RDKit: RDKit::RWMol Class Reference

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RDKit::RWMol Class Reference

RWMol is a molecule class that is intended to be edited. More...

`#include <RWMol.h>`

Inheritance diagram for RDKit::RWMol:

## Public Member Functions
| RWMol ()
| RWMol (const ROMol &other, bool quickCopy=false, int confId=-1)
| copy constructor with a twist More...
RWMol & | operator= (const RWMol &)
void | insertMol (const ROMol &other)
| insert the atoms and bonds from `other` into this molecule More...
void | clear ()
| removes all atoms, bonds, properties, bookmarks, etc. More...
Atoms
unsigned int | addAtom (bool updateLabel=true)
| adds an empty Atom to our collection More...
unsigned int | addAtom (Atom *atom, bool updateLabel=true, bool takeOwnership=false)
| adds an Atom to our collection More...
unsigned int | addAtom (ATOM_SPTR atom, bool updateLabel=true)
| adds an Atom to our collection More...
void | replaceAtom (unsigned int idx, Atom *atom, bool updateLabel=false)
| replaces a particular Atom More...
Atom * | getLastAtom ()
| returns a pointer to the highest-numbered Atom More...
Atom * | getActiveAtom ()
| returns a pointer to the "active" Atom More...
void | setActiveAtom (Atom *atom)
| sets our `activeAtom` More...
void | setActiveAtom (unsigned int idx)
void | removeAtom (unsigned int idx)
| removes an Atom from the molecule More...
void | removeAtom (Atom *atom)
Bonds
unsigned int | addBond (unsigned int beginAtomIdx, unsigned int endAtomIdx, Bond::BondType order=Bond::UNSPECIFIED)
| adds a Bond between the indicated Atoms More...
unsigned int | addBond (ATOM_SPTR beginAtom, ATOM_SPTR endAtom, Bond::BondType order=Bond::UNSPECIFIED)
unsigned int | addBond (Atom *beginAtom, Atom *endAtom, Bond::BondType order=Bond::UNSPECIFIED)
unsigned int | addBond (Bond *bond, bool takeOwnership=false)
| adds a Bond to our collection More...
unsigned int | addBond (BOND_SPTR bsp)
| adds a Bond to our collection More...
Bond * | createPartialBond (unsigned int beginAtomIdx, Bond::BondType order=Bond::UNSPECIFIED)
| starts a Bond and sets its beginAtomIdx More...
unsigned int | finishPartialBond (unsigned int endAtomIdx, int bondBookmark, Bond::BondType order=Bond::UNSPECIFIED)
| finishes a partially constructed bond More...
void | removeBond (unsigned int beginAtomIdx, unsigned int endAtomIdx)
| removes a bond from the molecule More...
Public Member Functions inherited from RDKit::ROMol
| ROMol ()
| ROMol (const ROMol &other, bool quickCopy=false, int confId=-1)
| copy constructor with a twist More...
| ROMol (const std::string &binStr)
| construct a molecule from a pickle string More...
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
unsigned int | getNumAtoms (bool onlyExplicit=1) const
| returns our number of atoms More...
unsigned int | getNumHeavyAtoms () const
| returns our number of heavy atoms (atomic number > 1) More...
Atom * | getAtomWithIdx (unsigned int idx)
| returns a pointer to a particular Atom More...
const Atom * | getAtomWithIdx (unsigned int idx) const
template<class U >
Atom * | getAtomWithIdx (const U idx)
template<class U >
const Atom * | getAtomWithIdx (const U idx) const
unsigned int | getAtomDegree (const Atom *at) const
| returns the degree (number of neighbors) of an Atom in the graph More...
unsigned int | getAtomDegree (ATOM_SPTR at) const
unsigned int | getNumBonds (bool onlyHeavy=1) const
| returns our number of Bonds More...
Bond * | getBondWithIdx (unsigned int idx)
| returns a pointer to a particular Bond More...
const Bond * | getBondWithIdx (unsigned int idx) const
template<class U >
Bond * | getBondWithIdx (const U idx)
template<class U >
const Bond * | getBondWithIdx (const U idx) const
Bond * | getBondBetweenAtoms (unsigned int idx1, unsigned int idx2)
| returns a pointer to the bond between two atoms, Null on failure More...
const Bond * | getBondBetweenAtoms (unsigned int idx1, unsigned int idx2) const
template<class U , class V >
Bond * | getBondBetweenAtoms (const U idx1, const V idx2)
template<class U , class V >
const Bond * | getBondBetweenAtoms (const U idx1, const V idx2) const
void | setAtomBookmark (ATOM_SPTR at, int mark)
| associates an Atom pointer with a bookmark More...
void | setAtomBookmark (Atom *at, int mark)
void | replaceAtomBookmark (ATOM_SPTR at, int mark)
| associates an Atom pointer with a bookmark More...
void | replaceAtomBookmark (Atom *at, int mark)
Atom * | getAtomWithBookmark (int mark)
| returns the first Atom associated with the `bookmark` provided More...
ATOM_PTR_LIST & | getAllAtomsWithBookmark (int mark)
| returns all Atoms associated with the `bookmark` provided More...
void | clearAtomBookmark (const int mark)
| removes a `bookmark` from our collection More...
void | clearAtomBookmark (const int mark, const Atom *atom)
| removes a particular Atom from the list associated with the `bookmark` More...
void | clearAtomBookmark (const int mark, ATOM_SPTR atom)
void | clearAllAtomBookmarks ()
| blows out all atomic `bookmarks` More...
bool | hasAtomBookmark (int mark) const
| queries whether or not any atoms are associated with a `bookmark` More...
ATOM_BOOKMARK_MAP * | getAtomBookmarks ()
