From fb808a244f789ebeb19a8e9a630c828d5eb4c7b9 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 26 Jul 2024 08:57:58 +0200
Subject: [PATCH] scoring: reduce compute time for GDT with minimal decrease in
accuracy
---
modules/mol/alg/pymod/scoring.py | 17 +++++++++++------
1 file changed, 11 insertions(+), 6 deletions(-)
diff --git a/modules/mol/alg/pymod/scoring.py b/modules/mol/alg/pymod/scoring.py
index 24a676fb9..52be442df 100644
--- a/modules/mol/alg/pymod/scoring.py
+++ b/modules/mol/alg/pymod/scoring.py
@@ -385,7 +385,7 @@ class Scorer:
self._rigid_n_target_not_mapped = None
self._rigid_transform = None
- self._gdt_window_sizes = [5, 7, 9, 12, 24, 36, 48]
+ self._gdt_window_sizes = [7, 9, 12, 24, 48]
self._gdt_05 = None
self._gdt_1 = None
self._gdt_2 = None
@@ -1477,7 +1477,8 @@ class Scorer:
"""
if self._gdt_05 is None:
N = list()
- for window_size in self._gdt_window_sizes:
+ wsizes = self._gdt_window_sizes + [len(self.rigid_mapped_model_pos)]
+ for window_size in wsizes:
n = GDT(self.rigid_mapped_model_pos,
self.rigid_mapped_target_pos,
window_size, 1000, 0.5)[0]
@@ -1501,7 +1502,8 @@ class Scorer:
"""
if self._gdt_1 is None:
N = list()
- for window_size in self._gdt_window_sizes:
+ wsizes = self._gdt_window_sizes + [len(self.rigid_mapped_model_pos)]
+ for window_size in wsizes:
n = GDT(self.rigid_mapped_model_pos,
self.rigid_mapped_target_pos,
window_size, 1000, 1.0)[0]
@@ -1526,7 +1528,8 @@ class Scorer:
"""
if self._gdt_2 is None:
N = list()
- for window_size in self._gdt_window_sizes:
+ wsizes = self._gdt_window_sizes + [len(self.rigid_mapped_model_pos)]
+ for window_size in wsizes:
n = GDT(self.rigid_mapped_model_pos,
self.rigid_mapped_target_pos,
window_size, 1000, 2.0)[0]
@@ -1550,7 +1553,8 @@ class Scorer:
"""
if self._gdt_4 is None:
N = list()
- for window_size in self._gdt_window_sizes:
+ wsizes = self._gdt_window_sizes + [len(self.rigid_mapped_model_pos)]
+ for window_size in wsizes:
n = GDT(self.rigid_mapped_model_pos,
self.rigid_mapped_target_pos,
window_size, 1000, 4.0)[0]
@@ -1573,7 +1577,8 @@ class Scorer:
"""
if self._gdt_8 is None:
N = list()
- for window_size in self._gdt_window_sizes:
+ wsizes = self._gdt_window_sizes + [len(self.rigid_mapped_model_pos)]
+ for window_size in wsizes:
n = GDT(self.rigid_mapped_model_pos,
self.rigid_mapped_target_pos,
window_size, 1000, 8.0)[0]
--
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