* fix for calculation of prinicipal moments of inertia
* fix a typo
update expected values
* PMI and NPR tests working
* cleanup some of the other descriptors and tests
* Test against Moments.py descriptors
* add new tests from Brian
* remove some warnings
* fix compatibility with PostgreSQL 9.2
* get tests working on pgsql92; the Makefile does not currently work
* simplify 9.2 handling
* seems to work on 9.6 and 9.2 now
* - fixed issue with weighted formal charges being stored as unsigned rather than as signed int
- the sum of formal charge and multiple bond indices is now used as last resort sort criterion to achieve stable sorting of degenerate resonance structures
* - added C++ and Python tests for GItHub #1166
* Added getAlignmentTransform to ROMol.i to expose in Java SWIG wrapper
* Added missing argument
Added missing argument to call to getAlignmentTransform causing build failure
* Added test case for getAlignmentTransform
* Update AlignTests.java
* Update AlignTests.java
* Update AlignTests.java
* Expose RDKit's DetectBondStereoChemistry to python.
* Adding a test case for DetectBondStereoChemistry from python.
This test case ensures a new molecule can be constructed from scratch
and DetectBondStereoChemistry detects the correct bond stereo from the
3D coordinates alone.
* Fix a bug in the python DistGeom tests.
* test new features
* add simple parameter objects for ETDG, ETKDG, and KDG
* Update conformation generation documentation to use the new parameter objects.
* Adds C++ Enumeration Engine to the RDKit
* Adds Sanitization helpers, wrappers and tests
* Clang format
* Remove unused enumerationStateOnly flag
* Fixes docStrings to current API
* Adds doc strings
* Removes RGroupPosition, adds getPosition to EnumerationBase
* Fixes readability.
* Adds EnumerateLibraryBase::reset and getReaction
* Added getReagents method to EnumerateLibrary
* Make the tests have the same naming
* Need to save the initial state for resetting.
* Stupid case-insensitive file systems
* Moves ResetState to EnumerateLibraryBase
* Adds removeNonmatchingReagents helper
* Renames currentPosition to getPosition
* Adds Enumeration Toolkit tutorial
* Fixes Python3 serialization and enumerators
* Verified to run on python2 and 3
* Fixes integer issues on windows
* The number of enumeration should be unsigned.
* Adds deserialization constructor
* Moves boost_serialization to the end
* Deprecates Clone in favor of copy
* Update tests to use copy.copy not Clone
* Move RGROUPS and BBS into an EnumerationTypes namespace
* Make sure old pickles work
* Adds pickle for backwards compatibility
* Moves to uint64_t from size_t for public api
* Whups, accidentally used the binary archiver.
* Commits boost 1.55 serialization
* Makes serialization turnoffable Like Filter Catalog
* Fixes tests when serialization not available. Adds more enumeration strategy tests
* Fixes a syntax error on some versions of python
* Fixes sanitizeRxn to actually make proper RGroup atoms
* Updates SanitizeRXN python API
* Updates Enumeration API to a parameter class - fixes reagent removal
* Adds a mess of tests
* Change stats to return a string.
* Exposes EvenPairSamplingStrategy Stats to python
* Fixes a crash bug in SanitizeRxn
* Adds better testing of the even pair sampling
* Fixes namespace
* One more try to fix gcc
* Enum classes are c++11 and a microsoft extension.
* Fix typo
* Fixes np.median for python3
* Fixes atom iterators
* Adds virtual tags to derived virtual functions (for clarity)
* Fixes size comparison issues
* Adds doc string
* Small cleanup (has no effect since flags aren’t used)
* fixes crash bug on windows
* get the tests working on windows
* Updates tutorial
* Adds Glare implementation to Contrib
* first pass at RWMol::replaceBond()
* get ready for the changes
* rename some options
add bond options (not doing anything with them yet)
update tests to reflect new options
* backup
* re-enable the rest of the tests
* patch from Roger Sayle to support nucleic acids as well as amino acids
* add some tests which do not yet pass
* fix a bug I introduced in residue name parsing
* basic sequence testing
* add some more tests
* initial version; no actual testing yet
* start on tests
* rename seed->randomSeed; add tests
* add support in java wrapper
* add support in python wrapper
* initial version; no actual testing yet
* start on tests
* rename seed->randomSeed; add tests
* add support in java wrapper
* add support in python wrapper
* yapf
* document the parameter object;
introduce pre-defined const objects for ETDG, ETKDG, and KDG
* this is why we write tests
* swig did not like the initialization in the header file
* findSSSR performance improvements for fragments without rings
This makes Chem.SanitizeMol significantly faster when dealing with
molecules with lots of disconnected fragments (like a box of water).
