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

Add debugging

b68dbab12ffca44c374c68bc6578a67383f14000 authored about 7 years ago

Add distance geometry test with some initial cases

47e417c948e71cd3f3ca55411befbff800b33da7 authored about 7 years ago

Updates to improve distance geometry generation

4e3a53a39c9e173575d0ea11ce747ef36c6890a0 authored about 7 years ago

Merge pull request #1736 from ghutchis/fix-distgeom-triangles

Fix code error found from @baoilleach compiler warnings

94f963bef3090eed057e4260f5b4d9150c0cc604 authored about 7 years ago

Merge pull request #1734 from ghutchis/tinker-custom-atom-types

Add support for using atom classes as Tinker atom types.

201d477423208f973cfcd21b4e3125de27463cea authored about 7 years ago

Fix code error found from @baoilleach compiler warnings

Resolves #1735

0db5bc02e7d0ebf888a04668ca1eb38d9e8744cf authored about 7 years ago

Add support for using atom classes as Tinker atom types.

Resolves feature request #1732
`obabel -:'[C:345]([H:34])([H:34])([H:34])[C:234]([H:34])([H:34])...

ea801f59d989e32877c371c79cbeed878e100cb1 authored about 7 years ago

Merge pull request #1724 from baoilleach/IsInRing

Make sure that OBAtom::IsInRing always triggers ring perception if not set as perceived

1dacb36ba92063b9673cf072290183eb2ebed63a authored about 7 years ago

Merge pull request #1580 from kyle-roberts-arzeda/no_resonance_vinylogy

Remove the change in resonance structure from the vinylogous carboxylic acid pH model

8e30bdb559a9d086d5b2cc88e91321a06a5e3497 authored about 7 years ago

Merge pull request #1725 from baoilleach/SmilesSpeedImprov

Reserve string buffers to improve performance

310e721599a1849c10c00b06465e8296d4de4a36 authored about 7 years ago

Merge pull request #1729 from baoilleach/SwigIterators

In the Python bindings, avoid adding methods from the iterated object to the iterator itself

959119249b6afdab8b31e28bafea2eeaa27a312a authored about 7 years ago

Merge pull request #1733 from adalke/fastindex-compressed-datafile-msgs

warning/error messages for fastindex when the structure file is compressed

fe498e7ecd9affd327842b9de29d4d9e000ced93 authored about 7 years ago

During index creation, warn that gzip files will fail during fastindex search. Added error message in search if using a gzip file.

gzip files don't work because the fastsearch code has the index in the uncompressed file, but th...

dfed9c829b1f84e53de899756cf6744dc9e12b40 authored about 7 years ago

Merge pull request #1715 from baoilleach/AvoidSSSR

Speed up SMILES writer by replacement of SSSR in SMILES writer with a bounded BFS

127101b98fc0f03a954ec979cd3139a0a4a9226f authored about 7 years ago

Reduce Python bindings by 20% by avoiding adding methods from the iterated object to the iterator

b893521c2e4dc3fba5ba8f8ee07a120b6e3b1684 authored about 7 years ago

Merge pull request #1728 from baoilleach/AvoidStringCopy

In the SMILES reader, avoid allocating a BUFSIZE buffer, and the associated string copy

74e382f51291f0fef0116b6ba7de639adc542a26 authored about 7 years ago

In the SMILES reader, avoid the allocation of the BUFSIZE buffer, and the associated string copy.

8e4c8836474d4f2daa42bbaa40e6957b90236ec2 authored about 7 years ago

Add some std::vector reserves to speed things up

a43121b22c2422d114ee7882bcd65f9844530d96 authored about 7 years ago

Correct the comparison. I was stripping the stereo from the wrong double bonds.

74da3ead7007d3644aa68a2348fdd629589be977 authored about 7 years ago

Merge pull request #1718 from baoilleach/SmilesOptions

Minor speedup to avoid repeated calls to IsOption by caching some options

c36e1ee1646041e7249bb8d572807d18fc4c9cb4 authored about 7 years ago

Merge pull request #1723 from baoilleach/FixBadNoelRingClosure

Fixes for ring closure parsing

872c7e584a1354b8cca45d542167972acc17c017 authored about 7 years ago

Add the bounded BFS for smallest ring to the API

ea8b0f0d9456863b8eed24c15fe3b4c4e6aab65b authored about 7 years ago

Also cache option 'o'

86dfe8b51a28cc0b4d947d906da16dac8d0fba6b authored about 7 years ago

Make sure that OBAtom::IsInRing always triggers ring perception if not set as perceived

9ab4c6476798094ed6abd8ef412adfffe8fa0158 authored about 7 years ago

Add test cases that would have failed previously

574bcbacaa399b541bb344952a03cde49c03b3ec authored about 7 years ago

Fix parsing of %NN notation and %(NNN) notation

29adec8bbd8976e5a24485c32ebf8d8a4b1b66a1 authored about 7 years ago

Merge pull request #1721 from baoilleach/fix_uninitialized_read

Fix uninitialized read in kekulize.cpp found by Dr Memory.

