Skip to content

Add Residue Interaction Log Odds (RILO) and Packing Score #57

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
yusuf1759 wants to merge 2 commits into
base: main
Choose a base branch
from
+714 −6
Open

Add Residue Interaction Log Odds (RILO) and Packing Score #57

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
a893d7f
chore: add log-odds scores
yusuf1759 Sep 17, 2025
44c82a8
chore: add packing scores scores
yusuf1759 Sep 18, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
15 changes: 15 additions & 0 deletions src/peppr/clashes.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -112,3 +112,18 @@ def _to_sparse_indices(all_contacts: NDArray[np.int_]) -> NDArray[np.int_]:
combined_indices = np.stack([query_indices, contact_indices], axis=1)
# Remove the padding values
return combined_indices[contact_indices != -1]


def _find_interface_contacts(
atoms1: struc.AtomArray,
atoms2: struc.AtomArray,
inclusion_radius: float,
) -> NDArray[np.int_]:
last_index_atoms1 = atoms1.array_length()
combined_atoms = struc.concatenate((atoms1, atoms2))
contacts = _find_contacts(combined_atoms, inclusion_radius)
# Only keep contacts between atoms1 and atoms2
interface_contacts = contacts[
(contacts[:, 0] < last_index_atoms1) & (contacts[:, 1] >= last_index_atoms1)
]
return interface_contacts
1 change: 1 addition & 0 deletions src/peppr/contacts.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -609,6 +609,7 @@ def _find_charged_atoms_in_resonance_structures(
"""
pos_mask = np.zeros(mol.GetNumAtoms(), dtype=bool)
neg_mask = np.zeros(mol.GetNumAtoms(), dtype=bool)

resonance_supplier = Chem.ResonanceMolSupplier(mol)
for resonance_mol in resonance_supplier:
if resonance_mol is None:
Expand Down
329 changes: 329 additions & 0 deletions src/peppr/logodds.py
View file
Open in desktop
Copy link
Copy Markdown
Contributor

@OleinikovasV OleinikovasV Oct 9, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

What is the source of these values? Should we link in some documentations?

Original file line number Diff line number Diff line change
@@ -0,0 +1,329 @@
PLI_LOG_ODDS = {
Copy link
Copy Markdown
Collaborator

@padix-key padix-key Oct 16, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Due to the large number of values, we should probably put them into a JSON file

"CATION_PI": {
"ALA": 0.0,
"ARG": 0.335,
"ASN": 0.0,
"ASP": 0.0,
"CYS": 0.755,
"GLN": 0.0,
"GLU": 0.0,
"GLY": 0.591,
"HIS": 0.0,
"ILE": 0.0,
"LEU": 0.0,
"LYS": 0.42,
"MET": 0.0,
"PHE": 0.0,
"PRO": 0.0,
"SER": 0.0,
"THR": 0.0,
"TRP": 0.0,
"TYR": 0.0,
"VAL": 0.0,
"XXX": 0.0
},
"HALOGEN_BOND": {
"ALA": 0.0,
"ARG": 0.0,
"ASN": 0.0,
"ASP": 0.0,
"CYS": 0.0,
"GLN": 0.0,
"GLU": 0.0,
"GLY": 0.0,
"HIS": 0.0,
"ILE": 0.0,
"LEU": 0.0,
"LYS": 0.0,
"MET": 0.0,
"PHE": 0.0,
"PRO": 0.0,
"SER": 0.0,
"THR": 0.0,
"TRP": 0.0,
"TYR": 0.0,
"VAL": 0.0,
"XXX": 0.0
},
"HBOND_DONOR_LIGAND": {
"ALA": -0.077,
"ARG": -1.094,
"ASN": 0.144,
"ASP": 0.466,
"CYS": 0.052,
"GLN": 0.062,
"GLU": 0.48,
"GLY": -0.237,
"HIS": 0.141,
"ILE": 0.2,
"LEU": 0.147,
"LYS": -1.061,
"MET": 0.144,
"PHE": -0.443,
"PRO": 0.586,
"SER": -0.079,
"THR": -0.099,
"TRP": -0.843,
"TYR": -0.013,
"VAL": 0.252,
"XXX": 0.379
},
"HBOND_DONOR_RECEPTOR": {
"ALA": 0.146,
"ARG": -0.015,
"ASN": 0.064,
"ASP": -0.776,
"CYS": 0.103,
"GLN": 0.113,
"GLU": -0.711,
"GLY": 0.157,
"HIS": -0.205,
"ILE": 0.057,
"LEU": 0.034,
"LYS": 0.016,
"MET": 0.053,
"PHE": -0.489,
"PRO": 0.0,
"SER": 0.149,
"THR": 0.156,
"TRP": -0.044,
"TYR": -0.035,
"VAL": 0.019,
"XXX": 0.0
},
"IONIC_BOND": {
"ALA": 0.0,
"ARG": 0.549,
"ASN": 0.0,
"ASP": 0.168,
"CYS": 0.0,
"GLN": 0.0,
"GLU": 0.11,
"GLY": -0.988,
"HIS": 0.0,
"ILE": 0.0,
"LEU": 0.0,
"LYS": 0.485,
"MET": 0.0,
"PHE": 0.0,
"PRO": 0.0,
"SER": 0.0,
"THR": 0.0,
"TRP": 0.0,
"TYR": 0.0,
"VAL": 0.0,
"XXX": 0.0
},
"PI_CATION": {
"ALA": 0.0,
"ARG": 0.0,
"ASN": 0.0,
"ASP": 0.0,
"CYS": 0.0,
"GLN": 0.0,
"GLU": 0.0,
"GLY": 0.0,
"HIS": 0.71,
"ILE": 0.0,
"LEU": 0.0,
"LYS": 0.0,
"MET": 0.0,
"PHE": 0.689,
"PRO": 0.0,
"SER": 0.0,
"THR": 0.0,
"TRP": 1.068,
"TYR": 0.642,
"VAL": 0.0,
"XXX": 0.0
},
"PI_STACKING": {
"ALA": 0.0,
"ARG": 0.0,
"ASN": 0.0,
"ASP": 0.0,
"CYS": 0.0,
"GLN": 0.0,
"GLU": 0.0,
"GLY": 0.0,
"HIS": 0.632,
"ILE": 0.0,
"LEU": 0.0,
"LYS": 0.0,
"MET": 0.0,
"PHE": 1.071,
"PRO": 0.0,
"SER": 0.0,
"THR": 0.0,
"TRP": 0.786,
"TYR": 0.591,
"VAL": 0.0,
"XXX": 0.0
}
}

