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v 1.3 w. compare across files functionality"
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‎CHANGELOG.txt

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@@ -1,3 +1,7 @@
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**VERSION 1.3.0**
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- added script and module function to compare SMILE strings across 2 files.
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**VERSION 1.2.0**
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- added Python 2.x support

‎README.md

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@@ -7,11 +7,14 @@ smilite is a Python module to download and analyze SMILE strings (Simplified Mol
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Now supports both Python 3.x and Python 2.x.
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####Sections
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<p><a href="#installation">Installation</a><br>
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<p><a href="#documentation">Documentation</a><br>
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<p><a href="#examples">Command Line Scripts Examples</a><br>
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<p><a href="#contact">Contact</a><br>
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<p><a href="#changelog">Changelog</a><br>
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&#8226; <a href="#installation">Installation</a><br>
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&#8226; <a href="#documentation">Documentation</a><br>
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&#8226; <a href="#examples">Command Line Scripts Examples</a><br>
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&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&#45; <a href="#gen_zincid">gen_zincid_smile_csv.py (downloading SMILES)</a><br>
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&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&#45; <a href="#comp_smile">comp_smile_strings.py (checking for duplicates within 1 file)</a><br>
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&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&#45; <a href="#comp_2_smile">comp_2_smile_files.py (checking for duplicates across 2 files)</a><br>
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&#8226; <a href="#contact">Contact</a><br>
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&#8226; <a href="#changelog">Changelog</a><br>
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<br>
@@ -42,47 +45,92 @@ Documentation
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After you installed the smilite module, you can import it in Python via `import smilite`.
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The current functions include:
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<pre>def get_zinc_smile(zinc_id):
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Gets the corresponding SMILE string for a ZINC ID query from
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the ZINC online database. Requires an internet connection.
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Keyword arguments:
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zinc_id (str): A valid ZINC ID, e.g. 'ZINC00029323'
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Returns the SMILE string for the corresponding ZINC ID.
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E.g., 'COc1cccc(c1)NC(=O)c2cccnc2'</pre>
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<div style="background: #ffffff; overflow:auto;width:auto;border:solid gray;border-width:.1em .1em .1em .8em;padding:.2em .6em;"><pre style="margin: 0; line-height: 125%"><span style="color: #008800; font-weight: bold">def</span> <span style="color: #0066BB; font-weight: bold">get_zinc_smile</span>(zinc_id):
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<span style="color: #DD4422">&quot;&quot;&quot;</span>
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<span style="color: #DD4422"> Gets the corresponding SMILE string for a ZINC ID query from</span>
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<span style="color: #DD4422"> the ZINC online database. Requires an internet connection.</span>
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<span style="color: #DD4422"> Keyword arguments:</span>
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<span style="color: #DD4422"> zinc_id (str): A valid ZINC ID, e.g. &#39;ZINC00029323&#39;</span>
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<span style="color: #DD4422"> Returns the SMILE string for the corresponding ZINC ID.</span>
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<span style="color: #DD4422"> E.g., &#39;COc1cccc(c1)NC(=O)c2cccnc2&#39;</span>
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<span style="color: #DD4422"> &quot;&quot;&quot;</span>
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</pre></div>
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<div style="background: #ffffff; overflow:auto;width:auto;border:solid gray;border-width:.1em .1em .1em .8em;padding:.2em .6em;"><pre style="margin: 0; line-height: 125%"><span style="color: #008800; font-weight: bold">def</span> <span style="color: #0066BB; font-weight: bold">simplify_smile</span>(smile_str):
