metrics.py¶
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class
src.metrics.metrics.Builder(is_AF=False)¶ Bases:
Bio.PDB.StructureBuilder.StructureBuilderSubclassing of Bio.PDB.StructureBuilder.StructureBuilder to incorporate metrics.ModRes and metrics.ModStructure into the Bio.PDB hierarchy.
Usage: Pass a Builder instance to the PDBParser as a structure_builder parameter.
Example: >>> parser = PDBParser(QUIET=1, structure_builder=Builder()) >>> s = parser.get_structure(“code”, “1ris.pdb”)
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get_structure()¶ For AlphaFold structures containing floppy N and C terminal, residues are removed until the first residue with a pLDDT (confidence) > 80.
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init_residue(resname, field, resseq, icode)¶ Instantiate residue as src.metrics.metrics.ModRes object. Overrides Bio.PDB.StructureBuilder.init_residue.
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init_structure(structure_id)¶ Instantiate structure object as a metrics.ModStructure object. Overrides Bio.PDB.StructureBuilder.init_structure.
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class
src.metrics.metrics.ModRes(id, resname, segid)¶ Bases:
Bio.PDB.Residue.Residue-
is_buried(threshold=0.25)¶ Return boolean depending on ratio of residue SASA with respect to literature values in GLYXGLY_ASA.
- Parameters
threshold (float) – ratio (0, 1) of residue’s SASA over reference Gly-X-Gly polymer value.
- Returns
bool
- Raises
AttributeError – if the ModRes.monosara attribute is not set; if ModStructure.calculate_sasa didn’t run.
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class
src.metrics.metrics.ModStructure(id)¶ Bases:
Bio.PDB.Structure.StructureSubclass of Bio.PDB.Structure containing new methods and attributes for the estimation of protein physichochemical properties from their PDB coordinates.
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aminocount()¶ Return the amount of positive, negative and hydrophobic residues.
- Parameters
self – Structure entity
- Returns
Amount of positive, negative and hydrophobic residues in protein.
- Return type
tuple
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classmethod
anglemeasurement(v, u)¶ Calculate angle between any two vectors v and u, in degrees.
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calculate_sasa()¶ Perform SASA calculation with ShrakeRupley algorithm for the individual chains (monomers). Attach results to residue objects as Residue.monosasa.
- Parameters
self – Structure entity
- Returns
Solvent accessible surface area (SASA)
- Return type
int
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dipolemoment()¶ Calculation of the dipole moment from the dipole vector.
- Parameters
self – Structure entity
- Returns
Dipole moment
- Return type
int
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dipolevector()¶ Return dipole moment calculated from the position of the positive and negative residues. Source for dipolemoment equation: Felder, Prilusky, Silman, Sussman Nucleic Acids Research 2007
- Parameters
self – Structure entity
- Returns
Dipole vector
- Return type
tuple
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getlength()¶ Return length of the protein sequence.
- Parameters
self – Structure entity
- Returns
Length of sequence
- Return type
int
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hydrophobicmoment()¶ Calculate first order hydrophobic moment. Source for hydrophobicmoment equation: Silverman PNAS 2001, eq. 13
- Parameters
self – Structure entity
- Returns
Hydrophobic momemnt
- Return type
int
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hydrophobicvector()¶ Calculate first order hydrophobic moment vector.
- Parameters
self – Structure entity
- Returns
Hydrophobic vector
- Return type
tuple
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measure()¶ Assigns measurement to an attribute.
- Parameters
self – Structure entity
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molecularweight()¶ Return molecular weight of the protein sequence.
- Parameters
self – Structure entity
- Returns
Molecular weight
- Return type
int
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netcharge()¶ Return the net charge of the protein from the amount of positive and negative amino acids.
- Parameters
self – Structure entity
- Returns
Net charge
- Return type
int
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netchargedensity()¶ Return net charge density from net charge and total SASA of the residues.
- Parameters
self – Structure entity
- Returns
Net charge density
- Return type
int
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save_pdb(outfname)¶ Save structure as pdb file. Typically used together with trimming.
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sequencer()¶ Return polypeptide sequence from peptides.
- Parameters
self – Structure entity
- Returns
Amino acid sequence in one letter code
- Return type
str
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serializer()¶ Returns a dictionary representing the structure’s physicochemical properties.
- Parameters
self – Structure entity
- Returns
Dictionary of attributes
- Return type
dict
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truehydrophobicity()¶ Calculate total hydrophobicity for residues that are more than 25% exposed to the surface.
- Parameters
self – Structure entity
- Returns
Hydrophobicity for exposed amino acids
- Return type
int
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