removed hyphen from python file names

InformaticsMatters · Jul 16, 2020 · 1d97336 · 1d97336
1 parent c8cd73b
commit 1d97336
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Showing 6 changed files with 14 additions and 12 deletions.
diff --git a/requirements-rdkit.txt b/requirements-rdkit.txt
@@ -5,3 +5,4 @@ molvs==0.1.1
 standardiser==0.1.9
 pandas==1.0.1
 scikit-learn==0.22.1
+requests==2.24.0
diff --git a/src/nextflow/xchem/featurestein.nf b/src/nextflow/xchem/featurestein.nf
@@ -20,7 +20,7 @@ process generate_feat_maps {
     file 'featurestein.p' into fmaps
 
     """
-    python -m pipelines.xchem.featurestein-generate -i '$fragments' -f featurestein.p
+    python -m pipelines.xchem.featurestein_generate -i '$fragments' -f featurestein.p
     """
 }
 
@@ -51,7 +51,7 @@ process score {
     file 'scored_part*.sdf' into scored_parts
 
     """
-    python -m pipelines.xchem.featurestein-score -i '$part' -f '$fmaps' -o '${part.name.replace('inputs', 'scored')[0..-8]}' -of sdf --no-gzip
+    python -m pipelines.xchem.featurestein_score -i '$part' -f '$fmaps' -o '${part.name.replace('inputs', 'scored')[0..-8]}' -of sdf --no-gzip
     """
 }
 

diff --git a/.../pipelines/xchem/featurestein-generate.py → .../pipelines/xchem/featurestein_generate.py b/.../pipelines/xchem/featurestein-generate.py → .../pipelines/xchem/featurestein_generate.py
@@ -17,7 +17,7 @@
 """
 Ligand pose scoring using 'FeatureStein'.
 This module generates a merged feature map from a set of 3D ligands.
-The output is a pickle of the merged feature map that can be read by the featurestein-score.py module to
+The output is a pickle of the merged feature map that can be read by the featurestein_score.py module to
 generate scores.
 """
 
@@ -82,12 +82,13 @@ def build_feat_data(mols):
 
 def find_closest(scores):
     #print('Find closest for', len(scores), len(scores[0]))
-    best_score = 0
+    best_score = -1.0
     for i in range(len(scores)):
         for j in range(len(scores)):
             if i == j:
                 continue
             score = scores[i][j]
+            utils.log('Score:', score)
             if score > best_score:
                 best_score = score
                 best_row = i
@@ -151,7 +152,7 @@ def process(inputs, fname):
 def main():
 
     # Example usage:
-    # python -m pipelines.xchem.featurestein-generate -i ../../data/mpro/hits-17.sdf.gz -f mpro-fstein.p
+    # python -m pipelines.xchem.featurestein_generate -i ../../data/mpro/hits-17.sdf.gz -f mpro-fstein.p
 
     global fmaps
 

diff --git a/...ipelines/xchem/featurestein-generate.test → ...ipelines/xchem/featurestein_generate.test b/...ipelines/xchem/featurestein-generate.test → ...ipelines/xchem/featurestein_generate.test
@@ -4,11 +4,11 @@
 
     version = 1,
 
-    // Testing featurestein-generate.py
+    // Testing featurestein_generate.py
     // reading from STDIN and writing to STDOUT
     test_featurestein_generate = [
 
-        command: '''python -m pipelines.rdkit.featurestein-generate
+        command: '''python -m pipelines.xchem.featurestein_generate
                  -i ${PIN}/mpro/hits-17.sdf.gz
                  -f ${POUT}featurestein.p''',
 

diff --git a/...hon/pipelines/xchem/featurestein-score.py → ...hon/pipelines/xchem/featurestein_score.py b/...hon/pipelines/xchem/featurestein-score.py → ...hon/pipelines/xchem/featurestein_score.py
@@ -18,7 +18,7 @@
 Ligand pose scoring using 'FeatureStein'.
 FeatureStein is a merged RDKit feature map that estimates the overlap of a ligand with a set of ligands (e.g. fragment
 screening hits) based on the RDKit feature maps.
-See featurestein-generate.py for how to generate the merged feature maps.
+See featurestein_generate.py for how to generate the merged feature maps.
 """
 
 from __future__ import print_function
@@ -96,7 +96,7 @@ def process(inputs, writer):
 def main():
 
     # Example usage
-    # python -m pipelines.xchem.featurestein-score -i ../../data/mpro/poses.sdf.gz -f mpro-fstein.p -o fstein
+    # python -m pipelines.xchem.featurestein_score -i ../../data/mpro/poses.sdf.gz -f mpro-fstein.p -o fstein
 
     global fmaps
 
@@ -110,7 +110,7 @@ def main():
     args = parser.parse_args()
     utils.log("FeatureStein Args: ", args)
 
-    source = "featurestein-score.py"
+    source = "featurestein_score.py"
     datasetMetaProps = {"source":source, "description": "FeatureStein scoring using RDKit " + rdBase.rdkitVersion}
 
     clsMappings = {}

diff --git a/...n/pipelines/xchem/featurestein-score.test → ...n/pipelines/xchem/featurestein_score.test b/...n/pipelines/xchem/featurestein-score.test → ...n/pipelines/xchem/featurestein_score.test
@@ -4,11 +4,11 @@
 
     version = 1,
 
-    // Testing featurestein-score.py
+    // Testing featurestein_score.py
     // reading from STDIN and writing to STDOUT
     test_featurestein_score = [
 
-        command: '''python -m pipelines.xchem.featurestein-score
+        command: '''python -m pipelines.xchem.featurestein_score
                  -i ${PIN}/mpro/poses.sdf.gz
                  -f ${PIN}/mpro/featurestein.p
                  -o ${POUT}fstein''',