From 8a8c5ede1573a9a781c7e5c0977baf3e1a48d7a4 Mon Sep 17 00:00:00 2001
From: Sulstice <sharifsuliman1@gmail.com>
Date: Thu, 31 Mar 2022 07:51:13 -0400
Subject: [PATCH] ss-main: added first pass

---
 .../global_chem_extensions.py                 | 23 ++++++++++++-
 .../smarts_pattern_visualizer.py              |  7 ----
 .../__init__.py                               |  0
 .../smarts_visualizer/smarts_visualizer.py    | 34 +++++++++++++++++++
 global_chem_extensions/setup.py               |  2 +-
 5 files changed, 57 insertions(+), 9 deletions(-)
 delete mode 100644 global_chem_extensions/global_chem_extensions/software_adapters/smarts_pattern_visualizer/smarts_pattern_visualizer.py
 rename global_chem_extensions/global_chem_extensions/software_adapters/{smarts_pattern_visualizer => smarts_visualizer}/__init__.py (100%)
 create mode 100644 global_chem_extensions/global_chem_extensions/software_adapters/smarts_visualizer/smarts_visualizer.py

diff --git a/global_chem_extensions/global_chem_extensions/global_chem_extensions.py b/global_chem_extensions/global_chem_extensions/global_chem_extensions.py
index 2c312548..48c7b6eb 100644
--- a/global_chem_extensions/global_chem_extensions/global_chem_extensions.py
+++ b/global_chem_extensions/global_chem_extensions/global_chem_extensions.py
@@ -17,11 +17,15 @@
 from global_chem_extensions.analysis_tools.drug_design_filters.drug_design_filters import DrugDesignFilters
 from global_chem_extensions.analysis_tools.node_pca_analysis.node_pca_analysis import PCAAnalysis
 
-# Adapters
+# Software Adapters
 
 from global_chem_extensions.software_adapters.pdf_adapter.molpdf_parser import MolPDFAdapter
 from global_chem_extensions.software_adapters.networkx_adapter.networkx_adapter import NetworkxAdapter
+from global_chem_extensions.software_adapters.smarts_visualizer.smarts_visualizer import SmartsVisualizer
 from global_chem_extensions.software_adapters.dimorphite_dl_adapter.dimorphite_dl import DimorphiteAdapter
+
+# Language Adapters
+
 from global_chem_extensions.language_adapters.amino_acid_converter.amino_acid_converter import AminoAcidConverter
 
 # Machine Learning
@@ -474,3 +478,20 @@ def initialize_cgenff_molecule(stream_file):
 
         return cgenff_molecule
 
+
+    @staticmethod
+    def visualize_smarts(smarts):
+
+        '''
+
+        Arguments:
+            smarts (String): Viusalize the SMARTS string
+
+        '''
+
+        visualizer = SmartsVisualizer(
+            smarts
+        )
+
+        return visualizer.get_image()
+
diff --git a/global_chem_extensions/global_chem_extensions/software_adapters/smarts_pattern_visualizer/smarts_pattern_visualizer.py b/global_chem_extensions/global_chem_extensions/software_adapters/smarts_pattern_visualizer/smarts_pattern_visualizer.py
deleted file mode 100644
index 03d09984..00000000
--- a/global_chem_extensions/global_chem_extensions/software_adapters/smarts_pattern_visualizer/smarts_pattern_visualizer.py
+++ /dev/null
@@ -1,7 +0,0 @@
-#!/usr/bin/env python3
-#
-# GlobalChemExtensions - SMARTS Pattern Visualizer
-#
-# ------------------------------------------------
-
-
diff --git a/global_chem_extensions/global_chem_extensions/software_adapters/smarts_pattern_visualizer/__init__.py b/global_chem_extensions/global_chem_extensions/software_adapters/smarts_visualizer/__init__.py
similarity index 100%
rename from global_chem_extensions/global_chem_extensions/software_adapters/smarts_pattern_visualizer/__init__.py
rename to global_chem_extensions/global_chem_extensions/software_adapters/smarts_visualizer/__init__.py
diff --git a/global_chem_extensions/global_chem_extensions/software_adapters/smarts_visualizer/smarts_visualizer.py b/global_chem_extensions/global_chem_extensions/software_adapters/smarts_visualizer/smarts_visualizer.py
new file mode 100644
index 00000000..544dfa21
--- /dev/null
+++ b/global_chem_extensions/global_chem_extensions/software_adapters/smarts_visualizer/smarts_visualizer.py
@@ -0,0 +1,34 @@
+#!/usr/bin/env python3
+#
+# GlobalChemExtensions - SMARTS Pattern Visualizer
+#
+# ------------------------------------------------
+
+
+# Imports
+# -------
+
+import urllib
+import requests
+
+from rdkit import Chem
+from IPython.display import Image
+
+class SmartsVisualizer(object):
+
+    __version__ = '0.0.1'
+
+
+    def __init__(self,
+                 smarts_pattern
+        ):
+
+        self.smarts_pattern = smarts_pattern
+
+        self.base_url = "https://smarts.plus/smartsview/download_rest?"
+        self.url = self.base_url + f"smarts={self.smarts_pattern}"
+
+    def get_image(self):
+
+        res = requests.get(self.url)
+        return Image(res.content)
\ No newline at end of file
diff --git a/global_chem_extensions/setup.py b/global_chem_extensions/setup.py
index 91fbea7b..41c63c1e 100644
--- a/global_chem_extensions/setup.py
+++ b/global_chem_extensions/setup.py
@@ -36,7 +36,7 @@
 # ----
 setup(
     name="global_chem_extensions",
-    version="0.6.6",
+    version="0.7.5",
     packages=find_packages(),
     license='MPL 2.0',
     author="Suliman Sharif",