ost.mol.alg.lddt Namespace Reference

Data Structures
class	CustomCompound
class	lDDTScorer
class	SymmetrySettings

Functions
	cdist (p1, p2)
	blockwise_cdist (A, B, block_size=1000)
	GetDefaultSymmetrySettings ()
	DisableChainPairContacts (scorer, excluded_interfaces)

Function Documentation

blockwise_cdist()

blockwise_cdist	(		A,
			B,
			block_size = 1000
	)

 Memory efficient cdist implementation that performs blockwise operations

scipy cdist uses 64 bit floats (double) which can scratch at the upper
memory end for most machines when number of positions become larger.
E.g. ~4000 residues might for example have 35000 atom positions. That's
Almost 10GB to hold all pairwise distances in 64bit floats. This function
calls cdist blockwise and stores the results in a 32bit float matrix.

This function is adapted from chatgpt output

Definition at line 19 of file lddt.py.

cdist()

cdist	(		p1,
			p2
	)

Definition at line 12 of file lddt.py.

DisableChainPairContacts()

DisableChainPairContacts	(		scorer,
			excluded_interfaces
	)

Copy interchain reference distances of *scorer* with contacts
for a selection of interfaces switched off

:param scorer: Scorer from which to derive the interchain reference
               distances
:type scorer: :class:`lDDTScorer`
:param excluded_interfaces: Interfaces for which contacts should be
                            disabled. Each element is a pair of chain
                            names.
:type excluded_interfaces: :class:`list` of :class:`tuple` with two
                           :class:`str`
:returns: Tuple with 4 elements that are copies of
          (scorer.ref_indices_ic, scorer.ref_distances_ic,
          scorer.sym_ref_indices_ic, scorer.sym_ref_distances_ic) with
          any contact belonging to one of *excluded_interfaces* removed

Definition at line 1686 of file lddt.py.

GetDefaultSymmetrySettings()

GetDefaultSymmetrySettings

(

)

Constructs and returns :class:`SymmetrySettings` object for natural amino
acids

Definition at line 103 of file lddt.py.