From a8d7b5d22e8fe947a47b15574638ec2647114cc8 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Mon, 9 May 2022 14:28:40 +0200
Subject: [PATCH] lDDT: consistent use of ndarrays, also in case of empty
default values
---
modules/mol/alg/pymod/lddt.py | 24 ++++++++++++------------
1 file changed, 12 insertions(+), 12 deletions(-)
diff --git a/modules/mol/alg/pymod/lddt.py b/modules/mol/alg/pymod/lddt.py
index 40e98d90c..e58784bd4 100644
--- a/modules/mol/alg/pymod/lddt.py
+++ b/modules/mol/alg/pymod/lddt.py
@@ -841,10 +841,10 @@ class lDDTScorer:
"""Compute distance related members of lDDTScorer
"""
# init
- self._ref_indices = [[] for idx in range(self.n_atoms)]
- self._ref_distances = [[] for idx in range(self.n_atoms)]
- self._sym_ref_indices = [[] for idx in range(self.n_atoms)]
- self._sym_ref_distances = [[] for idx in range(self.n_atoms)]
+ self._ref_indices = [np.asarray([], dtype=np.int64) for idx in range(self.n_atoms)]
+ self._ref_distances = [np.asarray([], dtype=np.float64) for idx in range(self.n_atoms)]
+ self._sym_ref_indices = [np.asarray([], dtype=np.int64) for idx in range(self.n_atoms)]
+ self._sym_ref_distances = [np.asarray([], dtype=np.float64) for idx in range(self.n_atoms)]
# initialize positions with values far in nirvana. If a position is not
# set, it should be far away from any position in target (or at least
@@ -888,10 +888,10 @@ class lDDTScorer:
"""Select subset of contacts only covering intra-chain contacts
"""
# init
- self._ref_indices_sc = [[] for idx in range(self.n_atoms)]
- self._ref_distances_sc = [[] for idx in range(self.n_atoms)]
- self._sym_ref_indices_sc = [[] for idx in range(self.n_atoms)]
- self._sym_ref_distances_sc = [[] for idx in range(self.n_atoms)]
+ self._ref_indices_sc = [np.asarray([], dtype=np.int64) for idx in range(self.n_atoms)]
+ self._ref_distances_sc = [np.asarray([], dtype=np.float64) for idx in range(self.n_atoms)]
+ self._sym_ref_indices_sc = [np.asarray([], dtype=np.int64) for idx in range(self.n_atoms)]
+ self._sym_ref_distances_sc = [np.asarray([], dtype=np.float64) for idx in range(self.n_atoms)]
# start from overall contacts
ref_indices = self.ref_indices
@@ -920,10 +920,10 @@ class lDDTScorer:
"""Select subset of contacts only covering inter-chain contacts
"""
# init
- self._ref_indices_ic = [[] for idx in range(self.n_atoms)]
- self._ref_distances_ic = [[] for idx in range(self.n_atoms)]
- self._sym_ref_indices_ic = [[] for idx in range(self.n_atoms)]
- self._sym_ref_distances_ic = [[] for idx in range(self.n_atoms)]
+ self._ref_indices_ic = [np.asarray([], dtype=np.int64) for idx in range(self.n_atoms)]
+ self._ref_distances_ic = [np.asarray([], dtype=np.float64) for idx in range(self.n_atoms)]
+ self._sym_ref_indices_ic = [np.asarray([], dtype=np.int64) for idx in range(self.n_atoms)]
+ self._sym_ref_distances_ic = [np.asarray([], dtype=np.float64) for idx in range(self.n_atoms)]
# start from overall contacts
ref_indices = self.ref_indices
--
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