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PyModSim Version 1.0
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================================================================================
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PyModSim is a standalone *Python* package to create protein homology models from
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a sequence using **AlphaFold**, refine protein models using **MODELLER**, and
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standardize the orientation of protein models using **PPM**.
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**PyModSim** is hosted in GitHub at:
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<https://github.com/rlvandenbroek/pymodsim>
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You can download any version of **PyModSim** by cloning the repository to your
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local machine using git.
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You will need to create a free personal account at github and send
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and e-mail to: [r.l.van.den.broek@umail.leidenuniv.nl](r.l.van.den.broek@umail.leidenuniv.nl)
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requesting access to the code. After request processing from us you will be
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given access to the free repository.
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To install **PyModSim** follow these steps:
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0. Install/prepare all **PyModSim** dependencies:
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Python 3.X (extensively tested on Python 3.10)
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Python modules:
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- modeller 10.2 - (https://salilab.org/modeller/release.html)
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AlphaFold 2.0 - (https://github.com/deepmind/alphafold)
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PPM 3.0 - (https://console.cloud.google.com/storage/browser/opm-assets/ppm3_code)
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1. Clone **PyModSim** for Python 3.X with the *modeller* module:
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git clone https://username@github.com/rlvandenbroek/pymodsim.git
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Make sure to change *username* to the one you have created at
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github.
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2. The previous command will create a *pymodsim* directory. Now you
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have to tell your operating system how to find that folder. You
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achieve this by declaring the location of the directory in a .bashrc
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file .cshrc or .zshrc file in your home folder. An example of what you will
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have to include in your .bashrc file follows:
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export PYMODSIM=/home/username/software/pymodsim
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export PATH=$PYMODSIM:$PATH
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or if your shell is csh then in your .cshrc file you can add:
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setenv PYMODSIM /home/username/software/pymodsim
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set path = ($path $PYMODSIM)
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Notice that I have cloned *pymodsim* in the software folder in my
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home folder, you will have to adapt this to wherever it is that you
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downloaded your *pymodsim* to.
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After including the route to your *pymodsim* directory in your
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.bashrc file make sure to issue the command:
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source .bashrc
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or open a new terminal.
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To check if you have defined the route to the *pymodsim* directory
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correctly try to run the main program called pymodsim in a terminal:
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pymodsim -h
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You should obtain the following help output:
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usage: pymodsim [-h] [-v] [-n NSTEP] [-s SEQUENCE] [-p PDB] [-N NTERM] [-C CTERM] [-l LOOP] [-f LOOP_FILL]
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[-t TOPOLOGY]
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== Create prepared homology models given a sequence. ==
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options:
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-h, --help show this help message and exit
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-v, --version show program's version number and exit
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-n NSTEP, --nstep NSTEP
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PyModSim steps you wish to execute. This allowes you modify the model preparation steps -
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see documentation Options: (0) Full, (1) Homology|AlphaFold, (2) ModPrep|MODELLER, (3)
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Orientation|PPM
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-s SEQUENCE, --seq SEQUENCE
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Name of the sequence for which to create an homology model. -s is only required if -n = 0,
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1 or 2. Use the fasta extension. (example: -s myseq.fasta)
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-p PDB, --pdb PDB Name of the protein to process. -p is only required if -n = 2 or 3. Use the pdb extension.
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(example: -p myprot.pdb)
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-N NTERM, --Nterm NTERM
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Residue number at which to cut the N-terminus. Note: the chain up AND including the given
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residue will be removed. -N is only used if -n = 2. If you wish to use the default cutoff,
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don't specify -N. If you wish not to cut the N-term: set -N = 0
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-C CTERM, --Cterm CTERM
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Residue number at which to cut the C-terminus. Note: the chain from AND including the given
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residue will be removed. -C is only used if -n = 2. If you wish to use the default cutoff,
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don't specify -C. If you wish not to cut the C-term: set -C = 0
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-l LOOP, --loop LOOP Residue numbers at which to cut loop(s). Define the first and last residue of the loop you
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wish to cut ('-' delimited) If there are multiple loops to cut, delimit the loop cuts with
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a ',' (example: -l 101-131,230-250). If you do not with to cut any loops: set -l = 0
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-f LOOP_FILL, --loop_fill LOOP_FILL
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Amount of Å per AA to fill cut loops. The total distance is calculated from the coordinates
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of the remaining residues. The AA contour length is 3.4-4.0 Å, To allow for flexibility in
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the loop, 2.0 Å/AA (default) is suggested. (example: -f 2.0)
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-t TOPOLOGY, --topology TOPOLOGY
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Indicate the topology of the N-term within the protein structure. 'out': extracellular
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N-term (default), 'in': intracellular N-term.