The following is the runtime of Chem.SanitizeMol while adding 10,000
waters with explicit hydrogens when running Chem.SanitizeMol on every
1,000th water added.
Before:
0 add_water = 0.00007s
0 Chem.SanitizeMol = 0.01991s
1000 add_water = 0.00009s
1000 Chem.SanitizeMol = 0.99659s
2000 add_water = 0.00013s
2000 Chem.SanitizeMol = 3.94565s
3000 add_water = 0.00018s
3000 Chem.SanitizeMol = 8.94760s
4000 add_water = 0.00023s
4000 Chem.SanitizeMol = 15.75187s
5000 add_water = 0.00035s
5000 Chem.SanitizeMol = 24.59318s
6000 add_water = 0.00048s
6000 Chem.SanitizeMol = 37.23530s
7000 add_water = 0.00042s
7000 Chem.SanitizeMol = 47.70860s
8000 add_water = 0.00105s
8000 Chem.SanitizeMol = 62.21912s
9000 add_water = 0.00056s
9000 Chem.SanitizeMol = 80.08511s
After:
0 add_water = 0.00003s
0 Chem.SanitizeMol = 0.01219s
1000 add_water = 0.00004s
1000 Chem.SanitizeMol = 0.01004s
2000 add_water = 0.00012s
2000 Chem.SanitizeMol = 0.01058s
3000 add_water = 0.00018s
3000 Chem.SanitizeMol = 0.01158s
4000 add_water = 0.00018s
4000 Chem.SanitizeMol = 0.01530s
5000 add_water = 0.00022s
5000 Chem.SanitizeMol = 0.02010s
6000 add_water = 0.00036s
6000 Chem.SanitizeMol = 0.02397s
7000 add_water = 0.00033s
7000 Chem.SanitizeMol = 0.02978s
8000 add_water = 0.00037s
8000 Chem.SanitizeMol = 0.04446s
9000 add_water = 0.00040s
9000 Chem.SanitizeMol = 0.04419s
* Refactor new_timings.py script a bit to be able to run only the first (reading molecules) test.
* Removing O(N^2) behavior of finding the number of bonds in the fragment during SSSR.
This only improves the case when there are long chains and a small
number of rings in the fragment. Many ring systems are still dominated
by the rest of the SSSR algorithm, and fragments with no ring systems
don't reach this part of the code.
For a test case with a single cyclicpropane and adding carbons while
calling Chem.SanitizeMol every 10,000 carbons added yield the
following improvement in performance:
before:
0 add_carbon = 0.00001s
0 Chem.SanitizeMol = 0.01237s
10000 add_carbon = 0.00017s
10000 Chem.SanitizeMol = 0.04453s
20000 add_carbon = 0.00017s
20000 Chem.SanitizeMol = 0.13038s
30000 add_carbon = 0.00029s
30000 Chem.SanitizeMol = 0.27671s
40000 add_carbon = 0.00063s
40000 Chem.SanitizeMol = 0.44774s
50000 add_carbon = 0.00106s
50000 Chem.SanitizeMol = 0.69433s
60000 add_carbon = 0.00181s
60000 Chem.SanitizeMol = 1.00577s
after:
0 add_carbon = 0.00001s
0 Chem.SanitizeMol = 0.01264s
10000 add_carbon = 0.00013s
10000 Chem.SanitizeMol = 0.01349s
20000 add_carbon = 0.00022s
20000 Chem.SanitizeMol = 0.02724s
30000 add_carbon = 0.00040s
30000 Chem.SanitizeMol = 0.04292s
40000 add_carbon = 0.00076s
40000 Chem.SanitizeMol = 0.06172s
50000 add_carbon = 0.00193s
50000 Chem.SanitizeMol = 0.07658s
60000 add_carbon = 0.00147s
60000 Chem.SanitizeMol = 0.08625s
Note, couldn't actually test a higher number of carbons as it led to a
stack overflow due to recursion in findSSSR.
