Merge pull request #93 from volkamerlab/rm-wip-disclaimer

Minor repo improvements (env, README, docs)
volkamerlab · Sep 16, 2021 · 80285a7 · 80285a7
2 parents b6be420 + bdb2235
commit 80285a7
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Showing 7 changed files with 51 additions and 118 deletions.
diff --git a/README.md b/README.md
@@ -30,9 +30,7 @@ Take a look at the [repository `kissim_app`](https://github.com/volkamerlab/kiss
 
 ## Documentation
 
-> This package is still in development.
-
-The `kissim` package documentation is available [here](https://kissim.readthedocs.io/).
+The `kissim` package documentation is available [here](https://kissim.readthedocs.io/), including [installation instructions](https://kissim.readthedocs.io/en/latest/installing.html).
 
 ## Contact
 
@@ -73,7 +71,7 @@ The `kissim` project is a collaboration between the Volkamer Lab (Dominique Sydo
 - Data science (PyData stack):
   [`numpy`](https://numpy.org/),
   [`pandas`](https://pandas.pydata.org/),
-  [`scikit-learn`](https://scikit-learn.org/),
+  [`scipy`](https://scipy.org/),
   [`jupyter`](https://jupyter.org/),
   [`ipywidgets`](https://ipywidgets.readthedocs.io)
 - Data visualization:

diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
@@ -11,7 +11,7 @@ dependencies:
   - biopython=1.77
   - numpy
   - scipy
-  - matplotlib
+  - matplotlib-base
   - seaborn
   - jupyter
   - jupyterlab>=3

