Merge remote-tracking branch 'origin/master'

Author: marioernestovaldes

GMXMMPBSA/main.py

@@ -1274,8 +1274,16 @@ def get_iec2entropy(self, from_calc):
         allowed_met = ['gb', 'pb', 'rism std', 'rism gf', 'rism pcplus', 'gbnsr6']
         if self.INPUT['general']['interaction_entropy']:
             self.calc_types.normal['ie'] = {}
+            if self.INPUT['ala']['alarun']:
+                self.calc_types.mutant['ie'] = {}
+                if not self.INPUT['ala']['mutant_only']:
+                    self.calc_types.mut_norm['ie'] = {}
         if self.INPUT['general']['c2_entropy']:
             self.calc_types.normal['c2'] = {}
+            if self.INPUT['ala']['alarun']:
+                self.calc_types.mutant['c2'] = {}
+                if not self.INPUT['ala']['mutant_only']:
+                    self.calc_types.mut_norm['c2'] = {}
 
         for key in allowed_met:
             if self.INPUT['general']['interaction_entropy']:

GMXMMPBSA/make_top.py

@@ -1276,6 +1276,8 @@ def check_structures(self, com_str, rec_str=None, lig_str=None):
                                     'based on the reference structure. Please check that the reference structure is '
                                     'correct')
                 com_str.residues[c].chain = res.chain
+                # update the chain id (https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/issues/354)
+                self.resl[c].chain = res.chain
                 i = self.resl[c].id_index - 1
                 if self.resl[c].is_receptor():
                     rec_str.residues[i].chain = res.chain

GMXMMPBSA/output_file.py

@@ -178,7 +178,7 @@ def write_outputs(app):
                         final_output.add_section(ie_dict['mutant'][key].summary_output())
                         ie_inconsistent = ie_dict['mutant'][key]['sigma'] > 3.6
 
-            if INPUT['ala']['alarun'] and not INPUT['mutant_only']:
+            if INPUT['ala']['alarun'] and not INPUT['ala']['mutant_only']:
                 final_output.writeline(f'Delta ( Mutant - Normal ) [ Δ(-TΔS) ]')
                 final_output.writeline('ENTROPY RESULTS (INTERACTION ENTROPY):')
                 for key in allowed_met:

GMXMMPBSA/utils.py

@@ -423,34 +423,36 @@ def get_indexes(com_ndx, rec_ndx=None, lig_ndx=None):
 
 
 def _get_dup_args(args):
-    flags_values_list = []
-    cv = []
-    current_flag = None
-    for o in args:
+    flag_index = []
+    flags = []
+
+    for i, o in enumerate(args):
         if o.startswith('-'):
-            if current_flag:
-                flags_values_list.append([current_flag, cv])
-            current_flag = o
-            cv = []
-        else:
-            cv.append(o)
+            flag_index.append(i)
+            flags.append(o)
 
     opt_duplicates = []
-    args_duplicates = []
-    flags = [a[0] for a in flags_values_list]
-
-    for x in flags:
-        if flags.count(x) > 1 and x not in opt_duplicates:
-            opt_duplicates.append(x)
+    flags_values = {}
+    for i, f in enumerate(flags):
+        if flags.count(f) > 1 and f not in opt_duplicates:
+            opt_duplicates.append(f)
+        if i == len(flags) - 1:
+            flags_values[f] = [args[x] for x in range(flag_index[i] + 1, len(args))]
+            print('tets')
+        elif flag_index[i] - flag_index[i+1]:
+            flags_values[f] = [args[x] for x in range(flag_index[i]+1, flag_index[i+1])]
+        else:
+            flags_values[f] = []
 
     if opt_duplicates:
         GMXMMPBSA_ERROR('Several options are duplicated in the command-line...\n'
                         f"Duplicated options:\n\t{', '.join(opt_duplicates)}")
 
-    flags_values_dict = dict(flags_values_list)
+    args_duplicates = []
     unique_args = []
     inverted_args_dict = {}
-    for k, v in flags_values_dict.items():
+    for k, v in flags_values.items():
+        # skip this options since they can share the same group number/name
         if k in ['-cg', '-rg', '-lg']:
             continue
         for a in v:
@@ -460,8 +462,8 @@ def _get_dup_args(args):
             else:
                 args_duplicates.append([k, a])
 
-    text_out = '\n'.join([f"\t{inverted_args_dict[a]} {' '.join(flags_values_dict[inverted_args_dict[a]])} <---> "
-                          f"{k} {' '.join(flags_values_dict[k])}"
+    text_out = '\n'.join([f"\t{inverted_args_dict[a]} {' '.join(flags_values[inverted_args_dict[a]])} <---> "
+                          f"{k} {' '.join(flags_values[k])}"
                           for k, a in args_duplicates])
     if args_duplicates:
         GMXMMPBSA_ERROR('Several args are duplicated in the command-line...\n'
@@ -669,8 +671,7 @@ def selector(selection: str):
             for r in resl:
                 rr = r.split('-')
                 if len(rr) == 1:
-                    ci = rr[0].split(':')
-                    ri = [chain, int(ci[0]), ''] if len(ci) == 1 else [chain, int(ci[0]), ci[1]]
+                    ri = [chain, int(rr[0]), ''] if rr[0][-1] not in ascii_letters else [chain, int(rr[0][:-1]), rr[0][-1]]
                     if ri in res_selections:
                         logging.warning('Found duplicated residue in selection: CHAIN:{} RES_NUM:{} ICODE: '
                                         '{}'.format(*ri))

docs/input_file.md

@@ -710,8 +710,8 @@ the same used for `print_res` variable in `&decomp` namelist.
                 insertion code are contained in the range
 
                 **Individual selection**
-                :   `qm_residues="A/5,6:B,6:C,7` Will treat with quantum mechanic all mentioned residues except the 
-                residues A:6:A and A:6:D from chain A
+                :   `qm_residues="A/5,6B,6C,7` Will treat with quantum mechanic all mentioned residues except the 
+                residues 6A and 6D from chain A
 
                 **Multiple chain selection**
                 :   `qm_residues="A/5-10,100 B/34,56` Will treat with quantum mechanic residues 5 through 10, and 100 from 
@@ -1877,7 +1877,8 @@ sufficient in most cases, however we have added several additional notations
                         contained in the range
 
                     **Individual selection**
-                    :   `print_res="A/5,6:B,6:C,7 B/25` Will print all mentioned residues except the residues A:6:A and A:6:D
+                    :   `print_res="A/5,6B,6C,7 B/25` Will print all mentioned residues except the residues 6A and 
+                        6D from chain A
 
                 === "Wrong notation"
                     `print_res="A/5-6B,6D-7` Will end in error.