Secondary structure determination

.travis.yml

@@ -28,12 +28,14 @@ env:
     - SETUP_CMD="${PYTEST_FLAGS}"
     - BUILD_CMD="pip install -e package/ && (cd testsuite/ && python setup.py build)"
     - CONDA_MIN_DEPENDENCIES="mmtf-python mock six biopython networkx cython matplotlib scipy griddataformats hypothesis gsd codecov"
-    - CONDA_DEPENDENCIES="${CONDA_MIN_DEPENDENCIES} seaborn>=0.7.0 clustalw=2.1 netcdf4 scikit-learn joblib>=0.12 chemfiles"
+    - CONDA_DEPENDENCIES="${CONDA_MIN_DEPENDENCIES} seaborn>=0.7.0 clustalw=2.1 netcdf4 scikit-learn joblib>=0.12 chemfiles mdtraj"
     - CONDA_CHANNELS='biobuilds conda-forge'
     - CONDA_CHANNEL_PRIORITY=True
     - PIP_DEPENDENCIES="duecredit parmed"
     - NUMPY_VERSION=stable
     - INSTALL_HOLE="true"
+    - INSTALL_DSSP="true"
+    - INSTALL_STRIDE="true"
     - CYTHON_TRACE_NOGIL=1
 
   matrix:
@@ -55,6 +57,8 @@ matrix:
            BUILD_DOCS=true
            BUILD_CMD="cd ${TRAVIS_BUILD_DIR}/package && python setup.py build_ext --inplace"
            INSTALL_HOLE="false"
+           INSTALL_DSSP="false"
+           INSTALL_STRIDE="false"
            PIP_DEPENDENCIES="${PIP_DEPENDENCIES} sphinx==1.8.5 sphinx-sitemap sphinx_rtd_theme"
 
     - env: NAME="Lint"
@@ -64,6 +68,8 @@ matrix:
            BUILD_CMD=""
            CONDA_DEPENDENCIES=""
            INSTALL_HOLE="false"
+           INSTALL_DSSP="false"
+           INSTALL_STRIDE="false"
 
     - env: NAME="python 2.7"
            PYTHON_VERSION=2.7
@@ -97,6 +103,8 @@ matrix:
            PIP_DEPENDENCIES=""
            CONDA_DEPENDENCIES=${CONDA_MIN_DEPENDENCIES}
            INSTALL_HOLE="false"
+           INSTALL_DSSP="false"
+           INSTALL_STRIDE="false"
            CODECOV="true" SETUP_CMD="${PYTEST_FLAGS} --cov=MDAnalysis"
 
   allow_failures:
@@ -120,6 +128,16 @@ install:
         HOLE_BINDIR="${HOME}/hole2/exe"; \
         export PATH=${PATH}:${HOLE_BINDIR}; \
     fi
+    if [[ $INSTALL_DSSP == 'true' ]]; then \
+        bash ./maintainer/install_dssp.sh $TRAVIS_OS_NAME "${HOME}"; \
+        DSSP_BINDIR="${HOME}/dssp-3.1.4"; \
+        export PATH=${PATH}:${DSSP_BINDIR}; \
+    fi
+    if [[ $INSTALL_STRIDE == 'true' ]]; then \
+        bash ./maintainer/install_stride.sh $TRAVIS_OS_NAME "${HOME}"; \
+        STRIDE_BINDIR="${HOME}/stride"; \
+        export PATH=${PATH}:${STRIDE_BINDIR}; \
+    fi
   - git clone git://github.com/astropy/ci-helpers.git
   - source ci-helpers/travis/setup_conda.sh
   - eval $BUILD_CMD

