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

Set the valence field if setting M RAD to make sure that the number of hydrogens is read correctly

9b473d3224e958a436ba7c9c57346ca208be202e authored over 7 years ago

Minor fix to get radical test passing again

133dc3239d31eee772c211b446edb953a385cb71 authored over 7 years ago

Merge branch 'master' into radicals

c04f53b06aaa93317a24b3d9f535b77b71a8f986 authored over 7 years ago

Merge pull request #1610 from baoilleach/fix_slow_molfile_writing

Fix underflow causing a noticeable delay when e.g. writing a molfile

1517ddbf4ea50e132a852f6d8fba2e2621ad0677 authored over 7 years ago

Merge pull request #1601 from baoilleach/elements

Improve performance of element handling

4931b9abca7aef6c3ec7782f497172948e122bb3 authored over 7 years ago

Merge pull request #1609 from baoilleach/implicitH_tweak

Tweak the handling of implicit Hs when reading SMILES

4f47382a6ecc5d3b5447732ff9879b3c51c76da5 authored over 7 years ago

Fix underflow causing a noticeable delay when writing a MOL file with a single atom.

e34041448215be1191b6cfbf1e937d03713ea4ff authored over 7 years ago

Merge

3c8bc425102e2a0b5f589b33c67843f29da93441 authored over 7 years ago

Simplification/correction for calculation of number of implicit hydrogens when reading SMILES

681a004d47f0853ac97b20bf52c6b32e2470173b authored over 7 years ago

added matrix-matrix multiplication to the csharp bindings

711b1f8f2071c35c2db2f3bd80fb97608b4fae0a authored over 7 years ago

added ability to carry out matrix-vector multiplication to csharp bindings

18e475146e391c024c224dfa74df252df7f46a5b authored over 7 years ago

fixed some small misspellings in the csharp bindings

066ad0ee5d4cc1dd775f59a3d7cb02437bd694bf authored over 7 years ago

Handle interaction of valence field and M RAD when reading MOL file. Tested against Symyx Draw.

4678bcaad7fc26b1bebcccedd86b2bf5a757ad27 authored over 7 years ago

Correctly read the valence field in a MOL file

67872fd7afe44c250a1f498c47e9f7bd06db3e60 authored over 7 years ago

Merge pull request #1606 from baoilleach/Fix1605

Fix for calculating implicit H count when reading SMILES

3bcf71e4f06d418f1f3481ce3fb1472fcbf3ea36 authored over 7 years ago

Set the valence field in a MOL file if the number of hydrogens is not consistent with the MDL valence model.

a18681e499a002d394ee2b06e56f6d271a9724d8 authored over 7 years ago

Fix #1605. Forgot that GetValence returns the degree not the valence.

d3081acefd40410bf966b5b84828479ee9669dd6 authored over 7 years ago

Correct MM3 carboxyl oxygen atom type definition

c89ccb9634e78f9a99f5315e63ba0cd53ee7fd8c authored over 7 years ago

Remove old isotope data files

f6f84d4ea8295e3d1482d3d3d62fa7cba3123966 authored over 7 years ago

Remove all mention of OBIsotopeTable and isotab

444be6e64a46c405dc4e1b7d88fc49f5a6d56572 authored over 7 years ago

Add a test to check that a new element has been correctly added.

8ded1713ba23d6c758d0758b188366d93d647e4d authored over 7 years ago

Update comments

209308c67dc3881c2614bbfb0657c950306dbf09 authored over 7 years ago

Add some notes on how to add a new element. I will write some tests to enforce these rules.

bf109afd7eebf5b1b1eea48fb0d0a0adf7ce5e7e authored over 7 years ago

Add the isotope lookup to OBElements namespace

91a320713f498e78db1b3e4579a1a87478f0c55a authored over 7 years ago

Remove previous element table

fcf60e7aba011ff44c0fd60260cd2059c0cbc555 authored over 7 years ago

Update Python bindings

0d2d13e6a6193bf388aa217ccd9a9c62ac9d1acc authored over 7 years ago

Document the new element code

6d1e1ff7c6012aa6e39df90e02a723243c33d0cb authored over 7 years ago

Remove OBElement and OBElementTable.

eff3c755e6922b6adddfe13e8325dac10a8e5838 authored over 7 years ago

Removing final uses of GetNumberOfElements

30424498d2c519d92526dc355b5d634b99ead202 authored over 7 years ago

Removing use of GetNumberOfElements: first test has no effect, and no need for the second.

