RDCode: RDKit::ROMol Class Reference

# RDKit::ROMol Class Reference

ROMol is a molecule class that is intended to have a fixed topology. More...

`#include <ROMol.h>`

Inheritance diagram for RDKit::ROMol:

List of all members.

## Public Member Functions
| ROMol ()
| ROMol (const ROMol &other, bool quickCopy=false)
| copy constructor with a twist
| ROMol (const std::string &binStr)
| construct a molecule from a pickle string
virtual | ~ROMol ()
ATOM_SPTR | operator[] (const vertex_descriptor &v)
const ATOM_SPTR | operator[] (const vertex_descriptor &v) const
BOND_SPTR | operator[] (const edge_descriptor &e)
const BOND_SPTR | operator[] (const edge_descriptor &e) const
Atoms
unsigned int | getNumAtoms (bool onlyHeavy=1) const
| returns our number of Atoms
Atom * | getAtomWithIdx (unsigned int idx)
| returns a pointer to a particular Atom
const Atom * | getAtomWithIdx (unsigned int idx) const
unsigned int | getAtomDegree (const Atom *at) const
| returns the degree (number of neighbors) of an Atom in the graph
unsigned int | getAtomDegree (ATOM_SPTR at) const
Bonds
unsigned int | getNumBonds (bool onlyHeavy=1) const
| returns our number of Bonds
Bond * | getBondWithIdx (unsigned int idx)
| returns a pointer to a particular Bond
const Bond * | getBondWithIdx (unsigned int idx) const
Bond * | getBondBetweenAtoms (unsigned int idx1, unsigned int idx2)
| returns a pointer to the bond between two atoms, Null on failure
const Bond * | getBondBetweenAtoms (unsigned int idx1, unsigned int idx2) const
Bookmarks
void | setAtomBookmark (ATOM_SPTR at, int mark)
| associates an Atom pointer with a bookmark
void | setAtomBookmark (Atom *at, int mark)
Atom * | getAtomWithBookmark (int mark)
| returns the first Atom associated with the `bookmark` provided
ATOM_PTR_LIST & | getAllAtomsWithBookmark (int mark)
| returns all Atoms associated with the `bookmark` provided
void | clearAtomBookmark (const int mark)
| removes a `bookmark` from our collection
void | clearAtomBookmark (const int mark, const Atom *atom)
| removes a particular Atom from the list associated with the `bookmark`
void | clearAtomBookmark (const int mark, ATOM_SPTR atom)
void | clearAllAtomBookmarks ()
| blows out all atomic `bookmarks`
bool | hasAtomBookmark (int mark) const
| queries whether or not any atoms are associated with a `bookmark`
ATOM_BOOKMARK_MAP * | getAtomBookmarks ()
| returns a pointer to all of our atom `bookmarks`
void | setBondBookmark (BOND_SPTR bond, int mark)
| associates a Bond pointer with a bookmark
void | setBondBookmark (Bond *bond, int mark)
Bond * | getBondWithBookmark (int mark)
| returns the first Bond associated with the `bookmark` provided
BOND_PTR_LIST & | getAllBondsWithBookmark (int mark)
| returns all bonds associated with the `bookmark` provided
void | clearBondBookmark (int mark)
| removes a `bookmark` from our collection
void | clearBondBookmark (int mark, const Bond *bond)
| removes a particular Bond from the list associated with the `bookmark`
void | clearBondBookmark (int mark, BOND_SPTR bond)
void | clearAllBondBookmarks ()
| blows out all bond `bookmarks`
bool | hasBondBookmark (int mark) const
| queries whether or not any bonds are associated with a `bookmark`
BOND_BOOKMARK_MAP * | getBondBookmarks ()
| returns a pointer to all of our bond `bookmarks`
Conformers
const Conformer & | getConformer (int id=-1) const
Conformer & | getConformer (int id=-1)
void | removeConformer (unsigned int id)
| Delete the conformation with the specified ID.
void | clearConformers ()
