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

Bases: enum.Enum

An enumeration.

AlphaHelix = 2
AntiparallelPleatedSheet = 8
CollagenHelix = 5
Custom = 9
CustomAngles = 10
Extended = 1
LeftHandedAlphaHelix = 6
ParallelPleatedSheet = 7
PiHelix = 3
ThreeTenHelix = 4
__class__

alias of enum.EnumMeta

__members__ = mappingproxy(OrderedDict([('Extended', <SECONDARY_STRUCTURE.Extended: 1>), ('AlphaHelix', <SECONDARY_STRUCTURE.AlphaHelix: 2>), ('PiHelix', <SECONDARY_STRUCTURE.PiHelix: 3>), ('ThreeTenHelix', <SECONDARY_STRUCTURE.ThreeTenHelix: 4>), ('CollagenHelix', <SECONDARY_STRUCTURE.CollagenHelix: 5>), ('LeftHandedAlphaHelix', <SECONDARY_STRUCTURE.LeftHandedAlphaHelix: 6>), ('ParallelPleatedSheet', <SECONDARY_STRUCTURE.ParallelPleatedSheet: 7>), ('AntiparallelPleatedSheet', <SECONDARY_STRUCTURE.AntiparallelPleatedSheet: 8>), ('Custom', <SECONDARY_STRUCTURE.Custom: 9>), ('CustomAngles', <SECONDARY_STRUCTURE.CustomAngles: 10>)]))
__module__ = 'schrodinger.protein.buildpeptide'
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.

:rtype (int, int)

schrodinger.protein.buildpeptide.build_peptide(sequence, 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 (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