2ac019f7a164c1f26f442507d4d82fa1226306a5 authored over 7 years ago

Correction for previous commit

7a2a31455eced6ac1d3c768149b890f759fef824 authored over 7 years ago

Port GetRGB from etab to OBElements.

83432fce8816bfaeafd5689b28cf77511c199f20 authored over 7 years ago

Port uses of CorrectedBondRad to OBElements.

eb007e116375727d7ecdd12ac454b20f9b3e30b7 authored over 7 years ago

Replace final uses of etab.GetAtomicNum with OBElements.

a489bb8bbf70218d611a160df19d0d74f32f41b3 authored over 7 years ago

Merge pull request #1593 from keipertk/master

Change silicon to correct MM3 atom type

646f579c2d0fdeb848bc8ce23df5d66f0f61f620 authored over 7 years ago

Add missing include

5a3843dc18a0de227554a5cf3e4a568f332545a7 authored over 7 years ago

Replace etab.GetAtomicNum() with OBElements::GetAtomicNum for most cases.

1ffcea83c5d203ddf131e2fa09cebe6f86e80488 authored over 7 years ago

Change silicon to correct MM3 atom type

cf8a22121924fcb5bf69c3c9ff6082fbe59bc594 authored over 7 years ago

Merge pull request #1578 from afonari/patch-14

Parse _space_group_symop_operation_xyz in mmcif

9359f9e266c2c970026ea56f51a1af91e27b2e41 authored over 7 years ago

Fix wrong spin multiplicity assignment

3b32b219cccdb548c7103e3431a8f5f0616a4fc3 authored over 7 years ago

Merge pull request #1586 from mwojcikowski/fix-msvc

Introduce std:isnan for older versions of MSVC

f460d04ab9572153d30f302c1b533cbe652eb792 authored over 7 years ago

Merge pull request #1 from baoilleach/my_fix-msvc

Define OB_ISNAN to handle differences between MSVC versions

ac0fd291d423903fbada0aa5a9fa273cf4f1306c authored over 7 years ago

Define OB_ISNAN to handle differences between MSVC versions

357bde11e8a25eaad2267bf69cfe72cf9393aac9 authored over 7 years ago

Correct function name (GetAtomicMass) in OBElements to match the original in etab (GetMass).

a0cbf38e5ca9bb0c8482c9817b3b3b052dce1446 authored over 7 years ago

Replace two more etab methods.

98a11a12744f56f3a9387d3da1a1de1bbce3ff59 authored over 7 years ago

Add a few missing includes.

bce40a8a65fc1eb857e9481609c9d7f707173b82 authored over 7 years ago

Replace multiple etab multiple with the corresponding OBElements:: method.

f6cbee1adca3b163d6e1016f64046c83e1c5802a authored over 7 years ago

Replace etab.GetCovalentRad with OBElements::GetCovalentRad.

a894cc48436dd9acf4c55b418002604c9d60a708 authored over 7 years ago

Replace etab.GetSymbol with OBElements::GetSymbol.

6fc7c9a49b922034730e5020e9b487b63e4b7980 authored over 7 years ago

Remove IsHydrogen() and friends. Also IsNotCorH().

5e5755e4430675dcf6d06ea78b498b741db64ddf authored over 7 years ago

Port remaining instances of IsHydrogen(). Part Two.

66683da373e8ae9f9660a50c918a3c7d308b08f1 authored over 7 years ago

Port remaining instances of IsHydrogen().

50801704a1210de250abd0be171ddab65902459d authored over 7 years ago

Port instances of !IsHydrogen().

bd7a1156ed00720c991ba8d95f4baa08da914c48 authored over 7 years ago

Port IsPhosphorus() to the new code.

