stcrpy.tcr_interactions package

Submodules

stcrpy.tcr_interactions.PLIPParser module

class stcrpy.tcr_interactions.PLIPParser.PLIPParser[source]

Bases: object

This class is used to parse the interactions of a TCR-pMHC complex using PLIP.

parse_complex(complex: plip.structure.preparation.PDBComplex, tcr_pmhc_complex: abTCR | gdTCR = None, renumbering=None, domain_assignment=None) → DataFrame[source]

Parses PLIP profiled interactions and maps them back onto a syctpy TCR object.

Parameters:

  • complex (plip.structure.preparation.PDBComplex)

  • tcr_pmhc_complex (Union["abTCR", "gdTCR"], optional) – _description_. Defaults to None.

  • renumbering (_type_, optional) – _description_. Defaults to None.

  • domain_assignment (_type_, optional) – _description_. Defaults to None.

Returns:

_description_

Return type:

pd.DataFrame

stcrpy.tcr_interactions.TCRInteractionProfiler module

class stcrpy.tcr_interactions.TCRInteractionProfiler.TCRInteractionProfiler(**kwargs)[source]

Bases: object

create_pymol_session(tcr_pmhc: TCR, save_as=None, antigen_residues_to_highlight=None)[source]
get_interaction_heatmap(tcr, renumber=True, **plotting_kwargs)[source]
get_interactions(tcr, renumber=True, save_as_csv=None)[source]
reset_parameters()[source]
set_interaction_parameters(**kwargs)[source]

Function to set global PLIP detection parameters, ie. the stcrpy API for PLIP config parameters. See https://github.com/pharmai/plip/blob/master/plip/plipcmd.py for how these are set in native PLIP See https://github.com/pharmai/plip/blob/master/plip/basic/config.py for the default values

Default Parameters (from PLIP distribution):

BS_DIST = 7.5 # Determines maximum distance to include binding site residues AROMATIC_PLANARITY = 5.0 # Determines allowed deviation from planarity in aromatic rings MIN_DIST = 0.5 # Minimum distance for all distance thresholds HYDROPH_DIST_MAX = 4.0 # Distance cutoff for detection of hydrophobic contacts HBOND_DIST_MAX = 4.1 # Max. distance between hydrogen bond donor and acceptor (Hubbard & Haider, 2001) + 0.6 A HBOND_DON_ANGLE_MIN = 100 # Min. angle at the hydrogen bond donor (Hubbard & Haider, 2001) + 10 PISTACK_DIST_MAX = 5.5 # Max. distance for parallel or offset pistacking (McGaughey, 1998) PISTACK_ANG_DEV = 30 # Max. Deviation from parallel or perpendicular orientation (in degrees) PISTACK_OFFSET_MAX = 2.0 # Maximum offset of the two rings (corresponds to the radius of benzene + 0.5 A) PICATION_DIST_MAX = 6.0 # Max. distance between charged atom and aromatic ring center (Gallivan and Dougherty, 1999) SALTBRIDGE_DIST_MAX = 5.5 # Max. distance between centers of charge for salt bridges (Barlow and Thornton, 1983) + 1.5 HALOGEN_DIST_MAX = 4.0 # Max. distance between oxy. and halogen (Halogen bonds in biological molecules., Auffinger)+0.5 HALOGEN_ACC_ANGLE = 120 # Optimal acceptor angle (Halogen bonds in biological molecules., Auffinger) HALOGEN_DON_ANGLE = 165 # Optimal donor angle (Halogen bonds in biological molecules., Auffinger) HALOGEN_ANGLE_DEV = 30 # Max. deviation from optimal angle WATER_BRIDGE_MINDIST = 2.5 # Min. distance between water oxygen and polar atom (Jiang et al., 2005) -0.1 WATER_BRIDGE_MAXDIST = 4.1 # Max. distance between water oxygen and polar atom (Jiang et al., 2005) +0.5 WATER_BRIDGE_OMEGA_MIN = 71 # Min. angle between acceptor, water oxygen and donor hydrogen (Jiang et al., 2005) - 9 WATER_BRIDGE_OMEGA_MAX = 140 # Max. angle between acceptor, water oxygen and donor hydrogen (Jiang et al., 2005) WATER_BRIDGE_THETA_MIN = 100 # Min. angle between water oxygen, donor hydrogen and donor atom (Jiang et al., 2005) METAL_DIST_MAX = 3.0 # Max. distance between metal ion and interacting atom (Harding, 2001) MAX_COMPOSITE_LENGTH = 200 # Filter out ligands with more than 200 fragments

Raises:

  • AttributeError – Raised if parameter being modified does not exist in config

  • ValueError – Raised if value being set is not permitted.

stcrpy.tcr_interactions.TCRpMHC_PLIP_Model_Parser module

class stcrpy.tcr_interactions.TCRpMHC_PLIP_Model_Parser.TCRpMHC_PLIP_Model_Parser(tmp_dir=None)[source]

Bases: object

map_amino_acids_to_ligands(ligand_pdb, ligand_sdf)[source]
parse_tcr_pmhc_complex(tcr_pmhc_complex: TCR, delete_tmp_files=True, renumber=True) → PDBComplex[source]

stcrpy.tcr_interactions.utils module

class stcrpy.tcr_interactions.utils.Interaction(type, protein_atom, protein_chain, protein_residue, protein_number, ligand_atom, distance, angle, plip_id)[source]

Bases: object

to_tuple()[source]
stcrpy.tcr_interactions.utils.parse_interaction(interaction) → Interaction[source]
stcrpy.tcr_interactions.utils.process_hbond(interaction)[source]
stcrpy.tcr_interactions.utils.process_hydrophobic(interaction)[source]
stcrpy.tcr_interactions.utils.process_pi_stack(interaction)[source]
stcrpy.tcr_interactions.utils.process_saltbridge(interaction)[source]
stcrpy.tcr_interactions.utils.return_interactions(protein_file=None, ligand_file=None, complex_file=None, pymol_visualization=False)[source]

Module contents