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

For right now, turn off distance geometry building by default.

Since we cannot guarantee stereochemistry, we should stick to the
existing method. Revisions wil...

f840204c77d2e8c2ed45f5de5e941e5c39749e31 authored almost 9 years ago

Merge pull request #269 from dspoel/master

Moved storing total charge in gaussformat.cpp

3c199b7c335d779465ab57be0a73da97d4fbc939 authored almost 9 years ago

Moved storing total charge in gaussformat.cpp

The total charge in an OBMol may be changed by EndModify or
other routines involved with changin...

fed6145d48d8c5d509675622a1dbd7c877497c6e authored almost 9 years ago

Moved storing total charge in gaussformat.cpp

The total charge in an OBMol may be changed by EndModify or
other routines involved with changin...

1ca2c68edf5230fe04c9095d35c920c941185230 authored almost 9 years ago

Moved storing total charge in gaussformat.cpp

The total charge in an OBMol may be changed by EndModify or
other routines involved with changin...

b6555f5d9150105ee7606233a05a0499a340d7bd authored almost 9 years ago

Merge pull request #267 from afonari/patch-11

Test for decaying to P1 (pull request #261)

f3fbd8e01219366ac431bdd48d94c7eec6571cd5 authored almost 9 years ago

Add a test

d6c141dcbbf5a52431f42c2137772500d2b7b195 authored almost 9 years ago

Update CMakeLists.txt

66b072e874f1a227e1479343af667e948d0d33be authored almost 9 years ago

bondtyp.txt

1c896a515e049d5ad18e9c5ad58c6f11c44e3755 authored almost 9 years ago

bondtyp.txt

ad2fb115958759e8086251bbfb362d6bad5cb73c authored almost 9 years ago

Merge pull request #265 from afonari/patch-10

Correctly parse symmetry transformations

3a63a9849f8d9719c5989c43875d51be50c53019 authored almost 9 years ago

Make test run

0ca06e748c8d3e0c864252fc7d3f286c66bed0a4 authored almost 9 years ago

Add tests

92dc3233a9a6843f3996627d20780d68c38b5903 authored almost 9 years ago

Update cifspacegrouptest.cpp

a8076aa24d3d421551a647ba9a9e544654e871ee authored almost 9 years ago

Merge pull request #261 from afonari/patch-8

Correctly convert to P1 cell in mmcif format when space group is not found

b885ade539294f0f924759a3b90d9ce6403b2fe2 authored almost 9 years ago

Merge pull request #257 from smoe/master

Add support for PDB insertion codes

e3db4783155e05e20ab6c9cd92407b53a9650e16 authored almost 9 years ago

Merge pull request #264 from afonari/patch-9

Make unit tests from #262 actually run

87f43483143a482fdbcf10bc6fe4d6eb2f1ed181 authored almost 9 years ago

Improved cif checking

a542cfd21c88d8934244e27654263f8332ca585c authored almost 9 years ago

Update CMakeLists.txt

91f06633cb5f79ec4daa8c510bce610ecea06efd authored almost 9 years ago

Merge branch 'master' of https://github.com/openbabel/openbabel into patch-8

70337b9b9b189f56168c4a070425d6b8c3152c55 authored almost 9 years ago

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

3278fb081b16456b2229eccd753f5d432d1a638f authored about 9 years ago

Added test for PDB insertion codes

6e9ef2cb56df4de10a94d9744c769d56d7d4e4ea authored about 9 years ago

Merge pull request #262 from afonari/patch-9

Add unit tests for pull requests: #254 #255 #260

4e375e4650fe099f205e3e1ed42c112bf520c24e authored about 9 years ago

Update cifspacegrouptest.cpp

1c896174a5e50210cabb6680dde66125bb377aec authored about 9 years ago

Create test02.cif

36935bef8266bbc6ac65e7e9d0d8d68ab8112a3a authored about 9 years ago

Create test01.cif

f9df3bb65592eec25ffa578c76e5f80612249c34 authored about 9 years ago

Create cifspacegrouptest.cpp

dfaf4486e6ce2d2d631713652aa59f2638831bd1 authored about 9 years ago

Update CMakeLists.txt

09ee47e66404a57e32f3e2c6d314e1e5620869c4 authored about 9 years ago

Update mmcifformat.cpp