27421ffa6dd9da84dd8dae87b9961428d0be389b authored over 7 years ago

Port IsSulfur() to new code.

c0ce17f93a4505a9a343390e2b672b39c80028c6 authored over 7 years ago

Port IsOxygen() to new code.

e7153a2595ce82806dc6ccb6afcad0010d3bebab authored over 7 years ago

Port IsNitrogen() usages.

cf3f9521d43beedaf11682377fe0c1c41ac1f7ea authored over 7 years ago

Replace instances of IsCarbon().

dd241c464922fe7778d6f60595d78a0329afec08 authored over 7 years ago

Rewrite the conditionals

682931dd86a870ab9b2d46682f1db77a375271e4 authored over 7 years ago

Check-in new code for handling elements. (I haven't replaced the old code yet.)

5e869499182d4029dbe49eabfb7c6865d6a615a9 authored over 7 years ago

Merge pull request #1589 from baoilleach/smilesatomtypes

Improve performance of SMILES parser

829aa40444475831029e6c1a098808db6de0a12f authored over 7 years ago

Merge pull request #1588 from barrymoo/prepend_to_ld_library_path

Prepend to LD_LIBRARY_PATH instead of overwrite

360669bd1b05aad37a4e4eceb1d9a94bcc3a2a30 authored over 7 years ago

1. Add aromatic boron to parse complex.

2. When kekulizing, treat like pyrrole nitrogen
3. Add tests for parsing aromatic atoms in organi...

cd481d4685d1f9e153a6bee752e22e85bc4c82a0 authored over 7 years ago

Prepend to LD_LIBRARY_PATH instead of overwrite

4c82eee800b876b88906669af3157111e52b69c0 authored over 7 years ago

Merge pull request #1576 from baoilleach/workingimph

Keep count of implicit hydrogens instead of inferring them

172fc44a6a8f5bfa706fac1b67980ed4e9b342eb authored over 7 years ago

SMILES parsing performance improvements

1. Don't call SetType() during SMILES parsing.
2. Use a single switch for both aromatic and non-a...

35bb0fc90ae95d0afb2623e900b263111253eb21 authored over 7 years ago

Introduce std:isnan for older versions of MSVC

2329958316d976a5b170f613f2bc5f88feb63f22 authored over 7 years ago

Merge pull request #1582 from fredrikw/stereodepictfix

Fix wedge/hash in cyclopropyl

aef0f25a3c0e73a2b8c4ef1bfc55fd68afba4562 authored over 7 years ago

Added some comments in the code as to why the change is there.

7d1ecb6d905e0ba182619dd650bb8e28537e9257 authored over 7 years ago

Merge pull request #1585 from fredrikw/depictfragmentsfix

Fix multifragment depiction. Fixes #1357 and #1584.

341d49bc551e602b45283a90d58330634aa36ecc authored over 7 years ago

Made the code a bit more efficient (after suggestions from @baoilleach)

e9a592e105d7d9038d4e30e005de19373127fd65 authored over 7 years ago

Calculate a scalefactor for depiction of multifragment molecules without bonds (e.g. salts).

c940608d64edf7c20e6c41fd638527399d1341fd authored over 7 years ago

Fix 'regression' due to GetSize() returning zero for OBAtomTyper - this was causing an

error message about failure to initialize database.

1ac83a830a19846d965aef2cd89323deafb33c51 authored over 7 years ago

Made TetStereoToWedgeHash handle negative scores for very unfavorable wedge/hash bonds. Fixes #1581.

91e9a6a867200d2be46338a4e88fbbc1a76e9ff8 authored over 7 years ago

Removed the change in resonance structure from the vinylogous carboxylic acid pH model.

c6dcd70613f43946eb5f336148c86deb96f13efe authored over 7 years ago

Merge pull request #1575 from susilehtola/fpic

Compile position independent code for shared libraries.

59789f3ca3370b6f48ac4c5808bda8e7d6b9db60 authored over 7 years ago

Tidy some comments. Remove some commented out code.