960303b3d4cb23e1fbfb5af2ddccb27b59a7943d authored about 7 years ago

Read reaction map inside CDX

3df490a496c3e016faffee20918a52f4d89e3eb0 authored about 7 years ago

Merge pull request #1712 from baoilleach/SmilesAtomOrder2

Make generation of the SMILES atom order vector optional (Take 2)

1c7c093c1583d0e3aa9194ee9296e2263c6fbda5 authored about 7 years ago

Merge pull request #1719 from baoilleach/FixImplicitRef

Fix bug when copying stereo during obmol += obmolB

d80d036199dffe538b1e72db4c5b5f41a23a050e authored about 7 years ago

Add test case

fe6c1485bdc0671794df0729fdd5c439a9ba09d6 authored about 7 years ago

Minor speedup to avoid repeated calls to IsOption by caching some options

20bc70432c0eb444b7e540ddde181b92e945b966 authored about 7 years ago

Merge pull request #1716 from baoilleach/SmilesReader

When reading, don't pre-scan the SMILES string for illegal characters

8a79ebea8f469e0432e667e57f73b76f075d8eb6 authored about 7 years ago

Changes to avoid scanning over the string in the SMILES reader

b44045f18459913dc6578f95e392fbc653ebc0c9 authored about 7 years ago

Replace use of SSSR in SMILES writer with a bounded BFS search

c9915d67d40f405308392172df25f920a04b551f authored about 7 years ago

Merge pull request #1714 from baoilleach/LogMessages

Avoid logging messages that are taking time

b372010f7374a05d413e3fe233bc1833e0b4785e authored about 7 years ago

Avoid logging messages that are taking time

d0e8c1c903101019d7b278357a1222d14f2541ca authored about 7 years ago

When adding one molecule to another, and copying the stereo refs, make sure that implicitrefs are copied (and not just set to 0).

1c0ba799dfe385d738821c097d67309845d00d87 authored about 7 years ago

Make generation of the SMILES atom order vector optional, but also more efficient. Ensure that option 'x' keeps working.

325150e7880a19e41ba85a186a897fc81b70e285 authored about 7 years ago

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

4d168b3f062d4a29ffecb706370b5e01a3ddec6a authored about 7 years ago

Merge pull request #1706 from baoilleach/FastSmiles2

Faster SMILES: Replace std::endl by "\n"

d07d4ecad386474f6d6a9b4de7b3e7240529d4e6 authored about 7 years ago

Merge pull request #1707 from baoilleach/AvoidAuditMsg

Remove some audit messages

5e132000e0bab2ab97e870f4d40b9bb92767998d authored about 7 years ago

Remove some audit messages that copy the entire format description and then substring it.

fb19e7cf2e304ab2945ab9d375307b8c245c32c5 authored about 7 years ago

Use \r\n for Windows, which is the behaviour of the current release.

8dfaa8f6ad9cc4962f4a0d8f8eedad7d227f193c authored about 7 years ago

Avoid use of std::endl, as 3.5% of the conversion time from smi->smi is spent on that. Also, just have a single write to the output file stream.

043a2f38682081a4973a15e88ca92f6b1ace7c61 authored about 7 years ago

Merge pull request #1704 from baoilleach/fix_for_1701

Fix #1701

615f1046fa005edfb54bf70b8db0944425813003 authored about 7 years ago

Fix for #1701 as reported by @balducci. Wrong return value from function caused compiler error.

7a57706c2ccf5b9ee7177e01b6a108b18a0f56ff authored about 7 years ago

Fix uninitialized read in kekulize.cpp found by Dr Memory.

f640d8a124014d0515ec2eb70dc3e91038d06972 authored about 7 years ago

Merge pull request #1699 from baoilleach/fastersmi

Speed up the SMILES writer

5a9457ab01b473d1057ecd1dca107f4d49844c75 authored about 7 years ago

Remove final strcpys from smiles

76a7d9c7f389340ff99e722eed70deefa014137d authored about 7 years ago

Fix failing test, where '[' was being returned by the SMILES writer for a too-large value of the isotope.I've changed it to report a warning and ignore the value.

84e097bca467348cb9ad4fc5425ef155903f0753 authored about 7 years ago

Another round (the final?) of removing string copies.