diff --git a/docs/tutorials/io.ipynb b/docs/tutorials/io.ipynb
diff --git a/kissim/tests/api/test_api_subset.py b/kissim/tests/api/test_api_subset.py
@@ -122,5 +122,4 @@ def test_subset_fingerprint_generator_data(
     fp_subset_sum_calculated = np.nansum(
         fingerprint_generator_data[structure_klifs_id].values_array()
     )
-    print(fp_subset_sum_calculated)
     assert pytest.approx(fp_subset_sum_calculated, abs=1e-3) == fp_subset_sum
diff --git a/kissim/tests/data/KLIFS_download/klifs_metadata.csv b/kissim/tests/data/KLIFS_download/klifs_metadata.csv
@@ -1,4 +1,4 @@
-species.klifs,structure.pdb_id,structure.alternate_model,structure.chain,ligand.expo_id,ligand_allosteric.expo_id,structure.rmsd1,structure.rmsd2,structure.qualityscore,structure.pocket,structure.resolution,structure.missing_residues,structure.missing_atoms,interaction.fingerprint,structure.fp_i,structure.fp_ii,structure.bp_i_a,structure.bp_i_b,structure.bp_ii_in,structure.bp_ii_a_in,structure.bp_ii_b_in,structure.bp_ii_out,structure.bp_ii_b,structure.bp_iii,structure.bp_iv,structure.bp_v,kinase.names,kinase.hgnc_name,kinase.klifs_name,kinase.family,kinase.group,ligand.name,ligand_allosteric.name,structure.dfg,structure.ac_helix,structure.filepath,structure.klifs_id,kinase.klifs_id
+species.klifs,structure.pdb_id,structure.alternate_model,structure.chain,ligand.expo_id,ligand_allosteric.expo_id,structure.rmsd1,structure.rmsd2,structure.qualityscore,structure.pocket,structure.resolution,structure.missing_residues,structure.missing_atoms,interaction.fingerprint,structure.fp_i,structure.fp_ii,structure.bp_i_a,structure.bp_i_b,structure.bp_ii_in,structure.bp_ii_a_in,structure.bp_ii_b_in,structure.bp_ii_out,structure.bp_ii_b,structure.bp_iii,structure.bp_iv,structure.bp_v,kinase.names,kinase.gene_name,kinase.klifs_name,kinase.family,kinase.group,ligand.name,ligand_allosteric.name,structure.dfg,structure.ac_helix,structure.filepath,structure.klifs_id,kinase.klifs_id
 Human,3gvu,B,A,STI,STI,0.896,2.289,9.8,HKLGGGQYGEVYVVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIVTEYMPYGNLLDYLREYLEKKNFIHRDLAARNCLVVADFGLS,2.05,0,2,0000000000000010000000000000000000000000000000000101000000000000000000100000000000000000000000000010000001000000100000000000000000000000000000000000000000000000010001000000000000000010000001000000000000000000001000000000000000000000000000000000010000000000000000000000000000000000000000000000001000000000000010001000000000110000010010000000000000000010000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000010000001000100100010010000000000000000000000000000000000000000000000000000000100000000000000000000100000010010001010000000000000000000000000,0.0,0.0,1.0,1.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,0.0,['ABL2'],ABL2,ABL2,Abl,TK,4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE,4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE,out,out,HUMAN/ABL2/3gvu_altB_chainA,109,393
 Human,3hmi,B,A,DKI,-,0.846,2.155,9.5,HKLGGGQYGEVYVVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIVTEYMPYGNLLDYLREYLEKKNFIHRDLAARNCLVVADFGLS,1.65,0,5,0000000000000010000001000000000000000000000000000110000000000000000000100000000000000000000000000010000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000010000000000000000000000000000000000000000000000000000000000000000000000000100110000010011000000000000000010000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000100000010000000000000100000000000000000000100000000000001010000000000000000000000000,1.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,['ABL2'],ABL2,ABL2,Abl,TK,"5-AMINO-3-{[4-(AMINOSULFONYL)PHENYL]AMINO}-N-(2,6-DIFLUOROPHENYL)-1H-1,2,4-TRIAZOLE-1-CARBOTHIOAMIDE",-,out-like,in,HUMAN/ABL2/3hmi_altB_chainA,118,393
 Human,2xyn,A,A,VX6,-,0.78,2.126,8.0,HKLGGGQYGEVYVVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIVTEYMPYGNLLDYLREYLEKKNFIHRDLAARNCLVVADFGLS,2.81,0,34,0000000000000010000001000000000000000000000000000110000000000000000000100000000000000000000000000010000000000000100000000000000000000000000000000000000000000000010000000000000000000000000001000000000000000000000000000000000000000000000000000000010000000000000000000000000000000000000000000000001000000000000010000000000000110000010001001000000100000010000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000100000000000000000000000000010001000000000000000000000000000000,0.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,['ABL2'],ABL2,ABL2,Abl,TK,CYCLOPROPANECARBOXYLIC ACID {4-[4-(4-METHYL-PIPERAZIN-1-YL)-6-(5-METHYL-2H-PYRAZOL-3-YLAMINO)-PYRIMIDIN-2-YLSULFANYL]-PHENYL}-AMIDE,-,in,in,HUMAN/ABL2/2xyn_altA_chainA,110,393

diff --git a/kissim/tests/encoding/test_fingerprint.py b/kissim/tests/encoding/test_fingerprint.py
@@ -111,8 +111,6 @@ def test_values_array(self, structure_klifs_id, values_array_mean):
 
         fingerprint = Fingerprint.from_structure_klifs_id(structure_klifs_id, LOCAL)
         values_array_mean_calculated = np.nanmean(fingerprint.values_array(True, True, True))
-        print(fingerprint.values_array(True, True, True)[:8])
-        print(fingerprint.values_array(True, True, True)[17 * 8 : 18 * 8])
         assert pytest.approx(values_array_mean_calculated, abs=1e-4) == values_array_mean
 
         # Test the different lengths of the final fingerprint based on the selection of

diff --git a/kissim/viewer/base.py b/kissim/viewer/base.py
@@ -150,6 +150,8 @@ def _from_structure_klifs_ids(cls, structure_klifs_ids, klifs_session=None):
         texts = {}
         for structure_klifs_id in structure_klifs_ids:
             try:
+                # Hack! KLIFS IDs may be of type numpy.int32, cast to int!
+                structure_klifs_id = int(structure_klifs_id)
                 texts[structure_klifs_id] = klifs_session.coordinates.to_text(
                     structure_klifs_id, "complex", "pdb"
                 )