| Clear all the conformations on the molecule.
unsigned int | addConformer (Conformer *conf, bool assignId=false)
| Add a new conformation to the molecule.
unsigned int | getNumConformers () const
Topology
RingInfo * | getRingInfo () const
ADJ_ITER_PAIR | getAtomNeighbors (Atom const *at) const
| provides access to all neighbors around an Atom
ADJ_ITER_PAIR | getAtomNeighbors (ATOM_SPTR at) const
OBOND_ITER_PAIR | getAtomBonds (Atom const *at) const
| provides access to all Bond objects connected to an Atom
ATOM_ITER_PAIR | getVertices ()
| returns an iterator pair for looping over all Atoms
BOND_ITER_PAIR | getEdges ()
| returns an iterator pair for looping over all Bonds
ATOM_ITER_PAIR | getVertices () const
BOND_ITER_PAIR | getEdges () const
MolGraph const & | getTopology () const
| brief returns a pointer to our underlying BGL object
Iterators
AtomIterator | beginAtoms ()
| get an AtomIterator pointing at our first Atom
ConstAtomIterator | beginAtoms () const
AtomIterator | endAtoms ()
| get an AtomIterator pointing at the end of our Atoms
ConstAtomIterator | endAtoms () const
BondIterator | beginBonds ()
| get a BondIterator pointing at our first Bond
ConstBondIterator | beginBonds () const
BondIterator | endBonds ()
| get a BondIterator pointing at the end of our Bonds
ConstBondIterator | endBonds () const
AromaticAtomIterator | beginAromaticAtoms ()
| get an AtomIterator pointing at our first aromatic Atom
ConstAromaticAtomIterator | beginAromaticAtoms () const
AromaticAtomIterator | endAromaticAtoms ()
| get an AtomIterator pointing at the end of our Atoms
ConstAromaticAtomIterator | endAromaticAtoms () const
HeteroatomIterator | beginHeteros ()
| get an AtomIterator pointing at our first hetero Atom
ConstHeteroatomIterator | beginHeteros () const
HeteroatomIterator | endHeteros ()
| get an AtomIterator pointing at the end of our Atoms
ConstHeteroatomIterator | endHeteros () const
QueryAtomIterator | beginQueryAtoms (QueryAtom const *query)
| get an AtomIterator pointing at our first Atom that matches `query`
ConstQueryAtomIterator | beginQueryAtoms (QueryAtom const *) const
QueryAtomIterator | endQueryAtoms ()
| gte an AtomIterator pointing at the end of our Atoms
ConstQueryAtomIterator | endQueryAtoms () const
ConformerIterator | beginConformers ()
ConformerIterator | endConformers ()
ConstConformerIterator | beginConformers () const
ConstConformerIterator | endConformers () const
Properties
STR_VECT | getPropList (bool includePrivate=true, bool includeComputed=true) const
| returns a list with the names of our `properties`
template<typename T>
void | setProp (const char *key, T val, bool computed=false) const
| sets a `property` value
template<typename T>
void | setProp (const std::string key, T val, bool computed=false) const
template<typename T>
void | getProp (const char *key, T &res) const
| allows retrieval of a particular property value
template<typename T>
void | getProp (const std::string key, T &res) const
bool | hasProp (const char *key) const
| returns whether or not we have a `property` with name `key`
bool | hasProp (const std::string key) const
void | clearProp (const char *key) const
| clears the value of a `property`
void | clearProp (const std::string key) const
void | clearComputedProps (bool includeRings=true) const
| clears all of our `computed` `properties`
void | updatePropertyCache (bool strict=true)
| calculates any of our lazy `properties`
Misc
void | debugMol (std::ostream &str) const
| sends some debugging info to a stream
## Friends
class | MolPickler
class | RWMol

