Commit Graph

8 Commits

Author SHA1 Message Date
Greg Landrum
ba12d98ad0 Removes ATOM/BOND_SPTR in boost::graph in favor of raw pointers (#1713)
* Removes ATOM/BOND_SPTR in boost::graph in favor of raw pointers

* Actually delete atoms and bonds...

* RWMol::clear now calls destroy to handle atom/bond deletion

* Changes broken Atom lookup for windows/gcc

* Adds tests for running with valgrind

* Adds test designed for valgrind and molecule deletions

* Removes RNG, actually tests bond deletions

* update swig wrappers

* deal with most recent changes on the main branch
2018-01-07 14:19:47 -05:00
Greg Landrum
636a0f6e69 Cleanup a bunch of compiler warnings (#1697)
* remove a bunch of compiler warnings

* remove some more warnings on windows (there are still plenty to go...)
2017-12-22 12:59:52 +01:00
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
Greg Landrum
adad6e55c2 Fix two problems with the PDB parsing (#1341)
* Fixes #1029

* Fixes #1340

* add test files
2017-03-04 12:34:27 -05:00
Greg Landrum
e08e0d16d8 first pass, using google style 2015-11-14 14:58:11 +01:00
Brian Kelley
a146c3826a Remove unused variables/functions and register keyword 2015-10-18 10:01:00 -04:00
Greg Landrum
53a2937eb6 Fixes #194 2014-01-15 03:19:26 -05:00
Greg Landrum
35147eb749 integrate Roger's bond-perception/assignment code 2013-09-30 05:04:01 +02:00