RDCode: SLNAttribs.h Source File

# SLNAttribs.h

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    00001 //
    00002 //  Copyright (c) 2008, Novartis Institutes for BioMedical Research Inc.
    00003 //  All rights reserved.
    00004 //
    00005 // Redistribution and use in source and binary forms, with or without
    00006 // modification, are permitted provided that the following conditions are
    00007 // met:
    00008 //
    00009 //     * Redistributions of source code must retain the above copyright
    00010 //       notice, this list of conditions and the following disclaimer.
    00011 //     * Redistributions in binary form must reproduce the above
    00012 //       copyright notice, this list of conditions and the following
    00013 //       disclaimer in the documentation and/or other materials provided
    00014 //       with the distribution.
    00015 //     * Neither the name of Novartis Institutes for BioMedical Research Inc.
    00016 //       nor the names of its contributors may be used to endorse or promote
    00017 //       products derived from this software without specific prior
    00018 //       written permission.
    00019 //
    00020 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
    00021 // "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
    00022 // LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
    00023 // A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
    00024 // OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
    00025 // SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
    00026 // LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
    00027 // DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
    00028 // THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
    00029 // (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
    00030 // OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
    00031 //
    00032 // Created by Greg Landrum, September 2006
    00033 //
    00034 #ifndef __RD_SLNATTRIBS_H__
    00035 #define __RD_SLNATTRIBS_H__
    00036
    00037 #include <string>
    00038 #include <vector>
    00039 #include <boost/smart_ptr.hpp>
    00040
    00041 namespace RDKit{
    00042   class Atom;
    00043   class Bond;
    00044
    00045   namespace SLNParse {
    00046     typedef enum {
    00047       AttribLowPriAnd=0,
    00048       AttribOr,
    00049       AttribAnd,
    00050       AttribNot
    00051     } AttribCombineOp;
    00052
    00053     class AttribType {
    00054     public:
    00055       AttribType() :first(""),second(""),op(""),negated(false),structQuery(0) {};
    00056       std::string first;
    00057       std::string second;
    00058       std::string op;
    00059       bool negated;
    00060       void *structQuery;
    00061     };
    00062
    00063     typedef std::vector< std::pair<AttribCombineOp,boost::shared_ptr<AttribType> > > AttribListType;
    00064
    00065     //! parses the attributes provided for an atom and sets
    00066     // the appropriate RD properties/queries.
    00067     // NOTES:
    00068     //    1) Some SLN query values cannot be properly set until the molecule is fully/
    00069     //       initialized. These are handled by parseFinalAtomAttribs()
    00070     //
    00071     void parseAtomAttribs(Atom *atom,AttribListType attribs,bool doingQuery);
    00072     void parseFinalAtomAttribs(Atom *atom,bool doingQuery);
    00073
    00074     //! parses the attributes provided for a bond and sets
    00075     // the appropriate RD properties/queries.
    00076     // NOTES:
    00077     //    1) Some SLN query values cannot be properly set until the molecule is fully/
    00078     //       initialized. These are handled by parseFinalBondAttribs()
    00079     void parseBondAttribs(Bond *bond,AttribListType attribs,bool doingQuery);
    00080     void parseFinalBondAttribs(Bond *bond,bool doingQuery);
    00081
    00082     //! parses the attributes provided for a ctab and sets
    00083     // the appropriate RD properties/queries.
    00084     void parseMolAttribs(ROMol *mol,AttribListType attribs);
    00085
    00086     void adjustAtomChiralities(RWMol *mol);
    00087   }
    00088 }
    00089 #endif