diff --git a/deeprank/features/FullPSSM.py b/deeprank/features/FullPSSM.py index ec88b0fd..1c641097 100644 --- a/deeprank/features/FullPSSM.py +++ b/deeprank/features/FullPSSM.py @@ -120,7 +120,7 @@ def read_PSSM_data(self): self.pssm_res_id = np.array(raw_data)[:, :3] self.pssm_res_id = [(r[0], int(r[1]), r[2]) for r in self.pssm_res_id] - self.pssm_data = np.array(raw_data)[:, 3:].astype(np.float) + self.pssm_data = np.array(raw_data)[:, 3:].astype(np.float32) # new format with ≥2 files (each chain has one file) # and aligned mapping and IC (i.e. the iScore format) @@ -148,9 +148,9 @@ def read_PSSM_data(self): rd = np.array(raw_data)[1:, :2] rd = [(chainID, int(r[0]), resmap[r[1]]) for r in rd] if self.out_type == 'pssmvalue': - pd = np.array(raw_data)[1:, 4:-1].astype(np.float) + pd = np.array(raw_data)[1:, 4:-1].astype(np.float32) else: - pd = np.array(raw_data)[1:, -1].astype(np.float) + pd = np.array(raw_data)[1:, -1].astype(np.float32) pd = pd.reshape(pd.shape[0], -1) if iiter == 0: diff --git a/deeprank/learn/rankingMetrics.py b/deeprank/learn/rankingMetrics.py index 8fadb17f..33f242ed 100644 --- a/deeprank/learn/rankingMetrics.py +++ b/deeprank/learn/rankingMetrics.py @@ -47,7 +47,7 @@ def success(rs): """ success = np.cumsum(rs) > 0 - return success.astype(np.int) + return success.astype(np.int32) def avprec(rs): diff --git a/deeprank/tools/sasa.py b/deeprank/tools/sasa.py index e3b262eb..37e2cdaf 100644 --- a/deeprank/tools/sasa.py +++ b/deeprank/tools/sasa.py @@ -58,8 +58,8 @@ def get_residue_center(self, chain1='A', chain2='B'): resA = np.array(sql.get('resSeq,resName', chainID=chain1)) resB = np.array(sql.get('resSeq,resName', chainID=chain2)) - resSeqA = np.unique(resA[:, 0].astype(np.int)) - resSeqB = np.unique(resB[:, 0].astype(np.int)) + resSeqA = np.unique(resA[:, 0].astype(np.int32)) + resSeqB = np.unique(resB[:, 0].astype(np.int32)) self.xyz = {} @@ -106,14 +106,14 @@ def get_residue_carbon_beta(self, chain1='A', chain2='B'): chainID=chain2)) sql._close() - assert len(resA[:, 0].astype(np.int).tolist()) == len( - np.unique(resA[:, 0].astype(np.int)).tolist()) - assert len(resB[:, 0].astype(np.int).tolist()) == len( - np.unique(resB[:, 0].astype(np.int)).tolist()) + assert len(resA[:, 0].astype(np.int32).tolist()) == len( + np.unique(resA[:, 0].astype(np.int32)).tolist()) + assert len(resB[:, 0].astype(np.int32).tolist()) == len( + np.unique(resB[:, 0].astype(np.int32)).tolist()) self.xyz = {} - self.xyz[chain1] = resA[:, 2:].astype(np.float) - self.xyz[chain2] = resB[:, 2:].astype(np.float) + self.xyz[chain1] = resA[:, 2:].astype(np.float32) + self.xyz[chain2] = resB[:, 2:].astype(np.float32) self.resinfo = {} self.resinfo[chain1] = resA[:, :2] diff --git a/deeprank/utils/cal_hitrate_successrate.py b/deeprank/utils/cal_hitrate_successrate.py index ef424f47..13e17999 100644 --- a/deeprank/utils/cal_hitrate_successrate.py +++ b/deeprank/utils/cal_hitrate_successrate.py @@ -103,9 +103,9 @@ def evaluate(data): for caseID, df_one_case in df_grped: df_sorted = df_one_case.sort_values(by=M, ascending=True) hitrate.extend(rankingMetrics.hitrate( - df_sorted['target'].astype(np.int))) + df_sorted['target'].astype(np.int32))) success.extend(rankingMetrics.success( - df_sorted['target'].astype(np.int))) + df_sorted['target'].astype(np.int32))) caseIDs.extend([caseID] * len(df_one_case)) # success =[0, 0, 1, 1, 1,...]: starting from rank 3 this case is a success