| returns a pointer to all of our atom `bookmarks` More...
void | setBondBookmark (BOND_SPTR bond, int mark)
| associates a Bond pointer with a bookmark More...
void | setBondBookmark (Bond *bond, int mark)
Bond * | getBondWithBookmark (int mark)
| returns the first Bond associated with the `bookmark` provided More...
BOND_PTR_LIST & | getAllBondsWithBookmark (int mark)
| returns all bonds associated with the `bookmark` provided More...
void | clearBondBookmark (int mark)
| removes a `bookmark` from our collection More...
void | clearBondBookmark (int mark, const Bond *bond)
| removes a particular Bond from the list associated with the `bookmark` More...
void | clearBondBookmark (int mark, BOND_SPTR bond)
void | clearAllBondBookmarks ()
| blows out all bond `bookmarks` More...
bool | hasBondBookmark (int mark) const
| queries whether or not any bonds are associated with a `bookmark` More...
BOND_BOOKMARK_MAP * | getBondBookmarks ()
| returns a pointer to all of our bond `bookmarks` More...
const Conformer & | getConformer (int id=-1) const
Conformer & | getConformer (int id=-1)
void | removeConformer (unsigned int id)
| Delete the conformation with the specified ID. More...
void | clearConformers ()
| Clear all the conformations on the molecule. More...
unsigned int | addConformer (Conformer *conf, bool assignId=false)
| Add a new conformation to the molecule. More...
unsigned int | getNumConformers () const
RingInfo * | getRingInfo () const
ADJ_ITER_PAIR | getAtomNeighbors (Atom const *at) const
| provides access to all neighbors around an Atom More...
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 More...
ATOM_ITER_PAIR | getVertices ()
| returns an iterator pair for looping over all Atoms More...
BOND_ITER_PAIR | getEdges ()
| returns an iterator pair for looping over all Bonds More...
ATOM_ITER_PAIR | getVertices () const
BOND_ITER_PAIR | getEdges () const
MolGraph const & | getTopology () const
| brief returns a pointer to our underlying BGL object More...
AtomIterator | beginAtoms ()
| get an AtomIterator pointing at our first Atom More...
ConstAtomIterator | beginAtoms () const
AtomIterator | endAtoms ()
| get an AtomIterator pointing at the end of our Atoms More...
ConstAtomIterator | endAtoms () const
BondIterator | beginBonds ()
| get a BondIterator pointing at our first Bond More...
ConstBondIterator | beginBonds () const
BondIterator | endBonds ()
| get a BondIterator pointing at the end of our Bonds More...
ConstBondIterator | endBonds () const
AromaticAtomIterator | beginAromaticAtoms ()
| get an AtomIterator pointing at our first aromatic Atom More...
ConstAromaticAtomIterator | beginAromaticAtoms () const
AromaticAtomIterator | endAromaticAtoms ()
| get an AtomIterator pointing at the end of our Atoms More...
ConstAromaticAtomIterator | endAromaticAtoms () const
HeteroatomIterator | beginHeteros ()
| get an AtomIterator pointing at our first hetero Atom More...
ConstHeteroatomIterator | beginHeteros () const
HeteroatomIterator | endHeteros ()
| get an AtomIterator pointing at the end of our Atoms More...
ConstHeteroatomIterator | endHeteros () const
QueryAtomIterator | beginQueryAtoms (QueryAtom const *query)
| get an AtomIterator pointing at our first Atom that matches `query` More...
ConstQueryAtomIterator | beginQueryAtoms (QueryAtom const *) const
QueryAtomIterator | endQueryAtoms ()
| get an AtomIterator pointing at the end of our Atoms More...
ConstQueryAtomIterator | endQueryAtoms () const
MatchingAtomIterator | beginMatchingAtoms (bool(*query)(Atom *))
| get an AtomIterator pointing at our first Atom that matches `query` More...
ConstMatchingAtomIterator | beginMatchingAtoms (bool(*query)(const Atom *)) const
MatchingAtomIterator | endMatchingAtoms ()
| get an AtomIterator pointing at the end of our Atoms More...
ConstMatchingAtomIterator | endMatchingAtoms () const
ConformerIterator | beginConformers ()
ConformerIterator | endConformers ()
ConstConformerIterator | beginConformers () const
ConstConformerIterator | endConformers () const
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 char *key, T val, bool computed=false) const
| sets a `property` value More...
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 More...
template<typename T >
void | getProp (const std::string &key, T &res) const
template<typename T >
T | getProp (const char *key) const
template<typename T >
T | getProp (const std::string &key) const
template<typename T >
bool | getPropIfPresent (const char *key, T &res) const
template<typename T >
bool | getPropIfPresent (const std::string &key, T &res) const
bool | hasProp (const char *key) const
| returns whether or not we have a `property` with name `key` More...
bool | hasProp (const std::string &key) const
void | clearProp (const char *key) const
| clears the value of a `property` More...
void | clearProp (const std::string &key) const
void | clearComputedProps (bool includeRings=true) const
| clears all of our `computed` `properties` More...
void | updatePropertyCache (bool strict=true)
| calculates any of our lazy `properties` More...
bool | needsUpdatePropertyCache () const
void | debugMol (std::ostream &str) const
| sends some debugging info to a stream More...