PPI_LOG_ODDS = {
"CATION_PI": {
"ALA": 0.0,
"ARG": 0.441,
"ASN": 0.0,
"ASP": 0.0,
"CYS": 0.0,
"GLN": 0.0,
"GLU": 0.0,
"GLY": 0.342,
"HIS": 0.0,
"ILE": 0.0,
"LEU": 0.0,
"LYS": 0.585,
"MET": 0.0,
"PHE": 0.0,
"PRO": 0.83,
"SER": 0.0,
"THR": 0.0,
"TRP": 0.0,
"TYR": 0.0,
"VAL": 0.0,
"XXX": 0.859
},
"HALOGEN_BOND": {
"ALA": 0.0,
"ARG": 0.0,
"ASN": 0.0,
"ASP": 0.0,
"CYS": 0.0,
"GLN": 0.0,
"GLU": 0.0,
"GLY": 0.0,
"HIS": 0.0,
"ILE": 0.0,
"LEU": 0.0,
"LYS": 0.0,
"MET": 0.0,
"PHE": 0.0,
"PRO": 0.0,
"SER": 0.0,
"THR": 0.0,
"TRP": 0.0,
"TYR": 0.0,
"VAL": 0.0,
"XXX": 0.0
},
"HBOND_DONOR_LIGAND": {
"ALA": 0.154,
"ARG": -0.719,
"ASN": 0.094,
"ASP": 0.116,
"CYS": 0.167,
"GLN": 0.092,
"GLU": 0.112,
"GLY": 0.136,
"HIS": -0.008,
"ILE": 0.175,
"LEU": 0.173,
"LYS": -0.524,
"MET": 0.295,
"PHE": -0.206,
"PRO": 0.41,
"SER": 0.091,
"THR": 0.134,
"TRP": -0.505,
"TYR": -0.044,
"VAL": 0.171,
"XXX": 0.097
},
"HBOND_DONOR_RECEPTOR": {
"ALA": 0.084,
"ARG": 0.165,
"ASN": 0.191,
"ASP": -0.838,
"CYS": 0.109,
"GLN": 0.193,
"GLU": -0.872,
"GLY": 0.12,
"HIS": -0.051,
"ILE": 0.132,
"LEU": 0.091,
"LYS": 0.133,
"MET": -0.123,
"PHE": -0.255,
"PRO": 0.0,
"SER": 0.193,
"THR": 0.163,
"TRP": -0.019,
"TYR": 0.054,
"VAL": 0.093,
"XXX": -0.292
},
"IONIC_BOND": {
"ALA": -0.704,
"ARG": 0.25,
"ASN": 0.0,
"ASP": 0.345,
"CYS": 0.0,
"GLN": 0.0,
"GLU": 0.355,
"GLY": -0.898,
"HIS": 0.0,
"ILE": 0.0,
"LEU": -0.81,
"LYS": 0.248,
"MET": 0.0,
"PHE": 0.0,
"PRO": 0.0,
"SER": -1.085,
"THR": 0.0,
"TRP": 0.0,
"TYR": 0.0,
"VAL": -0.649,
"XXX": 0.096
},
"PI_CATION": {
"ALA": 0.0,
"ARG": 0.0,
"ASN": 0.0,
"ASP": 0.0,
"CYS": 0.0,
"GLN": 0.0,
"GLU": 0.0,
"GLY": 0.0,
"HIS": 0.751,
"ILE": 0.0,
"LEU": 0.0,
"LYS": 0.0,
"MET": 0.0,
"PHE": 0.905,
"PRO": 0.0,
"SER": 0.0,
"THR": 0.0,
"TRP": 1.032,
"TYR": 0.628,
"VAL": 0.0,
"XXX": 0.0
},
"PI_STACKING": {
"ALA": 0.0,
"ARG": 0.0,
"ASN": 0.0,
"ASP": 0.0,
"CYS": 0.0,
"GLN": 0.0,
"GLU": 0.0,
"GLY": 0.0,
"HIS": 0.761,
"ILE": 0.0,
"LEU": 0.0,
"LYS": 0.0,
"MET": 0.0,
"PHE": 1.029,
"PRO": 0.0,
"SER": 0.0,
"THR": 0.0,
"TRP": 0.821,
"TYR": 0.638,
"VAL": 0.0,
"XXX": 0.0
}
}

SCALING_FACTORS = {"upper_asymptote": 2.0, "midpoint": 0.0, "steepness": 100.0, "lower_asymptote": -1}
Loading