From 4cc873d78ce72b0dd209ea4d95cf3fe6a3cd3336 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Tue, 25 Jun 2024 13:14:46 +0000 Subject: [PATCH] Upload documentation from latest commit --- api/autoapi/reciprocalspaceship.DataSet.html | 18 +- developers/utilities.html | 8 +- examples/7_makingADifferenceMap.html | 10 +- examples/7_makingADifferenceMap.ipynb | 490 +++++++++---------- 4 files changed, 263 insertions(+), 263 deletions(-) diff --git a/api/autoapi/reciprocalspaceship.DataSet.html b/api/autoapi/reciprocalspaceship.DataSet.html index 60e1aaa9..b0886157 100644 --- a/api/autoapi/reciprocalspaceship.DataSet.html +++ b/api/autoapi/reciprocalspaceship.DataSet.html @@ -101,7 +101,7 @@

DataSet

-class reciprocalspaceship.DataSet(data=None, index=None, columns=None, dtype=None, copy=False, spacegroup=None, cell=None, merged=None)[source]
+class reciprocalspaceship.DataSet(data=None, index=None, columns=None, dtype=None, copy=False, spacegroup=None, cell=None, merged=None)[source]

Bases: DataFrame

Representation of a crystallographic dataset.

A DataSet object provides a tabular representation of reflection data. @@ -299,7 +299,7 @@

DataSet
-canonicalize_phases(inplace=False)[source]
+canonicalize_phases(inplace=False)[source]

Canonicalize columns with phase data to fall in the interval between -180 and 180 degrees. This method will modify the values within any column composed of data with the PhaseDtype.

@@ -355,7 +355,7 @@

DataSet
-expand_anomalous()[source]
+expand_anomalous()[source]

Expands data by applying Friedel operator (-x, -y, -z). The necessary phase shifts are made for columns of complex dtypes or PhaseDtypes.

@@ -368,7 +368,7 @@

DataSet
-expand_to_p1()[source]
+expand_to_p1()[source]

Generates all symmetrically equivalent reflections. The spacegroup symmetry is set to P1.

@@ -495,7 +495,7 @@

DataSet
-get_reciprocal_grid_size(dmin=None, sample_rate=3.0)[source]
+get_reciprocal_grid_size(dmin=None, sample_rate=3.0)[source]

Determine an appropriate 3D grid size for reflection data.

Returns the smallest grid size that yields a real-space grid spacing of at most dmin/sample_rate (in Å). The returned grid size will @@ -518,7 +518,7 @@

DataSet
-hkl_to_asu(inplace=False, anomalous=False)[source]
+hkl_to_asu(inplace=False, anomalous=False)[source]

Map HKL indices to the reciprocal space asymmetric unit. If phases are included in the DataSet, they will be changed according to the phase shift associated with the necessary symmetry operation.

@@ -549,7 +549,7 @@

DataSet
-hkl_to_observed(m_isym=None, inplace=False)[source]
+hkl_to_observed(m_isym=None, inplace=False)[source]

Map HKL indices to their observed index using an M/ISYM column. This method applies the symmetry operation specified by the M/ISYM column to each Miller index in the DataSet. If phases are included @@ -946,7 +946,7 @@

DataSet
-to_reciprocal_grid(key, sample_rate=3.0, dmin=None, grid_size=None)[source]
+to_reciprocal_grid(key, sample_rate=3.0, dmin=None, grid_size=None)[source]

Set up reciprocal grid with values from column, key, indexed by Miller indices.

Notes

@@ -986,7 +986,7 @@

DataSet
-to_reciprocalgrid(key, sample_rate=3.0, dmin=None, gridsize=None)[source]
+to_reciprocalgrid(key, sample_rate=3.0, dmin=None, gridsize=None)[source]

Deprecated: Set up reciprocal grid with values from column, key, indexed by Miller indices.

diff --git a/developers/utilities.html b/developers/utilities.html index 97a1911d..fc1fcea9 100644 --- a/developers/utilities.html +++ b/developers/utilities.html @@ -250,7 +250,7 @@
-reciprocalspaceship.utils.compute_dHKL(H, cell)[source]
+reciprocalspaceship.utils.compute_dHKL(H, cell)[source]

Compute the real space lattice plane spacing, d, associated with miller indices and cell.