725711ec67748852d5805ea815ed8727e4c9ea99 authored over 7 years ago

Merge pull request #1579 from aandi/patch-2

UFF: Fix conversion constant

2328def50bb5ff321214ca68bb3c4771d8181d53 authored over 7 years ago

Update UFF test case energies

Update energies, related to 347190265a17d994680d674e2cb7e8b3350055db

f88027b25037021361a1eaa84f849de814db6368 authored over 7 years ago

UFF: Fix conversion constant

Probably a typo, the constant 2G=664.12 (not 644...) converts units to kcal/mol, see also equati...

347190265a17d994680d674e2cb7e8b3350055db authored over 7 years ago

Remove duplicate line in a test

7e69177f294b79e21575a3b4b93fcbb6d246ee5c authored over 7 years ago

Added a test

e07c2e86f861639850a7b5813bdeaa21c7e6df49 authored over 7 years ago

Parse _space_group_symop_operation_xy in mmcif

c151584339589f9052d44e5352b88a1fa636a33e authored over 7 years ago

Final tidies

5c3211dc51b7763ec3c7ff738a3823b705d559c4 authored over 7 years ago

Check in some missing header files. obfunctions.h should be renamed after discussion.

a9354de723b4398f3e659b96d4cb7693e8160563 authored over 7 years ago

Compile position independent code for shared libraries.

ecd7dc73dad4e7d81c7f0c0d659dabc962d6d948 authored over 7 years ago

Merge pull request #1572 from serval2412/master

cppcheck: Condition '1==0' is always false

5b67af61725c694e4ddbcb26263332d88063e190 authored over 7 years ago

Merge pull request #1558 from afonari/patch-12

Allow to set space group origin in PDB CRYST1 section

acf242e88876768b5736fd8743d9ea62da060a1e authored over 7 years ago

Fixed ZTS calculation reading from the latest nwchem.

4f340fc78e42e68d1274755d84d46812445a063a authored over 7 years ago

Fixed inconsistent number of frequencies and intensities

12db2b10cb36c298eca89980dc14665eb4f4dd1a authored over 7 years ago

Fixed ineffective memory usage while frequency calculation reading

0cf2c99181b9891cc13672ff9c64a9a0e8c9d768 authored over 7 years ago

Change calls from const string& to const char*

ddcbb5d574031fa2cddb2d8bf24e556ecf129740 authored over 7 years ago

Rename Get/SetImplicitHydrogen to Get/SetImplicitHCount

85c43296275d4352199d918222f95e4744f8514b authored over 7 years ago

1. Remove all references to SetImplicitvalence, SetNoImplicitH and ForceImplH and suchlike.

2. Commented out the ZBO extension code in MDLFormat for now. Will need to either remove or updat...

6ed745f93b6dd130aebb25e4dbda0fe5092d4e4c authored over 7 years ago

Remove all references to GetImplicitValence, ImplicitHydrogenCount, and the associated implicit valence typer.

0a15ddda868d9802bb01ca0b1fa4079ce6bf791c authored over 7 years ago

1. Get rid of text of OBMol::AssignSpinMultiplicity() as it doesn't do anything now

2. Update OBMol::AssignTotalChargeToAtoms() for change to implicit valence. This required a littl...

ceb7d55a8d09061fa52d44ffe0661e27d4653911 authored over 7 years ago

Update ref to GetImplicitValence in pdbqtformat.cpp

3dbfab76f54014ef96d1bf9ca8c01ae48bfc781d authored over 7 years ago

Removing GetImplicitValence(): Update OBMol::AddHydrogens(OBAtom*) and GetGIVector()

3d7e83e7ef02f52d776bc003da05a055580eed3b authored over 7 years ago

Removing GetImplicitValence(): Change IsPrimaryAmide and friends

ef0f3fb5bbbff5982d4c8c8748baa2740d3e3d46 authored over 7 years ago

Get tautomertest to pass by:

1. Porting to new implicit H system
2. Fixed bug in original code for generation of canonical tau...

6839e180d2f28871bf67c9ccb9fab39d0ae559a9 authored over 7 years ago