Bonds

class tissue_forge.Bond

Bonds apply a potential to a particular set of particles.

If you’re building a model, you should probably instead be working with a BondHandle.

static create(potential: _Potential, i: ParticleHandle, j: ParticleHandle, half_life: FPTYPE * = None, dissociation_energy: FPTYPE * = None, flags: uint32_t = 0) → TissueForge::BondHandle *

Construct a new bond handle and underlying bond.

Automatically updates when running on a CUDA device.

Parameters:

  • potential (Potential) – bond potential

  • i (ParticleHandle) – ith particle

  • j (ParticleHandle) – jth particle

  • half_life (float) – bond half life

  • dissociation_energy (float) – dissociation energy

  • flags (int) – bond flags

toString() → std::string

Get a JSON string representation

static fromString(str: std::string const &) → TissueForge::Bond *

Create from a JSON string representation.

The returned bond is not automatically registered with the engine.

Parameters:

str (string) –

__reduce__()

Helper for pickle.

class tissue_forge.BondHandle(*args)

Handle to a bond

This is a safe way to work with a bond.

Overload 1:

Construct a new bond handle and do nothing Subsequent usage will require a call to ‘init’


Overload 2:

Construct a new bond handle from an existing bond id

Parameters:

id (int) – id of existing bond


Overload 3:

Construct a new bond handle and underlying bond.

Automatically updates when running on a CUDA device.

Parameters:

  • potential (Potential) – bond potential

  • i (int) – id of ith particle

  • j (int) – id of jth particle

  • half_life (float) – bond half life

  • bond_energy (float) – bond energy

  • flags (int) – bond flags

property length

bond length

property energy

bond energy

property parts

bonded particles

property potential

bond potential

property id

bond id

property dissociation_energy

bond dissociation energy

property half_life

bond half life

property style

bond style

property age

bond age

has(*args) → bool

Overload 1: Test whether the bond has an id


Overload 2: Test whether the bond has a particle

__str__() → str

Return str(self).

__getitem__(index: int)
__contains__(item)
__lt__(rhs) → bool

Return self<value.

__gt__(rhs) → bool

Return self>value.

__le__(rhs) → bool

Return self<=value.

__ge__(rhs) → bool

Return self>=value.

__eq__(rhs) → bool

Return self==value.

__ne__(rhs) → bool

Return self!=value.

get() → TissueForge::Bond *

Gets the underlying bond

Return type:

Bond

Returns:

bond, if available

static pairwise(pot: _Potential, parts: ParticleList, cutoff: FPTYPE const &, ppairs: vectorPairParticleType_ParticleType, half_life: FPTYPE const &, bond_energy: FPTYPE const &, flags: uint32_t) → std::vector< TissueForge::BondHandle,std::allocator< TissueForge::BondHandle > >

Apply bonds to a list of particles.

Automatically updates when running on a CUDA device.

Parameters:

  • pot (Potential) – the potential of the created bonds

  • parts (ParticleList) – list of particles

  • cutoff (float) – cutoff distance of particles that are bonded

  • ppairs (std::vector< std::pair< TissueForge::ParticleType *,TissueForge::ParticleType * > *,std::allocator< std::pair< TissueForge::ParticleType *,TissueForge::ParticleType * > * > >) – type pairs of bonds

  • half_life (float) – bond half life

  • bond_energy (float) – bond energy

  • flags (int) – bond flags

Return type:

std::vector< TissueForge::BondHandle,std::allocator< TissueForge::BondHandle > >

Returns:

created bonds

destroy() → HRESULT

Destroy the bond.

Automatically updates when running on a CUDA device.

static items() → std::vector< TissueForge::BondHandle,std::allocator< TissueForge::BondHandle > >

Gets all bonds in the universe

decays() → bool

Tests whether this bond decays

Return type:

boolean

Returns:

true when the bond should decay

class tissue_forge.Angle

A bond concerning an angle

If you’re building a model, you should probably instead be working with a AngleHandle.

static create(potential: _Potential, p1: ParticleHandle, p2: ParticleHandle, p3: ParticleHandle, flags: uint32_t = 0) → TissueForge::AngleHandle *

Creates an angle bond.

