* enable Werror on Mac and Linux
* do not fail on boost multiprecision pessimizing move
* fix eigen array_bounds warning
* Fix unused arg in Rascal MCS
* fix range-loop-construct warning in Rascal MCES
* fix sign mismatched comparison
* drop unused lambda capture
* allow FMCS timeout test more time under Debug (not a warning!)
* fix fwd declaration of struct RascalClusterOptions
* fix deallocator mismatch
* fix two minor leaks
* fix a real leak
* more minor leaks
* fix another real leak, plus some potential ones
* fix std::move preventing copy ellision
* allow longer run time for debug builds
* make maxBondMatchPairs and getLargestFragSize unsigned int
* make snake case camel case
* update to current master, fix new warnings
* update again and more fixes
* add #include <optional>
* fix char array deallocation
* update and fixes in Marvin writer
* unsigned int
* more copy ellision fixes
* more copy ellision fixes, and typos
* and some more
* cleanup a bunch of g++ warnings
* make it work with clang
* remove some additional warnings based on CI builds
* fix that version number
* stop being verbose when building
* change minimal cmake version to a consistent 3.5
* progress towards a cleanup
* get the basic python deps working
* two more libs
* another round of changes
all tests pass at this point
* next round of changes
all tests pass at this point
* close to done
all tests pass
* very close
* almost done
* shift the RDBoost dependencies around a bit
* remove an extraneous python linkage
this is trying to get the mac builds working again
* Only link to python if it was built shared (#3091)
* change in response to review
Co-Authored-By: Ric <ricrogz@users.noreply.github.com>
* move that suppression of the maybe-uninitialized warning to BoostStartInclude.h
Co-authored-by: Brian Kelley <fustigator@gmail.com>
Co-authored-by: Ric <ricrogz@users.noreply.github.com>
* add a SmilesParserParams object to prepare for this
* add a SmilesParserParams object to prepare for this
* add tests for the SmilesParseParmas
* support name parsing, should it be the default?
* rename CXNSmiles to CXSmiles;
add a spirit parser for CXSmiles coordinate that is at least syntax correct
* abandon boost::spirit for now; crude atom token parser
* support params in smiles parser (not tested, may not build)
* can read coords and atom labels along with mol names; crude, but works
* read coordinate bonds
* remove some compiler warnings with VS2015
* remove a bunch of compiler warnings on windows
* remove more warnings on windows
* remove more warnings on windows
* backup commit: first pass at parsing query features
* radical spec parsing
* handle attachment points using atom mapping
* switch to a named property for atom labels
* fix handling of the "A" atom query
* add functions to construct A and Q queries (needs more work)
* fix a problem created while cleaning up warnings earlier
* add some additional convenience functions for making generic atoms.
Still need M and to recognize these while writing CXSMILES
* add M queries; update some tests
* fix a linux compile problem
* get the cxsmiles stuff working in python; basic testing
* support "M" in CXSMILES
* Remove a bunch of warnings
The biggest change here is to treat the boost includes as system libraries.
This causes g++ to ignore warnings from boost.
This change still needs to be tested with clang and on Windows
* suppress a bunch of warnings on clang
* 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.
