* first pass, does not yet actually work
* pass2, same problems
* pass2, same problems
* another test
* new tests; bugfix
* move the code out to a header
* add a double bond example
* enable auto-downloads of the code
* move the function to its own namespace
* first pass at a basic python wrapper
* change coordgen commit used
* try supporting bond stereo; does not currently work
* cis/trans seems to now work.
* first pass at templates; needs testing
* use the fixed flag too
* need mol align
* expand test
* initial pass at python wrapper for template
* simplify tests
* add an option to directly use a substructure match for alignment
* scaling
* add #define
* Define a cache setting for RDK_COORDGEN_LIBS to allow these to be used in other packages
* return the conformer id from addCoords
* Make CoordGen the default when it’s available.
This is a backup commit… the tests don’t even come close to passing.
* add some debugging options for a bit
* add alignment step to testing when using non-fixed coords
* Add global to allow use of CoordGen to be disabled
get the basic depictor tests working
* make coordgen the default when it is available
* make sure things continue to work when coordgen is disabled
* get windows builds working
* mods to get this building on windows.
something is screwy with the fileParsersTest1
* no need to generate coords for the 1K C string
* fix java wrappers
* works on linux
* update the (stupid) way dependencies were handled on windows.
this allows a lot of cleanup of cmake files (still more to do)
the linux build is unlikely to work due to the way _statics aren't handled
* docs
* extend forceRDKit applicability
* switch coordgen version
* try using templates
* try to get the template dir finding reasonably robust w.r.t. conda install
* continuing to iterate on the way the template file is installed
* fix a problem caused by the merge
* remove test that should never have been checked in
* update expected results for cartridge tests
* switch back to using the RDKit as the default coordinate generator
* Fixes atom documentation
* Fixes#1461
This is a complicated one. Basically URANGE_CHECK when
used on unsigned integers has a problem when the size of
the range it’s checking is 0. The standard operations is
to check
URANGE(num, size-1)
Which (for unsigned integers) obviously rolls over.
This fixes all usage cases to be
URANGE(num+1, size)
And fixes the bugs found. (addBond and the mmff tests)
* Fixes#1461 - Updates URANGE_CHECK to be 0<=x<hi
* add a test (currently fails, of course)
* backup, not really working
* Fixes#1240
* a bit more parameter tweaking to get some more structures to embed
* - optimization to UFF and MMFF forcefields
* - further optimizations (memset, factoring unnecessary in-loop
initialization out of the loop, replacing if clause with pre-increment)
* - fixed a couple of stylistic glitches
* - the torsionSmarts parameter in addTorsions() is now a const std::string&
* - implemented the DefaultTorsionBondSmarts singleton using boost::call_once()
* passes all tests, but is still not 100 percent there
* generalize _centerInVolume for possible future use
* better testing of tetrahedral centers
update tests
* only test ring atoms
* handle 4-coordinate n too
* add a volume check; not all tests pass
* turn off debug printing
* rearrange the order of tests.
if this is not done, we get a seg fault when the github55 test runs.
the whole thing needs to be run under valgrind to track this down
* clear up a memory leak
* a bit more documentation
add a constant for one of the threshold values
* get more permissive on the energy tests.
Only do the extra tetrahedral tests for atoms in at least two rings.
* add a DEBUG_EMBEDDING option to make tracking down failures easier
* enable better debugging when the flag is set
* remove a FIX
* remove some debug printing from the tests
* enforce planarity
* increase the force constant for the impropers
* force constant adapted
* reduced tolerance for planarity and force constants changed for some torsions
* tolerance for planarity increased a bit again
* cerr outputs removed
* planarity tolerance increased
* boost log added in planarity check
o rdkit gains a RDKit::common_properties namespace that contains common string value properties
o Dict.h and below gain getPropIfPresent that attempts to retrieve a property and returns
true/false on success or failure. This is used to optimize access.
o rdkit learns how to pass property keys by reference, not value.
A new namespace has been added to RDKit, common_properties
that contains the std::string values for commonly used
properties. This helps to avoid typos in string values
but also avoids a creation of std::strings from character
values. All accessors (has/get/clear and getPropIfPresent) now pass
the key by reference.
Additionally, getPropIfPresent removes the double lookup
of hasProp/getProp which can be a significant speedup
in the smiles and smarts parsers (10-20%)
which caused issues with negative angles
- made also UFF/AngleConstraint.cpp and MMFF/AngleConstraint.cpp more
robust against angle ranges involving negative values
- added relevant C++ and Python tests
(i.e., equilibrium distances/angles and force constants) from
UFF and MMFF in response to two requests recently appeared
on the RDKit-discuss mailing list:
http://sourceforge.net/p/rdkit/mailman/message/32953737/http://sourceforge.net/p/rdkit/mailman/message/32880156/
- did some clean up on the MMFF code
- NB there are two ABI changes:
1) StretchBendContrib(ForceField *owner,
const unsigned int idx1, const unsigned int idx2, const unsigned int idx3,
const MMFFStbn *mmffStbnParams, const MMFFAngle *mmffAngleParams,
const MMFFBond *mmffBondParams1, const MMFFBond *mmffBondParams2);
previously was:
StretchBendContrib(ForceField *owner,
const unsigned int idx1, const unsigned int idx2, const unsigned int idx3,
const std::pair<bool, const MMFFStbn *> mmffStbnParams,
const MMFFAngle *mmffAngleParams, const MMFFBond *mmffBondParams1,
const MMFFBond *mmffBondParams2);
2) std::pair<double, double> calcStbnForceConstants(const MMFFStbn *mmffStbnParams);
previously was:
std::pair<double, double> calcStbnForceConstants
(const std::pair<bool, const MMFFStbn *> mmffStbnParams);
The two changes are NOT mandatory - however, both the StretchBendContrib constructor
and calcStbnForceConstants(), though public, are basically "internal" method that
most likely no-one has ever invoked. Given that the current API is MUCH better
and cleaner, I would really advise for the new version.
to segfault when a system not listed in the MMFFBndk
table was found. THe Herschbach-Laurie fallback according
to MMFF.V was implemented and a relevant test was added
in testMMFFHelpers.cpp
- fixed a bug in Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.cpp
which caused misassignment of atom types in CYGUAN01 upon shuffling
the order of atoms in the validation SDF files
- added checks for acos and asin function parameters to be within
a (-1, 1) range
