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Bond.h
Go to the documentation of this file.
//
// Copyright (C) 2001-2021 Greg Landrum and other RDKit contributors
//
// @@ 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>
#include <utility>
// Ours
#include <RDGeneral/Invariant.h>
#include <Query/QueryObjects.h>
#include <RDGeneral/types.h>
#include <RDGeneral/RDProps.h>
#include <GraphMol/details.h>
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
STEREOATROPCW, // atropisomer clockwise rotation
STEREOATROPCCW, // atropisomer counter clockwise rotation
} BondStereo;
Bond();
//! construct with a particular BondType
explicit Bond(BondType bT);
Bond(const Bond &other);
virtual ~Bond();
Bond &operator=(const Bond &other);
Bond(Bond &&o) noexcept : RDProps(std::move(o)) {
df_isAromatic = o.df_isAromatic;
df_isConjugated = o.df_isConjugated;
d_bondType = o.d_bondType;
d_dirTag = o.d_dirTag;
d_stereo = o.d_stereo;
d_index = o.d_index;
d_beginAtomIdx = o.d_beginAtomIdx;
d_endAtomIdx = o.d_endAtomIdx;
// NOTE: this is somewhat fraught for bonds associated with molecules since
// the molecule will still be pointing to the original object
dp_mol = std::exchange(o.dp_mol, nullptr);
dp_stereoAtoms = std::exchange(o.dp_stereoAtoms, nullptr);
}
Bond &operator=(Bond &&o) noexcept {
if (this == &o) {
return *this;
}
RDProps::operator=(std::move(o));
df_isAromatic = o.df_isAromatic;
df_isConjugated = o.df_isConjugated;
d_bondType = o.d_bondType;
d_dirTag = o.d_dirTag;
d_stereo = o.d_stereo;
d_index = o.d_index;
d_beginAtomIdx = o.d_beginAtomIdx;
d_endAtomIdx = o.d_endAtomIdx;
// NOTE: this is somewhat fraught for bonds associated with molecules since
// the molecule will still be pointing to the original object
delete dp_stereoAtoms;
dp_mol = std::exchange(o.dp_mol, nullptr);
dp_stereoAtoms = std::exchange(o.dp_stereoAtoms, nullptr);
return *this;
}
//! 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
*/
virtual 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); }
// inverts the chirality of an atropisomer
bool invertChirality();
//! 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 != STEREOCIS && what != STEREOTRANS) ||
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); }
ROMol *dp_mol;
INT_VECT *dp_stereoAtoms;
atomindex_t d_index;
atomindex_t d_beginAtomIdx, d_endAtomIdx;
bool df_isAromatic;
bool df_isConjugated;
std::uint8_t d_bondType;
std::uint8_t d_dirTag;
std::uint8_t d_stereo;
void initBond();
};
inline bool isDative(const Bond::BondType bt) {
return bt == Bond::BondType::DATIVE || bt == Bond::BondType::DATIVEL ||
bt == Bond::BondType::DATIVER || bt == Bond::BondType::DATIVEONE;
}
inline bool isDative(const Bond &bond) {
auto bt = bond.getBondType();
return isDative(bt);
}
inline bool canSetDoubleBondStereo(const Bond &bond) {
auto bondType = bond.getBondType();
return (bondType == Bond::SINGLE || bondType == Bond::AROMATIC ||
isDative(bond));
}
inline bool canHaveDirection(const Bond &bond) {
auto bondType = bond.getBondType();
return (bondType == Bond::SINGLE || bondType == Bond::AROMATIC);
}
//! returns twice the \c bondType
//! (e.g. SINGLE->2, AROMATIC->3, etc.)
RDKIT_GRAPHMOL_EXPORT extern uint8_t getTwiceBondType(const RDKit::Bond &b);
}; // 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
operator<<
RDKIT_GRAPHMOL_EXPORT std::ostream & operator<<(std::ostream &target, const RDKit::Bond &b)
allows Bond objects to be dumped to streams
Invariant.h
PRECONDITION
#define PRECONDITION(expr, mess)
Definition Invariant.h:109
QueryObjects.h
Pulls in all the query types.
RDProps.h
Queries::Query
Base class for all queries.
Definition Query.h:45
RDKit::Atom
The class for representing atoms.