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<span style="color: #DD4422">&quot;&quot;&quot; </span>
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<span style="color: #DD4422"> Simplifies a SMILE string by removing hydrogen atoms (H), </span>
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<span style="color: #DD4422"> chiral specifications (&#39;@&#39;), charges (+ / -), &#39;#&#39;-characters,</span>
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<span style="color: #DD4422"> and square brackets (&#39;[&#39;, &#39;]&#39;).</span>
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<span style="color: #DD4422"> Keyword Arguments:</span>
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<span style="color: #DD4422"> smile_str (str): A smile string, e.g., C[C@H](CCC(=O)NCCS(=O)(=O)[O-])</span>
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<span style="color: #DD4422"> </span>
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<span style="color: #DD4422"> Returns a simplified SMILE string, e.g., CC(CCC(=O)NCCS(=O)(=O)O)</span>
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<span style="color: #DD4422"> &quot;&quot;&quot;</span>
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</pre></div>
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<pre>def generate_zincid_smile_csv(zincid_list, out_file):
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Generates a CSV file of ZINC_ID,SMILE_string entries by querying the ZINC online
55-
database.
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Keyword arguments:
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zincid_list (str): Path to a UTF-8 or ASCII formatted file
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that contains 1 ZINC_ID per row. E.g.,
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ZINC0000123456
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ZINC0000234567
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[...]
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out_file (str): Path to a new output CSV file that will be written.
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print_prgress_bar (bool): Prints a progress bar to the screen if True.</pre>
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<pre>def check_duplicate_smiles(zincid_list, out_file, compare_simplified_smiles=False,
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print_progress_bar=False):
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Scans a ZINC_ID,SMILE_string CSV file for duplicate SMILE strings.
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Keyword arguments:
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zincid_list (str): Path to a UTF-8 or ASCII formatted file that
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contains 1 ZINC_ID per row.
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E.g.,
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ZINC12345678,Cc1ccc(cc1C)OCCOc2c(cc(cc2I)/C=N/n3cnnc3)OC
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ZINC01234567,C[C@H]1CCCC[NH+]1CC#CC(c2ccccc2)(c3ccccc3)O
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[...]
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out_file (str): Path to a new output CSV file that will be written.
76-
compare_simplified_smiles (bool): If true, SMILE strings will be simplified
77-
for the comparison.</pre>
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<div style="background: #ffffff; overflow:auto;width:auto;border:solid gray;border-width:.1em .1em .1em .8em;padding:.2em .6em;"><pre style="margin: 0; line-height: 125%"><span style="color: #008800; font-weight: bold">def</span> <span style="color: #0066BB; font-weight: bold">generate_zincid_smile_csv</span>(zincid_list, out_file, print_progress_bar<span style="color: #333333">=</span><span style="color: #007020">False</span>):
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<span style="color: #DD4422">&quot;&quot;&quot;</span>
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<span style="color: #DD4422"> Generates a CSV file of ZINC_ID,SMILE_string entries by querying the ZINC online</span>
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<span style="color: #DD4422"> database.</span>
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<span style="color: #DD4422"> Keyword arguments:</span>
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<span style="color: #DD4422"> zincid_list (str): Path to a UTF-8 or ASCII formatted file </span>
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<span style="color: #DD4422"> that contains 1 ZINC_ID per row. E.g., </span>
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<span style="color: #DD4422"> ZINC0000123456</span>
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<span style="color: #DD4422"> ZINC0000234567</span>
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<span style="color: #DD4422"> [...]</span>
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<span style="color: #DD4422"> out_file (str): Path to a new output CSV file that will be written.</span>
