diff --git a/.gitignore b/.gitignore index 73346d4b3ea9405ee6dc8d852a57b261ff81e7f1..075c900f1fcb3eab244ca4ac90b26c82f267dd8c 100644 --- a/.gitignore +++ b/.gitignore @@ -1,8 +1,10 @@ SSBtoolkit-Tutorial1-DEV.ipynb SSBtoolkit-Tutorial2-DEV.ipynb +SSBtoolkit-Tutorial3A-DEV.ipynb SSBtoolkit-Tutorial4-OXTR-DEV.ipynb src/lib/__pycache__/ src/lib/autogrid_reference_files/ src/lib/autogrids/ +src/lib/ssbtoolkit_BK.py .ipynb_checkpoints/ debugging.txt diff --git a/SSBtoolkit-Tutorial2-EBRAINS.ipynb b/SSBtoolkit-Tutorial2-EBRAINS.ipynb index c16479c474c082af8b5f169d22322de95a90add9..b7a2aae4983bedac3732c2fcc032378ccca2ada8 100644 --- a/SSBtoolkit-Tutorial2-EBRAINS.ipynb +++ b/SSBtoolkit-Tutorial2-EBRAINS.ipynb @@ -441,35 +441,6 @@ "💡 The potency predicted values can be exported as a python dictionary using the function `sim.PotencyToDict()` or saved in a csv file: `sim.PotencyToCSV()`. " ] }, - { - "cell_type": "markdown", - "id": "7650013b", - "metadata": {}, - "source": [ - "## Save results on Google Drive" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "2d5ed71a", - "metadata": {}, - "outputs": [], - "source": [ - "from google.colab import drive\n", - "drive.mount('/gdrive')" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "16081378", - "metadata": {}, - "outputs": [], - "source": [ - "sim.PotencyToCSV(path='/gdrive/MyDrive/XX') ## change XX accordingly. " - ] - }, { "cell_type": "markdown", "id": "f2f97975", diff --git a/SSBtoolkit-Tutorial3A-EBRAINS.ipynb b/SSBtoolkit-Tutorial3A-EBRAINS.ipynb index c120758427995c5be6c1667d95f9ef6bd3cf2111..656fe1569f65c2540cb2a22f11bf123214b28a11 100644 --- a/SSBtoolkit-Tutorial3A-EBRAINS.ipynb +++ b/SSBtoolkit-Tutorial3A-EBRAINS.ipynb @@ -384,35 +384,6 @@ "💡 The potency predicted values can be exported as a python dictionary using the function `sim.PotencyToDict()` or saved in a csv file: `sim.PotencyToCSV()`. " ] }, - { - "cell_type": "markdown", - "id": "fe6271ed", - "metadata": {}, - "source": [ - "## Save results on Google Drive" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "c5f82273", - "metadata": {}, - "outputs": [], - "source": [ - "from google.colab import drive\n", - "drive.mount('/gdrive')" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "bd888ea5", - "metadata": {}, - "outputs": [], - "source": [ - "sim.PotencyToCSV(path='/gdrive/MyDrive/XX') ## change XX accordingly." - ] - }, { "cell_type": "markdown", "id": "a7c9bbc4", diff --git a/SSBtoolkit-Tutorial3B-tauRAMD-EBRAINS.ipynb b/SSBtoolkit-Tutorial3B-tauRAMD-EBRAINS.ipynb index 4a8b8f2e6d85e6db42adf3266d65423c4770deba..9953102d96ae95f328d113b639ee3f811eebba34 100644 --- a/SSBtoolkit-Tutorial3B-tauRAMD-EBRAINS.ipynb +++ b/SSBtoolkit-Tutorial3B-tauRAMD-EBRAINS.ipynb @@ -458,35 +458,6 @@ "💡 The potency predicted values can be exported as a python dictionary using the function `sim.PotencyToDict()` or saved in a csv file: `sim.PotencyToCSV()`. " ] }, - { - "cell_type": "markdown", - "id": "e9e16ef7", - "metadata": {}, - "source": [ - "## Save results on Google Drive" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "d3ace9c6", - "metadata": {}, - "outputs": [], - "source": [ - "from google.colab import drive\n", - "drive.mount('/gdrive')" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "2df68659", - "metadata": {}, - "outputs": [], - "source": [ - "sim.PotencyToCSV(path='/gdrive/MyDrive/XX') ## change XX accordingly." - ] - }, { "cell_type": "markdown", "id": "65febe37", diff --git a/SSBtoolkit-Tutorial4-OXTR-EBRAINS.ipynb b/SSBtoolkit-Tutorial4-OXTR-EBRAINS.ipynb index 6ace35fda1ed250e0b812200ab93d3019ebdf737..0ed02cb64d492dc626399a52b10661456fccd0b0 100644 --- a/SSBtoolkit-Tutorial4-OXTR-EBRAINS.ipynb +++ b/SSBtoolkit-Tutorial4-OXTR-EBRAINS.ipynb @@ -285,35 +285,6 @@ "sim.plotCurves()" ] }, - { - "cell_type": "markdown", - "id": "5fd46fe3", - "metadata": {}, - "source": [ - "## Save results on Google Drive" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "3e476cad", - "metadata": {}, - "outputs": [], - "source": [ - "from google.colab import drive\n", - "drive.mount('/gdrive')" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "b98afd3b", - "metadata": {}, - "outputs": [], - "source": [ - "sim.plotCurves(save=True, filename='/gdrive/MyDrive/XX') ## change XX accordingly. " - ] - }, { "cell_type": "markdown", "id": "ff3d7f41", diff --git a/src/lib/pathways/__pycache__/Gs.cpython-39.pyc b/src/lib/pathways/__pycache__/Gs.cpython-39.pyc index f2526a339a1f76d36c791c488a40bd6551e3282a..e02e32e3bab2e6b49e52d2b05a528f23cf2d6d92 100644 Binary files a/src/lib/pathways/__pycache__/Gs.cpython-39.pyc and b/src/lib/pathways/__pycache__/Gs.cpython-39.pyc differ diff --git a/src/lib/ssbtoolkit.py b/src/lib/ssbtoolkit.py index 7b20da16249ac93c4c027396f7580cea893825db..23b9aa89abfa86294f84c26e27e5d0ad7ec0d846 100644 --- a/src/lib/ssbtoolkit.py +++ b/src/lib/ssbtoolkit.py @@ -648,9 +648,9 @@ class simulation: except: self._PathwayParameters = self._DefaultPathwayParametersDataFrame.set_index('Parameter').iloc[:,0].to_dict() - elif self._DefaultPathwayParametersDataFrame.empty and self._binding_kinetic_parameters is not None: - self._DefaultPathwayParametersDataFrame = pd.read_csv('src/lib/pathways/{}_parameters.csv'.format(self._pathway)) - self._PathwayParameters = {**self._DefaultPathwayParametersDataFrame.set_index('Parameter').iloc[:,0].to_dict(), **self._binding_kinetic_parameters} + #elif self._DefaultPathwayParametersDataFrame.empty and self._binding_kinetic_parameters is not None: + # self._DefaultPathwayParametersDataFrame = pd.read_csv('src/lib/pathways/{}_parameters.csv'.format(self._pathway)) + #self._PathwayParameters = {**self._DefaultPathwayParametersDataFrame.set_index('Parameter').iloc[:,0].to_dict(), **self._binding_kinetic_parameters} elif self._DefaultPathwayParametersDataFrame.empty is False and self._binding_kinetic_parameters is not None: try: @@ -673,6 +673,12 @@ class simulation: data=[] utils.printProgressBar(0, len(self._lig_conc_range), prefix = "{:<15}".format(ligand_name[:15]), suffix = 'Complete', length = 50) + ###DANGER ZONE### + if self._DefaultPathwayParametersDataFrame.empty and self._binding_kinetic_parameters is not None: + self._DefaultPathwayParametersDataFrame = pd.read_csv('src/lib/pathways/{}_parameters.csv'.format(self._pathway)) + self._PathwayParameters = {**self._DefaultPathwayParametersDataFrame.set_index('Parameter').iloc[:,0].to_dict(), **self._binding_kinetic_parameters[self._ligands.index(ligand)]} + ###################### + for idx in range(len(self._lig_conc_range)): ligand_conc = self._lig_conc_range[idx]