From b7dc72a63a3cde6920dd48f4c7fc40174c86127c Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Tue, 31 Jul 2018 10:39:33 +0200
Subject: [PATCH] SCHWED-3472: Removed SM specific HHblits code.
---
modules/bindings/pymod/hhblits.py | 14 +-------------
1 file changed, 1 insertion(+), 13 deletions(-)
diff --git a/modules/bindings/pymod/hhblits.py b/modules/bindings/pymod/hhblits.py
index 7ad416987..eacdcc50e 100644
--- a/modules/bindings/pymod/hhblits.py
+++ b/modules/bindings/pymod/hhblits.py
@@ -429,17 +429,6 @@ def ParseHHM(profile):
return profile_dict
-def EstimateMemConsumption():
- """
- Estimate the memory needed by HHblits. By default it uses not more than 3G.
- Also for small sequences it already uses quite some memnmory (46AA, 1.48G).
- And since the memory consumption could depend on the iterative search runs,
- how many hits are found in each step, we just go with 4G, here.
-
- :return: Assumed memory consumtion
- :rtype: (:class:`float`, :class:`str`)
- """
- return 4.0, 'G'
class HHblits:
"""
@@ -459,7 +448,6 @@ class HHblits:
:param working_dir: Directory for temporary files. Will be created if not
present but **not** automatically deleted.
:type working_dir: :class:`str`
-
"""
OUTPUT_PREFIX = 'query_hhblits'
def __init__(self, query, hhsuite_root, hhblits_bin=None, working_dir=None):
@@ -736,7 +724,7 @@ class HHblits:
__all__ = ['HHblits', 'HHblitsHit', 'HHblitsHeader',
'ParseHHblitsOutput', 'ParseA3M', 'ParseHHM',
- 'ParseHeaderLine', 'EstimateMemConsumption']
+ 'ParseHeaderLine']
# LocalWords: HHblits MSA hhblits hhtools PSIPRED addss param nrdb str mact
# LocalWords: cpu hhm func ParseHHblitsOutput ss pred conf msa hhsuite dir
--
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