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<span style="color: #DD4422"> print_prgress_bar (bool): Prints a progress bar to the screen if True.</span>
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<span style="color: #DD4422"> &quot;&quot;&quot;</span>
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</pre></div>
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<div style="background: #ffffff; overflow:auto;width:auto;border:solid gray;border-width:.1em .1em .1em .8em;padding:.2em .6em;"><pre style="margin: 0; line-height: 125%"><span style="color: #008800; font-weight: bold">def</span> <span style="color: #0066BB; font-weight: bold">check_duplicate_smiles</span>(zincid_list, out_file, compare_simplified_smiles<span style="color: #333333">=</span><span style="color: #007020">False</span>):
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<span style="color: #DD4422">&quot;&quot;&quot;</span>
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<span style="color: #DD4422"> Scans a ZINC_ID,SMILE_string CSV file for duplicate SMILE strings.</span>
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<span style="color: #DD4422"> Keyword arguments:</span>
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<span style="color: #DD4422"> zincid_list (str): Path to a UTF-8 or ASCII formatted file that </span>
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<span style="color: #DD4422"> contains 1 ZINC_ID + 1 SMILE String per row.</span>
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<span style="color: #DD4422"> E.g., </span>
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<span style="color: #DD4422"> ZINC12345678,Cc1ccc(cc1C)OCCOc2c(cc(cc2I)/C=N/n3cnnc3)OC</span>
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<span style="color: #DD4422"> ZINC01234567,C[C@H]1CCCC[NH+]1CC#CC(c2ccccc2)(c3ccccc3)O</span>
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<span style="color: #DD4422"> [...]</span>
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<span style="color: #DD4422"> out_file (str): Path to a new output CSV file that will be written.</span>
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<span style="color: #DD4422"> compare_simplified_smiles (bool): If true, SMILE strings will be simplified</span>
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<span style="color: #DD4422"> for the comparison.</span>
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<span style="color: #DD4422"> </span>
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<span style="color: #DD4422"> &quot;&quot;&quot;</span>
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</pre></div>
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<div style="background: #ffffff; overflow:auto;width:auto;border:solid gray;border-width:.1em .1em .1em .8em;padding:.2em .6em;"><pre style="margin: 0; line-height: 125%"><span style="color: #008800; font-weight: bold">def</span> <span style="color: #0066BB; font-weight: bold">comp_two_files</span>(zincid_list1, zincid_list2, out_file, compare_simplified_smiles<span style="color: #333333">=</span><span style="color: #007020">False</span>):
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<span style="color: #DD4422">&quot;&quot;&quot;</span>
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<span style="color: #DD4422"> Compares SMILE strings across two ZINC_ID files for duplicates </span>
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<span style="color: #DD4422"> (does not check for duplicates within each file).</span>
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<span style="color: #DD4422"> Keyword arguments:</span>
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<span style="color: #DD4422"> zincid_list1 (str): Path to a UTF-8 or ASCII formatted file that </span>
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<span style="color: #DD4422"> contains 1 ZINC_ID + 1 SMILE String per row.</span>
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<span style="color: #DD4422"> E.g., </span>
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<span style="color: #DD4422"> ZINC12345678,Cc1ccc(cc1C)OCCOc2c(cc(cc2I)/C=N/n3cnnc3)OC</span>
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<span style="color: #DD4422"> ZINC01234567,C[C@H]1CCCC[NH+]1CC#CC(c2ccccc2)(c3ccccc3)O</span>
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<span style="color: #DD4422"> [...]</span>
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<span style="color: #DD4422"> zincid_list2 (str): Second ZINC_ID list file, similarly </span>
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<span style="color: #DD4422"> out_file (str): Path to a new output CSV file that will be written.</span>
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<span style="color: #DD4422"> compare_simplified_smiles (bool): If true, SMILE strings will be simplified</span>
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<span style="color: #DD4422"> for the comparison.</span>
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<span style="color: #DD4422"> </span>
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<span style="color: #DD4422"> &quot;&quot;&quot;</span>
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</pre></div>
78133