maintainer/install_dssp.sh

@@ -0,0 +1,127 @@
+#!/usr/bin/env bash
+#
+# Written by Lily Wang, 2020
+#
+# This script is placed into the Public Domain using the CC0 1.0 Public Domain
+# Dedication https://creativecommons.org/publicdomain/zero/1.0/
+#
+#
+# NOTE: IF YOU RUN THIS SCRIPT YOU MUST BE ABLE TO COMPLY WITH THE DSSP
+#       LICENSE BELOW.
+#
+# Boost Software License - Version 1.0 - August 17th, 2003 
+# Permission is hereby granted, free of charge, to any person or organization 
+# obtaining a copy of the software and accompanying documentation covered by 
+# this license (the "Software") to use, reproduce, display, distribute, execute, 
+# and transmit the Software, and to prepare derivative works of the Software, 
+# and to permit third-parties to whom the Software is furnished to do so, all 
+# subject to the following:
+
+# The copyright notices in the Software and this entire statement, including 
+# the above license grant, this restriction and the following disclaimer, 
+# must be included in all copies of the Software, in whole or in part, and all 
+# derivative works of the Software, unless such copies or derivative works are 
+# solely in the form of machine-executable object code generated by a source 
+# language processor.
+
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 
+# FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT 
+# SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE FOR 
+# ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE, ARISING 
+# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS 
+# IN THE SOFTWARE. 
+# 
+#
+# Install DSSP from https://swift.cmbi.umcn.nl/gv/dssp/
+#
+# arguments
+#    OSNAME : linux | darwin
+#    PREFIX : "path/to/installdir"
+#
+# PREFIX can be relative to CWD or an absolute path; it will be created
+# and DSSP unpacked under PREFIX (the tar file contains "dssp-xx.xx.xx/...")
+#
+#
+
+
+set -o errexit -o nounset
+
+SCRIPT=$(basename $0)
+
+
+DOWNLOAD_URL='https://github.com/cmbi/dssp/archive/3.1.4.tar.gz'
+TARFILE='3.1.4.tar.gz'
+
+
+# path to dir with executables in the current HOLE distribution
+DSSP_EXE_DIR=dssp-3.1.4
+
+function die () {
+    local msg="$1" err=$2
+    echo "[${SCRIPT}] ERROR: $msg [$err]"
+    exit $err
+}
+
+function is_native_executable () {
+    local filename="$1" OSNAME="$2"
+    file "${filename}" | grep -qi ${OFORMAT}
+    return $?
+}
+
+OSNAME="$1"
+case "$OSNAME" in
+    Linux|linux)
+	OSNAME=Linux
+	OFORMAT=Linux
+	sudo apt-get -y install libboost-all-dev autoconf automake autotools-dev
+	;;
+    OSX|osx|Darwin|darwin)
+	OSNAME=Darwin
+	OFORMAT="Mach-O"
+	;;
+    *)
+	die "OS '${OSNAME}' not supported." 10;;
+esac
+
+
+PREFIX="$2"
+test -n "$PREFIX" || die "missing argument PREFIX (installation directory)" 10
+
+#------------------------------------------------------------
+# start installation
+#------------------------------------------------------------
+
+mkdir -p "$PREFIX" && cd "$PREFIX" || die "Failed to create and cd to $PREFIX" 1
+if ! test -f ${TARFILE}; then
+    echo "Downloading ${TARFILE} from ${DOWNLOAD_URL}..."
+    # fixing curl on travis/anaconda, see http://stackoverflow.com/a/31060428/334357
+    export CURL_CA_BUNDLE=/etc/ssl/certs/ca-certificates.crt
+    curl -L ${DOWNLOAD_URL} -o ${TARFILE} || \
+    die "Failed to download ${TARFILE} from ${DOWNLOAD_URL}" 1
+fi
+
+# only install the executables in DSSP_EXE_DIR 
+tar xvf ${TARFILE} ${DSSP_EXE_DIR} || die "Failed 'tar xvf ${TARFILE} ${DSSP_EXE_DIR}'" 1
+
+MDA_DSSP_BINDIR="${PWD}/${DSSP_EXE_DIR}"
+DSSP_EXE="${MDA_DSSP_BINDIR}/mkdssp"
+
+cd $MDA_DSSP_BINDIR
+
+echo "Configuring"
+./autogen.sh
+./configure
+echo "Making"
+make
+
+test -f "${DSSP_EXE}" || die "mkdssp executable ${DSSP_EXE} not installed" 2
+is_native_executable ${DSSP_EXE} ${OFORMAT} || \
+    { file ${DSSP_EXE}; \
+      die "${DSSP_EXE} will not run on ${OSNAME} (object format ${OFORMAT})" 3; }
+
+echo "mkdssp was installed into ${MDA_DSSP_BINDIR}"
+echo ">>> export PATH=\${PATH}:${MDA_DSSP_BINDIR}"
+
+# repeat this line in .travis.yml
+export PATH=${PATH}:${MDA_DSSP_BINDIR}

