Maciej Wójcikowski 10fbd483bb [MRG] Fix PDB reader + add argument to toggle proximity bonding (#1629) ...

* Add parameter to skip proximity bonding during PDB reading

* Test proximityBonding flag

* Remove multivalent Hs and bonds to metals in PDB

* Add tests for multivalent Hs and metal unbinding

* Remove covalent bonds to waters

* Test unbinding of HOHs

* Refactor funxtions

* Rename flag for cosistency

* Include flavor in double bond perception

* Add metalorganic test (APW ligand)

* Validate input foe IsBlacklistedPair and minor changes.

2017-11-15 06:53:31 +01:00

..

test

Add StructChecker functionality

2016-10-24 08:00:07 +02:00

Wrap

yapf formatting of recent changes to Python code in rdkit and Code

2016-10-24 11:57:08 -04:00

AtomSymbolMatch.cpp

run clang-format with c++-11 style over that

2017-04-22 17:19:10 +02:00

AugmentedAtomData.cpp

Add StructChecker functionality

2016-10-24 08:00:07 +02:00

CMakeLists.txt

Add StructChecker functionality

2016-10-24 08:00:07 +02:00

Pattern.cpp

another pass of clang modernize

2017-10-12 06:35:51 +02:00

Pattern.h

Add StructChecker functionality

2016-10-24 08:00:07 +02:00

ReCharge.cpp

run clang-format with c++-11 style over that

2017-04-22 17:19:10 +02:00

ReCharge.h

Add StructChecker functionality

2016-10-24 08:00:07 +02:00

Stereo.cpp

run clang-format with c++-11 style over that

2017-04-22 17:19:10 +02:00

Stereo.cpp.bak

[MRG] Fix PDB reader + add argument to toggle proximity bonding (#1629)

2017-11-15 06:53:31 +01:00

Stereo.h

Add StructChecker functionality

2016-10-24 08:00:07 +02:00

StripSmallFragments.cpp

another clang-format run

2017-10-12 06:42:15 +02:00

StripSmallFragments.h

Add StructChecker functionality

2016-10-24 08:00:07 +02:00

StructChecker.cpp

Add StructChecker functionality

2016-10-24 08:00:07 +02:00

StructChecker.h

update documentation

2016-10-24 08:45:58 +02:00

StructCheckerOptions.cpp

a number of other small changes from manually reviewing the PR

2017-04-22 17:24:57 +02:00

StructureFlags.cpp

clang-tidy output

2017-04-22 17:09:24 +02:00

Tautomer.cpp

run clang-format with c++-11 style over that

2017-04-22 17:19:10 +02:00

Tautomer.h

Add StructChecker functionality

2016-10-24 08:00:07 +02:00

testStructChecker.cpp

run clang-format with c++-11 style over that

2017-04-22 17:19:10 +02:00

Utilites.cpp

run clang-format with c++-11 style over that

2017-04-22 17:19:10 +02:00

Utilites.h

Add StructChecker functionality

2016-10-24 08:00:07 +02:00