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RDKit
Open-source cheminformatics and machine learning.
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The class for representing SubstanceGroups. More...
#include <SubstanceGroup.h>
Classes | |
struct | AttachPoint |
struct | CState |
Public Types | |
enum | BondType { BondType::XBOND, BondType::CBOND } |
Bond type (see V3000 spec) More... | |
typedef std::array< RDGeom::Point3D, 3 > | Bracket |
Public Member Functions | |
SubstanceGroup ()=delete | |
No default constructor. More... | |
SubstanceGroup (ROMol *owning_mol, const std::string &type) | |
SubstanceGroup (const SubstanceGroup &other)=default | |
SubstanceGroup (SubstanceGroup &&other)=default | |
SubstanceGroup & | operator= (const SubstanceGroup &other)=default |
SubstanceGroup & | operator= (SubstanceGroup &&other)=default |
~SubstanceGroup () | |
Destructor. More... | |
bool | hasOwningMol () const |
returns whether or not this belongs to a molecule More... | |
ROMol & | getOwningMol () const |
Get the molecule that owns this instance. More... | |
unsigned int | getIndexInMol () const |
void | addAtomWithIdx (unsigned int idx) |
void | addParentAtomWithIdx (unsigned int idx) |
void | addBondWithIdx (unsigned int idx) |
void | addAtomWithBookmark (int mark) |
void | addParentAtomWithBookmark (int mark) |
void | addBondWithBookmark (int mark) |
void | addBracket (const Bracket &bracket) |
void | addCState (unsigned int bondIdx, const RDGeom::Point3D &vector) |
void | addAttachPoint (unsigned int aIdx, int lvIdx, const std::string &idStr) |
BondType | getBondType (unsigned int bondIdx) const |
const std::vector< unsigned int > & | getAtoms () const |
const std::vector< unsigned int > & | getParentAtoms () const |
const std::vector< unsigned int > & | getBonds () const |
const std::vector< Bracket > & | getBrackets () const |
const std::vector< CState > & | getCStates () const |
const std::vector< AttachPoint > & | getAttachPoints () const |
void | setOwningMol (ROMol *mol) |
bool | operator== (const SubstanceGroup &other) const |
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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 |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. More... | |
template<typename T > | |
bool | getPropIfPresent (const std::string &key, T &res) const |
bool | hasProp (const std::string &key) const |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. More... | |
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... | |
Additional Inherited Members | |
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Dict | d_props |
The class for representing SubstanceGroups.
Notes:
Definition at line 52 of file SubstanceGroup.h.
typedef std::array<RDGeom::Point3D, 3> RDKit::SubstanceGroup::Bracket |
Definition at line 60 of file SubstanceGroup.h.
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strong |
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delete |
No default constructor.
RDKit::SubstanceGroup::SubstanceGroup | ( | ROMol * | owning_mol, |
const std::string & | type | ||
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Main Constructor. Ownership is only set on this side of the relationship: mol->addSubstanceGroup(sgroup) still needs to be called to get ownership on the other side.
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default |
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default |
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inline |
Destructor.
Definition at line 99 of file SubstanceGroup.h.
void RDKit::SubstanceGroup::addAtomWithBookmark | ( | int | mark | ) |
void RDKit::SubstanceGroup::addAtomWithIdx | ( | unsigned int | idx | ) |
void RDKit::SubstanceGroup::addAttachPoint | ( | unsigned int | aIdx, |
int | lvIdx, | ||
const std::string & | idStr | ||
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void RDKit::SubstanceGroup::addBondWithBookmark | ( | int | mark | ) |
void RDKit::SubstanceGroup::addBondWithIdx | ( | unsigned int | idx | ) |
void RDKit::SubstanceGroup::addBracket | ( | const Bracket & | bracket | ) |
void RDKit::SubstanceGroup::addCState | ( | unsigned int | bondIdx, |
const RDGeom::Point3D & | vector | ||
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void RDKit::SubstanceGroup::addParentAtomWithBookmark | ( | int | mark | ) |
void RDKit::SubstanceGroup::addParentAtomWithIdx | ( | unsigned int | idx | ) |
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inline |
Definition at line 128 of file SubstanceGroup.h.
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inline |
Definition at line 134 of file SubstanceGroup.h.
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inline |
Definition at line 130 of file SubstanceGroup.h.
BondType RDKit::SubstanceGroup::getBondType | ( | unsigned int | bondIdx | ) | const |
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inline |
Definition at line 132 of file SubstanceGroup.h.
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inline |
Definition at line 133 of file SubstanceGroup.h.
unsigned int RDKit::SubstanceGroup::getIndexInMol | ( | ) | const |
get the index of this sgroup in dp_mol's sgroups vector (do not mistake this by the ID!)
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inline |
Get the molecule that owns this instance.
Definition at line 105 of file SubstanceGroup.h.
References PRECONDITION.
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inline |
Definition at line 129 of file SubstanceGroup.h.
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inline |
returns whether or not this belongs to a molecule
Definition at line 102 of file SubstanceGroup.h.
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default |
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default |
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inline |
Definition at line 141 of file SubstanceGroup.h.
void RDKit::SubstanceGroup::setOwningMol | ( | ROMol * | mol | ) |
Set owning molecule This only updates atoms and bonds; parent sgroup has to be updated independently, since parent might not exist at the time this is called.