censo 3.0.6

No project description provided

CENSO - Commandline and Python Package for Conformer-Rotamer Ensembles

CENSO is a Python package designed to automate the refinement of Conformer-Rotamer Ensembles at the DFT level. It supports both command-line usage and usage via a fully implemented Python API. CENSO enables calculations of ensemble properties like NMR parameters, optical rotation, and UV-Vis spectra.

---

Key Features

• Prescreening, Screening, Optimization, and Refinement of conformer-rotamer ensembles.
  • Geometry Optimization using:
    • ORCA (native optimizer)
    • xtb (ANCOPT)
  • Thermal contributions using xtb Hessians
• Solvent Models:
  • ORCA: CPCM, SMD
  • Turbomole: COSMO, DCOSMORS, COSMORS
  • xtb: ALPB, GBSA
• Property Calculations:
  • NMR: ORCA, Turbomole
  • Optical Rotation: Turbomole
  • UV/Vis: ORCA
• Agnostic to global optimizer, input files just need to be in xyz-format (CLI)
• CLI and Python API

---

Update: CENSO 3.0

Version 3.0 introduces significant architectural improvements, particularly enhancing its usability as a Python package. Overall usage is also improved, e.g.:

• automatic system path exploration (finding program binaries, program versions, etc.),
• automatic system recognition,
• improved clarity for printout,
• improved logging,
• more configuration options for command-line interface.

Configuration is now managed using Pydantic V2, and several keywords have been updated. Refer to example.censo2rc for details.

Resources and tasks are now managed using Dask. This is in preparation of a multi-node implementation.

New auxiliary command-line scripts (nmrplot, uvvisplot, c2anmr) have been added for improved workflow support. nmrplot and uvvisplot are utilities for immediate visualization of NMR and UV/Vis data, respectively. c2anmr is a tool to ensure backwards compatibility with ANMR, due to the new directory structure since CENSO 2.0.

The documentation has also been updated to reflect the new version and includes more guidance on usage. It now also includes an example for the calculation of the NMR spectrum of glycerol.

---

Installation

Using pip

From pypi:

pip install censo

or after cloning the repository:

pip install .

To install additional command-line scripts and dependencies:

pip install .[scripts]

Manual Installation

1. Add CENSO/src to your $PYTHONPATH.
2. Add CENSO to your $PATH.

---

Usage

Command-Line Interface (CLI)

After installation, use the censo command. For help, run:

censo -h

Note: Opposed to previous versions, default values are now assumed for -i (crest_conformers.xyz) and --maxcores (total CPU cores).

In the CLI version, CENSO will try to automatically detect binary locations for necessary programs, as well as versions. If you want override, use the [paths] section in your .censo2rc file. Furthermore, it will try to automatically detect the number of available CPU cores. To override these settings, as well as general settings, you can use the command-line arguments.

usage: censo [-h] [--prescreening] [--screening] [--optimization] [--refinement] [--nmr] [--rot] [--uvvis] [-i INP] [-n NCONF] [-c CHARGE] [-u UNPAIRED] [-v] [--cleanup] [--cleanup-all]
             [--new-config] [--inprc INPRCPATH] [--constraints CONSTRAINTS] [--maxcores MAXCORES] [--omp-min OMPMIN] [--loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [--logpath LOGPATH]
             [--reload RELOAD [RELOAD ...]] [--keep-all] [--ignore-failed] [-T TEMPERATURE] [--trange start end step] [--bhess] [--consider-sym] [--sm-rrho SM_RRHO] [--evaluate-rrho]
             [--solvent SOLVENT] [--gas-phase] [--imagthr IMAGTHR] [--sthr STHR] [--scale SCALE]

Energetic sorting of Conformer Rotamer Ensembles (command line version).

options:
  -h, --help            show this help message and exit

RUN SETTINGS:
  --prescreening, -P    Enable the prescreening part.
  --screening, -S       Enable the screening part.
  --optimization, -O    Enable the optimization part.
  --refinement, -R      Enable the refinement part.
  --nmr                 Enable the NMR calculation part.
  --rot                 Enable the optical rotation calculation part.
  --uvvis               Enable the UV/Vis calculation part.
  -i, --input INP       Relative path to ensemble file, e.g. crest_conformers.xyz (default).
  -n, --nconf NCONF     The first 'nconf' conformers will be considered.
  -c, --charge CHARGE   Integer charge of the investigated molecule.
  -u, --unpaired UNPAIRED
                        Integer number of unpaired electrons of the investigated molecule.
  -v, --version         Print CENSO version and exit.
  --cleanup             Delete unneeded files from current working directory.
  --cleanup-all         Delete all CENSO files from previous runs from current working directory. Stronger than --cleanup !
  --new-config          Write new configuration file, which is placed into the current directory.
  --inprc INPRCPATH     Use to provide a path to the CENSO configuration file if you want to use a different one than the default (~/.censo2rc).
  --constraints CONSTRAINTS
                        Path to a file containing constraints in xtb format for use in geometry optimizations.
  --maxcores MAXCORES   Number of cores that should be used for CENSO on the machine. If this is not provided CENSO will use the maximum number available (also checks for slurm
                        environment variables).
  --omp-min OMPMIN      Minimum number of OpenMP threads per process, default is 4. This is mostly important if load balancing is enabled.
  --loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL}
                        Set the loglevel for all modules to a specified level.
  --logpath LOGPATH     Relative/absolute path to the logfile. If no path is provided, censo.log will be written in the output directory.
  --reload RELOAD [RELOAD ...]
                        Reload data from json output files. List all file names separated by spaces. Will be loaded in order (first to last). Note that all conformers from the current
                        ensemble need to be included in the output data keys.
  --keep-all            Do not cut down the ensemble, keep all conformers from start to end.
  --ignore-failed       Ignore failed calculations. If this is not set, failed calculations will raise RuntimeError.

