Analysis code and dataset for "multiphasic protein condensation governed by shape and valency"

The GitHub repository contains analysis programs for the study "the role of protein shape in multiphasic separation within condensates" by Pandey et al. [1]. All programs were written in Python3.8 (Windows) and designed for the analyses of output from the LASSI simulation engine [2].

[1] Pandey et al., 2025, Cell Reports

[2] https://github.com/Pappulab/LASSI

Directories

| directory | contents | | -------- | -------- | | bin |Executable programs | | lib| Shared libraries | | accessaries| Accessary programs | | example_data| Example data used below |

Basic procedure

Analyses are conducted through two steps: the conversion of lammpstrj files into intermediate data files and the visualization based on the intermediate data. Their directories and filenames are specified as instance variables of a superclass "SpecDatasets" in "specification_datasets.py." In the methods of "SpecDatasets", the instance variables below should be defined. They are referred by executable programs (bin/).

Instance variables of class "SpecDatasets" in "specification_datasets.py"

| instance variable | variable type | content | | -------- | -------- | -------- | | self.dir_lammpstrj | str | Directory for target lammpstrj files. | | self.dir_edited_data| str |Directory for intermediate data files. | | self.dir_imgs_root| str | Root directory for image files. | | self.filenames_lammpstrj| list/tuple | Filenames of target lammpstrj files. | | self.filenames_edited| list/tuple | Filenames of intermediate data files. | | self.filename_lammpstrj_matrix| func(v, l) | Filename of a target lammpstrj file specified by valency/GluN2B conc (v) and length/STG conc (l). It is used to draw matrix graphs and phase planes. | | self.filename_edited_matrix| func(v, l) | Filename of the intermediate data file specified by valency/GluN2B conc (v) and length/STG conc (l). It is used to draw matrix graphs and phase planes. |

Some .py files

| .py file | functions | | -------- | -------- | | lib/paramters.py | It defines basic parameters such as ID versus molecular name, the size of lattice space and so on. The defined variables (e.g., space) are referred such as "p.space" in executable programs (bin/). | | lib/colormap.py| It defines colors. The color universal design is utilized for color blindness. | | control_board_*.py| Workspaces. They would be edited for further simulation and analyses. |

Example

We would introduce an example procedure for analyses and visualization as a gateway to examine the analysis programs.

Programs and data

| diretory / file | contents | | -------- | -------- | | specification_datasets.py | The method "examples" is referred. | | control_board_example.py | It calls executables. | | example_data/lammpstrj| Zipped lammpstrj files (CG.zip, PS.zip, CGPS.zip). Please unzip them. | | example_data/edited| Zipped intermediate data files (CG.zip, PS.zip, CGPS.zip). Please unzip them. | | **`exampledata/imgs`**| Image file directories and images (profiles, profiles3dovito, profiles3dpyvista). |

controlboardexample.py

It creates objects of the classes below. Each object 'obj' first calls the 'examples' method to specify target files (obj.exmaples()), then executes a method for data conversion or visualization (obj.run()).

• EditData
• PlotProfiles
• Plot3dOvito
• Plot3dPyvista

EditData

The 'EditData' class converts the lammpstrj files ('CG.lammpstrj', 'PS.lammpstrj', and 'CGPS.lammpstrj' in exampledata/lammpstrj) into intermediate data files ('CG.pickle', 'PS.pickle', and 'CGPS.pickle'; example_data/edited). Each pickle file has a dict variable with the following keys:

| key | value type | description | | -------- | -------- | -------- | | mc_step | int | Sampled MC step. Final MC step is selected in general. | | sampling_frame | int | Sampled time frame. Final time frame is selected in general. | | region_condensate_in_grid_mesh | dict[Z] | Condensate region of X. Each condensate region is defined by the region over the half maximal levels of blurred Y. | | conc_condensate | dict[Y][X] | Conc of X in the condensate region Y. | | conc_periphery | dict[X] | Conc of X in the periphery region. The periphery region is defined by the region over d/2 distant from the center of the lattice space [d, d, d]. | | concs_in_grid_mesh | dict[X] | Conc of X in the 3d space (3d np.array, float). Grid locations of beads were blurred by the gaussian (sd: p.sigma in lattice unit). | | locs_in_grid_mesh | dict[X] | Conc of X in the 3d space (3d np.array, int). Grid locations of beads. | | rdf_bins| 1d np.array, int | Bins for radial distribution profile (RDP) (in lattice unit). | | rdf_sampling_frames| list, int | Sampled frames for RDP | | rdf| dict[X] | Radial distribution profile X (2d np.array, float) | | dir_lammpstrj| str | dirlammpstrj. | | **`filenamelammpstrj**| str | filename_lammpstrj. | | **rotatedregioncondensateingridmesh** | dict[X] | Same as ** regioncondensateingridmesh ** but rotated. Only in CGPS. | | **rotatedconcsingridmesh** | dict[X] | Same as **concsingridmesh`** but rotated. Only in CGPS. |

Here, X, Y ['All', 'CaMKII', 'GluN2B', 'STG', 'PSD95'], and Z ['All', 'CaMKII', 'GluN2B', 'STG', 'PSD95', 'dilute'].

PlotProfiles

It visualizes intensity levels at the section that divided the center of condensate as well as RDPs from condensate center-of-mass ('CG.png', 'PS.png', 'CGPS.png', 'CG.svg', 'PS.svg', and 'CGPS.svg' in example_data/imgs/profiles). Each image includes the panels showing intensity levels in the planes of 'yz', 'xy', 'zx', partition index, concentrations in the STG and CaMKII condensates, and RDPs.

Plot3dOvito

It visualizes protein bead distributions in the 3D lattice space ('CG.png', 'PS.png', 'CGPS.png', 'CG.svg', 'PS.svg', and 'CGPS.svg' in exampledata/imgs/profiles3d_ovito).

Plot3dPyvista

It visualizes the 3D shapes of condensates using their rendered volumes ('CG.png', 'PS.png', 'CGPS.png', 'CG.svg', 'PS.svg', and 'CGPS.svg' in exampledata/imgs/profiles3d_pyvista). Each image includes the panels showing rendered volumes in the planes of 'yz', 'xy', 'zx'.