## Detailed Description

ROMol is a molecule class that is intended to have a fixed topology.

This is the primary class for most molecule operations.

If you need to be manipulating the molecule (e.g. adding or deleting atoms or bonds, use an RWMol instead.

Notes:

- each ROMol maintains a Dict of `properties:`
  - Each `property` is keyed by name and can store an arbitrary type.
  - `Properties` can be marked as `calculated`, in which case they will be cleared when the `clearComputedProps()` method is called.
  - Because they have no impact upon chemistry, all `property` operations are `const`, this allows extra flexibility for clients who need to store extra data on ROMol objects.

- each ROMol has collections of `bookmarks` for Atoms and Bonds:
  - the Atom bookmarks and Bond bookmarks are stored separately from each other
  - each `bookmark`, an integer, can map to more than one Atom or Bond
  - these are currently used in molecule construction, but could also be useful for reaction mapping and the like

- information about rings (SSSR and the like) is stored in the molecule's RingInfo pointer.

Definition at line 98 of file ROMol.h.

## Constructor & Destructor Documentation

RDKit::ROMol::ROMol | ( |  | ) | `[inline]`

Definition at line 168 of file ROMol.h.

RDKit::ROMol::ROMol | ( | const ROMol & | other,
|  | bool | quickCopy = `false` |
| ) |  |  | `[inline]`

copy constructor with a twist

Parameters:

  | other | the molecule to be copied
  | quickCopy | (optional) if this is true, the resulting ROMol will not copy any of the properties or bookmarks and conformers from `other`. This can make the copy substantially faster (thus the name).

Definition at line 177 of file ROMol.h.

RDKit::ROMol::ROMol | ( | const std::string & | binStr | ) |

construct a molecule from a pickle string

virtual RDKit::ROMol::~ROMol | ( |  | ) | `[inline, virtual]`

Definition at line 181 of file ROMol.h.

## Member Function Documentation

unsigned int RDKit::ROMol::getNumAtoms | ( | bool | onlyHeavy = `1` | ) | const

returns our number of Atoms

Referenced by RDKit::RWMol::getLastAtom().

Atom* RDKit::ROMol::getAtomWithIdx | ( | unsigned int | idx | ) |

returns a pointer to a particular Atom

Referenced by RDKit::RWMol::getLastAtom().

const Atom* RDKit::ROMol::getAtomWithIdx | ( | unsigned int | idx | ) | const

unsigned int RDKit::ROMol::getAtomDegree | ( | const Atom * | at | ) | const

returns the degree (number of neighbors) of an Atom in the graph

unsigned int RDKit::ROMol::getAtomDegree | ( | ATOM_SPTR | at | ) | const

unsigned int RDKit::ROMol::getNumBonds | ( | bool | onlyHeavy = `1` | ) | const

returns our number of Bonds

Referenced by RDKit::FragCatalogEntry::getOrder().

Bond* RDKit::ROMol::getBondWithIdx | ( | unsigned int | idx | ) |

returns a pointer to a particular Bond

const Bond* RDKit::ROMol::getBondWithIdx | ( | unsigned int | idx | ) | const

Bond* RDKit::ROMol::getBondBetweenAtoms | ( | unsigned int | idx1,
|  | unsigned int | idx2 |
| ) |  |  |

returns a pointer to the bond between two atoms, Null on failure

const Bond* RDKit::ROMol::getBondBetweenAtoms | ( | unsigned int | idx1,
|  | unsigned int | idx2 |
| ) |  |  | const

void RDKit::ROMol::setAtomBookmark | ( | ATOM_SPTR | at,
|  | int | mark |
| ) |  |  | `[inline]`

associates an Atom pointer with a bookmark

Definition at line 219 of file ROMol.h.

Referenced by RDKit::SLNParse::bookmarkAtomID().

void RDKit::ROMol::setAtomBookmark | ( | Atom * | at,
|  | int | mark |
| ) |  |  | `[inline]`

Definition at line 221 of file ROMol.h.

