Module salt_bridge
Find salt-bridge interactions.
Examples
Find all salt bridge interactions within a protein:
st = StructureReader("protein.maegz").next()
for (atom1, atom2) in SaltBridgeFinder.find(st):
print "Salt bridge between atoms %i and %i" % (atom1, atom2)
Find all salt bridges within a single protein chain:
st = StructureReader("protein.maegz").next()
atoms = st.chain["C"].getAtomIndices()
for (atom1, atom2) in SaltBridgeFinder.find(st, atoms):
print "Salt bridge between atoms %i and %i" % (atom1, atom2)
Find all salt bridges between a protein and a ligand:
reader = StructureReader("protein_and_ligand.maegz")
prot = reader.next()
lig = reader.next()
for (atom1, atom2) in SaltBridgeFinder.find(prot, struc2=lig):
print "Salt bridge between atoms %i and %i" % (atom1, atom2)
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DEFAULT_MAX_DIST = 4.0
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__package__ = 'schrodinger.structutils.interactions' |
get_salt_bridges(struc1,
group1=None,
struc2=None,
group2=None,
cutoff=5,
order_by=<OrderBy.AnionCation: 1>)
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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 analyzegroup1 (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 bridgesorder_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: list
- A list of salt bridges, where each salt bridge is represented by
a tuple of two schrodinger.structure._StructureAtom
objects.
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_get_wrapped_sb_list(struc1,
group1,
struc2,
group2,
cutoff)
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Get the salt bridge list returned by schrodinger.infra.structure.get_salt_bridges.
- Parameters:
struc1 (schrodinger.structure.Structure) - The structure to analyzegroup1 (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 - Returns: list
- A list of salt bridges, where each salt bridge is represented by
a tuple of two schrodinger.infra.structure.StructureAtom
objects in (anion, cation) order.
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_convert_group(group,
struc)
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Convert a list of atom indices to a bitset.
- Parameters:
group (list) - A list of atom indices. If None, the bitset will contain all
atoms in struc.struc (schrodinger.structure.Structure) - The structure that the group atom indices refer to - Returns: mmbitset.Bitset
- The bitset
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_to_input_order(salt_bridge,
struc1,
bs1)
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Switch the salt bridge tuple from (anion, cation) order to input
order.
- Parameters:
- Returns: tuple
- The re-ordered salt bridge, as a tuple of schrodinger.structure._StructureAtom
objects.
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