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_data

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

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

Wrap

another pass of clang modernize

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

AUTOCORR2D.cpp

another clang-format run

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

AUTOCORR2D.h

another clang-format run

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

AUTOCORR3D.cpp

another pass of clang modernize

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

AUTOCORR3D.h

another clang-format run

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

CMakeLists.txt

assorted fixes to get the current master branch to build on Windows (#1495)

2017-07-18 08:04:23 +02:00

ConnectivityDescriptors.cpp

first pass, using google style

2015-11-14 14:58:11 +01:00

ConnectivityDescriptors.h

first pass, using google style

2015-11-14 14:58:11 +01:00

Crippen.cpp

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

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

Crippen.h

Dev/moldescriptors callables (#944)

2016-06-22 08:07:56 +02:00

Data3Ddescriptors.cpp

Add a collection of new 3D descriptors (#1467)

2017-07-02 11:28:48 +02:00

Data3Ddescriptors.h

Add a collection of new 3D descriptors (#1467)

2017-07-02 11:28:48 +02:00

datas.cpp

another clang-format run

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

GETAWAY.cpp

another clang-format run

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

GETAWAY.h

another clang-format run

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

Lipinski.cpp

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

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

Lipinski.h

Add feature for #1375 (#1384)

2017-03-28 16:02:21 -04:00

MolData3Ddescriptors.cpp

another clang-format run

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

MolData3Ddescriptors.h

Add a collection of new 3D descriptors (#1467)

2017-07-02 11:28:48 +02:00

MolDescriptors3D.h

Add a collection of new 3D descriptors (#1467)

2017-07-02 11:28:48 +02:00

MolDescriptors.cpp

Dev/moldescriptors callables (#944)

2016-06-22 08:07:56 +02:00

MolDescriptors.h

Add a collection of new 3D descriptors (#1467)

2017-07-02 11:28:48 +02:00

MolSurf.cpp

first pass, using google style

2015-11-14 14:58:11 +01:00

MolSurf.h

first pass, using google style

2015-11-14 14:58:11 +01:00

MORSE.cpp

Add a collection of new 3D descriptors (#1467)

2017-07-02 11:28:48 +02:00

MORSE.h

another clang-format run

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

MQN.cpp

first pass, using google style

2015-11-14 14:58:11 +01:00

MQN.h

first pass, using google style

2015-11-14 14:58:11 +01:00

PBF.cpp

clang-tidy output

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

PBF.h

Add some 3D molecular descriptors (#1084)

2016-10-10 08:34:08 -04:00

PMI.cpp

Fix/github1262 (#1265)

2017-01-22 05:49:52 +01:00

PMI.h

Fix/github1262 (#1265)

2017-01-22 05:49:52 +01:00

Property.cpp

clang-tidy output

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

Property.h

Dev/moldescriptors callables (#944)

2016-06-22 08:07:56 +02:00

RDF.cpp

Add a collection of new 3D descriptors (#1467)

2017-07-02 11:28:48 +02:00

RDF.h

another clang-format run

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

RegisterDescriptor.h

Dev/moldescriptors callables (#944)

2016-06-22 08:07:56 +02:00

test3D_old.py

Add a collection of new 3D descriptors (#1467)

2017-07-02 11:28:48 +02:00

test3D.cpp

Fix/github1262 (#1265)

2017-01-22 05:49:52 +01:00

test3D.cpp.hold

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

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

test3D.py

Add a collection of new 3D descriptors (#1467)

2017-07-02 11:28:48 +02:00

test_list.py

Issue1071/yapf (#1078)

2016-09-23 04:58:46 +02:00

test.cpp

another clang-format run

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

testAUTOCORR2D.cpp

another clang-format run

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

testAUTOCORR3D.cpp

another clang-format run

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

testGETAWAY.cpp

another clang-format run

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

testMORSE.cpp

another clang-format run

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

testPBF.cpp

another clang-format run

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

testRDF.cpp

another clang-format run

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

testSMWHIM.txt

Add a collection of new 3D descriptors (#1467)

2017-07-02 11:28:48 +02:00

testWHIM.cpp

another clang-format run

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

USRDescriptor.cpp

another clang-format run

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

USRDescriptor.h

another clang-format run

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

WHIM.cpp

another clang-format run

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

WHIM.h

another clang-format run

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