From 3d97c1910fff8467550596b4307699fd365891c0 Mon Sep 17 00:00:00 2001 From: Timothy Click Date: Thu, 14 Feb 2019 09:54:49 +0800 Subject: [PATCH] Deleted unused topology attributes. Signed-off-by: Timothy Click --- src/fluctmatch/models/topattrs.py | 69 ------------------------------- 1 file changed, 69 deletions(-) delete mode 100644 src/fluctmatch/models/topattrs.py diff --git a/src/fluctmatch/models/topattrs.py b/src/fluctmatch/models/topattrs.py deleted file mode 100644 index 61acd58..0000000 --- a/src/fluctmatch/models/topattrs.py +++ /dev/null @@ -1,69 +0,0 @@ -# -*- coding: utf-8 -*- -# -# python-fluctmatch - -# Copyright (c) 2019 Timothy H. Click, Ph.D. -# -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without -# modification, are permitted provided that the following conditions are met: -# -# Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# -# Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation -# and/or other materials provided with the distribution. -# -# Neither the name of the author nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE -# ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL -# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR -# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER -# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, -# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE -# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -# -# Timothy H. Click, Nixon Raj, and Jhih-Wei Chu. -# Simulation. Meth Enzymology. 578 (2016), 327-342, -# Calculation of Enzyme Fluctuograms from All-Atom Molecular Dynamics -# doi:10.1016/bs.mie.2016.05.024. - -from collections import defaultdict -from typing import ClassVar, Iterable, List, Mapping, Union - -import numpy as np -from MDAnalysis.core.groups import Atom, Residue, Segment, ComponentBase -from MDAnalysis.core.topologyattrs import Atomtypes - - -class XplorTypes(Atomtypes): - """String types for atoms used for XPLOR-PSF.""" - attriname: ClassVar[str] = "xplortypes" - singular: ClassVar[str] = "xplortype" - target_classes: ClassVar[List[ComponentBase]] = [Atom, Residue, Segment] - per_object: ClassVar[str] = "atom" - transplants: ClassVar[Mapping[List]] = defaultdict(list) - - def __init__(self, values: Union[Iterable, np.ndarray], - guessed: bool=False): - super().__init__(values, guessed) - - -class NumTypes(Atomtypes): - """Number types for atoms used for PSF.""" - attriname: ClassVar[str] = "numtypes" - singular: ClassVar[str] = "numtype" - target_classes: ClassVar[List[ComponentBase]] = [Atom, Residue, Segment] - per_object: ClassVar[str] = "atom" - transplants: ClassVar[Mapping[List]] = defaultdict(list) - - def __init__(self, values: Union[Iterable, np.ndarray], - guessed: bool=False): - super().__init__(values, guessed)