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Updates jupyter notebook #148

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DrPaulSharp merged 1 commit into from
Apr 17, 2025
Merged

Updates jupyter notebook #148

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16 changes: 8 additions & 8 deletions RATapi/examples/convert_rascal_project/convert_rascal.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
"source": [
"### RasCAL-1 to RAT\n",
"\n",
"RasCAL-1 (R1) project structs can be converted to RAT Project classes, and vice versa. This is done via the functions `r1_to_project_class` and `project_class_to_r1`.\n",
"RasCAL-1 (R1) project structs can be converted to RAT Projects, and vice versa. This is done via the functions `r1_to_project` and `project_to_r1`.\n",
"\n",
"Converting from R1 to a `Project` is very simple. We use the example R1 project in the file `R1monolayerVolumeModel.mat`, which is a project for analysing a monolayer of DSPC with various deuterations (tail-deuterated, head-deuterated, fully deuterated, hydrogenated)"
]
Expand All @@ -15,7 +15,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"Simply give the file path to the function `r1_to_project_class`, and it returns a RAT `Project` that you can use exactly like any other."
"Simply give the file path to the function `r1_to_project`, and it returns a RAT `Project` that you can use exactly like any other."
]
},
{
Expand All @@ -24,9 +24,9 @@
"metadata": {},
"outputs": [],
"source": [
"from RATapi.utils.convert import r1_to_project_class\n",
"from RATapi.utils.convert import r1_to_project\n",
"\n",
"project = r1_to_project_class(\"R1monolayerVolumeModel.mat\")\n",
"project = r1_to_project(\"R1monolayerVolumeModel.mat\")\n",
"print(project)"
]
},
Expand Down Expand Up @@ -108,7 +108,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"`project_class_to_r1` takes parameters `project` and `filename`, which are the `Project` object and filename for the produced .mat file respectively. This .mat file can then be loaded into RasCAL-1.\n",
"`project_to_r1` takes parameters `project` and `filename`, which are the `Project` object and filename for the produced .mat file respectively. This .mat file can then be loaded into RasCAL-1.\n",
"\n",
"Alternatively, if one sets `return_struct=True`, the struct is returned as a Python dictionary instead of being saved.\n",
"\n",
Expand All @@ -121,14 +121,14 @@
"metadata": {},
"outputs": [],
"source": [
"from RATapi.utils.convert import project_class_to_r1\n",
"from RATapi.utils.convert import project_to_r1\n",
"from pprint import pp # for printing the struct\n",
"\n",
"# save to a file called lipid_bilayer.mat\n",
"project_class_to_r1(lipid_bilayer_project, filename=\"lipid_bilayer.mat\")\n",
"project_to_r1(lipid_bilayer_project, filename=\"lipid_bilayer.mat\")\n",
"\n",
"# return as a Python dictionary\n",
"struct = project_class_to_r1(lipid_bilayer_project, return_struct=True)\n",
"struct = project_to_r1(lipid_bilayer_project, return_struct=True)\n",
"pp(struct)"
]
}
Expand Down