Atom* RDKit::ROMol::getAtomWithBookmark | ( | int | mark | ) |

returns the first Atom associated with the `bookmark` provided

ATOM_PTR_LIST& RDKit::ROMol::getAllAtomsWithBookmark | ( | int | mark | ) |

returns all Atoms associated with the `bookmark` provided

void RDKit::ROMol::clearAtomBookmark | ( | const int | mark | ) |

removes a `bookmark` from our collection

Referenced by clearAtomBookmark().

void RDKit::ROMol::clearAtomBookmark | ( | const int | mark,
|  | const Atom * | atom |
| ) |  |  |

removes a particular Atom from the list associated with the `bookmark`

void RDKit::ROMol::clearAtomBookmark | ( | const int | mark,
|  | ATOM_SPTR | atom |
| ) |  |  | `[inline]`

Definition at line 231 of file ROMol.h.

References clearAtomBookmark().

void RDKit::ROMol::clearAllAtomBookmarks | ( |  | ) | `[inline]`

blows out all atomic `bookmarks`

Definition at line 233 of file ROMol.h.

bool RDKit::ROMol::hasAtomBookmark | ( | int | mark | ) | const`[inline]`

queries whether or not any atoms are associated with a `bookmark`

Definition at line 235 of file ROMol.h.

Referenced by RDKit::SLNParse::bookmarkAtomID().

ATOM_BOOKMARK_MAP* RDKit::ROMol::getAtomBookmarks | ( |  | ) | `[inline]`

returns a pointer to all of our atom `bookmarks`

Definition at line 237 of file ROMol.h.

void RDKit::ROMol::setBondBookmark | ( | BOND_SPTR | bond,
|  | int | mark |
| ) |  |  | `[inline]`

associates a Bond pointer with a bookmark

Definition at line 240 of file ROMol.h.

void RDKit::ROMol::setBondBookmark | ( | Bond * | bond,
|  | int | mark |
| ) |  |  | `[inline]`

Definition at line 242 of file ROMol.h.

Bond* RDKit::ROMol::getBondWithBookmark | ( | int | mark | ) |

returns the first Bond associated with the `bookmark` provided

BOND_PTR_LIST& RDKit::ROMol::getAllBondsWithBookmark | ( | int | mark | ) |

returns all bonds associated with the `bookmark` provided

void RDKit::ROMol::clearBondBookmark | ( | int | mark | ) |

removes a `bookmark` from our collection

Referenced by clearBondBookmark().

void RDKit::ROMol::clearBondBookmark | ( | int | mark,
|  | const Bond * | bond |
| ) |  |  |

removes a particular Bond from the list associated with the `bookmark`

void RDKit::ROMol::clearBondBookmark | ( | int | mark,
|  | BOND_SPTR | bond |
| ) |  |  | `[inline]`

Definition at line 252 of file ROMol.h.

References clearBondBookmark().

void RDKit::ROMol::clearAllBondBookmarks | ( |  | ) | `[inline]`

blows out all bond `bookmarks`

Definition at line 254 of file ROMol.h.

bool RDKit::ROMol::hasBondBookmark | ( | int | mark | ) | const`[inline]`

queries whether or not any bonds are associated with a `bookmark`

Definition at line 256 of file ROMol.h.

Referenced by RDKit::SLNParse::bookmarkAtomID().

BOND_BOOKMARK_MAP* RDKit::ROMol::getBondBookmarks | ( |  | ) | `[inline]`

returns a pointer to all of our bond `bookmarks`

Definition at line 258 of file ROMol.h.

const Conformer& RDKit::ROMol::getConformer | ( | int | id = `-1` | ) | const

return the conformer with a specified ID if the ID is negative the first conformation will be returned

Conformer& RDKit::ROMol::getConformer | ( | int | id = `-1` | ) |

return the conformer with a specified ID if the ID is negative the first conformation will be returned

void RDKit::ROMol::removeConformer | ( | unsigned int | id | ) |

Delete the conformation with the specified ID.

void RDKit::ROMol::clearConformers | ( |  | ) | `[inline]`

Clear all the conformations on the molecule.

Definition at line 278 of file ROMol.h.

unsigned int RDKit::ROMol::addConformer | ( | Conformer * | conf,
|  | bool | assignId = `false` |
| ) |  |  |

Add a new conformation to the molecule.