maintainer/install_stride.sh

@@ -0,0 +1,117 @@
+#!/usr/bin/env bash
+#
+# Written by Lily Wang, 2020
+#
+# This script is placed into the Public Domain using the CC0 1.0 Public Domain
+# Dedication https://creativecommons.org/publicdomain/zero/1.0/
+#
+# NOTE: IF YOU RUN THIS SCRIPT YOU MUST BE ABLE TO COMPLY WITH THE DSSP
+#       LICENSE BELOW.
+#
+# All rights reserved, whether the	whole or part	of the program is
+# concerned. Permission to use, copy, and modify	this software and its
+# documentation is	granted	for academic use, provided that:
+#
+# i. this copyright notice appears in all copies of the	software and
+# related documentation;
+#
+# ii. the reference given below (Frishman and Argos, 1995) must be
+# cited in any publication of scientific results based in part or
+# completely	on the use of the program;
+#
+# iii. bugs will be reported to the authors.
+#
+# The use of the  software in  commercial	 activities  is	 not  allowed
+# without a prior written commercial license agreement.
+#
+# IF YOU USE STRIDE IN PUBLISHED WORK, PLEASE CITE:
+#
+# Frishman, D and Argos, P. (1995) Knowledge-based secondary structure
+# assignment. Proteins: structure, function and genetics, 23,  
+# 566-579.
+#
+# The source code is available at http://webclu.bio.wzw.tum.de/stride/
+#
+# arguments
+#    OSNAME : linux | darwin
+#    PREFIX : "path/to/installdir"
+#
+# PREFIX can be relative to CWD or an absolute path; it will be created
+# and STRIDE unpacked under PREFIX/stride.
+#
+#
+
+
+set -o errexit -o nounset
+
+SCRIPT=$(basename $0)
+
+
+DOWNLOAD_URL='http://webclu.bio.wzw.tum.de/stride/stride.tar.gz'
+TARFILE='stride.tar.gz'
+
+
+# path to dir with executables in the current HOLE distribution
+STRIDE_EXE_DIR=stride
+
+function die () {
+    local msg="$1" err=$2
+    echo "[${SCRIPT}] ERROR: $msg [$err]"
+    exit $err
+}
+
+function is_native_executable () {
+    local filename="$1" OSNAME="$2"
+    file "${filename}" | grep -qi ${OFORMAT}
+    return $?
+}
+
+OSNAME="$1"
+case "$OSNAME" in
+    Linux|linux)
+	OSNAME=Linux
+	OFORMAT=Linux
+	;;
+    OSX|osx|Darwin|darwin)
+	OSNAME=Darwin
+	OFORMAT="Mach-O"
+	;;
+    *)
+	die "OS '${OSNAME}' not supported." 10;;
+esac
+
+
+PREFIX="$2"
+test -n "$PREFIX" || die "missing argument PREFIX (installation directory)" 10
+PREFIX="${PREFIX}/${STRIDE_EXE_DIR}"
+
+#------------------------------------------------------------
+# start installation
+#------------------------------------------------------------
+
+mkdir -p "$PREFIX" && cd "$PREFIX" || die "Failed to create and cd to $PREFIX" 1
+if ! test -f ${TARFILE}; then
+    echo "Downloading ${TARFILE} from ${DOWNLOAD_URL}..."
+    # fixing curl on travis/anaconda, see http://stackoverflow.com/a/31060428/334357
+    export CURL_CA_BUNDLE=/etc/ssl/certs/ca-certificates.crt
+    curl -L ${DOWNLOAD_URL} -o ${TARFILE} || \
+    die "Failed to download ${TARFILE} from ${DOWNLOAD_URL}" 1
+fi
+
+# only install the executables in STRIDE_EXE_DIR 
+tar xvf ${TARFILE} || die "Failed 'tar xvf ${TARFILE}'" 1
+STRIDE_EXE="${PWD}/stride"
+
+echo "Making"
+make
+
+test -f "${STRIDE_EXE}" || die "stride executable ${STRIDE_EXE} not installed" 2
+is_native_executable ${STRIDE_EXE} ${OFORMAT} || \
+    { file ${STRIDE_EXE}; \
+      die "${STRIDE_EXE} will not run on ${OSNAME} (object format ${OFORMAT})" 3; }
+
+echo "stride was installed into ${PWD}"
+echo ">>> export PATH=\${PATH}:${PWD}"
+
+# repeat this line in .travis.yml
+export PATH=${PATH}:${PWD}

package/MDAnalysis/analysis/secondary_structure/__init__.py

@@ -0,0 +1,27 @@
+# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
+# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
+#
+# MDAnalysis --- https://www.mdanalysis.org
+# Copyright (c) 2006-2020 The MDAnalysis Development Team and contributors
+# (see the file AUTHORS for the full list of names)
+#
+# Released under the GNU Public Licence, v2 or any higher version
+#
+# Please cite your use of MDAnalysis in published work:
+#
+# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
+# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
+# MDAnalysis: A Python package for the rapid analysis of molecular dynamics
+# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th
+# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.
+# doi: 10.25080/majora-629e541a-00e
+#
+# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
+# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
+# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
+#
+
+from __future__ import absolute_import
+
+from .dssp import DSSP
+from .wrapper import DSSPWrapper, STRIDEWrapper