## Detailed Description

RWMol is a molecule class that is intended to be edited.

See documentation for ROMol for general remarks

Definition at line 30 of file RWMol.h.

## Constructor & Destructor Documentation

RDKit::RWMol::RWMol | ( |  | ) |
| inline

Definition at line 32 of file RWMol.h.

RDKit::RWMol::RWMol | ( | const ROMol & | other,
|  | bool | quickCopy = `false`,
|  | int | confId = `-1`
| ) |  |
| 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).
  confId | if this is >=0, the resulting ROMol will contain only the specified conformer from `other`.

Definition at line 44 of file RWMol.h.

## Member Function Documentation

unsigned int RDKit::RWMol::addAtom | ( | bool | updateLabel = `true` | ) |

adds an empty Atom to our collection

Parameters

  updateLabel | (optional) if this is true, the new Atom will be our `activeAtom`

Returns
  the new number of atoms

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

unsigned int RDKit::RWMol::addAtom | ( | Atom * | atom,
|  | bool | updateLabel = `true`,
|  | bool | takeOwnership = `false`
| ) |  |
| inline

adds an Atom to our collection

Parameters

  atom | pointer to the Atom to add
  updateLabel | (optional) if this is true, the new Atom will be our `activeAtom`
  takeOwnership | (optional) if this is true, we take ownership of `atom` instead of copying it.

Returns
  the new number of atoms

Definition at line 77 of file RWMol.h.

unsigned int RDKit::RWMol::addAtom | ( | ATOM_SPTR | atom,
|  | bool | updateLabel = `true`
| ) |  |
| inline

adds an Atom to our collection

Parameters

  atom | pointer to the Atom to add
  updateLabel | (optional) if this is true, the new Atom will be our `activeAtom`

Returns
  the new number of atoms

Note: since this is using a smart pointer, we don't need to worry about issues of ownership.

