SBHydrogenBondGroup

SBHydrogenBondGroup#

See also

SBHydrogenBond

Note

H-bonds are stored within an H-bond group, which itself is stored in a structural model.

Below are sample codes to add H-bonds based on a structural model or between receptors and ligands (see Selecting nodes for more information on how to get nodes):

Create hydrogen-bonds between atoms in a structural model#

# get an indexer of all structural models in the active document
structural_model_indexer = SAMSON.getNodes("node.type structuralModel")
# get the first structural model
structural_model = structural_model_indexer[0]

with SAMSON.holding("Add H-bonds"): # make it undoable
    # create an H-bond group object between atoms in a single node indexer
    h_bond_group = SBHydrogenBondGroup("H-bonds", structural_model_indexer)

    # compute H-bonds
    h_bond_group.update()

    # hold the node for undo/redo
    SAMSON.hold(h_bond_group)
    # create the H-bond group
    h_bond_group.create()

    # add the node to the active document
    structural_model.addChild(h_bond_group)

Create hydrogen-bonds between receptors and ligands#

# get an indexer of all structural models in the active document
structural_model_indexer = SAMSON.getNodes("node.type structuralModel")
# get the first structural model
structural_model = structural_model_indexer[0]

# get an indexer with receptor and ligand nodes
receptor_indexer = SAMSON.getNodes("node.category receptor")
ligand_indexer = SAMSON.getNodes("node.category ligand")

with SAMSON.holding("Add H-bonds"): # make it undoable
    # create an H-bond group object between atoms in two node indexers
    h_bond_group = SBHydrogenBondGroup("H-bonds between receptor and ligand",
                    receptor_indexer, ligand_indexer)

    # compute H-bonds
    h_bond_group.update()

    # hold the node for undo/redo
    SAMSON.hold(h_bond_group)
    # create the H-bond group
    h_bond_group.create()

    # add the node to the active document
    structural_model.addChild(h_bond_group)

You can remove H-bonds from an H-bond group based on some criteria, e.g., based on the donor-acceptor distance:

Remove H-bonds from an H-bonds group based on the donor-acceptor distance#

# get H-bonds from the H-bond group, excluding the H-bond group itself
hbond_indexer = h_bond_group.getNodes("not n.t hbg")
print(f"The total number of computed H-bonds is {len(hbond_indexer)}")

with SAMSON.holding("Remove some H-bonds"): # make it undoable
    for hbond in hbond_indexer:
        # check the donor-acceptor distance
        if hbond.donorAcceptorDistance > SBQuantity.angstrom(3.5):
            #print(hbond)
            h_bond_group.removeChild(hbond)

hbond_indexer = h_bond_group.getNodes("not n.t hbg")
print(f"The total number of computed H-bonds is {len(hbond_indexer)}")

You can also add new H-bonds in an H-bond group, as follows:

Add an H-bond in an H-bond group#

with SAMSON.holding("Add new H-bonds"): # make it undoable
    # create an H-bond object based on already defined acceptor, donor,
    # and (optionally) hydrogen atoms
    hbond = SBHydrogenBond(acceptor, donor) #, hydrogen
    # hold the node for undo/redo
    SAMSON.hold(hbond)
    # create the H-bond
    hbond.create()
    # add the H-bond in the H-bond group
    h_bond_group.addChild(hbond)

class samson.SBHydrogenBondGroup(*args, **kwargs)#

Bases: SBStructuralGroup

This class describes a Hydrogen-bond group in a structural model

Overloaded function.

__init__(self: samson.SBHydrogenBondGroup) -> None

Constructs a Hydrogen-bond group

__init__(self: samson.SBHydrogenBondGroup, name: str) -> None

Constructs a Hydrogen-bond group with the given name

__init__(self: samson.SBHydrogenBondGroup, name: str, nodeIndexer: samson.SBNodeIndexer) -> None

Constructs a Hydrogen-bond group with H-bonds within the system present in nodeIndexer

__init__(self: samson.SBHydrogenBondGroup, name: str, nodeIndexer1: samson.SBNodeIndexer, nodeIndexer2: samson.SBNodeIndexer) -> None

Constructs a Hydrogen-bond group with H-bonds between two systems present in nodeIndexer1 and nodeIndexer2

class HydrogenBondSystemSetupType(self: samson.SBHydrogenBondGroup.HydrogenBondSystemSetupType, value: int)#

Bases: pybind11_object

Members:

