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Merged
merged 5 commits into from
Apr 14, 2025
Merged

notebook for importing geometry #27

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e03949b
add example sysbio-1-antimony.ipynb to Colab link
jcschaff Apr 14, 2025
6ebe964
link to sysbio-2-parameters notebook in Colab
jcschaff Apr 14, 2025
6b4b580
added sysbio-3-geometry.ipynb
jcschaff Apr 14, 2025
93b4b34
comment out original colab notebook
jcschaff Apr 14, 2025
505d776
bump to 0.1.18
jcschaff Apr 14, 2025
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13 changes: 12 additions & 1 deletion README.md
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Expand Up @@ -5,7 +5,8 @@
[![codecov](https://codecov.io/gh/virtualcell/pyvcell/branch/main/graph/badge.svg)](https://codecov.io/gh/virtualcell/pyvcell)
[![Commit activity](https://img.shields.io/github/commit-activity/m/virtualcell/pyvcell)](https://img.shields.io/github/commit-activity/m/virtualcell/pyvcell)
[![License](https://img.shields.io/github/license/virtualcell/pyvcell)](https://img.shields.io/github/license/virtualcell/pyvcell)
[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/101BPDYqu4_PupqmunT6Qhextks_VT-8X?usp=sharing)

[//]: # "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/101BPDYqu4_PupqmunT6Qhextks_VT-8X?usp=sharing)"

This is the python wrapper for vcell modeling and simulation for

Expand Down Expand Up @@ -63,3 +64,13 @@ results.plotter.plot_concentrations()
# Documentation

coming soon.

# Examples:

### Antimony example

[![Open in Colab ](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1aGttld4SKxuC7Vh-h1A7gsPIJT8u00fN?usp=sharing)

### Parameters example

[![Open in Colab ](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1nNlMvXuZdn7Ay8la0KOKmSwi6dSurkte?usp=sharing)
422 changes: 422 additions & 0 deletions examples/notebooks/sysbio-3-geometry.ipynb
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2 changes: 1 addition & 1 deletion pyproject.toml
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@@ -1,6 +1,6 @@
[tool.poetry]
name = "pyvcell"
version = "0.1.17"
version = "0.1.18"
description = "This is the python wrapper for vcell modeling and simulation"
authors = ["Jim Schaff <[email protected]>"]
repository = "https://github.com/virtualcell/pyvcell"
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8 changes: 8 additions & 0 deletions pyvcell/vcml/models.py
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Expand Up @@ -291,6 +291,14 @@ def add_surface(self, name: str, sub_volume_1: SubVolume | str, sub_volume_2: Su
self.surface_classes.append(surface_class)
return surface_class

@property
def subvolume_names(self) -> list[str]:
return [subvolume.name for subvolume in self.subvolumes]

@property
def surface_class_names(self) -> list[str]:
return [surface_class.name for surface_class in self.surface_classes]


class StructureMapping(VcmlNode):
structure_name: str
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