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552a78ed3a
* 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.
127 lines
4.6 KiB
C++
127 lines
4.6 KiB
C++
//
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// Copyright (c) 2016, Novartis Institutes for BioMedical Research Inc.
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// All rights reserved.
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//
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// Redistribution and use in source and binary forms, with or without
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// modification, are permitted provided that the following conditions are
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// met:
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//
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// * Redistributions of source code must retain the above copyright
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// notice, this list of conditions and the following disclaimer.
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// * Redistributions in binary form must reproduce the above
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// copyright notice, this list of conditions and the following
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// disclaimer in the documentation and/or other materials provided
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// with the distribution.
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// * Neither the name of Novartis Institutes for BioMedical Research Inc.
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// nor the names of its contributors may be used to endorse or promote
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// products derived from this software without specific prior written
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// permission.
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//
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
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// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
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// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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//
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#ifndef RDKIT_PROPERTIES_H
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#define RDKIT_PROPERTIES_H
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#include <GraphMol/RDKitBase.h>
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#include <string>
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#include <RDGeneral/BoostStartInclude.h>
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#include <boost/shared_ptr.hpp>
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#include <RDGeneral/BoostEndInclude.h>
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#include <Query/Query.h>
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#include <RDGeneral/Exceptions.h>
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namespace RDKit {
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namespace Descriptors {
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struct PropertyFunctor {
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// Registry of property functions
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// See REGISTER_DESCRIPTOR
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std::string propName;
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std::string propVersion;
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double (*d_dataFunc)(const ROMol&);
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PropertyFunctor(const std::string &name, const std::string &version,
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double (*func)(const ROMol&)=NULL) :
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propName(name), propVersion(version), d_dataFunc(func) {
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}
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virtual ~PropertyFunctor() {};
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//! Compute the value of the property
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virtual double operator()(const RDKit::ROMol &) const = 0;
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//! Return the name of the property
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const std::string getName() const { return propName; }
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//! Return the properties version
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const std::string getVersion() const { return propVersion; }
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};
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//! Holds a collection of properties for computation purposes
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class Properties {
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protected:
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std::vector<boost::shared_ptr<PropertyFunctor> > m_properties;
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public:
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Properties();
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Properties(const std::vector<std::string> &propNames);
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std::vector<std::string> getPropertyNames() const;
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std::vector<double> computeProperties(const RDKit::ROMol &mol, bool annotate=false) const;
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void annotateProperties(RDKit::ROMol& mol) const;
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//! Register a property function - takes ownership
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static int registerProperty(PropertyFunctor *ptr);
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static boost::shared_ptr<PropertyFunctor> getProperty(const std::string &name);
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static std::vector<std::string> getAvailableProperties();
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static std::vector<boost::shared_ptr<PropertyFunctor> > registry;
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};
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typedef Queries::Query<bool, const ROMol &, true> PROP_BOOL_QUERY;
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typedef Queries::AndQuery<int, const ROMol &, true> PROP_AND_QUERY;
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typedef Queries::OrQuery<int, const ROMol &, true> PROP_OR_QUERY;
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typedef Queries::XOrQuery<int, const ROMol &, true> PROP_XOR_QUERY;
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typedef Queries::EqualityQuery<double, const ROMol &, true> PROP_EQUALS_QUERY;
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typedef Queries::GreaterQuery<double, const ROMol &, true> PROP_GREATER_QUERY;
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typedef Queries::GreaterEqualQuery<double, const ROMol &, true>
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PROP_GREATEREQUAL_QUERY;
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typedef Queries::LessQuery<double, const ROMol &, true> PROP_LESS_QUERY;
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typedef Queries::LessEqualQuery<double, const ROMol &, true> PROP_LESSEQUAL_QUERY;
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typedef Queries::RangeQuery<double, const ROMol &, true> PROP_RANGE_QUERY;
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template<class T>
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T* makePropertyQuery(const std::string &name, double what) {
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T *t = new T(what);
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t->setDataFunc( Properties::getProperty(name)->d_dataFunc );
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return t;
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}
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PROP_RANGE_QUERY *makePropertyRangeQuery(const std::string &name,
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double min,
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double max);
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}
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}
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#endif
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