@@ -376,7 +376,7 @@
-reciprocalspaceship.utils.generate_reciprocal_cell(cell, dmin, dtype=<class 'numpy.int32'>)[source]
+reciprocalspaceship.utils.generate_reciprocal_cell(cell, dmin, dtype=<class 'numpy.int32'>)[source]

Generate the miller indices of the full P1 reciprocal cell.

Parameters:
@@ -525,7 +525,7 @@
-reciprocalspaceship.utils.is_absent(H, spacegroup)[source]
+reciprocalspaceship.utils.is_absent(H, spacegroup)[source]

Determine if Miller indices are systematically absent in a given spacegroup.

@@ -543,7 +543,7 @@
-reciprocalspaceship.utils.is_centric(H, spacegroup)[source]
+reciprocalspaceship.utils.is_centric(H, spacegroup)[source]

Determine if Miller indices are centric in a given spacegroup

Parameters:
diff --git a/examples/7_makingADifferenceMap.html b/examples/7_makingADifferenceMap.html index 701a36ea..a2f12659 100644 --- a/examples/7_makingADifferenceMap.html +++ b/examples/7_makingADifferenceMap.html @@ -165,7 +165,7 @@

Load On<
-
+

@@ -179,7 +179,7 @@

Load On<
-
+

[5]:
@@ -475,7 +475,7 @@ 
Phasing the Difference Map
-
+
[17]:
@@ -641,11 +641,11 @@ 
Phasing the Difference Map
-
+

Good luck with your weighted difference map!

