* Add support for dative bonds to molfile reader plus writer and to SMILES reader (SMILES writer already supports it).
Initial V3000 molfile reader and writer dative bond support by Esben Jannik Bjerrum.
* first pass at adding -> as dative bond in smiles/smarts
more testing required
* all tests pass
* update .cmake files for lex
* 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.
o rdkit gains a RDKit::common_properties namespace that contains common string value properties
o Dict.h and below gain getPropIfPresent that attempts to retrieve a property and returns
true/false on success or failure. This is used to optimize access.
o rdkit learns how to pass property keys by reference, not value.
A new namespace has been added to RDKit, common_properties
that contains the std::string values for commonly used
properties. This helps to avoid typos in string values
but also avoids a creation of std::strings from character
values. All accessors (has/get/clear and getPropIfPresent) now pass
the key by reference.
Additionally, getPropIfPresent removes the double lookup
of hasProp/getProp which can be a significant speedup
in the smiles and smarts parsers (10-20%)
