Bond.h
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//
// Copyright (C) 2001-2017 Greg Landrum and Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <RDGeneral/export.h>
#ifndef _RD_BOND_H
#define _RD_BOND_H
// std stuff
#include <iostream>
// Ours
#include <RDGeneral/Invariant.h>
#include <Query/QueryObjects.h>
#include <RDGeneral/types.h>
#include <RDGeneral/RDProps.h>
#include <GraphMol/details.h>
#include <boost/foreach.hpp>
namespace RDKit {
class ROMol;
class RWMol;
class Atom;
//! class for representing a bond
/*!
<b>Notes:</b>
- many of the methods of Atom require that the Atom be associated
with a molecule (an ROMol).
- each Bond maintains a Dict of \c properties:
- Each \c property is keyed by name and can store an
arbitrary type.
- \c Properties can be marked as \c calculated, in which case
they will be cleared when the \c clearComputedProps() method
is called.
- Because they have no impact upon chemistry, all \c property
operations are \c const, this allows extra flexibility for
clients who need to store extra data on Bond objects.
*/
class RDKIT_GRAPHMOL_EXPORT Bond : public RDProps {
friend class RWMol;
friend class ROMol;
public:
// FIX: grn...
typedef Queries::Query<int, Bond const *, true> QUERYBOND_QUERY;
//! the type of Bond
typedef enum {
UNSPECIFIED = 0,
SINGLE,
DOUBLE,
TRIPLE,
QUADRUPLE,
QUINTUPLE,
HEXTUPLE,
ONEANDAHALF,
TWOANDAHALF,
THREEANDAHALF,
FOURANDAHALF,
FIVEANDAHALF,
AROMATIC,
IONIC,
HYDROGEN,
THREECENTER,
DATIVEONE, //!< one-electron dative (e.g. from a C in a Cp ring to a metal)
DATIVE, //!< standard two-electron dative
DATIVEL, //!< standard two-electron dative
DATIVER, //!< standard two-electron dative
OTHER,
ZERO //!< Zero-order bond (from
// http://pubs.acs.org/doi/abs/10.1021/ci200488k)
} BondType;
//! the bond's direction (for chirality)
typedef enum {
NONE = 0, //!< no special style
BEGINWEDGE, //!< wedged: narrow at begin
BEGINDASH, //!< dashed: narrow at begin
// FIX: this may not really be adequate
ENDDOWNRIGHT, //!< for cis/trans
ENDUPRIGHT, //!< ditto
EITHERDOUBLE, //!< a "crossed" double bond
UNKNOWN, //!< intentionally unspecified stereochemistry
} BondDir;
//! the nature of the bond's stereochem (for cis/trans)
typedef enum { // stereochemistry of double bonds
STEREONONE = 0, // no special style
STEREOANY, // intentionally unspecified
// -- Put any true specifications about this point so
// that we can do comparisons like if(bond->getStereo()>Bond::STEREOANY)
STEREOZ, // Z double bond
STEREOE, // E double bond
STEREOCIS, // cis double bond
STEREOTRANS // trans double bond
} BondStereo;
Bond();
//! construct with a particular BondType
explicit Bond(BondType bT);
Bond(const Bond &other);
virtual ~Bond();
Bond &operator=(const Bond &other);
//! returns a copy
/*!
<b>Note:</b> the caller is responsible for <tt>delete</tt>ing
the returned pointer.
*/
virtual Bond *copy() const;
//! returns our \c bondType
BondType getBondType() const { return static_cast<BondType>(d_bondType); };
//! sets our \c bondType
void setBondType(BondType bT) { d_bondType = bT; };
//! \brief returns our \c bondType as a double
//! (e.g. SINGLE->1.0, AROMATIC->1.5, etc.)
double getBondTypeAsDouble() const;
//! returns our contribution to the explicit valence of an Atom
/*!
<b>Notes:</b>
- requires an owning molecule
*/
double getValenceContrib(const Atom *at) const;
//! sets our \c isAromatic flag
void setIsAromatic(bool what) { df_isAromatic = what; };
//! returns the status of our \c isAromatic flag
bool getIsAromatic() const { return df_isAromatic; };
//! sets our \c isConjugated flag
void setIsConjugated(bool what) { df_isConjugated = what; };
//! returns the status of our \c isConjugated flag
bool getIsConjugated() const { return df_isConjugated; };
//! returns whether or not this instance belongs to a molecule
bool hasOwningMol() const { return dp_mol != nullptr; };
//! returns a reference to the ROMol that owns this instance
ROMol &getOwningMol() const {
PRECONDITION(dp_mol, "no owner");
return *dp_mol;
};
//! sets our owning molecule
void setOwningMol(ROMol *other);
//! sets our owning molecule
void setOwningMol(ROMol &other) { setOwningMol(&other); };
//! returns our index within the ROMol
/*!
