Several small changes for improving installation.

There is not any algorithmic changes in this version.
However, I made the following changes to make Python
and Docker installations better:
1-I changed base ubuntu from 20.04 to 22.04.
2-dssp 4.0 in Ubuntu 22.04 have a shitty requirement
 of CRYST record in the pdb file. Therefore, I manually
 installed dssp 3.
3-I needed at least Python 3.9 for importlib.resources
  and I made the required changes both in setup.py and
  Dockerfile for that.

Dockerfile

-FROM ubuntu:20.04
+FROM ubuntu:22.04
 
 LABEL maintainer="Mustafa Tekpinar <tekpinar@buffalo.edu>"
 LABEL description="ESGEMME: Evolutionary and Structural Global Epistatic Model for predicting Mutational Effects."
 
+ENV DEBIAN_FRONTEND=noninteractive
+
 WORKDIR /home/tekpinar/research/lcqb
 ENV JET2_PATH=/home/tekpinar/research/lcqb/JET2
 ENV ESGEMME_PATH=/home/tekpinar/research/lcqb/ESGEMME
@@ -25,10 +27,13 @@ COPY ./demust/ ./demust/
 RUN apt-get update --fix-missing && \
 apt-get install -y --no-install-recommends apt-utils &&\
 apt-get install -y software-properties-common && \
+apt-get install -y autotools-dev && \
+apt-get install -y automake && \
 apt-get install -y build-essential && \
+apt-get install -y python3-dev && \
+apt-get install -y python3-pip && \
 apt-get install -y r-base r-base-core && \
 apt-get install -y muscle && \
-apt-get install -y dssp && \
 apt-get install -y default-jre && \
 apt-get install -y ncbi-blast+ && \
 apt-get install -y nano && \
@@ -36,16 +41,22 @@ apt-get install -y less && \
 apt-get install -y wget && \
 apt-get install csh && \
 apt-get install -y hmmer && \
+apt-get install -y libboost-all-dev && \
 apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
-
-RUN add-apt-repository ppa:deadsnakes/ppa
-RUN apt-get update --fix-missing && \
-apt-get -y install python3.9 &&\
-apt-get install -y python3-dev && \
-apt-get install -y python3-pip && \
-apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
-
 ###################################################################
+#Install dssp v.3 because v.4 has some incompatibilites with biotite.
+RUN wget https://github.com/cmbi/dssp/archive/refs/heads/master.zip
+RUN unzip -o master.zip 
+WORKDIR /home/tekpinar/research/lcqb/dssp-master/
+RUN ./autogen.sh
+RUN ./configure 
+RUN make
+RUN make install
+RUN ln -s /usr/local/bin/mkdssp /usr/local/bin/dssp
+WORKDIR /home/tekpinar/research/lcqb
+RUN rm -rf dssp-master/
+RUN rm -f master.zip
+
 RUN wget https://github.com/soedinglab/hh-suite/releases/download/v3.3.0/hhsuite-3.3.0-AVX2-Linux.tar.gz
 RUN mkdir hhsuite
 RUN mv hhsuite-3.3.0-AVX2-Linux.tar.gz hhsuite/
@@ -55,35 +66,35 @@ RUN tar xvfz hhsuite-3.3.0-AVX2-Linux.tar.gz
 ENV PATH="/home/tekpinar/research/lcqb/hhsuite/bin:/home/tekpinar/research/lcqb/hhsuite/scripts:$PATH"
 RUN rm -f hhsuite-3.3.0-AVX2-Linux.tar.gz
 
-RUN ln -s /usr/bin/python3.9 /usr/bin/python
-
 WORKDIR /home/tekpinar/research/lcqb
 RUN pip3 install -e ./ESGEMME/
 RUN pip3 install -e ./demust/
 
 RUN Rscript -e 'install.packages("seqinr", repos="http://cran.us.r-project.org", dependencies=TRUE)'
 
-
 #PLMC and EVcouplings installation for obtaining sequences.
 RUN wget https://github.com/debbiemarkslab/plmc/archive/refs/heads/master.zip
-RUN unzip master.zip
+RUN unzip -o master.zip
+
 WORKDIR /home/tekpinar/research/lcqb/plmc-master
+RUN pwd
 RUN make all-openmp32
 RUN cp bin/plmc /usr/local/bin/
 WORKDIR /home/tekpinar/research/lcqb
-RUN rm -r master.zip plmc-master
-RUN pip3 install install https://github.com/debbiemarkslab/EVcouplings/archive/develop.zip
+RUN rm -rf master.zip plmc-master
+RUN pip3 install https://github.com/debbiemarkslab/EVcouplings/archive/develop.zip
 
+# If run command on M1 Mac with macOS Monterey, you can remove sudo
 # Build command
 # sudo docker build -t tekpinar/esgemme-docker:v1.3.0 .
 # sudo docker login
 # sudo docker push tekpinar/esgemme-docker:v1.3.0 
 
 # Pull command on M1 Mac with macOS Monterey
-# docker pull tekpinar/esgemme-docker:v1.3.0
+# sudo docker pull tekpinar/esgemme-docker:v1.3.0
 
-# Run command on M1 Mac with macOS Monterey
-# docker run -i -t -v $(pwd) --platform linux/amd64 tekpinar/esgemme-docker:v1.3.0 /bin/bash
+# Run commands
+# sudo docker run -i -t -v $(pwd) --platform linux/amd64 tekpinar/esgemme-docker:v1.3.0 /bin/bash
 
 # Bind your current folder to a particular folder in docker. 
 # docker run -ti --rm --mount type=bind,source=$PWD,target=/home/tekpinar/research/myexample tekpinar/esgemme-docker:v1.3.0

setup.py

@@ -32,7 +32,7 @@ from esgemme import __version__ as cp_vers
 
 setup(name='esgemme',
       version=cp_vers,
-      description="A Python program to predict mutational effects of proteins.",
+      description="ESGEMME: A Python program to predict mutational effects of proteins.",
       long_description=open('README.md').read(),
       long_description_content_type="text/markdown",
       author="Mustafa Tekpinar",
@@ -46,12 +46,13 @@ setup(name='esgemme',
           'Operating System :: POSIX',
           'Programming Language :: Python :: 3',
           'Programming Language :: Python :: 3.9',
+          'Programming Language :: Python :: 3.10',
           'License :: OSI Approved :: MIT License',
           'Intended Audience :: Science/Research',
           'Topic :: Scientific/Engineering :: Bio-Informatics',
           'Topic :: Scientific/Engineering :: Chemistry'
           ],
-      python_requires='>=3.6',
+      python_requires='>=3.9',
       install_requires=[i for i in [l.strip() for l in open("requirements.txt").read().split('\n')] if i],
       # zip_safe=False,
       packages=[p for p in find_packages() if p != 'tests'],