79-
<pre>def simplify_smile(smile_str):
80-
Simplifies a SMILE string by removing hydrogen atoms (H),
81-
chiral specifications ('@'), charges (+ / -), '#'-characters,
82-
and square brackets ('[', ']').
83-
Keyword Arguments:
84-
smile_str (str): A smile string, e.g., C[C@H](CCC(=O)NCCS(=O)(=O)[O-])
85-
Returns a simplified SMILE string, e.g., CC(CCC(=O)NCCS(=O)(=O)O)</pre>
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<br>
@@ -99,7 +147,9 @@ If you downloaded the smilite package from [https://pypi.python.org/pypi/smilite
99147
<br>
100148
<br>
101149

102-
###gen_zincid_smile_csv.py
150+
<p><a name="gen_zincid"></a></p>
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###gen_zincid_smile_csv.py (downloading SMILES)
103153

104154
Generates a ZINC_ID,SMILE_STR csv file from a input file of
105155
ZINC IDs. The input file should consist of 1 columns with 1 ZINC ID per row.
@@ -129,10 +179,11 @@ Downloading SMILES
129179

130180
<br>
131181
<br>
182+
<p><a name="comp_smile"></a></p>
132183

133-
###comp_smile_strings.py
184+
###comp_smile_strings.py (checking for duplicates within 1 file)
134185

135-
Compares SMILE strings in a 2 column CSV file (ZINC_ID,SMILE_string) to identify duplicates. Generates a new CSV file with ZINC IDs of identified
186+
Compares SMILE strings within a 2 column CSV file (ZINC_ID,SMILE_string) to identify duplicates. Generates a new CSV file with ZINC IDs of identified
136187
duplicates listed in a 3rd-nth column(s).
137188

138189
**Usage:**
@@ -173,6 +224,56 @@ Where
173224
![](https://raw.github.com/rasbt/smilite/master/images/comp_simple_smiles.png)
174225
[comp_simple_smiles.csv](https://raw.github.com/rasbt/smilite/master/examples/comp_simple_smiles.csv)
175226

227+
<br>
228+
<br>
229+
<p><a name="comp_2_smile"></a></p>
230+
231+
###comp_2_smile_files.py (checking for duplicates across 2 files)
232+
233+
Compares SMILE strings between 2 input CSV files, where each file consists of rows with 2 columns ZINC_ID,SMILE_string to identify duplicate SMILE string across both files.
234+
Generates a new CSV file with ZINC IDs of identified duplicates listed in a 3rd-nth column(s).
235+
236+
237+
**Usage:**
238+
`[shell]>> python3 comp_2_smile_files.py in1.csv in2.csv out.csv [simplify]`
239+
240+
**Example:**
241+
`[shell]>> python3 comp_2_smile_files.py ../examples/zid_smiles2.csv ../examples/zid_smiles3.csv ../examples/comp_2_files.csv`
242+
243+
244+
<br>
245+
246+
**Input example file 1:**
247+
![](https://raw.github.com/rasbt/smilite/master/images/zid_smiles2.png)
248+
[zid_smiles2.csv](https://raw.github.com/rasbt/smilite/master/examples/zid_smiles2.csv)
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250+
<br>
251+
252+
**Input example file 2:**
253+
![](https://raw.github.com/rasbt/smilite/master/images/zid_smiles3.png)
254+
[zid_smiles3.csv](https://raw.github.com/rasbt/smilite/master/examples/zid_smiles3.csv)
255+
256+
<br>
257+
258+
**Output example file format:**
259+
![](https://raw.github.com/rasbt/smilite/master/images/comp_2_files.png)
260+
[comp_2_files.csv](https://raw.github.com/rasbt/smilite/master/examples/comp_2_files.csv)
261+
262+
<br>
263+
264+
Where:
265+
- 1st column: name of the origin file
266+
- 2nd column: ZINC ID
267+
- 3rd column: SMILE string
268+
- 4th-nth column: ZINC IDs of duplicates
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270+
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272+
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176277
<br>
177278
<br>
178279

@@ -194,6 +295,11 @@ or Twitter: [@rasbt](https://twitter.com/rasbt)
194295
Changelog
195296
==========
196297

298+
**VERSION 1.3.0**
299+
300+
- added script and module function to compare SMILE strings across 2 files.
301+
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197303
**VERSION 1.2.0**
198304

