diff PDAUG_Peptide_Structure_Builder/PDAUG_Peptide_Structure_Builder.py @ 0:7557b48b2872 draft

"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PDAUG_Peptide_Structure_Builder/PDAUG_Peptide_Structure_Builder.py	Wed Oct 28 02:10:12 2020 +0000
@@ -0,0 +1,73 @@
+import tempfile
+import pandas as pd
+import shutil
+import sys
+import glob
+import fragbuilder
+import openbabel
+from fragbuilder import peptide
+
+import os
+
+
+def read_pep_file(pep_infile):
+    
+    file = open(pep_infile)
+    lines = file.readlines()
+
+    Index = []
+    list_pep_name = []
+
+    for line in lines:
+        if '>' in line:
+            Index.append(line.strip('\n'))
+        else:
+            line = line.strip('\n')
+            line = line.strip('\r')
+            list_pep_name.append(line.strip('\n'))
+
+    return list_pep_name
+
+def structure_gen(pep_seq, out_dir):
+
+    if not os.path.exists(os.path.join(out_dir, 'DataFile')):
+        os.makedirs(os.path.join(out_dir, 'DataFile'))
+
+    b = len(pep_seq)
+
+    for seq in pep_seq:
+
+        pep = peptide.Peptide(seq, nterm = "charged", cterm = "neutral")
+        pep.regularize()
+        pep.write_pdb(os.path.join(out_dir, 'DataFile', seq+".pdb"))
+
+        obConversion = openbabel.OBConversion()
+        obConversion.SetInAndOutFormats("pdb", "sdf")
+        mol = openbabel.OBMol()
+        obConversion.ReadFile(mol,  os.path.join(out_dir, 'DataFile', seq+".pdb")) 
+
+        mol.AddHydrogens()       
+
+    
+def main_process(str_pep_file, out_dir):
+      
+    my_pep = read_pep_file(str_pep_file) 
+    structure_gen(my_pep, out_dir)
+    
+    
+if __name__=="__main__":
+    
+    
+    import argparse
+    parser = argparse.ArgumentParser()
+    
+    parser.add_argument("-p", "--pep", required=True, default=None, help="pep file")                    
+    parser.add_argument("-o", "--OutDir", required=None, default=os.getcwd(), help="Path to out file")  
+                                               
+    args = parser.parse_args()
+    main_process(args.pep, args.OutDir)
+   
+    
+    
+   
+