Skip to content

Configuration

Basic configuration of PyHDX is done through a .yaml configuration file. By default, the configuration file in the user home directory is used (~/.pyhdx/config.yaml).
Individual or all config entries can be overwritten by loading (partial) config files.

In 'myconfigfile.yaml:

cluster:
  n_workers: 4
fitting: 
  dtype: float32
  device: cuda

Then to load the config:

from pyhdx.config import cfg
cfg.load_config('myconfigfile.yaml')
cfg.TORCH_DTYPE
>>> torch.float32

Default configuration

The default configuration file is shown below, and can be found in PyHDX source at pyhdx/config.yaml.

cluster:
  scheduler_address: "127.0.0.1:52123"
  n_workers: 10

server:
  assets_dir: ~/.pyhdx/assets
  log_dir: ~/.pyhdx/logs
  database_dir : ~/.hdxms_datasets/datasets

fitting:
  dtype: float64
  device: cpu

analysis:
  drop_first: 2
  weight_exponent: 1.0

plotting:
  # Sizes are in mm
  ncols: 2
  page_width: 160
  cbar_width: 2.5
  peptide_coverage_aspect: 3
  peptide_mse_aspect: 3
  residue_scatter_aspect: 3
  dG_aspect: 2.5
  linear_bars_aspect: 30
  loss_aspect: 2.5
  rainbowclouds_aspect: 4

Cluster

Settings related to the dask cluster for computation of \(\Delta G\) values.

  • scheduler_address: The address for the dask scheduler. If scheduler is found at this address, a new cluster is created.
  • n_workers: Number of workers for the cluster.

Server

Settings related to the panel web application.

  • assets_dir: Directory for static assets. Uploaded .pdb files for visualization are stored here.
  • log_dir: Directory for log files.

Fitting

Settings related to \(\Delta G\) fitting.

  • dtype: Data type for fitting. Can be float32 or float64.
  • device: Device for fitting. Can be cpu or cuda (GPU), if cuda is available.

Analysis

Settings related to analysis of HDX-MS data.

  • drop_first: Number of N-terminal residues to consider as completely back-exchanging.
  • weight_exponent: Exponent for calculating residue-level RFU values by weighted averaging.

Plotting

Settings related to output format of plots generated by the web interface. These include widths and aspect ratios of figures and plots, as well as the number of columns of plots to place into one figure.