199305
- added Python 2.x support

‎examples/comp_2_files.csv

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file_origin,zinc_id,smile_str,duplicates
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examples/zid_smiles2.csv,ZINC00029323,COc1cccc(c1)NC(=O)c2cccnc2,
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examples/zid_smiles2.csv,ZINC83310457,Cc1cccc(c1n2c(cc(c2C)/C=N\NC(=O)C(=O)Nc3ccc(cc3)[N+](=O)[O-])C)C,
4+
examples/zid_smiles2.csv,ZINC12345678,Cc1ccc(cc1C)OCCOc2c(cc(cc2I)/C=N/n3cnnc3)OC,ZINC12345678,
5+
examples/zid_smiles2.csv,ZINC12345678,Cc1ccc(cc1C)OCCOc2c(cc(cc2I)/C=N/n3cnnc3)OC,ZINC12345678,
6+
examples/zid_smiles3.csv,ZINC12345678,Cc1ccc(cc1C)OCCOc2c(cc(cc2I)/C=N/n3cnnc3)OC,ZINC12345678,ZINC12345678,
7+
examples/zid_smiles3.csv,ZINC01234567,C[C@H]1CCCC[NH+]1CC#CC(c2ccccc2)(c3ccccc3)O,
8+
examples/zid_smiles3.csv,ZINC03245324,c1ccc(c(c1)C#N)Sc2ccccc2C(=O)OCC(=O)Nc3ccc4c(c3)OCCO4,

‎examples/zid_smiles2.csv

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ZINC00029323,COc1cccc(c1)NC(=O)c2cccnc2
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ZINC83310457,Cc1cccc(c1n2c(cc(c2C)/C=N\NC(=O)C(=O)Nc3ccc(cc3)[N+](=O)[O-])C)C
3+
ZINC12345678,Cc1ccc(cc1C)OCCOc2c(cc(cc2I)/C=N/n3cnnc3)OC
4+

‎examples/zid_smiles3.csv

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ZINC12345678,Cc1ccc(cc1C)OCCOc2c(cc(cc2I)/C=N/n3cnnc3)OC
2+
ZINC01234567,C[C@H]1CCCC[NH+]1CC#CC(c2ccccc2)(c3ccccc3)O
3+
ZINC03245324,c1ccc(c(c1)C#N)Sc2ccccc2C(=O)OCC(=O)Nc3ccc4c(c3)OCCO4

‎images/comp_2_files.png

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‎images/zid_smiles2.png

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‎images/zid_smiles3.png

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‎scripts/comp_2_smile_files.py