Definition at line 96 of file RWMol.h.

unsigned int RDKit::RWMol::addBond | ( | unsigned int | beginAtomIdx,
|  | unsigned int | endAtomIdx,
|  | Bond::BondType | order = `Bond::UNSPECIFIED`
| ) |  |

adds a Bond between the indicated Atoms

Returns
  the number of Bonds

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

unsigned int RDKit::RWMol::addBond | ( | ATOM_SPTR | beginAtom,
|  | ATOM_SPTR | endAtom,
|  | Bond::BondType | order = `Bond::UNSPECIFIED`
| ) |  |

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

unsigned int RDKit::RWMol::addBond | ( | Atom * | beginAtom,
|  | Atom * | endAtom,
|  | Bond::BondType | order = `Bond::UNSPECIFIED`
| ) |  |

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

unsigned int RDKit::RWMol::addBond | ( | Bond * | bond,
|  | bool | takeOwnership = `false`
| ) |  |
| inline

adds a Bond to our collection

Parameters

  bond | pointer to the Bond to add
  takeOwnership | (optional) if this is true, we take ownership of `bond` instead of copying it.

Returns
  the new number of bonds

Definition at line 153 of file RWMol.h.

unsigned int RDKit::RWMol::addBond | ( | BOND_SPTR | bsp | ) |
| inline

adds a Bond to our collection

Parameters

  bsp | smart pointer to the Bond to add

Returns
  the new number of bonds

Note: since this is using a smart pointer, we don't need to worry about issues of ownership.

Definition at line 166 of file RWMol.h.

void RDKit::RWMol::clear | ( |  | ) |
| inline

removes all atoms, bonds, properties, bookmarks, etc.

Definition at line 212 of file RWMol.h.

References detail::computedPropName.

Bond* RDKit::RWMol::createPartialBond | ( | unsigned int | beginAtomIdx,
|  | Bond::BondType | order = `Bond::UNSPECIFIED`
| ) |  |

starts a Bond and sets its beginAtomIdx

Returns
  a pointer to the new bond

The caller should set a bookmark to the returned Bond in order to be able to later complete it:

      Bond *pBond = mol->createPartialBond(1);
      mol->setBondBookmark(pBond,666);
      ... do some other stuff ...
      mol->finishPartialBond(2,666,Bond::SINGLE);
      mol->clearBondBookmark(666,pBond);

or, if we want to set the `BondType` initially:

      Bond *pBond = mol->createPartialBond(1,Bond::DOUBLE);
      mol->setBondBookmark(pBond,666);
      ... do some other stuff ...
      mol->finishPartialBond(2,666);
      mol->clearBondBookmark(666,pBond);

the call to finishPartialBond() will take priority if you set the `BondType` in both calls.

unsigned int RDKit::RWMol::finishPartialBond | ( | unsigned int | endAtomIdx,
|  | int | bondBookmark,
|  | Bond::BondType | order = `Bond::UNSPECIFIED`
| ) |  |

finishes a partially constructed bond

Returns
  the final number of Bonds

See the documentation for createPartialBond() for more details

Atom* RDKit::RWMol::getActiveAtom | ( |  | ) |

returns a pointer to the "active" Atom

If we have an `activeAtom`, it will be returned, otherwise the results of getLastAtom() will be returned.

Atom* RDKit::RWMol::getLastAtom | ( |  | ) |
| inline

returns a pointer to the highest-numbered Atom

Definition at line 110 of file RWMol.h.

References RDKit::ROMol::getAtomWithIdx(), and RDKit::ROMol::getNumAtoms().

void RDKit::RWMol::insertMol | ( | const ROMol & | other | ) |

insert the atoms and bonds from `other` into this molecule

RWMol& RDKit::RWMol::operator= | ( | const RWMol & |  | ) |

void RDKit::RWMol::removeAtom | ( | unsigned int | idx | ) |

removes an Atom from the molecule

void RDKit::RWMol::removeAtom | ( | Atom * | atom | ) |

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

void RDKit::RWMol::removeBond | ( | unsigned int | beginAtomIdx,
|  | unsigned int | endAtomIdx
| ) |  |

removes a bond from the molecule

void RDKit::RWMol::replaceAtom | ( | unsigned int | idx,
|  | Atom * | atom,
|  | bool | updateLabel = `false`
| ) |  |

replaces a particular Atom

Parameters

  idx | the index of the Atom to replace
  atom | the new atom, which will be copied.
  updateLabel | (optional) if this is true, the new Atom will be our `activeAtom`

void RDKit::RWMol::setActiveAtom | ( | Atom * | atom | ) |

sets our `activeAtom`

void RDKit::RWMol::setActiveAtom | ( | unsigned int | idx | ) |

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

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

- RWMol.h