9b1588aee1596e03d254d9aa3e4eaadc53422c81 authored about 9 years ago

Allow fillUC plugin to use symmetry transformation

e966c88ea49a561dfc8892355f46df48b28b2fe1 authored about 9 years ago

Adding call to fillUC plugin to generate P1 cell

e5c812f407bc83aabf8312bcfa44b708656c51f8 authored about 9 years ago

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

9c5890a69946adf3e0228a3a3d88fb883bcda7b7 authored about 9 years ago

Merge pull request #260 from afonari/patch-7

Allow only unique symmetry transformations

a18da1bccab0ba213cb9a65fdba1b3fc61f223ce authored about 9 years ago

Allow only unique symmetry transformations

This should match the correct space group when the same transformation is present:

_symmetry_...

0d674ac479e205915cb4fa28bbaf6633d638b626 authored about 9 years ago

Also writing insertioncode in PDB entry

bf60af2d0677f649bfd50dc6ce5b74027c5da6f9 authored about 9 years ago

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

01a648cc396fd8aff3c2358a05310f68d5cc2b54 authored about 9 years ago

Interpretation of PDB InsertionCode

The PDB format features the line
27 AChar Code for insertion of residues.
which is meant to ...

46bb2d1d42b23938c6446680632477e950643e1d authored about 9 years ago

Merge branch 'alexandr-fonari-patch-2'

531f20353fc0722db52e0ec9ffa9512696e76063 authored about 9 years ago

Add another settings for 167 group

ccecd1ceed2e383192205ab7b0b1e3045f267f45 authored about 9 years ago

Add another settings for 166 group

3550d88f71a3e02b16c6862ce31dec84e3ebbbb0 authored about 9 years ago

Update PDB writer to obey PDB requirements

Requirement of PDB to name rhombohedral groups starting with H
(http://deposit.rcsb.org/adit/doc...

7d0ce2dc2206e32344417df124bbe0e14eef0b28 authored about 9 years ago

Merge pull request #256 from alexandr-fonari/patch-5

Add space group definitions

c35bbd093e227fa83b853bdfabee33675f832ad2 authored about 9 years ago

Add space group definitions

b624510a9bfd790f8f90e460a0dfd62ff89e352b authored about 9 years ago

[PATCH] New gaff.prm atomtyp.txt bondtyp.txt

f766148ed15fff827b60bbdc68bfa66dc1eca3a7 authored about 9 years ago

Merge branch 'master' of github.com:openbabel/openbabel into dist-geom-fixes

07b3585e72f5ebd4a2fea7921029bb70fe8ebbaa authored about 9 years ago

Merge pull request #254 from alexandr-fonari/patch-4

Clean space group name before anything

bce8a87d959c09bf98260412fb08b8e44f38528b authored about 9 years ago

Merge pull request #255 from alexandr-fonari/patch-3

Make transformation parser case insensitive

2d1730ecc89d369ebed7c94b9fe6676a3fc98151 authored about 9 years ago

Clean space group name before anything

This fixes the issue with reading space groups from PDB (and maybe other formats).

d5de951d606735b61d1686a0ea2321066956e085 authored about 9 years ago

Make transformation parser case insensitive

This needed in the cases like:

loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz...

8b14c1d8fc7a71e9ae224d8a4466dc54259be3de authored about 9 years ago

Merge pull request #132 from ghutchis/allow-ring-rotamers

Initial support for ring rotamer sampling.

8a6db30067e1484aa275f5deb537654c2f987808 authored about 9 years ago

Add option to sample ring conformers from command-line op and FF code.

74b422fcd2016b75a0b95dd06b9728a4c3d79292 authored about 9 years ago

Make sure all bonds have NULL parents unless set.

b12a49b693767462d696da03ec746208e77bad5a authored about 9 years ago

Fix crash on rotor unit test, ensure default is to not check rings.

4dc56646955c74e87878fe51b0f6dbebcf9c42ed authored about 9 years ago

Merge branch 'master' of github.com:openbabel/openbabel into allow-ring-rotamers

281d6dbf44d8346fa536b8056551f555b8f55998 authored about 9 years ago

Fix cppcheck reports from serval2412, closes #237.