Definition Atom.h:75
RDKit::Bond
class for representing a bond
Definition Bond.h:47
RDKit::Bond::getBeginAtomIdx
unsigned int getBeginAtomIdx() const
returns the index of our begin Atom
Definition Bond.h:218
RDKit::Bond::d_index
atomindex_t d_index
Definition Bond.h:378
RDKit::Bond::getEndAtom
Atom * getEndAtom() const
returns a pointer to our end Atom
RDKit::Bond::updatePropertyCache
void updatePropertyCache(bool strict=true)
calculates any of our lazy properties
Definition Bond.h:369
RDKit::Bond::getBondTypeAsDouble
double getBondTypeAsDouble() const
returns our bondType as a double (e.g. SINGLE->1.0, AROMATIC->1.5, etc.)
RDKit::Bond::setEndAtomIdx
void setEndAtomIdx(unsigned int what)
sets the index of our end Atom
RDKit::Bond::getOtherAtomIdx
unsigned int getOtherAtomIdx(unsigned int thisIdx) const
given the index of one Atom, returns the index of the other
RDKit::Bond::dp_stereoAtoms
INT_VECT * dp_stereoAtoms
Definition Bond.h:377
RDKit::Bond::~Bond
virtual ~Bond()
RDKit::Bond::BondType
BondType
the type of Bond
Definition Bond.h:56
RDKit::Bond::ZERO
@ ZERO
Zero-order bond (from.
Definition Bond.h:78
RDKit::Bond::DATIVER
@ DATIVER
standard two-electron dative
Definition Bond.h:76
RDKit::Bond::QUINTUPLE
@ QUINTUPLE
Definition Bond.h:62
RDKit::Bond::TWOANDAHALF
@ TWOANDAHALF
Definition Bond.h:65
RDKit::Bond::HYDROGEN
@ HYDROGEN
Definition Bond.h:71
RDKit::Bond::THREECENTER
@ THREECENTER
Definition Bond.h:72
RDKit::Bond::FIVEANDAHALF
@ FIVEANDAHALF
Definition Bond.h:68
RDKit::Bond::QUADRUPLE
@ QUADRUPLE
Definition Bond.h:61
RDKit::Bond::FOURANDAHALF
@ FOURANDAHALF
Definition Bond.h:67
RDKit::Bond::AROMATIC
@ AROMATIC
Definition Bond.h:69
RDKit::Bond::THREEANDAHALF
@ THREEANDAHALF
Definition Bond.h:66
RDKit::Bond::IONIC
@ IONIC
Definition Bond.h:70
RDKit::Bond::DOUBLE
@ DOUBLE
Definition Bond.h:59
RDKit::Bond::HEXTUPLE
@ HEXTUPLE
Definition Bond.h:63
RDKit::Bond::TRIPLE
@ TRIPLE
Definition Bond.h:60
RDKit::Bond::ONEANDAHALF
@ ONEANDAHALF
Definition Bond.h:64
RDKit::Bond::DATIVE
@ DATIVE
standard two-electron dative
Definition Bond.h:74
RDKit::Bond::SINGLE
@ SINGLE
Definition Bond.h:58
RDKit::Bond::OTHER
@ OTHER
Definition Bond.h:77
RDKit::Bond::DATIVEONE
@ DATIVEONE
one-electron dative (e.g. from a C in a Cp ring to a metal)
Definition Bond.h:73
RDKit::Bond::DATIVEL
@ DATIVEL
standard two-electron dative
Definition Bond.h:75
RDKit::Bond::UNSPECIFIED
@ UNSPECIFIED
Definition Bond.h:57
RDKit::Bond::Bond
Bond(const Bond &other)
RDKit::Bond::RWMol
friend class RWMol
Definition Bond.h:48
RDKit::Bond::initBond
void initBond()
RDKit::Bond::setIsAromatic
void setIsAromatic(bool what)
sets our isAromatic flag
Definition Bond.h:173
RDKit::Bond::getIdx
unsigned int getIdx() const
returns our index within the ROMol
Definition Bond.h:204
RDKit::Bond::setBeginAtom
void setBeginAtom(Atom *at)
sets our begin Atom
RDKit::Bond::getIsConjugated
bool getIsConjugated() const
returns the status of our isConjugated flag
Definition Bond.h:180
RDKit::Bond::hasOwningMol
bool hasOwningMol() const
returns whether or not this instance belongs to a molecule
Definition Bond.h:183
RDKit::Bond::getQuery
virtual QUERYBOND_QUERY * getQuery() const
NOT CALLABLE.
