![]() |
RDKit
Open-source cheminformatics and machine learning.
|
Class for storing Bond queries. More...
#include <QueryBond.h>
Public Types | |
typedef Queries::Query< int, Bond const *, true > | QUERYBOND_QUERY |
![]() | |
enum | BondType { UNSPECIFIED = 0, SINGLE, DOUBLE, TRIPLE, QUADRUPLE, QUINTUPLE, HEXTUPLE, ONEANDAHALF, TWOANDAHALF, THREEANDAHALF, FOURANDAHALF, FIVEANDAHALF, AROMATIC, IONIC, HYDROGEN, THREECENTER, DATIVEONE, DATIVE, DATIVEL, DATIVER, OTHER, ZERO } |
the type of Bond More... | |
enum | BondDir { NONE = 0, BEGINWEDGE, BEGINDASH, ENDDOWNRIGHT, ENDUPRIGHT, EITHERDOUBLE, UNKNOWN } |
the bond's direction (for chirality) More... | |
enum | BondStereo { STEREONONE = 0, STEREOANY, STEREOZ, STEREOE, STEREOCIS, STEREOTRANS } |
the nature of the bond's stereochem (for cis/trans) More... | |
typedef Queries::Query< int, Bond const *, true > | QUERYBOND_QUERY |
Public Member Functions | |
QueryBond () | |
QueryBond (BondType bT) | |
initialize with a particular bond order More... | |
QueryBond (const Bond &other) | |
initialize from a bond More... | |
QueryBond (const QueryBond &other) | |
~QueryBond () | |
virtual Bond * | copy () const |
returns a copy of this query, owned by the caller More... | |
QueryBond & | operator= (const QueryBond &other) |
void | setBondType (BondType bT) |
sets the BondType of this query: More... | |
void | setBondDir (BondDir bD) |
sets the BondDir of this query: More... | |
bool | Match (Bond const *what) const |
returns true if we match Bond what More... | |
bool | QueryMatch (QueryBond const *what) const |
returns true if our query details match those of QueryBond what More... | |
bool | hasQuery () const |
QUERYBOND_QUERY * | getQuery () const |
returns our current query More... | |
void | setQuery (QUERYBOND_QUERY *what) |
replaces our current query with the value passed in More... | |
void | expandQuery (QUERYBOND_QUERY *what, Queries::CompositeQueryType how=Queries::COMPOSITE_AND, bool maintainOrder=true) |
expands our current query More... | |
![]() | |
Bond () | |
Bond (BondType bT) | |
construct with a particular BondType More... | |
Bond (const Bond &other) | |
virtual | ~Bond () |
Bond & | operator= (const Bond &other) |
BondType | getBondType () const |
returns our bondType More... | |
void | setBondType (BondType bT) |
sets our bondType More... | |
double | getBondTypeAsDouble () const |
returns our bondType as a double (e.g. SINGLE->1.0, AROMATIC->1.5, etc.) More... | |
double | getValenceContrib (const Atom *at) const |
returns our contribution to the explicit valence of an Atom More... | |
void | setIsAromatic (bool what) |
sets our isAromatic flag More... | |
bool | getIsAromatic () const |
returns the status of our isAromatic flag More... | |
void | setIsConjugated (bool what) |
sets our isConjugated flag More... | |
bool | getIsConjugated () const |
returns the status of our isConjugated flag More... | |
ROMol & | getOwningMol () const |
returns a reference to the ROMol that owns this Bond More... | |
void | setOwningMol (ROMol *other) |
sets our owning molecule More... | |
void | setOwningMol (ROMol &other) |
sets our owning molecule More... | |
unsigned int | getIdx () const |
returns our index within the ROMol More... | |
void | setIdx (unsigned int index) |
sets our index within the ROMol More... | |
unsigned int | getBeginAtomIdx () const |
returns the index of our begin Atom More... | |
unsigned int | getEndAtomIdx () const |
returns the index of our end Atom More... | |
unsigned int | getOtherAtomIdx (unsigned int thisIdx) const |
given the index of one Atom, returns the index of the other More... | |
void | setBeginAtomIdx (unsigned int what) |
sets the index of our begin Atom More... | |
void | setEndAtomIdx (unsigned int what) |
sets the index of our end Atom More... | |
void | setBeginAtom (Atom *at) |
sets our begin Atom More... | |
void | setEndAtom (Atom *at) |
sets our end Atom More... | |
Atom * | getBeginAtom () const |
returns a pointer to our begin Atom More... | |
Atom * | getEndAtom () const |
returns a pointer to our end Atom More... | |
Atom * | getOtherAtom (Atom const *what) const |
returns a pointer to the other Atom More... | |
void | setBondDir (BondDir what) |
sets our direction More... | |
