Old esgemme.py script became escott.py

Dockerfile

@@ -11,15 +11,15 @@ ENV PRESCOTT_PATH=/home/tekpinar/research/lcqb/PRESCOTT
 COPY ./JET2/ /usr/local/JET2
 COPY ./naccess2.1.1 /usr/local/naccess2.1.1
 
-COPY ./PRESCOTT/esgemme/esgemme.py ./PRESCOTT/esgemme/esgemme.py
-COPY ./PRESCOTT/esgemme/alphabets ./PRESCOTT/esgemme/alphabets
-COPY ./PRESCOTT/esgemme/__init__.py ./PRESCOTT/esgemme/__init__.py
+COPY ./PRESCOTT/prescott/escott.py ./PRESCOTT/prescott/escott.py
+COPY ./PRESCOTT/prescott/alphabets ./PRESCOTT/prescott/alphabets
+COPY ./PRESCOTT/prescott/__init__.py ./PRESCOTT/prescott/__init__.py
 COPY ./PRESCOTT/setup.py ./PRESCOTT/setup.py
 COPY ./PRESCOTT/requirements.txt ./PRESCOTT/requirements.txt
 COPY ./PRESCOTT/README.md ./PRESCOTT/README.md 
-COPY ./PRESCOTT/esgemme/pred.R ./PRESCOTT/esgemme/pred.R
-COPY ./PRESCOTT/esgemme/computePred.R ./PRESCOTT/esgemme/computePred.R
-COPY ./PRESCOTT/esgemme/default.conf ./PRESCOTT/esgemme/default.conf
+COPY ./PRESCOTT/prescott/pred.R ./PRESCOTT/prescott/pred.R
+COPY ./PRESCOTT/prescott/computePred.R ./PRESCOTT/prescott/computePred.R
+COPY ./PRESCOTT/prescott/default.conf ./PRESCOTT/prescott/default.conf
 COPY ./PRESCOTT/data/ ./PRESCOTT/data/
 COPY ./PRESCOTT/examples/ ./PRESCOTT/examples/
 COPY ./demust/ ./demust/
@@ -75,8 +75,8 @@ ENV PATH="/home/tekpinar/research/lcqb/hhsuite/bin:/home/tekpinar/research/lcqb/
 RUN rm -f hhsuite-3.3.0-AVX2-Linux.tar.gz
 
 WORKDIR /home/tekpinar/research/lcqb
-RUN sed -i s#/home/tekpinar/research/lcqb/JET2/matrix#/usr/local/JET2/matrix#g ./PRESCOTT/esgemme/default.conf
-RUN sed -i s#/home/tekpinar/research/lcqb/naccess2.1.1/naccess#/usr/local/naccess2.1.1/naccess#g ./PRESCOTT/esgemme/default.conf
+RUN sed -i s#/home/tekpinar/research/lcqb/JET2/matrix#/usr/local/JET2/matrix#g ./PRESCOTT/prescott/default.conf
+RUN sed -i s#/home/tekpinar/research/lcqb/naccess2.1.1/naccess#/usr/local/naccess2.1.1/naccess#g ./PRESCOTT/prescott/default.conf
 RUN pip3 install ./PRESCOTT/
 RUN pip3 install -e ./demust/
 
@@ -96,21 +96,21 @@ RUN pip3 install https://github.com/debbiemarkslab/EVcouplings/archive/develop.z
 
 # If run command on M1 Mac with macOS Monterey, you can remove sudo
 # Build command
-# sudo docker build -t tekpinar/esgemme-docker:v1.4.0 .
+# sudo docker build -t tekpinar/prescott-docker:v1.4.0 .
 # sudo docker login
-# sudo docker push tekpinar/esgemme-docker:v1.4.0 
+# sudo docker push tekpinar/prescott-docker:v1.4.0 
 
 # Pull command on M1 Mac with macOS Monterey
-# sudo docker pull tekpinar/esgemme-docker:v1.4.0
+# sudo docker pull tekpinar/prescott-docker:v1.4.0
 
 # Run commands
-# sudo docker run -i -t -v $(pwd) --platform linux/amd64 tekpinar/esgemme-docker:v1.4.0 /bin/bash
+# sudo docker run -i -t -v $(pwd) --platform linux/amd64 tekpinar/prescott-docker:v1.4.0 /bin/bash
 
 # Bind your current folder to a particular folder in docker.
 # In this way, you fall into the bash terminal of the docker image. 
-# docker run -ti --rm --mount type=bind,source=$PWD,target=/home/tekpinar/research/lcqb tekpinar/esgemme-docker:v1.4.0
+# docker run -ti --rm --mount type=bind,source=$PWD,target=/home/tekpinar/research/lcqb tekpinar/prescott-docker:v1.4.0
 
 #If you want to use the docker image like an executable file:
 # Please note that you must have aliBLAT.fasta and blat-af2.pdb inside your current folder and run this command!
-# sudo docker run --rm -v $PWD:/home/tekpinar/research/lcqb tekpinar/esgemme-docker:v1.4.0 esgemme aliBLAT.fasta -r input -f aliBLAT.fasta --pdbfile  blat-af2.pdb
+# sudo docker run --rm -v $PWD:/home/tekpinar/research/lcqb tekpinar/prescott-docker:v1.4.0 escott aliBLAT.fasta -r input -f aliBLAT.fasta --pdbfile  blat-af2.pdb
 

esgemme/__init__.py → prescott/__init__.py

 """
-Program Name: esgemme
+Program Name: PRESCOTT
 Author      : Mustafa TEKPINAR
 Copyright   : Mustafa TEKPINAR - Alessandra Carbone- 2022-2023
 Email       : tekpinar@buffalo.edu
 Purpose     : A Python program to predict mutational effects of proteins.
 """
 
-__all__ = ['esgemme']
+__all__ = ['prescott']
 
-__version__ = '1.3.0'
+__version__ = '1.4.0'