schrodinger.protein.buildpeptide module¶
Module for converting protein residue sequences to 3D structures.
Copyright Schrodinger, LLC. All rights reserved.
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class
schrodinger.protein.buildpeptide.
SECONDARY_STRUCTURE
¶ Bases:
enum.Enum
An enumeration.
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AlphaHelix
= 2¶
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AntiparallelPleatedSheet
= 8¶
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CollagenHelix
= 5¶
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Custom
= 9¶
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CustomAngles
= 10¶
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Extended
= 1¶
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LeftHandedAlphaHelix
= 6¶
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ParallelPleatedSheet
= 7¶
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PiHelix
= 3¶
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ThreeTenHelix
= 4¶
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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
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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)
- st (
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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