7312f6df7f6fb3fa458a1a5da93158ff3ac9c0e5 authored about 7 years ago

Merge pull request #1696 from baoilleach/dont_perceive_stereo

By default, don't perceive stereo when reading SMILES, but have the option

d8af6a1f1ee8770f1e24e498679e28617f64106a authored about 7 years ago

Merge pull request #1698 from baoilleach/atommaps

Correct handling of atom maps

3cd84fbf29cd5be49d1b950494009f16a569565d authored about 7 years ago

Remove more strcpys, correct '[' instead of ']' and microopt AtomIsChiral

3fff8bb4e01b81dbdb95f63ca6a670d4b4743ed5 authored about 7 years ago

Replace another use of multiple obstereofacades in the smiles writer

16186370aff955f0b52aaf4bef2161af8abd8840 authored about 7 years ago

First round of removals of strcats and strlens from smiles writer

39022b1fe50e135c9c9cdb147c04b1e84df98f96 authored about 7 years ago

Speed up SMILES writing by avoiding creating a stereofacade multiple times

ed73bc4909e5bb999285693f4cedae899352fb5c authored about 7 years ago

Correct handling of atom maps by Open Babel. Atom maps were correctly handled when molecule was copied, added to another, or atoms deleted. Changed the behaviour to default to 0, and to allow values to be deleted (by setting to 0).

1ea4e3c3578b88b721594ba734bda3717381ede7 authored about 7 years ago

Merge pull request #1697 from cstein/expose-obfunctions_api

Expose obfunctions api through python bindings

34925bc47793372fb8d39471c70483cad4657109 authored about 7 years ago

Expose obfunctions api through python bindings

dd002f380d4a430cfa30469282fb157285735704 authored about 7 years ago

Add a comment explaining why the hybridisation flag needs to be set again.

Also trigger hybridisation perception before the molecule is copied or
workMol's bonds are deleted.

3d22141d7633177d8fa37ed6bee57beb24a46426 authored about 7 years ago

Make sure that a molecule copy copies the hybridisation flag. If it's already perceived, there's no need to reperceive and this would be unexpected as the molecule structure is unchanged on copy.

86bdc62bee7fcfcd7d2cad8346b0de12261bfe88 authored about 7 years ago

The other half of the 2nd last commit relating to the usage of OBRandom in vector3::randomUnitVector().

c4337343356707e2c343df7b03b6cc5d1f266ade authored about 7 years ago

Revert "If the hybridisation has not been perceived, this results in nans from GetNewBondVector() as GetHyb() returns 0. I don't understand why this statement was here."

This reverts commit a000bf72fe6407697b9a1411a5df7d1c596ca79d.

3b666b3b42386d272d397ab33b0e756999f0ba6f authored about 7 years ago

Drive-by fix for usage of OBRandom in vector3::randomUnitVector(). It was setting the timeseed each time a vector was requested. The granularity of this seed is one second, and so the same vector was being returned multiple times causing problems in the builder, which was repeatedly looping to get a non-colinear vector. I moved the timeseed down into the initialiser, but this is a bandaid and this whole OBRandom needs to be replaced.

bef0e66c5ab602600e1f858d6b6bdb6989dfe119 authored about 7 years ago

In order to properly mark unspecified cis/trans stereo, both gen2d and gen3d need to force reperception or else the unspecified centers will not be marked correctly.

09389ca4e14b3e6b35c0159c145b6224d2763da6 authored about 7 years ago

Update test to reflect new behavior. Unspecified tet centers no longer set parity to '3' in MOL files. This can only happen if 'S' is specified on reading to force reperception.

7717774ebc93935885f9d1ba9ebd5e3556a91e3a authored about 7 years ago

Add test case for reading stereo from SMILES with/out specifying the 'S' option for perceiving stereo on reading.

f1654feb6e5fc0c48db4bcb50fd67c4671cf7a3b authored about 7 years ago

Related to the previous commit. This test case no longer passes as this structure is no longer expected to have any stereo data associated with it when read from SMILES.

b57d6c549b29fb11a4df70bfa5041ec80910d1a2 authored about 7 years ago

Fix test failure where square planar stereo was not longer written by the SMILES writer. This was previously passing accidentally for the wrong reason, as the square planar center was being marked as an unspecified tetrahedral center.

f6902a6b44de4cb4f8c1be6ec7d5cadf03fc6359 authored about 7 years ago

Revert "Remove call to StereoFrom0D in MOL and CML handling."

This reverts commit f8aa3d679bdd4f442863740b8749ca004f383dd9.

d10772383c455b8b32591bd4766e1b18e8634f5f authored about 7 years ago

An update to the previous commit. Ensure that IsAromatic() always triggers aromaticity perception if the OBMol does not have the aromaticity perceived flag set.

63173f51907d6e7d4fe866708680065dcca9b624 authored about 7 years ago

Fix test failure. It turns out that UnsetAromaticPerceived() is not sufficient to trigger aromaticity perception when IsAromatic() is called. All of the aromaticity flags on atoms and bonds should be reset. I'm not sure if this is the correct behaviour but we can work with it for the moment.