BondDir | getBondDir () const |
returns our direction More... | |
void | setStereo (BondStereo what) |
sets our stereo code More... | |
BondStereo | getStereo () const |
returns our stereo code More... | |
void | setStereoAtoms (unsigned int bgnIdx, unsigned int endIdx) |
sets the atoms to be considered as reference points for bond stereo More... | |
const INT_VECT & | getStereoAtoms () const |
returns the indices of our stereo atoms More... | |
INT_VECT & | getStereoAtoms () |
void | updatePropertyCache (bool strict=true) |
calculates any of our lazy properties More... | |
![]() | |
RDProps () | |
RDProps (const RDProps &rhs) | |
RDProps & | operator= (const RDProps &rhs) |
void | clear () |
const Dict & | getDict () const |
gets the underlying Dictionary More... | |
Dict & | getDict () |
STR_VECT | getPropList (bool includePrivate=true, bool includeComputed=true) const |
returns a list with the names of our properties More... | |
template<typename T > | |
void | setProp (const std::string &key, T val, bool computed=false) const |
sets a property value More... | |
template<typename T > | |
void | getProp (const std::string &key, T &res) const |
allows retrieval of a particular property value More... | |
template<typename T > | |
T | getProp (const std::string &key) const |
template<typename T > | |
bool | getPropIfPresent (const std::string &key, T &res) const |
bool | hasProp (const std::string &key) const |
void | clearProp (const std::string &key) const |
clears the value of a property More... | |
void | clearComputedProps () const |
clears all of our computed properties More... | |
void | updateProps (const RDProps &source, bool preserveExisting=false) |
update the properties from another More... | |
Protected Attributes | |
QUERYBOND_QUERY * | dp_query |
![]() | |
bool | df_isAromatic |
sets our owning molecule More... | |
bool | df_isConjugated |
boost::uint8_t | d_bondType |
boost::uint8_t | d_dirTag |
boost::uint8_t | d_stereo |
atomindex_t | d_index |
atomindex_t | d_beginAtomIdx |
atomindex_t | d_endAtomIdx |
ROMol * | dp_mol |
INT_VECT * | dp_stereoAtoms |
![]() | |
Dict | dp_props |
Additional Inherited Members | |
![]() | |
void | initBond () |
Class for storing Bond queries.
QueryBond objects are derived from Bond objects, so they can be added to molecules and the like, but they have much fancier querying capabilities.
Definition at line 28 of file QueryBond.h.
typedef Queries::Query<int, Bond const *, true> RDKit::QueryBond::QUERYBOND_QUERY |
Definition at line 30 of file QueryBond.h.
|
inline |
Definition at line 32 of file QueryBond.h.
|
explicit |
initialize with a particular bond order
|
inlineexplicit |
initialize from a bond
Definition at line 36 of file QueryBond.h.
|
inline |
Definition at line 38 of file QueryBond.h.
RDKit::QueryBond::~QueryBond | ( | ) |
|
virtual |
returns a copy of this query, owned by the caller
Reimplemented from RDKit::Bond.
|
virtual |
expands our current query
what | the Queries::Query to be added |
how | the operator to be used in the expansion |
maintainOrder | (optional) flags whether the relative order of the queries needs to be maintained, if this is false, the order is reversed |
Notes:
what
should probably be constructed using one of the functions defined in QueryOps.hmaintainOrder
option can be useful because the combination operators short circuit when possible. Reimplemented from RDKit::Bond.
|
inlinevirtual |
returns our current query
Reimplemented from RDKit::Bond.
Definition at line 63 of file QueryBond.h.
|
inlinevirtual |
Reimplemented from RDKit::Bond.
Definition at line 60 of file QueryBond.h.
|
virtual |
returns true if we match Bond what
Reimplemented from RDKit::Bond.
bool RDKit::QueryBond::QueryMatch | ( | QueryBond const * | what | ) | const |
returns true if our query details match those of QueryBond what
void RDKit::QueryBond::setBondDir | ( | BondDir | bD | ) |
sets the BondDir of this query:
void RDKit::QueryBond::setBondType | ( | BondType | bT | ) |
sets the BondType of this query:
|
inlinevirtual |
replaces our current query with the value passed in
Reimplemented from RDKit::Bond.
Definition at line 65 of file QueryBond.h.
References Queries::COMPOSITE_AND.
|
protected |
Definition at line 91 of file QueryBond.h.