schrodinger.structutils.interactions.salt_bridge module

Find salt-bridge interactions.

Examples

Find all salt bridge interactions within a protein:

st = structure.Structure.read("protein.mae.gz")
for atom1, atom2 in get_salt_bridges(st):
    print(f"Salt bridge between atoms {atom1.index} and {atom2.index}")

Find all salt bridges within a single protein chain:

st = structure.Structure.read("protein.mae.gz")
atoms = st.chain["C"].getAtomIndices()
for atom1, atom2 in get_salt_bridges(st, atoms):
    print(f"Salt bridge between atoms {atom1.index} and {atom2.index}")

Find all salt bridges between a protein and a ligand:

with StructureReader("protein_and_ligand.mae.gz") as reader:
    prot, lib = reader
for atom1, atom2 in get_salt_bridges(prot, struc2=lig):
    print(f"Salt bridge between atoms {atom1.index} and {atom2.index}")
class schrodinger.structutils.interactions.salt_bridge.OrderBy

Bases: enum.Enum

An enumeration.

AnionCation = 1
InputOrder = 2
__class__

alias of enum.EnumMeta

__members__ = mappingproxy(OrderedDict([('AnionCation', <OrderBy.AnionCation: 1>), ('InputOrder', <OrderBy.InputOrder: 2>)]))
__module__ = 'schrodinger.structutils.interactions.salt_bridge'
schrodinger.structutils.interactions.salt_bridge.get_salt_bridges(struc1, group1=None, struc2=None, group2=None, cutoff=5, order_by=<OrderBy.AnionCation: 1>, honor_pbc=True)

Calculate all salt bridges within or between the specified atoms. If struc2 or group2 are given, then this function will return salt bridges between the two structures/groups of atoms. If neither struc2 nor group2 are given, then this function will return salt bridges within a single structure/group of atoms.

Parameters:
  • struc1 (schrodinger.structure.Structure) – The structure to analyze
  • group1 (list) – The list of atom indices in struc1 to analyze. If not given, all atoms in struc1 will be analyzed.
  • struc2 (schrodinger.structure.Structure) – The second structure to analyze. If group2 is given but struc2 is not, then struc1 will be used.
  • group2 (list) – The list of atom indices in struc2 to analyze. If struc2 is given but group2 is not, then all atoms in struc2 will be analyzed.
  • cutoff (float) – The maximum distance allowed for salt bridges
  • order_by (OrderBy) – How the returned salt bridge atom should be ordered. If OrderBy.AnionCation, then each salt bridge will be returned as a tuple of (anion atom, cation atom). If OrderBy.InputOrder, then each salt bridge will be returned as a tuple of (atom from struc1/group1, atom from struc2/group2).
Returns:

A list of salt bridges, where each salt bridge is represented by a tuple of two schrodinger.structure._StructureAtom objects.
Return type:

list
class schrodinger.structutils.interactions.salt_bridge.SaltBridgeFinder(cutoff=4.0)

Bases: object

DEPRECATED because it is inconsistent with Maestro.

Use get_salt_bridges() instead

PROT_CATIONS = {'ARG': {'NH1', 'NH2'}, 'HID': {'NE2'}, 'HIE': {'ND1'}, 'HIS': {'NE2'}, 'LYS': {'NZ'}}
PROT_ANIONS = {'ASP': {'OD1', 'OD2'}, 'GLU': {'OE1', 'OE2'}}
STANDARD_AAS = {'HID', 'PRO', 'CYS', 'PHE', 'HIP', 'HIS', 'ASN', 'NMA', 'LYS', 'MET', 'VAL', 'ILE', 'ASP', 'LEU', 'TYR', 'GLN', 'SER', 'GLU', 'ARG', 'ACE', 'HIE', 'THR', 'TRP', 'ALA', 'GLY'}
RES_TO_IGNORE = {'HOH'}
__init__(cutoff=4.0)

DEPRECATED for get_salt_bridges()

Parameters:cutoff (float) – The maximum distance allowed for salt bridges
classmethod find(struc1, group1=None, struc2=None, group2=None, cutoff=4.0, ignore_same_res=True)

