* atropisomer handling added
* fixed non-used variables, linking directives
* BOOST LIB start/stop fixes, linking fix
* Fixes for RDKIT CI errors
* minimalLib fix
* changed vector<enum> for java builds
* check for extra chars in CIP labeling
* removed wrong deprecated message
* fix ostrstream output error?
* restored _ChiralAtomRank to lowercase first letter
* changes for merged master
* Fixed catch label for new Catch package
* update expected psql results
* get swig wrappers building
* restore MolFileStereochem to FileParsers
* fix java wrapper for reapplyMolBlockWedging
* some suggestions
* move a couple functions out of Bond
* Merge branch 'master' into pr/atropisomers2
* merged master
* Renamed setStereoanyFromSquiggleBond
* atropisomers in cdxml, rationalize atrop wedging, stereoGroups in drawMol
* fix for CI build
* attempt to fix java build in CI
* attempt to fix java build in CI #2
* New routine to remove non-explicit 3D-geneated chirality
* changed to use pair for atrop atoms and related bonds
* Changes as per PR reviews
* PR review respnses
* PR review reponse - more
* Fix merge from master
* fixing java ci after merge
* Updated the help doc for atripisomers
* update the atropisomer docs
* improve the images
* add the source CXSMILES
---------
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* remove include from headers
* update implementation files
* completely remove BOOST_FOREACH (#7)
* convert those changes to use auto
* get rid of all usage of BOOST_FOREACH
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* run clang-tidy with modernize-use-default-member-init
* results from modernize-use-emplace
* one uniform initialization per line
otherwise SWIG is unhappy
Co-authored-by: Brian Kelley <fustigator@gmail.com>
* run clang-tidy with readability-braces-around-statements
clang-format the results
clean up all the parts that clang-tidy-8 broke
* fix problem on windows
* 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
* Adds a generic Property Calculation API
Property mw(Property::MW);
Property logp(Property::ALOGP);
// User based function
struct MyPropertyFunction : public PropertyFxn {
double compute(const ROMol &mol) const {
return rdcast<double>(mol.getNumAtoms());
}
bool isAdditive() const { return true; }
}
// Make the a num atom property
boost::shared_ptr<PropertyFxn> atomfxn(new MyPropertyFxn);
Property numAtoms("NumAtoms", atomfxn);
double alogp = logp.computeProperty(mol);
double nAtoms = numAtoms.computeProperty(mol);
And a ProperFilter API
// Molecular weight filter 0 ... 500.
PropertyFilter mw(PropertyFilter::MW, 0., 500.);
// log p Filter -5 ... 5
PropertyFilter logp(PropertyFilter::ALOGP, -5.0, 5.0);
// User based function
struct MyPropertyFunction : public PropertyFxn {
double compute(const ROMol &mol) const {
return rdcast<double>(mol.getNumAtoms());
}
}
// add num atom property 0. ... 50.
boost::shared_ptr<PropertyFxn> atomfxn(new MyPropertyFxn);
PropertyFilter natoms("NumAtoms", 0., 50., atomfxn);
if (natoms.accepts(mol)) {
// molecule is ok
} else {
// molecules is bad
}
* Adds missing includes
* Fixes g++ access to class based enums
* Updates to new API, adds better property registry
* Adds a generic Property Calculation API
Property mw(Property::MW);
Property logp(Property::ALOGP);
// User based function
struct MyPropertyFunction : public PropertyFxn {
double compute(const ROMol &mol) const {
return rdcast<double>(mol.getNumAtoms());
}
bool isAdditive() const { return true; }
}
// Make the a num atom property
boost::shared_ptr<PropertyFxn> atomfxn(new MyPropertyFxn);
Property numAtoms("NumAtoms", atomfxn);
double alogp = logp.computeProperty(mol);
double nAtoms = numAtoms.computeProperty(mol);
And a ProperFilter API
// Molecular weight filter 0 ... 500.
PropertyFilter mw(PropertyFilter::MW, 0., 500.);
// log p Filter -5 ... 5
PropertyFilter logp(PropertyFilter::ALOGP, -5.0, 5.0);
// User based function
struct MyPropertyFunction : public PropertyFxn {
double compute(const ROMol &mol) const {
return rdcast<double>(mol.getNumAtoms());
}
}
// add num atom property 0. ... 50.
boost::shared_ptr<PropertyFxn> atomfxn(new MyPropertyFxn);
PropertyFilter natoms("NumAtoms", 0., 50., atomfxn);
if (natoms.accepts(mol)) {
// molecule is ok
} else {
// molecules is bad
}
* Adds missing includes
* Fixes g++ access to class based enums
* Updates to new API, adds better property registry
* Fixes merge error
* Removes unused unordered_map include
* Adds calcClogP calcMR as functions.
* PropertyFxn ->PropertyFunctor, adds Queries::Query based queries.
* Adds Python PropertyFunctors (can’t be used as queries yet)
* Exposes PropertyRangeQueries
* Adds doc strings
* Throws error if stereo is not assigned.
* Adds molecule annotation.
Major changes in definition relative to the original GPS calculator:
Bonds linking ring systems:
- Single bonds between aliphatic ring Cs are always rotatable. This
means that the central bond in CC1CCCC(C)C1-C1C(C)CCCC1C is now
considered rotatable; it was not before
- Heteroatoms in the linked rings no longer affect whether or not
the linking bond is rotatable
- the linking bond in systems like Cc1cccc(C)c1-c1c(C)cccc1 is now
considered non-rotatable
we are no longer templating the descriptor functions and have moved the calculation
of the pattern matchers into statics inside the functions themselves.
This solves a crashing problem with the cartridge on the mac.
