From 4784da6f77f9be33cdc06f4d6318340737e7dd9d Mon Sep 17 00:00:00 2001
From: zinph <pkyawzi@ncsu.edu>
Date: Tue, 21 Jan 2020 21:39:52 -0500
Subject: [PATCH] name changed and data folder added

---
 Data/selected_extenders.txt  | 13 +++++++++++++
 Data/sugars                  |  7 +++++++
 PKS_Enumerator.py => SIME.py |  8 ++------
 main.py                      | 11 ++++++-----
 4 files changed, 28 insertions(+), 11 deletions(-)
 create mode 100644 Data/selected_extenders.txt
 create mode 100644 Data/sugars
 rename PKS_Enumerator.py => SIME.py (99%)

diff --git a/Data/selected_extenders.txt b/Data/selected_extenders.txt
new file mode 100644
index 0000000..b811abe
--- /dev/null
+++ b/Data/selected_extenders.txt
@@ -0,0 +1,13 @@
+[*R*]C[*R*]
+[*R*][C@@H](C)[*R*]
+[*R*][C@@H](CC)[*R*]
+[*R*][C@@H](O)[*R*]
+[*R*][C@@H](OC)[*R*]
+[*R*][C@@](O)(C)[*R*]
+[*R*][C@@](OC)(C)[*R*]
+[*R*][C@@H](CC=O)[*R*]
+[*R*]C(=O)[*R*]
+[*R*][C@](C)(F)[*R*]
+[*R*][C@@H](OC(=O)C)[*R*]
+[*R*][C@@]2(OC2)[*R*]
+[*R*][N@@](C)[*R*]
\ No newline at end of file
diff --git a/Data/sugars b/Data/sugars
new file mode 100644
index 0000000..8ba53ad
--- /dev/null
+++ b/Data/sugars
@@ -0,0 +1,7 @@
+[*R*][C@H](O[C@H]9C[C@@](C)(OC)[C@@H](O)[C@H](C)O9)[*R*]
+[*R*][C@H](O[C@@H]9O[C@H](C)C[C@@H]([C@H]9O)N(C)C)[*R*]
+[*R*][C@H](O[C@@H]9O[C@H](C)C[C@@H]([C@H]9OC(C)=O)N(C)C)[*R*]
+[*R*][C@H](O[C@H]9C[C@H](OC)O[C@@H](C)[C@@H]9OC(C)=O)[*R*]
+[*R*][C@H](O[C@H]9C[C@H](OC)[C@@H](O)[C@H](C)O9)[*R*]
+[*R*][C@H](O[C@H]9C[C@@H](O)[C@H](O)[C@@H](C)O9)[*R*]
+[*R*][C@H](O[C@@H]9O[C@H](C)C[C@H](NC)[C@H]9O)[*R*]
\ No newline at end of file
diff --git a/PKS_Enumerator.py b/SIME.py
similarity index 99%
rename from PKS_Enumerator.py
rename to SIME.py
index 41b57c1..52db618 100644
--- a/PKS_Enumerator.py
+++ b/SIME.py
@@ -22,7 +22,7 @@ from collections import Counter, defaultdict
 from rdkit.Chem.Scaffolds import MurckoScaffold
 from operator import itemgetter
 
-class PKS_Enumerator:
+class SIME:
 
     def __init__(self):
 
@@ -83,10 +83,6 @@ class PKS_Enumerator:
         self.info_manager.close()
 
 
-
-    def load_macrolide_cores(self):
-        pass
-
     def make_full_sugar_list(self):
         '''
         self.full_list contains all the sugars and hydroxyl groups.
@@ -343,4 +339,4 @@ class PKS_Enumerator:
         for j in full_indexes:
             template[j] = self.full_list
         # for sugars
-        return template
\ No newline at end of file
+        return template
diff --git a/main.py b/main.py
index 9164e2d..0c966e8 100644
--- a/main.py
+++ b/main.py
@@ -1,8 +1,9 @@
 #-------------------------------------------------------------------------------
-# Name:        module1
-# Purpose:
+# Name:        SIME
+# Purpose:     Scaffold-based enumeration method/software to design in-silico macrolide libraries
+
 #
-# Author:      kzphy
+# Author:      zinph
 #
 # Created:     27/02/2019
 # Copyright:   (c) kzphy 2019
@@ -20,12 +21,12 @@ def convert_time(second):
     second = round((minute - int(minute))*60,4)
     return(str(int(day)) + ' DAYS: '+ str(int(hour)) + ' HOURS: '+ str(int(minute)) + ' MINUTES: ' + str(second) + ' SECONDS')
 
-from PKS_Enumerator import *
+from SIME import *
 
 #ERY_core = 'CC[C@H]1OC(=O)[*][*sugar*][*][*sugar*][*]C[*]C(=O)[*][C@@H](O)[*]1'
 ERY_core = 'CC[C@H]1OC(=O)[*][*sugar*][C@H](C)[*sugar*][*]C[*]C(=O)[*][C@@H](O)[*]1'
 
-sample = PKS_Enumerator()
+sample = SIME()
 start_time = time.time()
 sample.generate_templates_withExtendersNSugars(ERY_core)
 duration = convert_time(time.time()-start_time)