schrodinger.protein.captermini module¶
Module for capping uncapped terminal residues in a protein structure by adding NME or ACE caps as appropriate. Also has functionality for adding a C-terminal oxygen in places where this is missing.
Usage for capping: capped_st = cap_termini(input_st)
Usage for adding C-terminal oxygens: capped_st = add_terminal_oxygens(input_st)
Copyright Schrodinger, LLC. All rights reserved.
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schrodinger.protein.captermini.
count_atom_hbonds
(st, atom)¶ Return the number of hydrogens bonds that the given atom is involved in.
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schrodinger.protein.captermini.
res_can_be_capped
(res)¶ Determines whether a fragment is able to be capped. Returns CAPN if specified residue can be N-capped, CAPC if C-capped; DONTCAP if it can’t be capped.
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class
schrodinger.protein.captermini.
CapTermini
(st, verbose=False, frag_min_atoms=150)¶ Bases:
object
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__init__
(st, verbose=False, frag_min_atoms=150)¶ Add caps to uncapped terminal residues in the input structure ‘st’. Returns a list of residues capped frag_min_atoms - peptide fragments with less than this number of atoms will not be capped (default 150). Set to 0 to cap all fragments.
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capSequences
(st)¶ Cap both ends of each sequence in the given structure.
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outputStructure
()¶
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cappedResidues
()¶ Returns residue strings for residues that were capped.
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capResidues
()¶ Returns residue strings for the added cap residues.
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findOxygenToReplace
(st, c_atom)¶ Check whether c_atom is bound to 2 terminal oxygens. If so, determine which one to replace with a cap, and return its atom index.
Return None if can’t find 2 terminal oxygens.
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adjustDihedral
(st, atom1, atom2, atom3, atom4)¶ Adjust dihedral between the original residue and the cap to 0 degrees.
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resCapped
(residue, capres)¶ Record this capping in the internal lists.
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attachCap
(residue, fromatom, replace_atom, fragname)¶ Attaches the specified fragment and returns the new Residue object
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schrodinger.protein.captermini.
cap_termini
(st)¶ Cap the termini on the specified st Function interface for CapTermini class
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schrodinger.protein.captermini.
add_terminal_oxygens
(st, frag_min_atoms=150)¶ Add OXT oxygen to the C-terminal of each poly-peptide chain. A hydrogen will first be added to the residue and converted to an oxygen. The bond length is not adjusted, and a minimization would be in order to fix this.