From 96d039d431af9c0cbfb8b4491006822c1d41064b Mon Sep 17 00:00:00 2001 From: dechin Date: Tue, 18 Apr 2023 17:43:13 +0800 Subject: [PATCH] Fix the rebuild_hydrogen paramter setting --- .../protein_relaxation/protein_relax.py | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/MindSPONGE/applications/molecular_dynamics/protein_relaxation/protein_relax.py b/MindSPONGE/applications/molecular_dynamics/protein_relaxation/protein_relax.py index f7507f915..334817537 100644 --- a/MindSPONGE/applications/molecular_dynamics/protein_relaxation/protein_relax.py +++ b/MindSPONGE/applications/molecular_dynamics/protein_relaxation/protein_relax.py @@ -32,7 +32,7 @@ from mindsponge import SimulationCell from mindsponge.callback import RunInfo from mindsponge.optimizer import SteepestDescent from mindsponge.potential.bias import OscillatorBias -from mindsponge.system.modeling.pdb_generator import gen_pdb +from mindsponge.system.modelling.pdb_generator import gen_pdb from mindsponge.common.utils import get_pdb_info from mindsponge.metrics.structure_violations import get_structural_violations @@ -104,7 +104,7 @@ def optimize_strategy(system, gds, loops, ads, adm, nonh_mask, mode=1): run_info = RunInfo(1) md.run(gds, callbacks=[run_info]) - if msnp.isnan(md.energy().sum()): + if msnp.isnan(md.calc_energy().sum()): return 0 for _ in range(loops): @@ -121,10 +121,10 @@ def optimize_strategy(system, gds, loops, ads, adm, nonh_mask, mode=1): for i, param in enumerate(opt.trainable_params()): print(i, param.name, param.shape) md = Sponge(simulation_network, optimizer=opt) - print(md.energy()) + print(md.calc_energy()) run_info = RunInfo(1) md.run(ads, callbacks=[run_info]) - if msnp.isnan(md.energy().sum()): + if msnp.isnan(md.calc_energy().sum()): return 0 if mode in (1, 3): @@ -136,10 +136,10 @@ def optimize_strategy(system, gds, loops, ads, adm, nonh_mask, mode=1): for i, param in enumerate(opt.trainable_params()): print(i, param.name, param.shape) md = Sponge(simulation_network, optimizer=opt) - print(md.energy()) + print(md.calc_energy()) run_info = RunInfo(1) md.run(ads, callbacks=[run_info]) - if msnp.isnan(md.energy().sum()): + if msnp.isnan(md.calc_energy().sum()): return 0 return system @@ -149,7 +149,7 @@ def main(): seed = 2333 ms.set_seed(seed) set_global_units("A", "kcal/mol") - system = Protein(pdb=pdb_name) + system = Protein(pdb=pdb_name, rebuild_hydrogen=True) nonh_mask = Tensor( np.where(system.atomic_number[0] > 1, 0, 1)[None, :, None], ms.int32 ) -- Gitee