* Add Double Cubic Lattice Volume (DCLV).
Method to compute the solvent accessible surface area and volume, van der Waals volume, compactness and packing density of a protein. Implemented from: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander and Michael Scharf, "The Double Cubic Lattice Method: Efficient Approaches to Numerical Integration of Surface Area and Volume and to Dot Surface Contouring of Molecular Assemblies", Journal of Computational Chemistry, Vol. 16, No. 3, pp. 273-284, 1995.
* refactor
* DCLV is no longer a configuration option
* add to the docs
* standalone test has been removed
* reduce use of pointers as args
* DCLV to catch_tests
* update python wrapper
* add copyright statements
---------
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* un/signed comparisons in molops
* reference in loop in EmbeddedFrag.cpp
* un/signed comparison in filtercatalogtest.cpp
* un/signed comparison in Descriptors/catch_tests.cpp
* un/signed comparisons in DetermineBonds.cpp
* drop unused 'params' arg from static functions in MolInterchange/Writer.cpp
* un/signed comparisons in MolDraw2D/catch_tests.cpp
* unused var in SubgraphUtils.cpp
* 'move' preventing copy ellision in CDXMLParser.cpp
* fix infinite recursive call in SubstructLibraryWrap.cpp
* First stab at disconnecting organometallics the Syngenta way.
* Add support for Li and Na compounds, with tests.
* Correct docstrings.
* Add -1 valence to sodium.
* Add changes from PR 5997.
* Move declaration of disconnectOrganometallics.
* Re-factor tests for disconnectOrganometallics to read V3000 files rather than hard-code in file.
* Add optional options to constructor.
* Python wrapping for disconnectOrganometallics.
* Python tests.
* Correct docString.
* Test using in place overload of disconnect free function.
* options_ should not be a reference.
* Re-work the wrappers.
* Added test MOL files.
* Correct charge on iron atoms.
* Fix tests for charged iron.
* Added some more test complexes.
* Port Marco's oxidation number Python to C++ Descriptor.
* Rename functions.
* Another test.
* Python wrappers.
* Comment in test.
* Throws exception if atom-based function called with non-kekulized parent.
* Fix typo.
* Allow potassium as well.
* Whole molecule calculations for oxidation number only.
Rename prop to OxidationNumber.
* Add OxidationNumber to common_properties.
* Extra comment.
* When deleting atom, update any ENDPTS props on bonds.
Copied in from stale PR ExtraDoc.
* Added hapticBondsToDative with python wrapper.
* Extra test.
* Re-factor endpts parsing.
* Typo.
* Add function for haptic end points inc. Python wrapper.
* Add dative bonds in separate step.
* C++ version of dativeBondstoHaptic.
* Update test mols.
* Python wrapper.
* Fix indents in Python test script.
* Corrected expected test result.
* Only do non-metal to metal conversion of single bond to dative if the explicit valence of the non-metal allows it.
* Fix test broken in a non-material way by previous change.
* Export for DLL.
* Remove redundant function declaration.
* Dave hates Windows.
* Move hapticBondEndpoints to Molops::details.
* And take it out of the Python wrappers.
* Run yapf on reformatted test script.
* Get the DLL builds going.
* addDativeBond -> addHapticBond.
* Batch edits.
* Position arithmetic.
* setQuery.
* Dummy positions for all confs.
* Fix tests for dummy positions for all confs.
* Move tests to catch_organometallics.cpp.
* Modern docString.
* Change member variable names.
* sProp length, bonus batchEdit.
* Add options object to disconnectOrganometallics.
* Tidied license.
Atom precondition.
* GetIntProp.
* Test opts aren't defaults.
* Python wrapper for disconnectOrganometallics with options.
* Minor edit.
* Slightly random attempt to fix Java build.
* Response to review.
* Another stab at the doc strings.
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
