which: no dssp in PATH while running LipIDens on CentOS 7.X

The official logo – taken from the github site.

I’m trying to install Lipidens, a simulation assisted interpreter of lipid densities under my clean conda installation of python-3.7.3. My roadmap is first to load the module, then to create the environment, then to install dependencies.

$ > module load python-3.7.3
$ > git clone https://github.com/TBGAnsell/LipIDens
$ > cd LipIDens/
$ > conda create -n LipIDens python=3.9
## we log out, maybe run conda init to add conda to our shell
$ > conda activate LipIDens
 which python
~/.conda/envs/LipIDens/bin/python
 python
Python 3.9.7 (default, Sep 16 2021, 13:09:58) 
[GCC 7.5.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> exit()
## so everything looks correct
pip install -r requirements.txt 
Looking in indexes: https://pypi.org/simple, https://pypi.ngc.nvidia.com
Collecting kneebow
... here a log of downloads ...
Successfully built kneebow mdtraj p-tqdm python-louvain
Installing collected packages: six, pyparsing, numpy, dill, threadpoolctl, scipy, pytz, python-dateutil, ppft, pox, pillow, packaging, multiprocess, kiwisolver, joblib, fonttools, cycler, tqdm, scikit-learn, patsy, pathos, pandas, networkx, matplotlib, astunparse, statsmodels, python-louvain, pbr, p-tqdm, mdtraj, logomaker, kneebow, vermouth, seaborn, pylipid
Successfully installed astunparse-1.6.3 cycler-0.11.0 dill-0.3.4 fonttools-4.30.0 joblib-1.1.0 kiwisolver-1.4.0 kneebow-0.1.1 logomaker-0.8 matplotlib-3.5.1 mdtraj-1.9.7 multiprocess-0.70.12.2 networkx-2.7.1 numpy-1.22.3 p-tqdm-1.3.3 packaging-21.3 pandas-1.4.1 pathos-0.2.8 patsy-0.5.2 pbr-5.8.1 pillow-9.0.1 pox-0.3.0 ppft-1.6.6.4 pylipid-1.5.14 pyparsing-3.0.7 python-dateutil-2.8.2 python-louvain-0.16 pytz-2021.3 scikit-learn-1.0.2 scipy-1.8.0 seaborn-0.11.2 six-1.16.0 statsmodels-0.13.2 threadpoolctl-3.1.0 tqdm-4.63.0 vermouth-0.7.2

Everything is ready to run. I don’t copy the output, only the error:

$ > conda activate LipIDens
cd LipIDens/
python lipidens_master_run.py
...here you enter all the run parameters...
which: no dssp in PATH

I follow this suggestion to install dssp, and run it agan. Now I get a crash:

$ > module load python-3.7.3 
$ > cd LipIDens/
$ > conda activate LipIDens
 python lipidens_master_run.py
Traceback (most recent call last):
File "lipidens_master_run.py", line 8, in <module>
import lipidens.test_PyLipID_cutoffs as lip_test
File "/PATH/__init__.py", line 3, in <module>
from .test_PyLipID_cutoffs import *
File "/PATH/test_PyLipID_cutoffs.py", line 15, in <module>
import pylipid
ModuleNotFoundError: No module named 'pylipid'

Also googling the error helps. We need the pylipid package. I install it in the same environment. It calls a lot of other packages. Have a look:

pip install pylipid 
... a lot of stuff being collected...
Successfully installed dill-0.3.4 fonttools-4.30.0 
kneebow-0.1.1 logomaker-0.8 matplotlib-3.5.1 
mdtraj-1.9.7 multiprocess-0.70.12.2 p-tqdm-1.3.3
pathos-0.2.8 pox-0.3.0 ppft-1.6.6.4 pylipid-1.5.14 
python-louvain-0.16

I open a new shell and load everything anew. It’s better to refresh the environment from time to time. Unfortunately the dssp warning is still there:

$ > conda activate LipIDens
cd LipIDens/
python lipidens_master_run.py
...here you enter all the run parameters...
which: no dssp in PATH

What is going on? I did clearly installed! It looks like now it has another name. I can fix it with one line:

~/.conda/envs/LipIDens/bin $ > ln -s mkdssp dssp

then I start a new shell (remember, refreshing is good!) and the warning is gone. Time to learn to use the tool!