GENERAL SETTINGS:
  -T, --temperature TEMPERATURE
                        Temperature in Kelvin for thermostatistical evaluation.
  --trange start end step
                        specify a temperature range [start, end, step] e.g.: 250.0 300.0 10.0 resulting in the range [250.0, 260.0, 270.0, 280.0, 290.0, 300.0].
  --bhess               Uses SPH and applies structure constraint to input/DFT geometry for mRRHO calcuation.
  --consider-sym        Consider symmetry in mRRHO calcuation (based on desy xtb threshold).
  --sm-rrho SM_RRHO     Solvation model used in xTB GmRRHO calculation. Applied if not in gas-phase. Options are 'gbsa' or 'alpb'.
  --evaluate-rrho       Evaluate mRRHO contribution.
  --solvent SOLVENT     Solvent to be used for Gsolv calculation.
  --gas-phase           Run calculation in gas-phase, overriding all solvation settings.
  --imagthr IMAGTHR     threshold for inverting imaginary frequencies for thermo in cm-1, e.g. -30.0.
  --sthr STHR           Rotor cut-off for thermo in cm-1, e.g. 50.0.
  --scale SCALE         Scaling factor for frequencies, e.g. 1.0.

---

Python API Usage

CENSO can be integrated into Python scripts for custom workflows. Below is a basic setup example:

from censo.ensemble import EnsembleData
from censo.config.setup import configure
from censo.ensembleopt import prescreening, screening, optimization
from censo.properties import nmr
from censo.config import PartsConfig
from censo.parallel import get_cluster

# CENSO outputs files in the current working directory (os.getcwd())
# When called from the CLI version, the output dir will be the same as the input file's location
input_path = "rel/path/to/your/inputfile"  # Relative to working directory
ensemble = EnsembleData()
ensemble.read_input(input_path)

# For charged/open-shell systems:
# ensemble = EnsembleData()
# ensemble.read_input(input_path, charge=-1, unpaired=1)

# Load a custom rcfile (optional)
config = configure(rcpath="/path/to/rcfile")

# Ensure valid configuration
config.general.solvent = "dmso"
config = PartsConfig.model_validate(
    config.model_dump(),
    context={"check": ["prescreening", "screening", "optimization", "nmr"]}
)
# passing a context enables paths and solvent validation, which is usually skipped

# Set up task management
cluster = get_cluster() # instead you can also supply your own cluster
client = cluster.get_client()

# Execute workflow steps
results = [
    part(ensemble, config, client)
    for part in [prescreening, screening, optimization, nmr]
]

# The results are then also output to json files in the working directory
# The molecules stored in the ensemble contain the most up-to-date energy values and geometries

Note: For multiple runs, rename or move output folders to avoid overwriting.

---

Development Environment Setup

• Python Version: Requires Python >= 3.12. Set up a virtual environment using your preferred method:

  • Conda: conda env create -f environment.yaml
  • Pipenv, venv, or others.

• Install the Package: Install the package and its dependencies in development mode:

  pip install -e '.[dev]'
  

• Pre-commit Hooks: Install pre-commit hooks:

  pre-commit install
  

• Testing:

  • Pytest Markers: Custom markers are available for conditional test execution. Optional tests (e.g., integration tests) require third-party programs like xtb, ORCA, Turbomole, or COSMOtherm.

    markers = [
        "optional: mark test as optional (e.g., integration tests)",
        "requires_xtb: skip test if xtb is not available",
        "requires_orca: skip test if ORCA is not available",
        "requires_turbomole: skip test if Turbomole is not available",
        "requires_cosmotherm: skip test if COSMOtherm is not available",
    ]
    

  • Run Tests:
    • Default (skip optional tests):

      pytest
      

    • Include optional tests:

      pytest --run-optional
      

  • Run Tox: Execute tests across multiple environments:

    tox
    

---

License

CENSO is free software under the GNU Lesser General Public License (LGPLv3). You may redistribute and modify it under the license terms. No warranty is provided. See the LGPLv3 for details.