Greg Landrum d15efc1ac9 Make the defaults for some functions less error prone. (#1690) ...

* auto generate coords in mol block writer if includeChirality = True

* default to include chirality when writing mol blocks/files

* make isomeric smiles the default; note that not all tests are passing at the moment

* update a reaction test

* update expected cartridge search results
at this point all python, c++, and cartridge tests pass

* docs

* update incompatibility docs

* update doctests

* these now build

* minor example update

* update expected c++

* typo

* make allowCXSMILES=true the default

* add auto perception of chirality when reading 3D structures from mol blocks

* explain changes in release notes

* further doc update

2017-12-22 08:09:36 -05:00

..

test_data

Issue1071/yapf (#1078)

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

Atom.cpp

Merge branch 'master' into modern_cxx

2017-10-05 05:58:38 +02:00

Bond.cpp

Merge branch 'master' into modern_cxx

2017-10-05 05:58:38 +02:00

CMakeLists.txt

Merge branch 'master' into modern_cxx

2017-10-05 05:58:38 +02:00

CompressedSDMolSupplier.cpp

first pass, using google style

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

Conformer.cpp

Conformer GetPos returns a numpy array rather than a tuple of tuples (#1087)

2016-10-14 05:02:59 +02:00

EditableMol.cpp

another clang-format run

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

ForwardSDMolSupplier.cpp

clang-tidy output

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

Mol.cpp

another clang-format run

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

MolBundle.cpp

Expose the MolBundle to python (#1583)

2017-09-26 13:00:53 -04:00

MolOps.cpp

Cleanup a bunch of compiler warnings (#1697)

2017-12-22 12:59:52 +01:00

MolSupplier.h

first pass, using google style

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

MonomerInfo.cpp

first pass, using google style

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

PDBWriter.cpp

clang-tidy output

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

props.hpp

Check for doubles after other integer types when reporting properties (#1115)

2016-10-21 20:43:43 -04:00

Queries.cpp

clang-tidy output

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

rdchem.cpp

Merge branch 'master' into modern_cxx

2017-10-05 05:58:38 +02:00

rdchem.h

Conformer GetPos returns a numpy array rather than a tuple of tuples (#1087)

2016-10-14 05:02:59 +02:00

rdmolfiles.cpp

Make the defaults for some functions less error prone. (#1690)

2017-12-22 08:09:36 -05:00

rdmolfiles.h

first pass, using google style

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

rdmolops.cpp

add some additional parameters tests to python wrapper;

2016-11-06 10:09:57 +01:00

rdmolops.h

first pass, using google style

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

rdqueries.cpp

Remove extra calls to python::register_exception_translator

2016-03-01 06:36:54 +01:00

rdTrajectory.cpp

- added miising Code/GraphMol/Wrap/rdTrajectory.cpp

2016-05-11 19:56:32 +01:00

ResonanceMolSupplier.cpp

another clang-format run

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

RingInfo.cpp

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

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

rough_test.py

Make the defaults for some functions less error prone. (#1690)

2017-12-22 08:09:36 -05:00

SDMolSupplier.cpp

first pass, using google style

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

SDWriter.cpp

clang-tidy output

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

seqs.hpp

Fix/github1366 (#1382)

2017-03-28 16:01:36 -04:00

SmilesMolSupplier.cpp

clang-tidy output

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

SmilesWriter.cpp

Make the defaults for some functions less error prone. (#1690)

2017-12-22 08:09:36 -05:00

substructmethods.h

Expose the MolBundle to python (#1583)

2017-09-26 13:00:53 -04:00

Table.cpp

Add python wraps (#1259)

2017-01-16 10:16:48 +01:00

TDTMolSupplier.cpp

first pass, using google style

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

TDTWriter.cpp

clang-tidy output

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

test_list.py

Issue1071/yapf (#1078)

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

testConformer.py

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

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

testThreads.py

Issue1071/yapf (#1078)

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

testTrajectory.py

Fix trajectory tests

2016-11-15 13:47:52 +00:00

Trajectory.cpp

clang-tidy output

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