#include <openbabel/builder.h>

Public Member Functions
	OBBuilder ()

void	LoadFragments ()

std::vector< vector3 >	GetFragmentCoord (std::string smiles)

Call the build algorithm
bool	Build (OBMol &mol, bool stereoWarnings=true)

Setup build parameters
void	SetKeepRings ()

void	UnsetKeepRings ()

Static Public Member Functions
static vector3	GetNewBondVector (OBAtom *atom)

static vector3	GetNewBondVector (OBAtom *atom, double length)

static bool	Connect (OBMol &mol, int a, int b, vector3 &newpos, int bondOrder=1)

static bool	Connect (OBMol &mol, int a, int b, int bondOrder=1)

static bool	Swap (OBMol &mol, int a, int b, int c, int d)

static bool	CorrectStereoBonds (OBMol &mol)

static bool	CorrectStereoAtoms (OBMol &mol, bool warn=true)

static bool	IsSpiroAtom (unsigned long atomId, OBMol &mol)

static OBBitVec	GetFragment (OBAtom *atom)

static void	AddNbrs (OBBitVec &fragment, OBAtom *atom)

Detailed Description

Class to build 3D structures.

Class for 3D structure generation.

Since: version 2.2

The OBBuilder class is used for generating 3D structures.

Below is and example which explain the basics.

//
// code to read molecule from smiles goes here...
//
OBBuilder builder;
builder.Build(mol);
//
// code to write molecule to 3D file format goes here...
//

Constructor & Destructor Documentation

◆ OBBuilder()

OBBuilder ( )

inline

Member Function Documentation

◆ Build()

bool Build	(	OBMol &	mol,
		bool	stereoWarnings = `true`
	)

The mol object contains all connectivity information (atomic numbers, bonds, bond orders, ..) but no 3D coordinates. Build generates these coordinates and assigns them.

Parameters

mol	Molecule with the connectivity (from SMILES for example). The coordinates are also changed in this mol.
stereoWarnings	Warn if the stereochemistry is incorrect (default is true)

Referenced by AliasData::Expand().

◆ SetKeepRings()

void SetKeepRings ( )

inline

If the molecule already contains 3D coordinates, if you set KeepRings to true it will use retain the 3D coordinates of the rings. By default KeepRings is false, and ring conformations are obtained by lookup in a library of ring conformers. However, since the ring conformer library is not exhaustive, if the ring system is not found in the library, the resulting 3D structure can be poor, and require geometry optimisation before it is reasonable. If your starting point is a 3D structure, you can set KeepRings to true, and the conformation will be taken from the input. The remaining (acyclic) bonds will still all be built by the builder.

◆ UnsetKeepRings()

void UnsetKeepRings ( )

inline

◆ LoadFragments()

void LoadFragments ( )

Load fragment info from file, if is it has not already been done.

◆ GetFragmentCoord()

std::vector< vector3 > GetFragmentCoord ( std::string smiles )

◆ GetNewBondVector() [1/2]

vector3 GetNewBondVector ( OBAtom * atom )

static

Get the position for a new neighbour on atom. Returns non-finite vector if there is no reasonable location.

Parameters

atom	Atom for which we want a new neighbour location.

Returns: The position for the new atom.

◆ GetNewBondVector() [2/2]

vector3 GetNewBondVector	(	OBAtom *	atom,
		double	length
	)

static

◆ Connect() [1/2]

bool Connect	(	OBMol &	mol,
		int	a,
		int	b,
		vector3 &	newpos,
		int	bondOrder = `1`
	)

static

Atoms a and b are part of two fragments that are not connected in mol. Connect will translate and rotate the fragment that contains b so that a and b are seperated by a bond. This bond is also added.

Parameters

mol	The molecule to be modified
a	Index for atom in fragment that should not be rotated.
b	Index for atom in fragment that should be rotated.
newpos	Direction for new bond between a and b
bondOrder	Bond order of the new bond between a and b.

Returns: true if succesful or fails when failed (most likely cause for failing: a and b are in the same fragment, they are connected)

Referenced by AliasData::Expand().

◆ Connect() [2/2]

bool Connect	(	OBMol &	mol,
		int	a,
		int	b,
		int	bondOrder = `1`
	)

static

Atoms a and b are part of two fragments that are not connected in mol. Connect will translate and rotate the fragment that contains b so that a and b are seperated by a bond. This bond is also added.

Parameters

mol	The molecule to be modified
a	Index for atom in fragment that should not be rotated.
b	Index for atom in fragment that should be rotated.
bondOrder	Bond order of the new bond bewtween a and b.

Returns: true if succesfull or fails when failed (most likely cause for failing: a and b are in the same fragment, they are connected)

◆ Swap()

bool Swap	(	OBMol &	mol,
		int	a,
		int	b,
		int	c,
		int	d
	)

static

Swap group b, bonded to a with group d, bonded to c. The bonds a-b and b-c cannot be part of a ring. Atoms a and b will not be moved. Atoms b, d and their connected atoms (after deleting bonds ab and cd) will be translated/rotated.

Example:

\ /                            /
 b                            d
  \     /     Swap(a,b,c,d)    \     /
   a---x          ---->         a---x
  /     \     /                /     \     /
 x       c---d                x       c---b
                                           \

This function can also be used to invert chiral centers if a and c are the same atom.

Example

   1                        3
   |      Swap(C,1,C,3)     |
2>-C-<3      ----->      2>-C-<1
   |                        |
   4                        4

◆ CorrectStereoBonds()

bool CorrectStereoBonds ( OBMol & mol )

static

Atoms a and b must be bonded and this bond cannot be part of a ring. The bond will be broken and the smiles fragment will be inserted bewteen the two remaining fragments. The fragment that contains a will not be translated or rotated. Parameters c and d are the index in the smiles to which atoms a and b will be connected respectivly.

Correct double bond stereochemistry

Returns: Success or failure

◆ CorrectStereoAtoms()

bool CorrectStereoAtoms	(	OBMol &	mol,
		bool	warn = `true`
	)

static

Correct stereochemistry at tetrahedral atoms with at least two non-ring bonds. It also works for spiro atoms.

Returns: Success or failure

◆ IsSpiroAtom()

bool IsSpiroAtom	(	unsigned long	atomId,
		OBMol &	mol
	)

static

Does this atom connect two rings which are not otherwise connected?

◆ GetFragment()

OBBitVec GetFragment ( OBAtom * atom )

static

Get the fragment to which this atom belongs.

Parameters

atom	Atom in the fragment.

Returns: The OBBitVec defining the fragment to which a belongs.

◆ AddNbrs()

void AddNbrs	(	OBBitVec &	fragment,
		OBAtom *	atom
	)

static

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

Public Member Functions

Static Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ OBBuilder()

Member Function Documentation

◆ Build()

◆ SetKeepRings()

◆ UnsetKeepRings()

◆ LoadFragments()

◆ GetFragmentCoord()

◆ GetNewBondVector() [1/2]

◆ GetNewBondVector() [2/2]

◆ Connect() [1/2]

◆ Connect() [2/2]

◆ Swap()

◆ CorrectStereoBonds()

◆ CorrectStereoAtoms()

◆ IsSpiroAtom()

◆ GetFragment()

◆ AddNbrs()