Parameters:

  | conf | - conformation to be added to the molecule, this molecule takes ownership of the conformer
  | assignId | - a unique ID will be assigned to the the conformation if true otherwise it is assumed that the conformation already has an (unique) ID set

unsigned int RDKit::ROMol::getNumConformers | ( |  | ) | const`[inline]`

Definition at line 289 of file ROMol.h.

RingInfo* RDKit::ROMol::getRingInfo | ( |  | ) | const`[inline]`

returns a pointer to our RingInfo structure Note: the client should not delete this.

Definition at line 301 of file ROMol.h.

Referenced by RDKit::queryAtomIsInRingOfSize(), RDKit::queryAtomMinRingSize(), RDKit::queryAtomRingBondCount(), RDKit::queryAtomRingMembership(), RDKit::queryBondIsInRingOfSize(), RDKit::queryBondMinRingSize(), RDKit::queryIsAtomInNRings(), RDKit::queryIsAtomInRing(), RDKit::queryIsBondInNRings(), and RDKit::queryIsBondInRing().

ADJ_ITER_PAIR RDKit::ROMol::getAtomNeighbors | ( | Atom const * | at | ) | const

provides access to all neighbors around an Atom

Parameters:

  | at | the atom whose neighbors we are looking for

Usage

            ... molPtr is a const ROMol & ...
            ... atomPtr is a const Atom * ...
            ROMol::ADJ_ITER nbrIdx,endNbrs;
            boost::tie(nbrIdx,endNbrs) = molPtr.getAtomNeighbors(atomPtr);
            while(nbrIdx!=endNbrs){
              const ATOM_SPTR at=molPtr[*nbrIdx];
              ... do something with the Atom ...
              ++nbrIdx;
            }

ADJ_ITER_PAIR RDKit::ROMol::getAtomNeighbors | ( | ATOM_SPTR | at | ) | const

OBOND_ITER_PAIR RDKit::ROMol::getAtomBonds | ( | Atom const * | at | ) | const

provides access to all Bond objects connected to an Atom

Parameters:

  | at | the atom whose neighbors we are looking for

Usage

            ... molPtr is a const ROMol * ...
            ... atomPtr is a const Atom * ...
            ROMol::OEDGE_ITER beg,end;
            boost::tie(beg,end) = molPtr->getAtomBonds(atomPtr);
            while(beg!=end){
              const BOND_SPTR bond=(*molPtr)[*beg];
              ... do something with the Bond ...
              ++beg;
            }

or, if you need a non-const Bond *:

            ... molPtr is a ROMol * ...
            ... atomPtr is a const Atom * ...
            ROMol::OEDGE_ITER beg,end;
            boost::tie(beg,end) = molPtr->getAtomBonds(atomPtr);
            while(beg!=end){
              BOND_SPTR bond=(*molPtr)[*beg];
              ... do something with the Bond ...
              ++beg;
            }

Referenced by RDKit::queryAtomRingBondCount().

ATOM_ITER_PAIR RDKit::ROMol::getVertices | ( |  | ) |

returns an iterator pair for looping over all Atoms

Usage

            ROMol::VERTEX_ITER atBegin,atEnd;
            boost::tie(atBegin,atEnd) = mol.getVertices();
            while(atBegin!=atEnd){
              ATOM_SPTR at2=mol[*atBegin];
              ... do something with the Atom ...
              ++atBegin;
            }

BOND_ITER_PAIR RDKit::ROMol::getEdges | ( |  | ) |

returns an iterator pair for looping over all Bonds

Usage

            ROMol::EDGE_ITER firstB,lastB;
            boost::tie(firstB,lastB) = mol.getEdges();
            while(firstB!=lastB){
              BOND_SPTR bond = mol[*firstB];
              ... do something with the Bond ...
              ++firstB;
            }

ATOM_ITER_PAIR RDKit::ROMol::getVertices | ( |  | ) | const

BOND_ITER_PAIR RDKit::ROMol::getEdges | ( |  | ) | const

MolGraph const& RDKit::ROMol::getTopology | ( |  | ) | const`[inline]`

brief returns a pointer to our underlying BGL object

This can be useful if you need to call other BGL algorithms:

Here's an example:

               ... mol is a const ROMol ...
               ... mapping is an INT_VECT ...
               mapping.resize(mol.getNumAtoms());
               const MolGraph &G_p = mol.getTopology();
               int res = boost::connected_components(G_p,&mapping[0]);

Definition at line 408 of file ROMol.h.