* StructChecker changes. Initial commit. First implementation. Added some tests.
* StructChecker: add GoodAtoms and AcidicAtoms. new updates
* StructChecker: add new tests
* StructChecker: added TransformAugmentedAtoms()
* StructCheck: add structCheck to GraphMol. Fix compilation errors.
* StructChecker: add stereo verification and some utilities.
* StructChecker: function FixDubious3DMolecule was added
* StructChecker: checkStereo added. done with stereo.
* StructChecker: add StripSmallFragments()
* StructChecker: add AtomClash() function. Some cosmetic + tests
* StructChecker: checkAtoms() was started
* StructChecker: checkAtoms is ready
* StructChecker: user RingInfo from RDkit. Start regarge
* StructChecker: ReCharge molecule method prototype
* StructChecker: updates for ReCharge. Almost finished
* StructChecker: all ReCharge is done except external data tables loading
* StructChecker: add path tables into API. ReCharge completed
* Adds augmented atom data
Signed-off-by: Brian Kelley <brian.kelley@novartis.com>
* Removes extra files
Signed-off-by: Brian Kelley <brian.kelley@novartis.com>
* Adds path to test data via RDBASE environment
Signed-off-by: Brian Kelley <brian.kelley@novartis.com>
* Revert "Struct checker apr15"
* StructChecker: add missing tautomer tests
* Updates test to use RDBASE
* Adds initialization of data from data section
* Adds Python API and tests
* Fixes namespace for enum
* StructChecker: update/imporve strip small fragments
* StructChecker: fix acidic atoms (but logic does not work)
* StructChecker: fix match issue for CheckAtoms
* Adds macro guards
* Adds loading API and proper constructor
* Fixes tests, adds stereo test
* Fixes crash bug, matches[0] was being accessed from an empty match vector
* Reverts crash fix - conflicts with previous
* Adds the rest of the structure checker options
* StructChecker: fix atom matching for aromatic rings
* StructChecker: add tautomers checks. Update some tests
* StructChecker: stereo fixes. Add some tests
* StructChecker: fix check atoms. Start ligand symbol list
* StructChecker: fix some check atoms validation. Add Tranform to query lists. Start correct loading augmented atoms
* update
* another set of fixes
* StructChecker: fix loadDefaultAugmentedAtoms. Some changes in CheckAtom + tests + debug conditional breakpoints (TEMP operators)
* StructChecker: rewrited RecMatch() to sequential. Changed bond matching algorithm. small bug fixes
* Adds better logging of mismatched atoms
* Removes duplicated negative charge
* Fixes charges
* Adds nitro group test
* StructChecker: add better logging
* remove double logging
* Reformats code using RDKit's clang-format style
* StructChecker: Fix charge reformat using RDKit format.
* StructChecker: compilation restore after merge
* restore bond matching
* Removes the same fragments that strucheck does in case of ties
* Don't resanitize - this adds aromaticity which mucks things up
* Adds empty molecule checks
* Fixes atom clashes.
* Removes debug printing
* Removes debug logging info
* First pass at stereo fixes
* Fixes off by one error for dubious stereo fix
* Fixes more off by one errors
* Fixes more off by one errors
* More off by one fixes.
* Another off by one
* Fixes chiral flag set in molfile check
* Copies chiral flag over to largest fragment if necessary
* Poor man’s parity check.
* Find unspecified chiral centers ala Avalon.
* StructChecker: fix recursive match. Fix transformations
* StructChecker: fix transformation for atom list (using query atoms)
* Fixes checks && to &
* StructChecker: fix carboxylic acids tranform issue. Atom list is changed only if different
* StructChecker: documentation was updated
* Fixes snprintf and silences some warnings
* Adds Get/Set StructCheckerOptions
* Adds default AugmentedAtomTransforms