7249f73654173eedd588873aded04ed2c5f75e00 authored about 9 years ago

Merge pull request #247 from Reinis/fix_cmake_pop_policy

cmake/modules/UsePythonTest.cmake: Pop policy on return

2d24be8b09bb20c39e166f1473e68d9df46d3495 authored about 9 years ago

Merge pull request #248 from alexandr-fonari/patch-1

Fix mmcifformat.cpp to allow correctly setting atom types from the atom names containing digits

83319dfc4f1da29f8a1bb54d74bbd8143554e33b authored about 9 years ago

Update mmcifformat.cpp

In the case of setting the atom type from the atom label, this change allows for correctly parsi...

337860c6da4a58b98f9c30ed040b8741029154e4 authored about 9 years ago

cmake/modules/UsePythonTest.cmake: Pop policy on return

Otherwise test build fails if Python interpreter is not found or is
unset.

80bfbca5509430cbaad2425d4d6878a27c15ab02 authored about 9 years ago

Merge pull request #241 from aandi/patch-1

Fix infinite loop in eem calculation

737e86079a6b8b732080abe37aaeac7fb388fb6e authored about 9 years ago

Fix comparison between signed and unsigned integer expressions

2e7b495c94aff9af6a4b9aa1945225861f49a9c6 authored about 9 years ago

Improve distance geometry coordinate generation methods.

Use partial metrization and damped stereochemical corrections.

ed88e51c4cc9b552e48d30346b86246ee2be8fd0 authored about 9 years ago

Merge pull request #243 from krab1k/master

Integrate Cheminf 2015 EEM parameters

3aa97b7223bbc46364046e6237b5952dade60067 authored about 9 years ago

Add Cheminf 2015 EEM parameters

66bd04c1622a9a2600852e1f70440a39520df582 authored about 9 years ago

Move EEM parameters from source code to the data file

ea01909f94e6cb5042ae7c9d7e89b378f1e58faf authored about 9 years ago

Add method which returns the maximum bond order for all bonds connected to an atom

e07849f8446be2cd36d1a4071b198d81e9c5235e authored about 9 years ago

Fix segmentation fault in EEM

Since for unsigned int i the expression i >= 0 is always true.

0b8ac51907a4c70237c7bd04bb3a49b3e4181c1f authored about 9 years ago

Fix memory leak in EEM

792bae8a1432e76022b6b4c5e75382855b611106 authored about 9 years ago

Merge pull request #244 from sforli/master

New OBAtom:IsHbondAcceptor() method

2418f57d7fa5fe41a5bc641bb6d4c2323c91c5c9 authored about 9 years ago

Try fixing Travis build for GCC by using -march=native.

050a1b262ef913653e6bc25d3dffe390e02d0d0f authored about 9 years ago

Merge pull request #239 from tootea/master

Fixes to ConnectTheDots and plugin loading

c52106ab673bc1d520881ab6d28e7ad009a5ec0b authored about 9 years ago

Merge pull request #225 from xomachine/master

NWChem format parser improvements

444a90c2026fd41d3825589fae21dcfa4a710187 authored about 9 years ago

Merge pull request #234 from dkoes/pluginfix

fix for segfaulting similarity search with fastsearch index

a664de0f1fde24a79c6b7c3fa916a86b849d7a07 authored about 9 years ago

Merge pull request #226 from baip/master

Fix compiling errors under Windows & Cygwin

b83b71b612a25903811787ef3774be870e8c3fb4 authored about 9 years ago

Merge pull request #232 from kartlee/master

Fixed the cubic space groups 200-206 and 221-230 to treat 3-bar(-3) as 3

4fb8d73cc1bb16ae4228eadecb851b4faccf9f59 authored about 9 years ago

Merge pull request #240 from jeffjanes/fix_fingerprint_224

Fix fingerprint bug #224

2ce306e7a9e03c7771c9a34871583a953584e6b4 authored about 9 years ago

Merge pull request #1 from sforli/sforli-hbondacceptor

Modified OBAtom::IsHbondAcceptor()

1094956ff72c84928bc41758457823f4be151b05 authored about 9 years ago

Merge pull request #2 from sforli/sforli-hbondacceptor-2

Added IsHbondAcceptorSimple() and IsSulfoneOxygen()

aab77abbeab7e9d6618f93b76c5e79ea8db00c9d authored about 9 years ago

Added IsHbondAcceptorSimple() and IsSulfoneOxygen()

The old IsHBondAcceptor() function has been renamed IsHbondAcceptorSimple() for providing backwa...

