bug fix

AstraZeneca · Mar 23, 2022 · f6c6891 · f6c6891
1 parent 5a23b11
commit f6c6891
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Showing 5 changed files with 26 additions and 16 deletions.
diff --git a/CHANGES.md b/CHANGES.md
@@ -1,5 +1,7 @@
 
-extn_coeff_fasta_v2.2/
+extn_coeff_fasta
+
+* 2022-03-23 bug fixed: fixed std ouput results display. "molid" changed to "mol_name" in the code and some code polishing. 
 
 2.2
 ---
@@ -19,11 +21,14 @@ pI_fasta_v1.4/
 
 
 
-rdkit_pI_v3.2/
+rdkit_pI/
 
 Changes
 =======
 
+2022-03-23 bug fix: the output was incomplete if the extra keys (print_fragmet_pkas, etc.) were switched on.
+
+
 3.2
 -----
 

diff --git a/extn_coeff_fasta/extn_coeff_fasta.py b/extn_coeff_fasta/extn_coeff_fasta.py
@@ -195,9 +195,11 @@ def calc_extn_coeff_single_sequence(sequence):
 
 
 def print_stdout(dict_in):
-    for molid_ind in dict_in['molid_ind_list']:
+    #for molid_ind in dict_in['molid_ind_list']:
+    for molid_ind in dict_in.keys():
         dict_extn_coeff = dict_in[molid_ind]
-        molid = dict_extn_coeff['molid']
+        print(dict_extn_coeff.keys())
+        molid = dict_extn_coeff['mol_name']
         print("======================================================================================================================================================")
         print("--- Molar absorption coefficient at different wavelength")
         print("mol ID: "+molid)

diff --git a/rdkit_pI/TEST/run_pI.sh b/rdkit_pI/TEST/run_pI.sh
@@ -15,6 +15,8 @@ if [ -z "$i" ]; then echo "no input.  $usage" ; fi
 if [ -z "$o" ]; then echo "no output.  $usage" ; fi
 
 #python ../rdkit_pI.py -i ${i} --plot_titration_curve --print_fragment_pkas --use_acdlabs &> $o
-python ../rdkit_pI.py -i ${i} --plot_titration_curve --print_fragment_pkas --use_dimorphite --json  &> $o
+#python ../rdkit_pI.py -i ${i} --plot_titration_curve --print_fragment_pkas --use_dimorphite --json  &> $o
+#python ../rdkit_pI.py -i ${i} --plot_titration_curve --print_fragment_pkas --use_dimorphite  &> $o
+python ../rdkit_pI.py -i ${i} --plot_titration_curve --print_fragment_pkas --use_dimorphite 
 
 
diff --git a/rdkit_pI/rdkit_pI.py b/rdkit_pI/rdkit_pI.py
@@ -626,16 +626,17 @@ def calc_rdkit_pI(options={'smiles':'','inputDict':{},'inputJSON':'','inputFile'
                                     'plot_filename':figFileName,
                                     'pI_interval_threshold':int_tr
                                     }
-        if args.l_print_pka_set:
-            dict_output_rdkit_pI[molid_ind]={'pKa_set':pKaset }
+        #if args.l_print_pka_set:
+        dict_output_rdkit_pI[molid_ind].update({'pKa_set':pKaset })
+
         if args.l_print_fragments:
-            dict_output_rdkit_pI[molid_ind]={
+            dict_output_rdkit_pI[molid_ind].update({
                                     'base_pkas_fasta':base_pkas_fasta,
                                     'acid_pkas_fasta':acid_pkas_fasta,
                                     'base_pkas_calc':base_pkas_calc,
                                     'acid_pkas_calc':acid_pkas_calc,
                                     'constant_Qs_calc':net_Qs
-                                    }
+                                    })
 
 
                                     #'diacid_pkas_calc':diacid_pkas_calc,
@@ -661,20 +662,20 @@ def print_output(dict_output_rdkit_pI,args):
         elif args.use_dimorphite: predition_tool = 'modified Dimorphite-DL'
 
         int_tr = dict_output_rdkit_pI[molid_ind]['pI_interval_threshold']
-        base_pkas_fasta = dict_output_rdkit_pI[molid_ind]['base_pkas_fasta']
-        acid_pkas_fasta = dict_output_rdkit_pI[molid_ind]['acid_pkas_fasta']
-        #diacid_pkas_fasta = dict_output_rdkit_pI[molid_ind]['diacid_pkas_fasta']
-        base_pkas_calc = dict_output_rdkit_pI[molid_ind]['base_pkas_calc']
-        acid_pkas_calc = dict_output_rdkit_pI[molid_ind]['acid_pkas_calc']
-        #diacid_pkas_calc = dict_output_rdkit_pI[molid_ind]['diacid_pkas_calc']
-        constant_Qs_calc = dict_output_rdkit_pI[molid_ind]['constant_Qs_calc']
         pKaset = dict_output_rdkit_pI[molid_ind]['pKa_set']
 
         print(" ")
         print("pH interval with charge between %4.1f and %4.1f for pKa set: %s and prediction tool: %s" % (-int_tr,int_tr,pKaset,predition_tool) )
         print("%4.1f - %4.1f" % (dict_output_rdkit_pI[molid_ind]['pI_interval'][0],dict_output_rdkit_pI[molid_ind]['pI_interval'][1]))
 
         if args.l_print_fragments:
+            base_pkas_fasta = dict_output_rdkit_pI[molid_ind]['base_pkas_fasta']
+            acid_pkas_fasta = dict_output_rdkit_pI[molid_ind]['acid_pkas_fasta']
+            #diacid_pkas_fasta = dict_output_rdkit_pI[molid_ind]['diacid_pkas_fasta']
+            base_pkas_calc = dict_output_rdkit_pI[molid_ind]['base_pkas_calc']
+            acid_pkas_calc = dict_output_rdkit_pI[molid_ind]['acid_pkas_calc']
+            #diacid_pkas_calc = dict_output_rdkit_pI[molid_ind]['diacid_pkas_calc']
+            constant_Qs_calc = dict_output_rdkit_pI[molid_ind]['constant_Qs_calc']
 
             # merge fasta and calcualted pkas
             base_pkas = base_pkas_fasta[pKaset] + base_pkas_calc

diff --git a/rdkit_pI/rdkit_pI.py.swp b/rdkit_pI/rdkit_pI.py.swp