RDKit::Bond::hasQuery
virtual bool hasQuery() const
Definition Bond.h:285
RDKit::Bond::setStereoAtoms
void setStereoAtoms(unsigned int bgnIdx, unsigned int endIdx)
sets the atoms to be considered as reference points for bond stereo
RDKit::Bond::setBeginAtomIdx
void setBeginAtomIdx(unsigned int what)
sets the index of our begin Atom
RDKit::Bond::setIsConjugated
void setIsConjugated(bool what)
sets our isConjugated flag
Definition Bond.h:178
RDKit::Bond::QUERYBOND_QUERY
Queries::Query< int, Bond const *, true > QUERYBOND_QUERY
Definition Bond.h:53
RDKit::Bond::getBondType
BondType getBondType() const
returns our bondType
Definition Bond.h:158
RDKit::Bond::getOwningMol
ROMol & getOwningMol() const
returns a reference to the ROMol that owns this instance
Definition Bond.h:186
RDKit::Bond::setQuery
virtual void setQuery(QUERYBOND_QUERY *what)
NOT CALLABLE.
RDKit::Bond::operator=
Bond & operator=(const Bond &other)
RDKit::Bond::setOwningMol
void setOwningMol(ROMol *other)
sets our owning molecule
RDKit::Bond::setBondType
void setBondType(BondType bT)
sets our bondType
Definition Bond.h:160
RDKit::Bond::df_isAromatic
bool df_isAromatic
Definition Bond.h:380
RDKit::Bond::Bond
Bond()
RDKit::Bond::d_beginAtomIdx
atomindex_t d_beginAtomIdx
Definition Bond.h:379
RDKit::Bond::d_endAtomIdx
atomindex_t d_endAtomIdx
Definition Bond.h:379
RDKit::Bond::getOtherAtom
Atom * getOtherAtom(Atom const *what) const
returns a pointer to the other Atom
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:357
RDKit::Bond::ROMol
friend class ROMol
Definition Bond.h:49
RDKit::Bond::BondDir
BondDir
the bond's direction (for chirality)
Definition Bond.h:83
RDKit::Bond::EITHERDOUBLE
@ EITHERDOUBLE
a "crossed" double bond
Definition Bond.h:90
RDKit::Bond::BEGINWEDGE
@ BEGINWEDGE
wedged: narrow at begin
Definition Bond.h:85
RDKit::Bond::ENDUPRIGHT
@ ENDUPRIGHT
ditto
Definition Bond.h:89
RDKit::Bond::UNKNOWN
@ UNKNOWN
intentionally unspecified stereochemistry
Definition Bond.h:91
RDKit::Bond::NONE
@ NONE
no special style
Definition Bond.h:84
RDKit::Bond::ENDDOWNRIGHT
@ ENDDOWNRIGHT
for cis/trans
Definition Bond.h:88
RDKit::Bond::BEGINDASH
@ BEGINDASH
dashed: narrow at begin
Definition Bond.h:86
RDKit::Bond::Bond
Bond(Bond &&o) noexcept
Definition Bond.h:115
RDKit::Bond::expandQuery
virtual void expandQuery(QUERYBOND_QUERY *what, Queries::CompositeQueryType how=Queries::COMPOSITE_AND, bool maintainOrder=true)
NOT CALLABLE.