Referenced by RDKit::queryAtomRingBondCount().

AtomIterator RDKit::ROMol::beginAtoms | ( |  | ) |

get an AtomIterator pointing at our first Atom

ConstAtomIterator RDKit::ROMol::beginAtoms | ( |  | ) | const

AtomIterator RDKit::ROMol::endAtoms | ( |  | ) |

get an AtomIterator pointing at the end of our Atoms

ConstAtomIterator RDKit::ROMol::endAtoms | ( |  | ) | const

BondIterator RDKit::ROMol::beginBonds | ( |  | ) |

get a BondIterator pointing at our first Bond

ConstBondIterator RDKit::ROMol::beginBonds | ( |  | ) | const

BondIterator RDKit::ROMol::endBonds | ( |  | ) |

get a BondIterator pointing at the end of our Bonds

ConstBondIterator RDKit::ROMol::endBonds | ( |  | ) | const

AromaticAtomIterator RDKit::ROMol::beginAromaticAtoms | ( |  | ) |

get an AtomIterator pointing at our first aromatic Atom

ConstAromaticAtomIterator RDKit::ROMol::beginAromaticAtoms | ( |  | ) | const

AromaticAtomIterator RDKit::ROMol::endAromaticAtoms | ( |  | ) |

get an AtomIterator pointing at the end of our Atoms

ConstAromaticAtomIterator RDKit::ROMol::endAromaticAtoms | ( |  | ) | const

HeteroatomIterator RDKit::ROMol::beginHeteros | ( |  | ) |

get an AtomIterator pointing at our first hetero Atom

ConstHeteroatomIterator RDKit::ROMol::beginHeteros | ( |  | ) | const

HeteroatomIterator RDKit::ROMol::endHeteros | ( |  | ) |

get an AtomIterator pointing at the end of our Atoms

ConstHeteroatomIterator RDKit::ROMol::endHeteros | ( |  | ) | const

QueryAtomIterator RDKit::ROMol::beginQueryAtoms | ( | QueryAtom const * | query | ) |

get an AtomIterator pointing at our first Atom that matches `query`

ConstQueryAtomIterator RDKit::ROMol::beginQueryAtoms | ( | QueryAtom const * |  | ) | const

QueryAtomIterator RDKit::ROMol::endQueryAtoms | ( |  | ) |

gte an AtomIterator pointing at the end of our Atoms

ConstQueryAtomIterator RDKit::ROMol::endQueryAtoms | ( |  | ) | const

ConformerIterator RDKit::ROMol::beginConformers | ( |  | ) | `[inline]`

Definition at line 459 of file ROMol.h.

ConformerIterator RDKit::ROMol::endConformers | ( |  | ) | `[inline]`

Definition at line 463 of file ROMol.h.

ConstConformerIterator RDKit::ROMol::beginConformers | ( |  | ) | const`[inline]`

Definition at line 467 of file ROMol.h.

ConstConformerIterator RDKit::ROMol::endConformers | ( |  | ) | const`[inline]`

Definition at line 471 of file ROMol.h.

STR_VECT RDKit::ROMol::getPropList | ( | bool | includePrivate = `true`,
|  | bool | includeComputed = `true` |
| ) |  |  | const`[inline]`

returns a list with the names of our `properties`

Definition at line 481 of file ROMol.h.