Automatically updates when running on a CUDA device.

Parameters:
Return type:

AngleHandle

Returns:

AngleHandle*

toString() → std::string

Get a JSON string representation

static fromString(str: std::string const &) → TissueForge::Angle *

Create from a JSON string representation.

The returned angle is not automatically registered with the engine.

Parameters:

str (string) –

__reduce__()

Helper for pickle.

class tissue_forge.AngleHandle(*args)

A handle to an angle bond

This is a safe way to work with an angle bond.

Construct a new angle handle from an existing angle id

Parameters:

id – id of existing angle

property angle

angle angle

property energy

angle energy

property parts

bonded particles

property potential

angle potential

property id

angle id

property dissociation_energy

bond dissociation energy

property half_life

angle half life

property style

angle style

property age

angle age

has(*args) → bool

Overload 1: Test whether the bond has an id


Overload 2: Test whether the bond has a particle

__str__() → str

Return str(self).

__getitem__(index: int)
__contains__(item)
__lt__(rhs) → bool

Return self<value.

__gt__(rhs) → bool

Return self>value.

__le__(rhs) → bool

Return self<=value.

__ge__(rhs) → bool

Return self>=value.

__eq__(rhs) → bool

Return self==value.

__ne__(rhs) → bool

Return self!=value.

get() → TissueForge::Angle *

Gets the angle of this handle

Return type:

Angle

Returns:

angle, if available

destroy() → HRESULT

Destroy the angle.

Automatically updates when running on a CUDA device.

static items() → std::vector< TissueForge::AngleHandle,std::allocator< TissueForge::AngleHandle > >

Gets all angles in the universe

decays() → bool

Tests whether this bond decays

Return type:

boolean

Returns:

true when the bond should decay

class tissue_forge.Dihedral

The dihedral structure

static create(potential: _Potential, p1: ParticleHandle, p2: ParticleHandle, p3: ParticleHandle, p4: ParticleHandle) → TissueForge::DihedralHandle *

Creates a dihedral bond

Parameters:
Return type:

DihedralHandle

Returns:

DihedralHandle*

toString() → std::string

Get a JSON string representation

static fromString(str: std::string const &) → TissueForge::Dihedral *

Create from a JSON string representation.

The returned dihedral is not automatically registered with the engine.

Parameters:

str (string) –

__reduce__()

Helper for pickle.

class tissue_forge.DihedralHandle(*args)

A handle to a dihedral bond

This is a safe way to work with a dihedral bond.

Construct a new dihedral handle from an existing dihedral id

Parameters:

id – id of existing dihedral

property angle

dihedral angle

property energy

dihedral energy

property parts

bonded particles

property potential

dihedral potential

property id

dihedral id

property dissociation_energy

bond dissociation energy

property half_life

dihedral half life

property style

dihedral style

property age

dihedral age

get() → TissueForge::Dihedral *

Gets the dihedral of this handle

Return type:

Dihedral

Returns:

dihedral, if available

has(*args) → bool

Overload 1: Test whether the bond has an id


Overload 2: Test whether the bond has a particle

__str__() → str

Return str(self).

__getitem__(index: int)
__contains__(item)
__lt__(rhs) → bool

Return self<value.

__gt__(rhs) → bool

Return self>value.

__le__(rhs) → bool

Return self<=value.

__ge__(rhs) → bool

Return self>=value.

__eq__(rhs) → bool

Return self==value.

__ne__(rhs) → bool

Return self!=value.

destroy() → HRESULT

Destroy the dihedral

static items() → std::vector< TissueForge::DihedralHandle,std::allocator< TissueForge::DihedralHandle > >

Gets all dihedrals in the universe

decays() → bool

Tests whether this bond decays

Return type:

boolean

Returns:

true when the bond should decay