<b>Notes:</b>
- this makes no sense if we do not have an owning molecule
*/
unsigned int getIdx() const { return d_index; };
//! sets our index within the ROMol
/*!
<b>Notes:</b>
- this makes no sense if we do not have an owning molecule
- the index should be <tt>< this->getOwningMol()->getNumBonds()</tt>
*/
void setIdx(unsigned int index) { d_index = index; };
//! returns the index of our begin Atom
/*!
<b>Notes:</b>
- this makes no sense if we do not have an owning molecule
*/
unsigned int getBeginAtomIdx() const { return d_beginAtomIdx; };
//! returns the index of our end Atom
/*!
<b>Notes:</b>
- this makes no sense if we do not have an owning molecule
*/
unsigned int getEndAtomIdx() const { return d_endAtomIdx; };
//! given the index of one Atom, returns the index of the other
/*!
<b>Notes:</b>
- this makes no sense if we do not have an owning molecule
*/
unsigned int getOtherAtomIdx(unsigned int thisIdx) const;
//! sets the index of our begin Atom
/*!
<b>Notes:</b>
- requires an owning molecule
*/
void setBeginAtomIdx(unsigned int what);
//! sets the index of our end Atom
/*!
<b>Notes:</b>
- requires an owning molecule
*/
void setEndAtomIdx(unsigned int what);
//! sets our begin Atom
/*!
<b>Notes:</b>
- requires an owning molecule
*/
void setBeginAtom(Atom *at);
//! sets our end Atom
/*!
<b>Notes:</b>
- requires an owning molecule
*/
void setEndAtom(Atom *at);
//! returns a pointer to our begin Atom
/*!
<b>Notes:</b>
- requires an owning molecule
*/
Atom *getBeginAtom() const;
//! returns a pointer to our end Atom
/*!
<b>Notes:</b>
- requires an owning molecule
*/
Atom *getEndAtom() const;
//! returns a pointer to the other Atom
/*!
<b>Notes:</b>
- requires an owning molecule
*/
Atom *getOtherAtom(Atom const *what) const;
// ------------------------------------
// Please see the note in Atom.h for some explanation
// of these methods
// ------------------------------------
// This method can be used to distinguish query bonds from standard bonds
virtual bool hasQuery() const { return false; };
// FIX: the const crap here is all mucked up.
//! NOT CALLABLE
virtual void setQuery(QUERYBOND_QUERY *what);
//! NOT CALLABLE
virtual QUERYBOND_QUERY *getQuery() const;
//! NOT CALLABLE
virtual void expandQuery(
QUERYBOND_QUERY *what,
Queries::CompositeQueryType how = Queries::COMPOSITE_AND,
bool maintainOrder = true);
//! returns whether or not we match the argument
/*!
<b>Notes:</b>
- for Bond objects, "match" means that either one of the Bonds
has \c bondType Bond::UNSPECIFIED or both Bonds have the
same \c bondType.
*/
virtual bool Match(Bond const *what) const;
//! sets our direction
void setBondDir(BondDir what) { d_dirTag = what; };
//! returns our direction
BondDir getBondDir() const { return static_cast<BondDir>(d_dirTag); };
//! sets our stereo code
/*!
STEREONONE, STEREOANY, STEREOE and STEREOZ can be set without
neighboring atoms specified in getStereoAtoms since they are
defined by the topology of the molecular graph. In order to set
STEREOCIS or STEREOTRANS the neighboring atoms must be set first
(using setStereoBonds()) to know what atoms are being considered.
<b>Notes:</b>
- MolOps::findPotentialStereoBonds can be used to set
getStereoAtoms before setting CIS/TRANS
*/
void setStereo(BondStereo what) {
PRECONDITION(what <= STEREOE || getStereoAtoms().size() == 2,
"Stereo atoms should be specified before specifying CIS/TRANS "
"bond stereochemistry")
d_stereo = what;
};
//! returns our stereo code
BondStereo getStereo() const { return static_cast<BondStereo>(d_stereo); };
//! sets the atoms to be considered as reference points for bond stereo
/*!
These do not necessarily need to be the highest 'ranking' atoms
like CIP stereo requires. They can be any arbitrary atoms
neighboring the begin and end atoms of this bond
respectively. STEREOCIS or STEREOTRANS is then set relative to
only these atoms.
If CIP rankings are desired, use
MolOps::findPotentialStereoBonds, but this is a more costly
function as it takes the whole molecule topology into account.
