Improve python script

- `from __future__ import print_function`
- replace deprecated `unittest.TestCase.assertEquals` ...

github.com/openbabel/openbabel - 6b57788a052643a56dd36d963ab5a60304bf4e3d authored almost 6 years ago

Update Gaussian format

- comment out route section of outputted Gaussian input
- add missing `gzmat` format
- update URLs

github.com/openbabel/openbabel - 79518c409296f53e7254c0c1832945f11d2e9867 authored almost 6 years ago

Remove deprecated OBAtom::GetNextAtom() which returned the next atom (by idx) of the parent molecule

github.com/openbabel/openbabel - 010606cd7361cf83c0e95e416d335ba29120c725 authored almost 6 years ago

Remove deprecated (renamed) GetCIdx() in atom.h

github.com/openbabel/openbabel - 8a2b8233b44c79d2140c01c1a54efa192e1ce143 authored almost 6 years ago

Change uses of deprecated bitvec methods. Also remove NewAtom/Bond/Residue from mol.h

github.com/openbabel/openbabel - 23ed36ba4c6606a42efbb65fcecfc3954e201628 authored almost 6 years ago

Remove deprecated bitvec methods

github.com/openbabel/openbabel - 1901e28e9fc743749a6564f93e405317bb7b624f authored almost 6 years ago

Merge pull request #1967 from baoilleach/oldstereo

Try again removing the old stereo code

github.com/openbabel/openbabel - 0b4078f51a7e8964dfed421eb38c8d48e85e95d3 authored almost 6 years ago

Get rid of unused stereo flags in OBBond and their associated methods. Comment out bitrotted code that still used old stereo IsUp() and IsDown().

github.com/openbabel/openbabel - be5f8863891e1aae73d8034aef2e460795f67fc1 authored almost 6 years ago

Get rid of OBEdgeBase typedef.

github.com/openbabel/openbabel - 24c66613ac422409139d866f9253108012b72043 authored almost 6 years ago

In the interests of time, retain current behavior of OBMol::IsChiral in mdlformat.cpp and reportformat.cpp. File bug to fix it.

github.com/openbabel/openbabel - 7a5b7ac0f79fd8cfd1ce6aca7878429b307169fd authored almost 6 years ago

Part of previous commit

github.com/openbabel/openbabel - b662d02bd95eb68c535354b7c45e4f0447db9dbd authored almost 6 years ago

Remove OBMol::IsChiral(). It doesn't check whether the molecule is chiral, nor is there any easy way to implement this quickly.

github.com/openbabel/openbabel - 282e1664a1e567d1d48ac4df7e02ab31ad63eec3 authored almost 6 years ago

Remove obchiral executable as it uses the old chirality. Also, it's functionality is covered by the report format. I think. In theory.

github.com/openbabel/openbabel - 8c83af91fead84f5e2153766534cf78435d61b55 authored almost 6 years ago

Update bindings for lack of ChiralData

github.com/openbabel/openbabel - f96f03580e0844ab366b0d19d1757253824ed65f authored almost 6 years ago

Remove stereo code deprecated since Tim's rewrite back in 2009.

github.com/openbabel/openbabel - e0a85995054cc25779f2abb181143e49b18f9631 authored almost 6 years ago

Merge pull request #1953 from baoilleach/bondorder

Remove OBBond::GetBO() and SetBO()

github.com/openbabel/openbabel - 3e4d4057b64c0bee844e6739fa43019ad6ccea94 authored almost 6 years ago