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1+
# Copyright 2014 Sebastian Raschka
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#
3+
# Compares SMILE strings between 2 input CSV files, where each file consists of rows
4+
# with 2 columns ZINC_ID,SMILE_string to identify duplicate SMILE string across both files.
5+
# Generates a new CSV file with ZINC IDs of identified
6+
# duplicates listed in a 3rd-nth column(s).
7+
#
8+
#
9+
# Input example file format:
10+
# ZINC00029323,COc1cccc(c1)NC(=O)c2cccnc2
11+
# ZINC00029323,COc1cccc(c1)NC(=O)c2cccnc2
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# ZINC83310457,Cc1cccc(c1n2c(cc(c2C)/C=N\NC(=O)C(=O)Nc3ccc(cc3)[N+](=O)[O-])C)C
13+
# ZINC01234567,C[C@H]1CCCC[NH+]1CC#CC(c2ccccc2)(c3ccccc3)O
14+
#
15+
# Output example file format:
16+
# file_origin,zinc_id,smile_str,duplicates
17+
# my_file1.csv,ZINC00029323,COc1cccc(c1)NC(=O)c2cccnc2,1,ZINC00029323,
18+
# my_file1.csv,ZINC83310457,Cc1cccc(c1n2c(cc(c2C)/C=N\NC(=O)C(=O)Nc3ccc(cc3)[N+](=O)[O-])C)C,0,
19+
# my_file1.csv,ZINC01234567,C[C@H]1CCCC[NH+]1CC#CC(c2ccccc2)(c3ccccc3)O,0,
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# my_file2.csv,ZINC00029323,COc1cccc(c1)NC(=O)c2cccnc2,1,ZINC00029323,
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# my_file2.csv,ZINC83310457,Cc1cccc(c1n2c(cc(c2C)/C=N\NC(=O)C(=O)Nc3ccc(cc3)[N+](=O)[O-])C)C,0,
22+
# my_file2.csv,ZINC01234567,C[C@H]1CCCC[NH+]1CC#CC(c2ccccc2)(c3ccccc3)O,0,
23+
#
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#
25+
#
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# Where
27+
# 1st column: name of the origin file
28+
# 2nd column: ZINC ID
29+
# 3rd column: SMILE string
30+
# 4th-nth column: ZINC IDs of duplicates
31+
#
32+
# Usage:
33+
# [shell]>> python3 comp_2_smile_files.py in1.csv in2.csv out.csv [simplify]
34+
#
35+
# Example1:
36+
# [shell]>> python3 comp_2_smile_files.py ../examples/zid_smiles2.csv ../examples/zid_smiles3.csv ../examples/comp_2_files.csv
37+
#
38+
# Example2:
39+
# [shell]>> python3 comp_2_smile_files.py ../examples/zid_smiles2.csv ../examples/zid_smiles3.csv ../examples/comp_2_files.csv simplify
40+
41+
42+
import smilite
43+
import sys
44+
45+
46+
def print_usage():
47+
print('\nUSAGE: python3 comp_2_smile_files.py in1.csv in2.csv out.csv [simplify]')
48+
print('\nEXAMPLE1: python3 comp_2_smile_files.py ../examples/zid_smiles2.csv ../examples/zid_smiles3.csv ../examples/comp_2_files.csv\n')
49+
print('\nEXAMPLE2: python3 comp_2_smile_files.py ../examples/zid_smiles2.csv ../examples/zid_smiles3.csv ../examples/comp_2_files.csv simplify\n')
50+
51+
52+
try:
53+
in_csv1 = sys.argv[1]
54+
in_csv2 = sys.argv[2]
55+
out_csv = sys.argv[3]
56+
simplify = False
57+
58+
if len(sys.argv) > 4:
59+
simplify = True
60+
61+
smilite.comp_two_files(in_csv1, in_csv2, out_csv, compare_simplified_smiles=simplify)
62+
63+
except IOError as err:
64+
print('\n\nERROR: {}'.format(err))
65+
print_usage()
66+
67+
except IndexError:
68+
print('\n\nERROR: Invalid command line arguments.')
69+
print_usage()
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‎scripts/comp_smile_strings.py

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# Copyright 2014 Sebastian Raschka
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#
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# Compares SMILE strings in a 2 column CSV file (ZINC_ID,SMILE_string) to
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# Compares SMILE strings within a 2 column CSV file (ZINC_ID,SMILE_string) to
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# identify duplicates. Generates a new CSV file with ZINC IDs of identified
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# duplicates listed in a 3rd-nth column(s).
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#

‎setup.py

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from distutils.core import setup
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setup(name='smilite',
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version='1.2.0',
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version='1.3.0',
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description='smilite is a Python module to download and analyze SMILE strings',
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author='Sebastian Raschka',
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author_email='se.raschka@gmail.com',
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('test', ['test/test_simplify_smile.py']),
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('examples', ['examples/comp_simple_smiles.csv']),
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('examples', ['examples/comp_smiles.csv']),
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('examples', ['examples/comp_2_files.csv']),
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('examples', ['examples/README.md']),
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('examples', ['examples/zid_smiles.csv']),
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('examples', ['examples/zid_smiles2.csv']),
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('examples', ['examples/zid_smiles3.csv']),
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('examples', ['examples/zinc_ids.csv']),
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('scripts', ['scripts/comp_smile_strings.py']),
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('scripts', ['scripts/gen_zincid_smile_csv.py']),
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('scripts', ['scripts/comp_2_smile_files.py']),
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],
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install_requires=['PyPrind>=2.3.1'],
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license='GPLv3',

‎smilite/__init__.py

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from .smilite import generate_zincid_smile_csv
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from .smilite import simplify_smile
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from .smilite import check_duplicate_smiles
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from .smilite import comp_two_files
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from .smilite import create_id_smile_list
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__version__ = '1.2.0'
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__version__ = '1.3.0'
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