*/
void setStereoAtoms(unsigned int bgnIdx, unsigned int endIdx);
//! returns the indices of our stereo atoms
const INT_VECT &getStereoAtoms() const {
if (!dp_stereoAtoms) {
const_cast<Bond *>(this)->dp_stereoAtoms = new INT_VECT();
}
return *dp_stereoAtoms;
};
//! \overload
INT_VECT &getStereoAtoms() {
if (!dp_stereoAtoms) dp_stereoAtoms = new INT_VECT();
return *dp_stereoAtoms;
};
//! calculates any of our lazy \c properties
/*!
<b>Notes:</b>
- requires an owning molecule
*/
void updatePropertyCache(bool strict = true) { (void)strict; }
protected:
//! sets our owning molecule
// void setOwningMol(ROMol *other);
//! sets our owning molecule
// void setOwningMol(ROMol &other) {setOwningMol(&other);};
bool df_isAromatic;
bool df_isConjugated;
std::uint8_t d_bondType;
std::uint8_t d_dirTag;
std::uint8_t d_stereo;
atomindex_t d_index;
atomindex_t d_beginAtomIdx, d_endAtomIdx;
ROMol *dp_mol;
INT_VECT *dp_stereoAtoms;
void initBond();
};
}; // namespace RDKit
//! allows Bond objects to be dumped to streams
RDKIT_GRAPHMOL_EXPORT extern std::ostream &operator<<(std::ostream &target,
const RDKit::Bond &b);
#endif
RDKit::Bond::BEGINDASH
dashed: narrow at begin
Definition: Bond.h:86
RDKit::Bond::DATIVEL
standard two-electron dative
Definition: Bond.h:75
RDKit::Bond::DATIVE
standard two-electron dative
Definition: Bond.h:74
RDKit::Bond::dp_mol
ROMol * dp_mol
Definition: Bond.h:340
RDKit::Bond::getStereo
BondStereo getStereo() const
returns our stereo code
Definition: Bond.h:292
RDKit::Bond::df_isAromatic
bool df_isAromatic
sets our owning molecule
Definition: Bond.h:333
RDKit::Bond::d_dirTag
std::uint8_t d_dirTag
Definition: Bond.h:336
Queries::COMPOSITE_AND
Definition: QueryObjects.h:36
RDKit::Bond::DATIVER
standard two-electron dative
Definition: Bond.h:76
RDKit::INT_VECT
std::vector< int > INT_VECT
Definition: types.h:254
QueryObjects.h
Pulls in all the query types.
types.h
RDKit::Bond::THREEANDAHALF
Definition: Bond.h:66
RDKit::Bond::updatePropertyCache
void updatePropertyCache(bool strict=true)
calculates any of our lazy properties
Definition: Bond.h:326
RDKit::Bond::setIsConjugated
void setIsConjugated(bool what)
sets our isConjugated flag
Definition: Bond.h:141
RDKit::Bond::dp_stereoAtoms
INT_VECT * dp_stereoAtoms
Definition: Bond.h:341
RDKit::Bond::EITHERDOUBLE
a "crossed" double bond
Definition: Bond.h:90
RDKit::Bond::hasOwningMol
bool hasOwningMol() const
returns whether or not this instance belongs to a molecule
Definition: Bond.h:146
RDKit::Bond::getStereoAtoms
INT_VECT & getStereoAtoms()
This is an overloaded member function, provided for convenience. It differs from the above function o...
Definition: Bond.h:316
RDKit::Bond
class for representing a bond
Definition: Bond.h:47
Queries::CompositeQueryType
CompositeQueryType
Definition: QueryObjects.h:36
RDKit::Bond::setIdx
void setIdx(unsigned int index)
sets our index within the ROMol
Definition: Bond.h:171
RDKit::RWMol
RWMol is a molecule class that is intended to be edited.
Definition: RWMol.h:31
operator<<
RDKIT_GRAPHMOL_EXPORT std::ostream & operator<<(std::ostream &target, const RDKit::Bond &b)
allows Bond objects to be dumped to streams
RDKit::Bond::SINGLE
Definition: Bond.h:58
RDKit::Bond::setOwningMol
void setOwningMol(ROMol &other)
sets our owning molecule
Definition: Bond.h:156
RDKit::Bond::UNKNOWN
intentionally unspecified stereochemistry
Definition: Bond.h:91
RDKit::Bond::setBondDir
void setBondDir(BondDir what)
sets our direction
Definition: Bond.h:269
RDKit::Bond::d_index
atomindex_t d_index
Definition: Bond.h:338
RDKit::Bond::ENDUPRIGHT
ditto
Definition: Bond.h:89
RDKit::Bond::BondType
BondType
the type of Bond
Definition: Bond.h:56
RDKit::Bond::IONIC
Definition: Bond.h:70
RDKit::Bond::QUINTUPLE
Definition: Bond.h:62
RDKit::Atom
The class for representing atoms.
