schrodinger.protein.buildpeptide module

Module for converting protein residue sequences to 3D structures.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.protein.buildpeptide.SECONDARY_STRUCTURE(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Bases: enum.Enum

Extended = 1
AlphaHelix = 2
PiHelix = 3
ThreeTenHelix = 4
CollagenHelix = 5
LeftHandedAlphaHelix = 6
ParallelPleatedSheet = 7
AntiparallelPleatedSheet = 8
Custom = 9
CustomAngles = 10
schrodinger.protein.buildpeptide.get_fragment_structure(fragname)

Return the fragment structure for the given peptide residue.

Parameters

fragname (str) – Fragment name (e.g. “ALA”)

Returns

Structure

Return type

structure.Structure

schrodinger.protein.buildpeptide.grow_fragment(st, fromatom, toatom, fraggroup, fragname, direction=None)

Grow the given fragment to the given ct, in alpha-helix configuration.

Parameters

  • st (structure.Structure) – Input structure

  • fromatom (int) – The “from” grow atom.

  • toatom (int) – The “to” grow atom.

  • fraggroup – Fragment group (e.g. “organic”)

  • fragname (str) – Fragment name (e.g. “Hydroxyl”)

  • direction (str) – Direction to grow in (e.g. “forward”)

Tupe fraggroup

str

Returns

(new from atom, new to atom) for the next grow operation.

Return type

(int, int)

schrodinger.protein.buildpeptide.build_peptide(sequence: Sequence[str], secondary_structure=None, ss_seq=None, angles=None, cap=False)

For each amino acid in the sequence, test to make sure that it is a valid code and build the peptide.

Parameters

  • sequence (Sequence[str]) – Amino acid sequence of the peptide to be built.

  • secondary_structure (enum SECONDARY_STRUCTURE) – A description of how the secondary structure can be set.

  • ss_seq (list) – If the secondary structure is Custom then this is sequence of secondary structure codes - one per residue

  • angles – If the secondary structure is Custom Angles then this is a list of pairs of Phi/Psi angles - two per residue

  • cap (bool) – Option to include capping groups.

Returns

Initial peptide structure

Return type

structure.Structure