80a108049fd7c64113e28babb0ff9befc1766e25 authored about 7 years ago

If the hybridisation has not been perceived, this results in nans from GetNewBondVector() as GetHyb() returns 0. I don't understand why this statement was here.

a000bf72fe6407697b9a1411a5df7d1c596ca79d authored about 7 years ago

Merge pull request #1686 from jeffjanes/SWIG_message

Clarify option needed to generate SWIG bindings.

9f2a742e113a500b99619e4f7ba27abbce3b3a5f authored about 7 years ago

Merge pull request #1687 from jeffjanes/perl_manifest

Correct spelling of file name for Perl bindings

689e5899eec8597718e593a72366986b971c60f5 authored about 7 years ago

Drive-by fix for bug where needs_kekulization is not initalized when reading XYZ etc files

17169439355d5101f2eff7578e02490f947e328b authored about 7 years ago

Fix shuffletest failure caused by an example molecule with a tet stereo

specified but with two methyls attached. It is now expected that these
cannot be kekulized correc...

74379df47c6e3b3eb54cc078a6e20c2027e5c970 authored about 7 years ago

Fix include directory for building Chemistry::OpenBabel

The header file openbabel/babelconfig.h is not in ../../include,
but rather is in ../../build/in...

2ccf8f70f4701782909d2d51b4a937b64c3d043c authored about 7 years ago

Correct spelling of file name for Perl bindings

The MANIFEST file has openbabel-perl.cpp spelled with
an underscore rather than a dash. This ca...

438474f24d0ea91c666c2d8c3ddfbc7a69117a66 authored about 7 years ago

Merge remote branch 'upstream/master' into SWIG_message

c1bb68475511e9b109173ffc3698c7882b91ba46 authored about 7 years ago

Clarify option needed to generate SWIG bindings.

If you try build bindings which have not been generated,
it provides a suggestion which, when co...

45c0b4c5fdb4c904a15b20d2addc2857fc020089 authored about 7 years ago

Remove call to StereoFrom0D in MOL and CML handling.

f8aa3d679bdd4f442863740b8749ca004f383dd9 authored about 7 years ago

Accept InChI stereo as given when reading

dffc219da2640589bd3619d1a0ab95d67cfdc71d authored about 7 years ago

When reading SMILES, avoid reperceiving the stereo unless option 'S' is specified.

be25837e0c860dae4c21d8f7e5bb423c19660661 authored about 7 years ago

Merge pull request #1596 from mcs07/pcjson

Fix pubchem JSON handling of enum types as ints

1711fbe82cf4c3b7bf07d8d989431e4ed1cbb7c9 authored about 7 years ago

Merge pull request #1678 from merkys/manpages

Adding missing manpags

cc38245afb96af845c046c2ff76131a60d0a1264 authored about 7 years ago

Merge pull request #1658 from ghutchis/Fix-Fingerprint-Folding

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

c3a62487b84f7736ef4cf1b12b11f5286abd062d authored about 7 years ago

Merge pull request #1667 from baoilleach/newrinchi

Add basic support for RInChI (Reaction InChI)

1278975e976d75b34a2af783cd34bec84ace88ef authored about 7 years ago

Merge pull request #1671 from openbabel/code-of-conduct

Create CODE_OF_CONDUCT.md

ac8f623ad69977dcfaf563b8b90574138ba862af authored about 7 years ago

Merge pull request #1677 from baoilleach/smiringclosure

Add support for %(NNN) notation for SMILES ring closures

7981240efcba73d125223859f4ef585a7bba0204 authored about 7 years ago

Weeding out the last .SH from manpage of obthermo.

7e3e3aed29ad67d43a3906dd239c7fc4222c9a48 authored over 7 years ago

Adding missing .El to manpage of obthermo.

a6186268dfadd96e18f6976d2073061efc68106b authored over 7 years ago

Reformatting manpage for obthermo.

a00965a9f0d50987d0f66fbc79b25fe066a138e0 authored over 7 years ago

Replacing .Sh via .SH in doc/obthermo.1.

2c57dc60224cf13e0247afe43f11b8cea9e07dae authored over 7 years ago

Adding manpage for obthermo.

50dd100935366c54ed13c3ecf6a0d570bb1a8510 authored over 7 years ago

Merge pull request #1673 from Acpharis/pybel_bytes_filename

Use isinstance to test if filename is bytes. Fixes #1615.

d11d46051419b8961ca5e9c131cc9dee5bd5bfc6 authored over 7 years ago

Adding manpage for obtautomer.

790b57015adfce0a43e84a074b98dd9ac102ebf4 authored over 7 years ago

Adding manpage for obsym.

671f09628d16f0f31f4162dff230c3a834f8d5df authored over 7 years ago