Definition: Atom.h:69
RDKit::Bond::getEndAtomIdx
unsigned int getEndAtomIdx() const
returns the index of our end Atom
Definition: Bond.h:185
RDKit::Bond::getIdx
unsigned int getIdx() const
returns our index within the ROMol
Definition: Bond.h:164
RDKit::Bond::FIVEANDAHALF
Definition: Bond.h:68
RDKit::Bond::QUADRUPLE
Definition: Bond.h:61
RDKit::ROMol
Definition: ROMol.h:171
RDKit::Bond::DOUBLE
Definition: Bond.h:59
RDKit::Bond::STEREOZ
Definition: Bond.h:100
BondStereo
BondStereo
Definition: nmmolhash.h:49
RDKit::Bond::getStereoAtoms
const INT_VECT & getStereoAtoms() const
returns the indices of our stereo atoms
Definition: Bond.h:309
RDKIT_GRAPHMOL_EXPORT
#define RDKIT_GRAPHMOL_EXPORT
Definition: export.h:307
RDProps.h
RDKit::Bond::BEGINWEDGE
wedged: narrow at begin
Definition: Bond.h:85
Invariant.h
RDKit::Bond::TWOANDAHALF
Definition: Bond.h:65
RDKit::RDProps
Definition: RDProps.h:10
RDKit::Bond::THREECENTER
Definition: Bond.h:72
RDKit::Bond::d_bondType
std::uint8_t d_bondType
Definition: Bond.h:335
RDKit::Bond::getBondDir
BondDir getBondDir() const
returns our direction
Definition: Bond.h:271
RDKit::Bond::HEXTUPLE
Definition: Bond.h:63
RDKit::Bond::df_isConjugated
bool df_isConjugated
Definition: Bond.h:334
RDKit::Bond::FOURANDAHALF
Definition: Bond.h:67
RDKit::Bond::QUERYBOND_QUERY
Queries::Query< int, Bond const *, true > QUERYBOND_QUERY
Definition: Bond.h:53
RDKit
Std stuff.
Definition: Atom.h:30
RDKit::Bond::ENDDOWNRIGHT
for cis/trans
Definition: Bond.h:88
RDKit::Bond::getIsConjugated
bool getIsConjugated() const
returns the status of our isConjugated flag
Definition: Bond.h:143
RDKit::Bond::setIsAromatic
void setIsAromatic(bool what)
sets our isAromatic flag
Definition: Bond.h:136
RDKit::Bond::setBondType
void setBondType(BondType bT)
sets our bondType
Definition: Bond.h:123
RDKit::Bond::STEREOE
Definition: Bond.h:101
RDKit::Bond::TRIPLE
Definition: Bond.h:60
RDKit::Bond::ONEANDAHALF
Definition: Bond.h:64
RDKit::Bond::hasQuery
virtual bool hasQuery() const
Definition: Bond.h:245
PRECONDITION
#define PRECONDITION(expr, mess)
Definition: Invariant.h:109
Queries::Query
Base class for all queries.
Definition: Query.h:46
RDKit::atomindex_t
std::uint32_t atomindex_t
Definition: details.h:14
RDKit::Bond::getBondType
BondType getBondType() const
returns our bondType
Definition: Bond.h:121
details.h
RDKit::Bond::BondStereo
BondStereo
the nature of the bond's stereochem (for cis/trans)
Definition: Bond.h:95
RDKit::Bond::HYDROGEN
Definition: Bond.h:71
RDKit::Bond::OTHER
Definition: Bond.h:77
RDKit::Bond::getOwningMol
ROMol & getOwningMol() const
returns a reference to the ROMol that owns this instance
Definition: Bond.h:149
RDKit::Bond::DATIVEONE
one-electron dative (e.g. from a C in a Cp ring to a metal)
Definition: Bond.h:73
RDKit::Bond::AROMATIC
Definition: Bond.h:69
RDKit::Bond::STEREOANY
Definition: Bond.h:97
RDKit::Bond::getIsAromatic
bool getIsAromatic() const
returns the status of our isAromatic flag
Definition: Bond.h:138
RDKit::Bond::d_stereo
std::uint8_t d_stereo
Definition: Bond.h:337
RDKit::Bond::BondDir
BondDir
the bond's direction (for chirality)
Definition: Bond.h:83
RDKit::Bond::getBeginAtomIdx
unsigned int getBeginAtomIdx() const
returns the index of our begin Atom
Definition: Bond.h:178
RDKit::Bond::setStereo
void setStereo(BondStereo what)
sets our stereo code
Definition: Bond.h:285
RDKit::Bond::d_endAtomIdx
atomindex_t d_endAtomIdx
Definition: Bond.h:339
RDKit::Bond::STEREOCIS
Definition: Bond.h:102
export.h