PiTS³

April 23^rd, 2025

(Semi)automatic pipeline for transition state (TS) search in molecular photoswitches.

Installation Instructions

Local

python -m venv PiTS3.venv
git clone https://github.com/CrespiLab/PiTS3/
source PiTS3.venv/bin/activate
(PiTS3.venv) sudo apt install libopenbabel-dev swig
(PiTS3.venv) pip install openbabel --global-option=build_ext --global-option="-I/usr/include/openbabel3" \
                      --global-option="-L/usr/lib/x86_64-linux-gnu/openbabel/3.1.1/"
(PiTS3.venv) cd PiTS3
(PiTS3.venv) pip install -e .

Adjust according to your folder structure: --global-option="-I/usr/include/openbabel3" and --global-option="-L/usr/lib/x86_64-linux-gnu/openbabel/3.1.1/"

Global environment

Note that xTB and CREST depend on OMP_NUM_THREADS global variable, which controls the number of cores available to those utilities. Adjust it accordingly.

By default, the tool will check the accessibility of crest, xtb, orca and pysis in your environment (in PATH). If you have multiple installations/versions of these utilities, make sure the right one is in your PATH or change ts_pipe/config.py accordingly (see instructions in the file). It is especially relevant for working in a supercomputer cluster environment, where you might have a module system for utility loading.

Programmes required

These programmes need to be callable from the command-line (i.e. should be available in your PATH). If not: adjust config.py and add paths to programmes.

• OpenBabel
• xTB
• CREST
• ORCA

Cluster

Test run

We provide a set of test examples. These can be run in the test folder using the provided bash script.

(PiTS3.venv) /PiTS3/test/test1_cdxml-to-xyz$ ./test1_cdxml-to-xyz.sh
(PiTS3.venv) /PiTS3/test/test2_fragments-combiner_tspipe_noorca$ ./test2_fragments-combiner_tspipe_noorca.sh
(PiTS3.venv) /PiTS3/test/test3_fragments-combiner_tspipe_orca$ ./test3_fragments-combiner_tspipe_orca.sh

Instructions

Full run (locally)

Example for stilbene, starting from fragments_1.cdxml (1 fragment) and fragments_2.cdxml (2 fragments). The fragment combiner tool yields Cartesian coordinate files of two molecules, named after their molecular formulas: C15H11N.xyz and C15H14O.xyz.

fragments_combiner stilbene_fragments_1.cdxml stilbene_fragments_2.cdxml
tspipe -m 'C-C=C-C' C15H11N.xyz C15H14O.xyz
ts_data_collector -m 'C-C=C-C' C15H11N C15H14O

List of Tools

• fragments_combiner
• tspipe
• ts_data_collector
• cdxml_to_xyz

Fragments Combiner Tool (fragments_combiner)

fragments_combiner frag1.cdxml frag2.cdxml

tspipe

tspipe -m 'C-C=C-C'    stilbene.xyz
tspipe -m 'C-C=N-C'    diarylimine.xyz
tspipe -m 'C1=CCNC=C1' ADAE.xyz
tspipe -m 'C1C=CCC=C1' NBD.xyz

ts_data_collector

ts_data_collector -m 'C-C=C-C'    stilbene
ts_data_collector -m 'C-C=N-C'    diarylimine 
ts_data_collector -m 'C1=CCNC=C1' ADAE
ts_data_collector -m 'C1C=CCC=C1' NBD