ss/MASTER added new code for 0.3.0

Sulstice · Jun 19, 2020 · fadecec · fadecec
1 parent 101b2e8
commit fadecec
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Showing 6 changed files with 20 additions and 7 deletions.
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -0,0 +1 @@
+include README.md requirements.in requirements.txt
diff --git a/README.md b/README.md
@@ -74,7 +74,7 @@ Generate a List a PDF of Amino Acids
     document.add_spacer()
 
     smiles_amino_acids = list(amino_acid_side_chains.values())
-    document.generate(smiles=smiles_amino_acids)
+    document.generate(smiles=smiles_amino_acids, include_failed_smiles=True)
     
 ```
 

diff --git a/examples/functional_groups.pdf b/examples/functional_groups.pdf
diff --git a/molpdf/molpdf.py b/molpdf/molpdf.py
@@ -325,26 +325,35 @@ def add_title(self, title):
         title = Paragraph(title, self.styles['Line_Label_Center_Big'])
         self.story.append(title)
 
-    def add_image(self, smiles, temporary_directory):
+    def add_image(self, smiles, temporary_directory, include_failed_smiles=False):
 
         """
 
         Arguments:
             smiles (String): smiles representation of the molecule
             temporary_directory (tempfile object): Temporary directory of the module
+            include_failed_smiles (Bool): whether the user would like to include failed smiles.
 
         """
 
         indigo = Indigo()
         renderer = IndigoRenderer(indigo)
 
-        molecule = indigo.loadMolecule(smiles)
+        try:
+            molecule = indigo.loadMolecule(smiles)
+        except IndigoException as e:
+            if include_failed_smiles:
+                self.add_row("Failed Rendering", smiles)
+            return
+
         molecule.layout() # if not called, will be done automatically by the renderer
         indigo.setOption("render-output-format", "png")
         indigo.setOption("render-image-size", 400, 400)
         indigo.setOption("render-background-color", 1.0, 1.0, 1.0)
 
-        path = os.path.join(temporary_directory, smiles + '.png')
+        import uuid
+
+        path = os.path.join(temporary_directory,  str(uuid.uuid4()) + '.png')
 
         renderer.renderToFile(molecule, filename=path)
         image = Image(path, 1 * inch, 1 * inch, hAlign='CENTER')
@@ -421,7 +430,7 @@ def add_row(self, image, smiles):
         self.story.append(table)
 
     @timeit
-    def generate(self, smiles):
+    def generate(self, smiles, include_failed_smiles=False):
 
 
         """
@@ -440,7 +449,7 @@ def generate(self, smiles):
             self.smiles = smiles
 
             for smiles in self.smiles:
-                self.add_image(smiles, tmp)
+                self.add_image(smiles, tmp, include_failed_smiles)
 
             # Build the initial PDF using Reportlab
             self.doc.build(self.story)

diff --git a/requirements.txt b/requirements.txt
@@ -1,6 +1,9 @@
 epam.indigo==1.4.0b0
 numpy==1.18.3
 opencv-python==4.2.0.34
+pdfminer==20191125
+pdfrw==0.4
 Pillow==7.1.1
+pycryptodome==3.9.7
 reportlab==3.5.42
 six==1.14.0
diff --git a/setup.py b/setup.py
@@ -35,7 +35,7 @@
 # ----
 setup(
     name="molpdf",
-    version="0.2.0",
+    version="0.3.0",
     packages=['molpdf'],
     license='MPL 2.0',
     author="Suliman Sharif",