i run the dockies with example/genscore.py with target name '11betahsd1' have error:
gen_score_file(protein_path=protein_path,ligand_path=ligand_path,cand_sdf_path=cand_decoys_sdf,out_put_path=cand_decoys_score_outpath,args=args)
File "evalation_with_dockies.py", line 10, in gen_score_file
ids, scores = genscore.scoring(prot=protein_path,
File "/home/internal-GenScore/example/genscore.py", line 86, in scoring
data = VSDataset(ligs=lig,
File "/home/internal-GenScore/example/../GenScore/data/data.py", line 130, in init
self.gp = prot_to_graph(self.prot, cutoff)
File "/home/internal-GenScore/example/../GenScore/feats/mol2graph_rdmda_res.py", line 40, in prot_to_graph
res_coods = th.tensor(np.array([np.concatenate([res.atoms.positions, np.full((RES_MAX_NATOMS-len(res.atoms), 3), np.nan)],axis=0) for res in u.residues]))
File "/home/internal-GenScore/example/../GenScore/feats/mol2graph_rdmda_res.py", line 40, in
res_coods = th.tensor(np.array([np.concatenate([res.atoms.positions, np.full((RES_MAX_NATOMS-len(res.atoms), 3), np.nan)],axis=0) for res in u.residues]))
File "/opt/conda/lib/python3.8/site-packages/numpy/core/numeric.py", line 343, in full
a = empty(shape, dtype, order)
ValueError: negative dimensions are not allowed
cause the error is RES_MAX_NATOMS=24 smaller than res_max_natoms = max([len(res.atoms) for res in u.residues]).
what happened?
i run the dockies with example/genscore.py with target name '11betahsd1' have error:
gen_score_file(protein_path=protein_path,ligand_path=ligand_path,cand_sdf_path=cand_decoys_sdf,out_put_path=cand_decoys_score_outpath,args=args)
File "evalation_with_dockies.py", line 10, in gen_score_file
ids, scores = genscore.scoring(prot=protein_path,
File "/home/internal-GenScore/example/genscore.py", line 86, in scoring
data = VSDataset(ligs=lig,
File "/home/internal-GenScore/example/../GenScore/data/data.py", line 130, in init
self.gp = prot_to_graph(self.prot, cutoff)
File "/home/internal-GenScore/example/../GenScore/feats/mol2graph_rdmda_res.py", line 40, in prot_to_graph
res_coods = th.tensor(np.array([np.concatenate([res.atoms.positions, np.full((RES_MAX_NATOMS-len(res.atoms), 3), np.nan)],axis=0) for res in u.residues]))
File "/home/internal-GenScore/example/../GenScore/feats/mol2graph_rdmda_res.py", line 40, in
res_coods = th.tensor(np.array([np.concatenate([res.atoms.positions, np.full((RES_MAX_NATOMS-len(res.atoms), 3), np.nan)],axis=0) for res in u.residues]))
File "/opt/conda/lib/python3.8/site-packages/numpy/core/numeric.py", line 343, in full
a = empty(shape, dtype, order)
ValueError: negative dimensions are not allowed
cause the error is RES_MAX_NATOMS=24 smaller than res_max_natoms = max([len(res.atoms) for res in u.residues]).
what happened?