SingleSystem : Within a single system

BetweenTwoSystems : Between two systems

BetweenTwoSystems = <HydrogenBondSystemSetupType.BetweenTwoSystems: 1>#

SingleSystem = <HydrogenBondSystemSetupType.SingleSystem: 0>#

property name#

property value#

getAcceptorElementsString(self: samson.SBHydrogenBondGroup) → str#: Returns a string with acceptor element types

getAngleThreshold(self: samson.SBHydrogenBondGroup) → samson.SBQuantity.unitsSI#: Returns the H-bond group’s D-H-A angle threshold

getDonorBorneHydrogen(self: samson.SBHydrogenBondGroup, donor: samson.SBAtom, acceptor: samson.SBAtom, angleThreshold: samson.SBQuantity.unitsSI) → samson.SBAtom#: Returns a donor-borne hydrogen atom

getDonorElementsString(self: samson.SBHydrogenBondGroup) → str#: Returns a string with donor element types

getHydrogenBondAtoms(self: samson.SBHydrogenBondGroup) → samson.SBNodeIndexer#: Gets atoms (acceptors, donors, hydrogens) of visible hydrogen bonds

getHydrogenBondSystemSetupType(self: samson.SBHydrogenBondGroup) → samson.SBHydrogenBondGroup.HydrogenBondSystemSetupType#: Returns the current hydrogen bond system setup type

getNumberOfVisibleHydrogenBonds(self: samson.SBHydrogenBondGroup) → int#: Returns the number of visible hydrogen bonds

getSystem1(self: samson.SBHydrogenBondGroup) → samson.SBNodeIndexer#: Returns an indexer of nodes in the system 1

getSystem2(self: samson.SBHydrogenBondGroup) → samson.SBNodeIndexer#: Returns an indexer of nodes in the system 2

getThresholdDistanceOfModerateHBond(self: samson.SBHydrogenBondGroup) → samson.SBQuantity.unitsSI#: Returns the H-bond group’s threshold distance for moderate H-bonds

getThresholdDistanceOfStrongHBond(self: samson.SBHydrogenBondGroup) → samson.SBQuantity.unitsSI#: Returns the H-bond group’s threshold distance for strong H-bonds

getThresholdDistanceOfWeakHBond(self: samson.SBHydrogenBondGroup) → samson.SBQuantity.unitsSI#: Returns the H-bond group’s threshold distance for weak H-bonds

resetDefaultParameters(self: samson.SBHydrogenBondGroup) → None#: Resets the H-bond group parameters to their default values

selectHydrogenBondAtoms(self: samson.SBHydrogenBondGroup) → None#: Selects atoms (acceptors, donors, hydrogens) of visible hydrogen bonds

setAngleThreshold(self: samson.SBHydrogenBondGroup, angle: samson.SBQuantity.unitsSI) → None#: Sets the H-bond group’s D-H-A angle threshold to angle

setSystem(*args, **kwargs)#

Overloaded function.

setSystem(self: samson.SBHydrogenBondGroup, nodeIndexer: samson.SBNodeIndexer) -> None

Sets a single system

setSystem(self: samson.SBHydrogenBondGroup, nodeIndexer1: samson.SBNodeIndexer, nodeIndexer2: samson.SBNodeIndexer) -> None

Sets two systems

setThresholdDistanceOfModerateHBond(self: samson.SBHydrogenBondGroup, distance: samson.SBQuantity.unitsSI) → None#: Sets the H-bond group’s threshold distance for moderate H-bonds to distance

setThresholdDistanceOfStrongHBond(self: samson.SBHydrogenBondGroup, distance: samson.SBQuantity.unitsSI) → None#: Sets the H-bond group’s threshold distance for strong H-bonds to distance

setThresholdDistanceOfWeakHBond(self: samson.SBHydrogenBondGroup, distance: samson.SBQuantity.unitsSI) → None#: Sets the H-bond group’s threshold distance for weak H-bonds to distance

update(self: samson.SBHydrogenBondGroup) → None#: Updates the hydrogen bonds in the hydrogen bond group

BetweenTwoSystems = <HydrogenBondSystemSetupType.BetweenTwoSystems: 1>#

SingleSystem = <HydrogenBondSystemSetupType.SingleSystem: 0>#

property hideLeastProbableHBondsFlag#: Whether the least probable H-bonds should be hidden

property showModerateHBondsFlag#: Whether to show the moderate H-bonds

property showStrongHBondsFlag#: Whether to show the strong H-bonds

property showWeakHBondsFlag#: Whether to show the weak H-bonds

SBHydrogenBondGroup

Contents

SBHydrogenBondGroup#