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)¶ Bases:
enum.Enum
An enumeration.
-
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)[source]¶ 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)[source]¶ Grow the given fragment to the given ct, in alpha-helix configuration.
- Parameters
st (
structure.Structure
) – Input structurefromatom (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)[source]¶ 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