diff --git a/examples/7_makingADifferenceMap.ipynb b/examples/7_makingADifferenceMap.ipynb index bc8b8b26..463f9377 100644 --- a/examples/7_makingADifferenceMap.ipynb +++ b/examples/7_makingADifferenceMap.ipynb @@ -20,10 +20,10 @@ "execution_count": 1, "metadata": { "execution": { - "iopub.execute_input": "2024-06-19T03:06:51.947956Z", - "iopub.status.busy": "2024-06-19T03:06:51.947782Z", - "iopub.status.idle": "2024-06-19T03:06:52.863060Z", - "shell.execute_reply": "2024-06-19T03:06:52.862527Z" + "iopub.execute_input": "2024-06-25T13:14:37.321894Z", + "iopub.status.busy": "2024-06-25T13:14:37.321719Z", + "iopub.status.idle": "2024-06-25T13:14:38.339022Z", + "shell.execute_reply": "2024-06-25T13:14:38.338391Z" } }, "outputs": [], @@ -40,10 +40,10 @@ "execution_count": 2, "metadata": { "execution": { - "iopub.execute_input": "2024-06-19T03:06:52.865463Z", - "iopub.status.busy": "2024-06-19T03:06:52.865220Z", - "iopub.status.idle": "2024-06-19T03:06:53.180296Z", - "shell.execute_reply": "2024-06-19T03:06:53.179741Z" + "iopub.execute_input": "2024-06-25T13:14:38.341898Z", + "iopub.status.busy": "2024-06-25T13:14:38.341407Z", + "iopub.status.idle": "2024-06-25T13:14:38.675138Z", + "shell.execute_reply": "2024-06-25T13:14:38.674506Z" } }, "outputs": [], @@ -56,10 +56,10 @@ "execution_count": 3, "metadata": { "execution": { - "iopub.execute_input": "2024-06-19T03:06:53.182980Z", - "iopub.status.busy": "2024-06-19T03:06:53.182423Z", - "iopub.status.idle": "2024-06-19T03:06:53.185993Z", - "shell.execute_reply": "2024-06-19T03:06:53.185411Z" + "iopub.execute_input": "2024-06-25T13:14:38.678080Z", + "iopub.status.busy": "2024-06-25T13:14:38.677581Z", + "iopub.status.idle": "2024-06-25T13:14:38.680878Z", + "shell.execute_reply": "2024-06-25T13:14:38.680340Z" } }, "outputs": [ @@ -90,10 +90,10 @@ "execution_count": 4, "metadata": { "execution": { - "iopub.execute_input": "2024-06-19T03:06:53.216214Z", - "iopub.status.busy": "2024-06-19T03:06:53.216029Z", - "iopub.status.idle": "2024-06-19T03:06:53.226186Z", - "shell.execute_reply": "2024-06-19T03:06:53.225572Z" + "iopub.execute_input": "2024-06-25T13:14:38.713544Z", + "iopub.status.busy": "2024-06-25T13:14:38.713105Z", + "iopub.status.idle": "2024-06-25T13:14:38.723840Z", + "shell.execute_reply": "2024-06-25T13:14:38.723287Z" } }, "outputs": [ @@ -107,7 +107,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "450b0cb530004dc3a4d213075e24ef8b", + "model_id": "d49dfa82f4554df09b0fe27ddcf97291", "version_major": 2, "version_minor": 0 }, @@ -128,7 +128,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "f121e493a17c4c1a85f39d9816213900", + "model_id": "9455e736fd404ad1b72a7d8af07d4e82", "version_major": 2, "version_minor": 0 }, @@ -159,10 +159,10 @@ "execution_count": 5, "metadata": { "execution": { - "iopub.execute_input": "2024-06-19T03:06:53.228421Z", - "iopub.status.busy": "2024-06-19T03:06:53.228078Z", - "iopub.status.idle": "2024-06-19T03:06:53.231518Z", - "shell.execute_reply": "2024-06-19T03:06:53.230945Z" + "iopub.execute_input": "2024-06-25T13:14:38.726289Z", + "iopub.status.busy": "2024-06-25T13:14:38.725750Z", + "iopub.status.idle": "2024-06-25T13:14:38.729392Z", + "shell.execute_reply": "2024-06-25T13:14:38.728820Z" } }, "outputs": [], @@ -182,10 +182,10 @@ "execution_count": 6, "metadata": { "execution": { - "iopub.execute_input": "2024-06-19T03:06:53.233661Z", - "iopub.status.busy": "2024-06-19T03:06:53.233344Z", - "iopub.status.idle": "2024-06-19T03:06:53.432612Z", - "shell.execute_reply": "2024-06-19T03:06:53.432085Z" + "iopub.execute_input": "2024-06-25T13:14:38.731632Z", + "iopub.status.busy": "2024-06-25T13:14:38.731290Z", + "iopub.status.idle": "2024-06-25T13:14:38.939742Z", + "shell.execute_reply": "2024-06-25T13:14:38.939219Z" } }, "outputs": [ @@ -219,10 +219,10 @@ "execution_count": 7, "metadata": { "execution": { - "iopub.execute_input": "2024-06-19T03:06:53.434731Z", - "iopub.status.busy": "2024-06-19T03:06:53.434455Z", - "iopub.status.idle": "2024-06-19T03:06:53.445980Z", - "shell.execute_reply": "2024-06-19T03:06:53.445534Z" + "iopub.execute_input": "2024-06-25T13:14:38.942073Z", + "iopub.status.busy": "2024-06-25T13:14:38.941698Z", + "iopub.status.idle": "2024-06-25T13:14:38.953695Z", + "shell.execute_reply": "2024-06-25T13:14:38.953228Z" } }, "outputs": [ @@ -247,10 +247,10 @@ "execution_count": 