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3. Updates are very easy thanks to the git versioning system. Once
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**PyModSim** has been downloaded (cloned) into its own *pymodsim* folder
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you just have to move to it and pull the newest changes:
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cd /home/username/software/pymodsim
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git pull
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5. To make sure that your AlphaFold and PPM installation is understood by
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**PyModSim** you will need to specify the path to where the sofware is
114-
installed in your system. To do this you will need to edit the
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settings.py file with any text editor (“vi” and “emacs” are common
116-
options in the unix environment). Make sure that only one line is
117-
uncommented, looking like: PPM_PATH = /apps/PPM_3.0 Provided that in
118-
your case PPM is installed in /apps. The program
119-
will prepend this line to the binaries names, so calling
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“/apps/PPM_3.0/immers should point to that binary.
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### Auxiliary Modules
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- **recipes.py**. Applies step by step instructions for carrying a
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modeling step.
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- **broker.py**. Proxy for printing messages
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- **settings.py**. This modules sets up the main environment variables needed
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to run the calculation, for example, the path to the AlphaFold and PPM binaries.
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### Execution Modules
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- **commands.py**. Defines the Commands and Wrapper objects. Commands will
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load the objects, recipes, and run them. Wrapper is a proxy for the
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commands. When a recipe entry is sent to it this returns the command to be run.
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- **modprep.py**. Runs commands using the *modeller* module.
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### Executable
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- **pymodsim** The main program to call which sends the run to a cluster.
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PyModSim Version 1.0
2+
================================================================================
3+
4+
PyModSim is a standalone *Python* package to create protein homology models from
5+
a sequence using **AlphaFold**, refine protein models using **MODELLER**, and
6+
standardize the orientation of protein models using **PPM**.
7+
8+
**PyModSim** is hosted in GitHub at:
9+
10+
<https://github.com/rlvandenbroek/pymodsim>
11+
12+
You can download any version of **PyModSim** by cloning the repository to your
13+
local machine using git.
14+
15+
You will need to create a free personal account at github and send
16+
and e-mail to: [r.l.van.den.broek@umail.leidenuniv.nl](r.l.van.den.broek@umail.leidenuniv.nl)
17+
requesting access to the code. After request processing from us you will be
18+
given access to the free repository.
19+
20+
To install **PyModSim** follow these steps:
21+
22+
0. Install/prepare all **PyModSim** dependencies:
23+
24+
Python 3.X (extensively tested on Python 3.10)
25+
Python modules:
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- modeller 10.2 (https://salilab.org/modeller/release.html)
27+
AlphaFold 2.0 - (https://github.com/deepmind/alphafold)
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PPM 3.0 - (https://console.cloud.google.com/storage/browser/opm-assets/ppm3_code)
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1. Clone **PyModSim** for Python 3.X with the *modeller* module:
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git clone https://username@github.com/rlvandenbroek/pymodsim.git
33+
34+
Make sure to change *username* to the one you have created at
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github.
36+
37+
2. The previous command will create a *pymodsim* directory. Now you
38+
have to tell your operating system how to find that folder. You
39+
achieve this by declaring the location of the directory in a .bashrc
40+
file .cshrc or .zshrc file in your home folder. An example of what you will
41+
have to include in your .bashrc file follows:
42+
43+
export PYMODSIM=/home/username/software/pymodsim
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export PATH=$PYMODSIM:$PATH
45+
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or if your shell is csh then in your .cshrc file you can add:
47+
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setenv PYMODSIM /home/username/software/pymodsim
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set path = ($path $PYMODSIM)
50+
51+
Notice that I have cloned *pymodsim* in the software folder in my
52+
home folder, you will have to adapt this to wherever it is that you
53+
downloaded your *pymodsim* to.
54+
55+
After including the route to your *pymodsim* directory in your
56+
.bashrc file make sure to issue the command:
57+
58+
source .bashrc
59+
60+
or open a new terminal.