8112fc4a6abaa2e63199ffee8d255d3421bf473f authored about 9 years ago

Modified OBAtom::IsHbondAcceptor()

Created a new OBAtom::IsHbondAcceptor() function which is based on more complex rules taking int...

c592a45e95a1b0ada102366caf2a55fef67d0146 authored about 9 years ago

Merge remote branch 'origin/fix_fingerprint_224' into fix_fingerprint_224

361dd0673dfd5e89365eb3907357b7ac9826d19f authored about 9 years ago

Merge branch 'master' into fix_fingerprint_224

0d1f73c7ee3c6dce25e800ddac0970fd57c363ce authored about 9 years ago

Clean up unneeded code.

I think that the only reason for this code was to spread the damage from
bug #224 from the ring ...

dc50c19301687c45e256fe699dcd3a1f7861d7c9 authored about 9 years ago

Fix another bug in fingerprinting FP2, #224

When we reach an atom which is connected back the first atom in ring,
it was closing the ring us...

e9a46f8315038cbe4c9c92ab4fb3ad5e9474a805 authored about 9 years ago

Merge remote-tracking branch 'upstream/master'

Syncing to upstream

ec725969cf01c5b3a62e3e4d0e9a6781060d4ede authored about 9 years ago

ConnectTheDots: fix hydrogen molecule

ConnectTheDots used to ignore all bonds between hydrogens, leading to
a missing bond in the H2 m...

dabd9f5fba5b56856ec676bc92d9b8aa1f3782cf authored about 9 years ago

OBPlugin::LoadAllPlugins: avoid infinite recursion

When no plugins are found for some reason, the OBPlugin::GetPlugin call
would recurse through Ge...

6d72726909d4fbeff7d341717acb562ebbcca4fd authored about 9 years ago

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

70c621a8feca625029a124e841bee7e6b5d062f2 authored about 9 years ago

Ignore unknown value for space group transformation block

Openbabel doesn't check if the values from _symmetry_equiv_pos_as_xyz
are unknown values (?) and...

4d9b605f793cf932c8fd6e3fc3770d385a683d4b authored about 9 years ago

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

8e2a14a3d0fc7dc3f6a8e8f6c32b76fd23eae3aa authored about 9 years ago

Merge pull request #233 from serval2412/master

cppcheck: fix reports "Prefer prefix ++/-- operators for non-primitiv…

8d258dda6e4d8a0f7f1495084d4a9a53e7cc7912 authored about 9 years ago

Merge pull request #235 from platinhom/master

The pqr format reader ignore the last element column...
Use the atom radius data saved in gener...

ea708051b48b43b9d999ae25f4ccf4a80c8810df authored about 9 years ago

Merge pull request #236 from tootea/builder_fixes

Builder fixes

afeb9dcf7ea6c94e8ac03b803a7b3c06261a8db5 authored about 9 years ago

Small cleanup in OBBuilder::GetNewBondVector

Remove redundant code called in both branches of if/else.

e62aa958cbfb42fa52fe6aa756b07c128245a8de authored about 9 years ago

Fix carboxylate handling in OBBuilder

Due to a logic error in GetNewBondVector, if the first found nbr2 that
IsOxygen() is the atom po...

8d0b96405068f49ca7e81502dca08c51aaea4ded authored about 9 years ago

a better fix?

ef9292bce177915a36b2ef31bfc9a5add5133e85 authored about 9 years ago

include pthreads

c0a2f1982e2cc86fa5ab536c55afc6fb918bbb31 authored about 9 years ago

maybe this fixes the deadlock?

b4735e85229c8b13817d08274c9083f52cc2ad32 authored about 9 years ago

fix for deadlock

319f8487b3efed083994ed03a1c653e98bc80a15 authored about 9 years ago

fix race condition in atomtyper

has to pull in boost for mutexes

15601ca09353e1c1172cb0c809301a3ddd6908a4 authored about 9 years ago