8, "metadata": { "execution": { - "iopub.execute_input": "2024-06-19T03:06:53.448097Z", - "iopub.status.busy": "2024-06-19T03:06:53.447674Z", - "iopub.status.idle": "2024-06-19T03:06:53.451026Z", - "shell.execute_reply": "2024-06-19T03:06:53.450471Z" + "iopub.execute_input": "2024-06-25T13:14:38.955847Z", + "iopub.status.busy": "2024-06-25T13:14:38.955493Z", + "iopub.status.idle": "2024-06-25T13:14:38.958828Z", + "shell.execute_reply": "2024-06-25T13:14:38.958381Z" } }, "outputs": [], @@ -266,10 +266,10 @@ "execution_count": 9, "metadata": { "execution": { - "iopub.execute_input": "2024-06-19T03:06:53.453001Z", - "iopub.status.busy": "2024-06-19T03:06:53.452832Z", - "iopub.status.idle": "2024-06-19T03:06:53.463815Z", - "shell.execute_reply": "2024-06-19T03:06:53.463252Z" + "iopub.execute_input": "2024-06-25T13:14:38.960897Z", + "iopub.status.busy": "2024-06-25T13:14:38.960542Z", + "iopub.status.idle": "2024-06-25T13:14:38.972877Z", + "shell.execute_reply": "2024-06-25T13:14:38.972409Z" } }, "outputs": [ @@ -302,10 +302,10 @@ "execution_count": 10, "metadata": { "execution": { - "iopub.execute_input": "2024-06-19T03:06:53.465960Z", - "iopub.status.busy": "2024-06-19T03:06:53.465642Z", - "iopub.status.idle": "2024-06-19T03:06:53.476769Z", - "shell.execute_reply": "2024-06-19T03:06:53.476329Z" + "iopub.execute_input": "2024-06-25T13:14:38.975043Z", + "iopub.status.busy": "2024-06-25T13:14:38.974702Z", + "iopub.status.idle": "2024-06-25T13:14:38.986796Z", + "shell.execute_reply": "2024-06-25T13:14:38.986328Z" } }, "outputs": [ @@ -330,10 +330,10 @@ "execution_count": 11, "metadata": { "execution": { - "iopub.execute_input": "2024-06-19T03:06:53.478708Z", - "iopub.status.busy": "2024-06-19T03:06:53.478385Z", - "iopub.status.idle": "2024-06-19T03:06:53.489094Z", - "shell.execute_reply": "2024-06-19T03:06:53.488534Z" + "iopub.execute_input": "2024-06-25T13:14:38.989012Z", + "iopub.status.busy": "2024-06-25T13:14:38.988664Z", + "iopub.status.idle": "2024-06-25T13:14:39.000278Z", + "shell.execute_reply": "2024-06-25T13:14:38.999826Z" } }, "outputs": [ @@ -368,10 +368,10 @@ "execution_count": 12, "metadata": { "execution": { - "iopub.execute_input": "2024-06-19T03:06:53.491060Z", - "iopub.status.busy": "2024-06-19T03:06:53.490891Z", - "iopub.status.idle": "2024-06-19T03:06:53.502940Z", - "shell.execute_reply": "2024-06-19T03:06:53.502346Z" + "iopub.execute_input": "2024-06-25T13:14:39.002205Z", + "iopub.status.busy": "2024-06-25T13:14:39.002047Z", + "iopub.status.idle": "2024-06-25T13:14:39.014437Z", + "shell.execute_reply": "2024-06-25T13:14:39.013944Z" } }, "outputs": [ @@ -413,10 +413,10 @@ "execution_count": 13, "metadata": { "execution": { - "iopub.execute_input": "2024-06-19T03:06:53.504988Z", - "iopub.status.busy": "2024-06-19T03:06:53.504672Z", - "iopub.status.idle": "2024-06-19T03:06:53.507576Z", - "shell.execute_reply": "2024-06-19T03:06:53.507059Z" + "iopub.execute_input": "2024-06-25T13:14:39.016523Z", + "iopub.status.busy": "2024-06-25T13:14:39.016211Z", + "iopub.status.idle": "2024-06-25T13:14:39.019432Z", + "shell.execute_reply": "2024-06-25T13:14:39.018951Z" } }, "outputs": [], @@ -434,10 +434,10 @@ "execution_count": 14, "metadata": { "execution": { - "iopub.execute_input": "2024-06-19T03:06:53.509561Z", - "iopub.status.busy": "2024-06-19T03:06:53.509233Z", - "iopub.status.idle": "2024-06-19T03:06:53.520908Z", - "shell.execute_reply": "2024-06-19T03:06:53.520440Z" + "iopub.execute_input": "2024-06-25T13:14:39.021510Z", + "iopub.status.busy": "2024-06-25T13:14:39.021162Z", + "iopub.status.idle": "2024-06-25T13:14:39.034394Z", + "shell.execute_reply": "2024-06-25T13:14:39.033888Z" } }, "outputs": [ @@ -470,10 +470,10 @@ "execution_count": 15, "metadata": { "execution": { - "iopub.execute_input": "2024-06-19T03:06:53.522962Z", - "iopub.status.busy": "2024-06-19T03:06:53.522546Z", - "iopub.status.idle": "2024-06-19T03:06:53.624140Z", - "shell.execute_reply": "2024-06-19T03:06:53.623645Z" + "iopub.execute_input": "2024-06-25T13:14:39.036510Z", + "iopub.status.busy": "2024-06-25T13:14:39.036119Z", + "iopub.status.idle": "2024-06-25T13:14:39.139835Z", + "shell.execute_reply": "2024-06-25T13:14:39.139282Z" } }, "outputs": [ @@ -541,10 +541,10 @@ "execution_count": 16, "metadata": { "execution": { - 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