References getProp(), hasProp(), and RDKit::Dict::keys().

template<typename T>

void RDKit::ROMol::setProp | ( | const char * | key,
|  | T | val,
|  | bool | computed = `false` |
| ) |  |  | const`[inline]`

sets a `property` value

Parameters:

  | key | the name under which the `property` should be stored. If a `property` is already stored under this name, it will be replaced.
  | val | the value to be stored
  | computed | (optional) allows the `property` to be flagged `computed`.

Definition at line 512 of file ROMol.h.

template<typename T>

void RDKit::ROMol::setProp | ( | const std::string | key,
|  | T | val,
|  | bool | computed = `false` |
| ) |  |  | const`[inline]`

Definition at line 518 of file ROMol.h.

References getProp(), and RDKit::Dict::setVal().

template<typename T>

void RDKit::ROMol::getProp | ( | const char * | key,
|  | T & | res |
| ) |  |  | const`[inline]`

allows retrieval of a particular property value

Parameters:

  | key | the name under which the `property` should be stored. If a `property` is already stored under this name, it will be replaced.
  | res | a reference to the storage location for the value.

Notes:

- if no `property` with name `key` exists, a KeyErrorException will be thrown.
- the `boost::lexical_cast` machinery is used to attempt type conversions. If this fails, a `boost::bad_lexical_cast` exception will be thrown.

Definition at line 545 of file ROMol.h.

References RDKit::Dict::getVal().

Referenced by clearProp(), getPropList(), and setProp().

template<typename T>

void RDKit::ROMol::getProp | ( | const std::string | key,
|  | T & | res |
| ) |  |  | const`[inline]`

Definition at line 550 of file ROMol.h.

References RDKit::Dict::getVal().

bool RDKit::ROMol::hasProp | ( | const char * | key | ) | const`[inline]`

returns whether or not we have a `property` with name `key`

Definition at line 556 of file ROMol.h.

References RDKit::Dict::hasVal().

Referenced by getPropList().

bool RDKit::ROMol::hasProp | ( | const std::string | key | ) | const`[inline]`

Definition at line 561 of file ROMol.h.

References RDKit::Dict::hasVal().

void RDKit::ROMol::clearProp | ( | const char * | key | ) | const`[inline]`

clears the value of a `property`

Notes:

- if no `property` with name `key` exists, a KeyErrorException will be thrown.
- if the `property` is marked as `computed`, it will also be removed from our list of `computedProperties`

Definition at line 575 of file ROMol.h.

void RDKit::ROMol::clearProp | ( | const std::string | key | ) | const`[inline]`

Definition at line 580 of file ROMol.h.

References RDKit::Dict::clearVal(), getProp(), and RDKit::Dict::setVal().

void RDKit::ROMol::clearComputedProps | ( | bool | includeRings = `true` | ) | const

clears all of our `computed` `properties`

void RDKit::ROMol::updatePropertyCache | ( | bool | strict = `true` | ) |

calculates any of our lazy `properties`

Notes:

- this calls `updatePropertyCache()` on each of our Atoms and Bonds

void RDKit::ROMol::debugMol | ( | std::ostream & | str | ) | const

sends some debugging info to a stream

ATOM_SPTR RDKit::ROMol::operator[] | ( | const vertex_descriptor & | v | ) | `[inline]`

Definition at line 611 of file ROMol.h.

const ATOM_SPTR RDKit::ROMol::operator[] | ( | const vertex_descriptor & | v | ) | const`[inline]`

Definition at line 612 of file ROMol.h.

BOND_SPTR RDKit::ROMol::operator[] | ( | const edge_descriptor & | e | ) | `[inline]`

Definition at line 614 of file ROMol.h.

const BOND_SPTR RDKit::ROMol::operator[] | ( | const edge_descriptor & | e | ) | const`[inline]`

Definition at line 615 of file ROMol.h.

## Friends And Related Function Documentation

friend class MolPickler`[friend]`

Definition at line 100 of file ROMol.h.

friend class RWMol`[friend]`

Definition at line 101 of file ROMol.h.

The documentation for this class was generated from the following file:

- ROMol.h