DEPRECATED for get_salt_bridges()

Parameters:
  • struc1 (schrodinger.structure.Structure) – The structure to analyze
  • group1 (list) – The list of atoms in struc1 to analyze. If not given, all atoms in struc1 will be analyzed.
  • struc2 (schrodinger.structure.Structure) – The second structure to analyze. If group2 is given but struc2 is not, then struc1 will be used.
  • group2 (list) – The list of atoms in struc2 to analyze. If struc2 is given but group2 is not, then all atoms in struc2 will be analyzed.
  • cutoff (float) – The maximum distance allowed for salt bridges
  • ignore_same_res (bool) – If True, salt bridges between atoms within the same residue will be ignored. If False, these salt bridges will be returned as normal. This option has no effect if struc2 or group2 are given. In those cases, the two structures/groups of atoms are assumed to be non-overlapping, so this option is irrelevant and no salt bridges are ignored. Also note that, if this option if False, there is no within-bonds restriction on salt bridges (ex. If there is an anion covalently bound to a cation, the pair will be returned as a salt bridge.)
Returns:

An iterator that provides pairs of atoms involved in salt bridges
Return type:

iter
Note:

If group2 are given and struc2 is None, then group1 and group2 are assumed to be non-overlapping. If these two lists contain the same atoms, then salt bridges may be returned twice.
calculateInter(struc1, group1, struc2, group2)

Return an iterator that provides salt bridges between two groups of atoms

Parameters:
Returns:

An iterator that provides salt bridge atoms as a tuple of (atom index from group1, atom index from group2)
Return type:

iter
calculateIntra(struc, atoms, ignore_same_res=True)

Return an iterator that provides salt bridges within a group of atoms

Parameters:
  • struc (schrodinger.structure.Structure) – The structure to analyze
  • atoms (list) – The list of atoms
  • ignore_same_res (bool) – If True, salt bridges between atoms within the same residue will be ignored. If False, these salt bridges will be returned as normal. Note that, if this option if False, there is no within-bonds restriction on salt bridges (ex. If there is an anion covalently bound to a cation, the pair will be returned as a salt bridge.)
Returns:

An iterator that provides salt bridge atoms as a tuple of two atom indices
Return type:

iter
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.structutils.interactions.salt_bridge', '__doc__': '\n DEPRECATED because it is inconsistent with Maestro.\n\n Use get_salt_bridges() instead\n ', 'PROT_CATIONS': {'LYS': {'NZ'}, 'ARG': {'NH1', 'NH2'}, 'HID': {'NE2'}, 'HIE': {'ND1'}, 'HIS': {'NE2'}}, 'PROT_ANIONS': {'GLU': {'OE1', 'OE2'}, 'ASP': {'OD1', 'OD2'}}, 'STANDARD_AAS': {'HID', 'PRO', 'CYS', 'PHE', 'HIP', 'HIS', 'ASN', 'NMA', 'LYS', 'MET', 'VAL', 'ILE', 'ASP', 'LEU', 'TYR', 'GLN', 'SER', 'GLU', 'ARG', 'ACE', 'HIE', 'THR', 'TRP', 'ALA', 'GLY'}, 'RES_TO_IGNORE': {'HOH'}, '_warned': False, '__init__': <function SaltBridgeFinder.__init__>, 'find': <classmethod object>, 'calculateInter': <function SaltBridgeFinder.calculateInter>, 'calculateIntra': <function SaltBridgeFinder.calculateIntra>, '_findChargedAtoms': <function SaltBridgeFinder._findChargedAtoms>, '_checkAtomCharge': <function SaltBridgeFinder._checkAtomCharge>, '_sumPartialCharges': <function SaltBridgeFinder._sumPartialCharges>, '_safeExtend': <function SaltBridgeFinder._safeExtend>, '_sbIterator': <function SaltBridgeFinder._sbIterator>, '_sameRes': <function SaltBridgeFinder._sameRes>, '__dict__': <attribute '__dict__' of 'SaltBridgeFinder' objects>, '__weakref__': <attribute '__weakref__' of 'SaltBridgeFinder' objects>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.structutils.interactions.salt_bridge'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)