RDKit::Bond::getBeginAtom
Atom * getBeginAtom() const
returns a pointer to our begin Atom
RDKit::Bond::setOwningMol
void setOwningMol(ROMol &other)
sets our owning molecule
Definition Bond.h:193
RDKit::Bond::getStereoAtoms
const INT_VECT & getStereoAtoms() const
returns the indices of our stereo atoms
Definition Bond.h:350
RDKit::Bond::d_stereo
std::uint8_t d_stereo
Definition Bond.h:384
RDKit::Bond::getStereo
BondStereo getStereo() const
returns our stereo code
Definition Bond.h:333
RDKit::Bond::setStereo
void setStereo(BondStereo what)
sets our stereo code
Definition Bond.h:325
RDKit::Bond::setIdx
void setIdx(unsigned int index)
sets our index within the ROMol
Definition Bond.h:211
RDKit::Bond::getEndAtomIdx
unsigned int getEndAtomIdx() const
returns the index of our end Atom
Definition Bond.h:225
RDKit::Bond::copy
virtual Bond * copy() const
returns a copy
RDKit::Bond::d_dirTag
std::uint8_t d_dirTag
Definition Bond.h:383
RDKit::Bond::d_bondType
std::uint8_t d_bondType
Definition Bond.h:382
RDKit::Bond::operator=
Bond & operator=(Bond &&o) noexcept
Definition Bond.h:129
RDKit::Bond::getValenceContrib
virtual double getValenceContrib(const Atom *at) const
returns our contribution to the explicit valence of an Atom
RDKit::Bond::setEndAtom
void setEndAtom(Atom *at)
sets our end Atom
RDKit::Bond::dp_mol
ROMol * dp_mol
Definition Bond.h:376
RDKit::Bond::setBondDir
void setBondDir(BondDir what)
sets our direction
Definition Bond.h:309
RDKit::Bond::BondStereo
BondStereo
the nature of the bond's stereochem (for cis/trans)
Definition Bond.h:95
RDKit::Bond::STEREOTRANS
@ STEREOTRANS
Definition Bond.h:103
RDKit::Bond::STEREOE
@ STEREOE
Definition Bond.h:101
RDKit::Bond::STEREOZ
@ STEREOZ
Definition Bond.h:100
RDKit::Bond::STEREOATROPCCW
@ STEREOATROPCCW
Definition Bond.h:105
RDKit::Bond::STEREOCIS
@ STEREOCIS
Definition Bond.h:102
RDKit::Bond::STEREONONE
@ STEREONONE
Definition Bond.h:96
RDKit::Bond::STEREOATROPCW
@ STEREOATROPCW
Definition Bond.h:104
RDKit::Bond::STEREOANY
@ STEREOANY
Definition Bond.h:97
RDKit::Bond::getIsAromatic
bool getIsAromatic() const
returns the status of our isAromatic flag
Definition Bond.h:175
RDKit::Bond::Match
virtual bool Match(Bond const *what) const
returns whether or not we match the argument
RDKit::Bond::getBondDir
BondDir getBondDir() const
returns our direction
Definition Bond.h:311
RDKit::Bond::invertChirality
bool invertChirality()
RDKit::Bond::Bond
Bond(BondType bT)
construct with a particular BondType
RDKit::Bond::df_isConjugated
bool df_isConjugated
Definition Bond.h:381
RDKit::RDProps::operator=
RDProps & operator=(const RDProps &rhs)
Definition RDProps.h:24
RDKit::RDProps::RDProps
RDProps()
Definition RDProps.h:22
RDKit::ROMol
Definition ROMol.h:199
RDKit::RWMol
RWMol is a molecule class that is intended to be edited.
Definition RWMol.h:32
details.h
export.h
RDKIT_GRAPHMOL_EXPORT
#define RDKIT_GRAPHMOL_EXPORT
Definition export.h:249
Queries::CompositeQueryType
CompositeQueryType
Definition QueryObjects.h:36
Queries::COMPOSITE_AND
@ COMPOSITE_AND
Definition QueryObjects.h:36
RDKit
Std stuff.
Definition Abbreviations.h:19
RDKit::INT_VECT
std::vector< int > INT_VECT
Definition types.h:300
RDKit::canHaveDirection
bool canHaveDirection(const Bond &bond)
Definition Bond.h:405
RDKit::canSetDoubleBondStereo
bool canSetDoubleBondStereo(const Bond &bond)
Definition Bond.h:399
RDKit::isDative
bool isDative(const Bond::BondType bt)
Definition Bond.h:389
RDKit::atomindex_t
std::uint32_t atomindex_t
Definition details.h:14
RDKit::getTwiceBondType
RDKIT_GRAPHMOL_EXPORT uint8_t getTwiceBondType(const RDKit::Bond &b)
types.h