61+
62+
To check if you have defined the route to the *pymodsim* directory
63+
correctly try to run the main program called pymodsim in a terminal:
64+
65+
pymodsim -h
66+
67+
You should obtain the following help output:
68+
69+
usage: pymodsim [-h] [-v] [-n NSTEP] [-s SEQUENCE] [-p PDB] [-N NTERM] [-C CTERM] [-l LOOP]
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[-f LOOP_FILL] [-t TOPOLOGY] [-c CHAIN]
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== Create prepared homology models given a sequence. ==
73+
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options:
75+
-h, --help show this help message and exit
76+
-v, --version show program's version number and exit
77+
-n NSTEP, --nstep NSTEP
78+
PyModSim steps you wish to execute. This allowes you modify the
79+
model preparation steps - see documentation Options: (0) Full, (1)
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Homology|AlphaFold, (2) ModPrep|MODELLER, (3) Orientation|PPM, and
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(23) ModPrep+Orientation
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-s SEQUENCE, --seq SEQUENCE
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Name of the sequence for which to create an homology model. -s is
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only required if -n = 0, 1 or 2. Use the fasta extension. (example:
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-s myseq.fasta)
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-p PDB, --pdb PDB Name of the protein to process. -p is only required if -n = 2 or 3.
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Use the pdb extension. (example: -p myprot.pdb)
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-N NTERM, --Nterm NTERM
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Residue number at which to cut the N-terminus. Note: the chain up
90+
AND including the given residue will be removed. -N is only used if
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-n = 2. If you wish to use the default cutoff, don't specify -N. If
92+
you wish not to cut the N-term: set -N = 0
93+
-C CTERM, --Cterm CTERM
94+
Residue number at which to cut the C-terminus. Note: the chain from
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AND including the given residue will be removed. -C is only used if
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-n = 2. If you wish to use the default cutoff, don't specify -C. If
97+
you wish not to cut the C-term: set -C = 0
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-l LOOP, --loop LOOP Residue numbers at which to cut loop(s). Define the first and last
99+
residue of the loop you wish to cut ('-' delimited) If there are
100+
multiple loops to cut, delimit the loop cuts with a ',' (example: -l
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101-131,230-250). If you do not with to cut any loops: set -l = 0
102+
-f LOOP_FILL, --loop_fill LOOP_FILL
103+
Amount of Å per AA to fill cut loops. The total distance is
104+
calculated from the coordinates of the remaining residues. The AA
105+
contour length is 3.4-4.0 Å, To allow for flexibility in the loop,
106+
2.0 Å/AA (default) is suggested. (example: -f 2.0)
107+
-t TOPOLOGY, --topology TOPOLOGY
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Indicate the topology of the N-term within the protein structure.
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'out': extracellular N-term (default), 'in': intracellular N-term.
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-c CHAIN, --chain CHAIN
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Only use if -n = 3 (i.e. only PPM). If more than 1 chain, add a
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comma-seperated list of the chain identifiers. (example: -c A,B,C)
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3. Updates are very easy thanks to the git versioning system. Once
115+
**PyModSim** has been downloaded (cloned) into its own *pymodsim* folder
116+
you just have to move to it and pull the newest changes:
117+
118+
cd /home/username/software/pymodsim
119+
git pull
120+
121+
5. To make sure that your AlphaFold and PPM installation is understood by
122+
**PyModSim** you will need to specify the path to where the sofware is
123+
installed in your system. To do this you will need to edit the
124+
settings.py file with any text editor (“vi” and “emacs” are common
125+
options in the unix environment). Make sure that only one line is
126+
uncommented, looking like: PPM_PATH = /apps/PPM_3.0 Provided that in
127+
your case PPM is installed in /apps. The program
128+
will prepend this line to the binaries names, so calling
129+
“/apps/PPM_3.0/immers should point to that binary.
130+
131+
132+
### Auxiliary Modules
133+
134+
- **recipes.py**. Applies step by step instructions for carrying a
135+
modeling step.
136+
- **broker.py**. Proxy for printing messages
137+
- **settings.py**. This modules sets up the main environment variables needed
138+
to run the calculation, for example, the path to the AlphaFold and PPM binaries.
139+
140+
141+
### Execution Modules
142+
143+
- **commands.py**. Defines the Commands and Wrapper objects. Commands will
144+
load the objects, recipes, and run them. Wrapper is a proxy for the
145+
commands. When a recipe entry is sent to it this returns the command to be run.
146+
- **modprep.py**. Runs commands using the *modeller* module.
147+
148+
### Executable
149+
150+
- **pymodsim** The main program to call which sends the run to a cluster.

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