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317 lines
8.8 KiB
OpenEdge ABL
317 lines
8.8 KiB
OpenEdge ABL
/*
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* $Id$
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*
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* Copyright (c) 2010, 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 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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%typemap(javaimports) RDKit::Atom "
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/**
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The class for representing atoms.
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<p>
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<p>
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@notes
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<li>many of the methods of Atom require that the Atom be associated with a molecule (an ROMol).
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<li>each Atom maintains a Dict of properties:
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<li>o Each property is keyed by name and can store an arbitrary type.
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<li>o Properties can be marked as calculated, in which case they will be cleared when the clearComputedProps() method is called.
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<li>o Because they have no impact upon chemistry, all property operations are const, this allows extra flexibility for clients who need to store extra data on Atom objects.
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<li>Atom objects are lazy about computing their explicit and implicit valence values. These will not be computed until their values are requested.
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Chirality:
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<p>
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The chirality of an Atom is determined by two things:
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<p>
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* its chiralTag
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* the input order of its bonds (see note below for handling of implicit Hs)
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<p>
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For tetrahedral coordination, the chiralTag tells you what direction you have to rotate to get from bond 2 to bond 3 while looking down bond 1. This is pretty much identical to the SMILES representation of chirality.
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<p>
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NOTE: if an atom has an implicit H, the bond to that H is considered to be at the *end* of the list of other bonds. */"
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%javamethodmodifiers RDKit::Atom::calcExplicitValence ( bool strict = true ) "
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/**
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<p>
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calculates and returns our explicit valence
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<p>
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<p>
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@notes
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<li>requires an owning molecule
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*/
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public";
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%javamethodmodifiers RDKit::Atom::calcImplicitValence ( bool strict = true ) "
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/**
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<p>
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calculates and returns our implicit valence
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<p>
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<p>
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@notes
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<li>requires an owning molecule
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*/
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public";
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%javamethodmodifiers RDKit::Atom::clearProp ( const std::string key ) const "
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/**
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<p>
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This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
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*/
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public";
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%javamethodmodifiers RDKit::Atom::clearProp ( const char * key ) const "
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/**
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<p>
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clears the value of a property
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<p>
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<p>
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@notes
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<li>if no property with name key exists, a KeyErrorException will be thrown.
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<li>if the property is marked as computed, it will also be removed from our list of computedProperties
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*/
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public";
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%javamethodmodifiers RDKit::Atom::copy ( ) const "
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/**
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<p>
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makes a copy of this Atom and returns a pointer to it.
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<p>
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<p>
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@notes
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Reimplemented in RDKit::QueryAtom.
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*/
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public";
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%javamethodmodifiers RDKit::Atom::getDegree ( ) const"
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/**
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<p>
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<p>
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@return
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the explicit degree of the Atom (number of bonded neighbors in the graph)
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<p>
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@notes
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<li>requires an owning molecule
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*/
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public";
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%javamethodmodifiers RDKit::Atom::getImplicitValence ( ) const"
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/**
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<p>
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<p>
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@return
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the implicit valence for this Atom
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<p>
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@notes
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<li>requires an owning molecule
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*/
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public";
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%javamethodmodifiers RDKit::Atom::getNumImplicitHs ( ) const"
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/**
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<p>
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<p>
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@return
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the number of implicit Hs this Atom is bound to
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<p>
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@notes
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<li>requires an owning molecule
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*/
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public";
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%javamethodmodifiers RDKit::Atom::getNumRadicalElectrons ( ) const "
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/**
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<p>
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<p>
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@return
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the number of radical electrons for this Atom
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<p>
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@notes
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<li>requires an owning molecule
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*/
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public";
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%javamethodmodifiers RDKit::Atom::getPerturbationOrder ( INT_LIST probe ) const"
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/**
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<p>
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returns the perturbation order for a list of integers
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<p>
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This value is associated with chirality.
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<p>
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<p>
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@param
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probe a list of bond indices. This must be the same length as our number of incoming bonds (our degree).
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<p>
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@return
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the number of swaps required to convert the ordering of the probe list to match the order of our incoming bonds: e.g. if our incoming bond order is: [0,1,2,3]
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getPerturbationOrder([1,0,2,3]) = 1
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getPerturbationOrder([1,2,3,0]) = 3
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getPerturbationOrder([1,2,0,3]) = 2
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See the class documentation for a more detailed description of our representation of chirality.
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<p>
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<p>
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@notes
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<li>requires an owning molecule
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template<typename T >
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*/
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public";
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%javamethodmodifiers RDKit::Atom::getProp ( const std::string key, T & res ) const "
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/**
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<p>
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This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
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template<typename T >
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*/
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public";
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%javamethodmodifiers RDKit::Atom::getProp ( const char * key, T & res ) const "
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/**
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<p>
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allows retrieval of a particular property value
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<p>
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<p>
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@param
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key the name under which the property should be stored. If a property is already stored under this name, it will be replaced.
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res a reference to the storage location for the value.
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<p>
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@notes
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<li>if no property with name key exists, a KeyErrorException will be thrown.
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<li>the boost::lexical_cast machinery is used to attempt type conversions. If this fails, a boost::bad_lexical_cast exception will be thrown.
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*/
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public";
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%javamethodmodifiers RDKit::Atom::getTotalDegree ( ) const"
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/**
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<p>
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<p>
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@return
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the total degree of the Atom (number of bonded neighbors + number of Hs)
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<p>
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@notes
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<li>requires an owning molecule
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*/
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public";
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%javamethodmodifiers RDKit::Atom::getTotalNumHs ( bool includeNeighbors = false ) const"
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/**
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<p>
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<p>
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@return
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the total number of Hs (implicit and explicit) that this Atom is bound to
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<p>
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@notes
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<li>requires an owning molecule
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*/
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public";
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%javamethodmodifiers RDKit::Atom::hasProp ( const std::string key ) const "
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/**
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<p>
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This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
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*/
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public";
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%javamethodmodifiers RDKit::Atom::Match ( const ATOM_SPTR what ) const "
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/**
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<p>
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This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
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<p>
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Reimplemented in RDKit::QueryAtom.
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*/
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public";
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%javamethodmodifiers RDKit::Atom::Match ( Atom const * what ) const "
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/**
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<p>
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<p>
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@return
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whether or not we match the argument
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<p>
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@notes
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<li>for Atom objects, 'match' means that atomic numbers are the same.
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Reimplemented in RDKit::QueryAtom.
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*/
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public";
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%javamethodmodifiers RDKit::Atom::setIdx ( unsigned int index ) "
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/**
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<p>
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sets our index within the ROMol
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<p>
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<p>
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@notes
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<li>this makes no sense if we do not have an owning molecule
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<li>the index should be < this->getOwningMol()->getNumAtoms()
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template<typename T >
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*/
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public";
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%javamethodmodifiers RDKit::Atom::setProp ( const std::string key, T val, bool computed = false ) const "
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/**
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<p>
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This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
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template<typename T >
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*/
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public";
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%javamethodmodifiers RDKit::Atom::setProp ( const char * key, T val, bool computed = false ) const "
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/**
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<p>
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sets a property value
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<p>
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<p>
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@param
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key the name under which the property should be stored. If a property is already stored under this name, it will be replaced.
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val the value to be stored
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computed (optional) allows the property to be flagged computed.
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*/
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public";
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%javamethodmodifiers RDKit::Atom::updatePropertyCache ( bool strict = true ) "
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/**
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<p>
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calculates any of our lazy properties
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<p>
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<p>
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@notes
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<li>requires an owning molecule
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<li>the current lazy properties are implicit and explicit valence
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*/
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public";
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