| |
| """Compare polar-atom selection conventions for 3D PSA on a finished run. |
| |
| The element-based selection (N, O, polar H) and the charge-threshold selection |
| used in the reference work give different absolute PSA values on the same |
| trajectory. This prints both, sweeping the charge threshold, so a gap against |
| published numbers can be attributed to convention rather than to conformation. |
| Charges come from the run's AM1-BCC cache, so nothing is recomputed. |
| |
| Takes a run name rather than a path and resolves <name>/<solvent>/ against the |
| current directory, so run it from the md folder. Solvent defaults to chloroform. |
| |
| Usage: |
| python psa_method_probe.py egfrvhl_rank4 [solvent] |
| """ |
| import json, glob, numpy as np, mdtraj as md |
| import xml.etree.ElementTree as ET |
|
|
| def cached_charges(cache_path): |
| d = json.load(open(cache_path)) |
| entry = list(list(d.values())[0].values())[0] |
| ffxml = entry["ffxml"] |
| root = ET.fromstring(ffxml) |
| |
| q_by_type = {} |
| for a in root.iter("Atom"): |
| if a.get("charge") is not None and a.get("type") is not None: |
| q_by_type[a.get("type")] = float(a.get("charge")) |
| |
| res = root.find(".//Residues/Residue") |
| order = [a.get("type") for a in res.findall("Atom")] |
| return np.array([q_by_type[t] for t in order]) |
|
|
| def main(): |
| import sys |
| NAME = sys.argv[1] if len(sys.argv) > 1 else "egfrvhl_rank4" |
| SOL = sys.argv[2] if len(sys.argv) > 2 else "chloroform" |
| q = cached_charges(f"{NAME}/{SOL}/ff_cache.json") |
| print(f"charges from cache: n={len(q)} range [{q.min():.2f},{q.max():.2f}] " |
| f"#|q|>1.0={(np.abs(q) > 1.0).sum()}") |
|
|
| top = glob.glob(f"{NAME}/{SOL}/*_solvated.pdb")[0] |
| reps = sorted(glob.glob(f"{NAME}/{SOL}/rep*/{NAME}_prod.dcd")) |
| tr = md.join([md.load(r, top=top) for r in reps]) |
| lig = [a.index for r in tr.topology.residues if not r.is_water and r.n_atoms > 5 |
| for a in r.atoms] |
| t = tr.atom_slice(lig); t.center_coordinates(); L = t.topology |
| syms = [a.element.symbol for a in L.atoms] |
| if len(syms) != len(q): |
| print(f"atom-count mismatch: cache {len(q)} vs MD {len(syms)}"); return |
| sasa = md.shrake_rupley(t, mode="atom", probe_radius=0.14) |
| def area(mask): return (sasa[:, mask].sum(1) * 100.0).mean() |
|
|
| nbr = {} |
| for b in L.bonds: |
| nbr.setdefault(b[0].index, []).append(b[1].index) |
| nbr.setdefault(b[1].index, []).append(b[0].index) |
| elem = np.array([i for i, a in enumerate(L.atoms) |
| if a.element.symbol in ("N", "O") or (a.element.symbol == "H" and |
| any(L.atom(j).element.symbol in ("N", "O") for j in nbr.get(a.index, [])))]) |
|
|
| print(f"\nelement selection (N, O, polar H): {area(elem):.0f} A2 ({len(elem)} atoms)") |
| print("charge-threshold selection:") |
| print(f" {'|q|>thr':>8s}{'#atoms':>8s}{'PSA':>7s}") |
| for thr in [0.10, 0.15, 0.20, 0.25, 0.30, 0.40, 0.50]: |
| m = np.abs(q) > thr |
| print(f" {thr:>8.2f}{int(m.sum()):>8d}{area(m):>7.0f}") |
| print("\nreference permeable band = 190-265 A2") |
|
|
| if __name__ == "__main__": |
| main() |
|
|
