Update dHisCu rotlibs to match those used in submitted manuscript. Enhance update_rotlib.py script.

scripts/update_rotlib.py

@@ -1,4 +1,5 @@
 #! /usr/bin/env python
+from pathlib import Path
 from zipfile import ZipFile
 from io import BytesIO
 import numpy as np
@@ -16,21 +17,36 @@
                                              '(compatible) versions.',
                                  )
 parser.add_argument('files_names', nargs='+', help='Names of the old rotlib files you wish to update')
+parser.add_argument('-d', '--description', default=None, help='Description text you would like to add to the rotamer '
+                                                              'library. Can be a string or a file')
+parser.add_argument('-c', '--comment',  default=None, help='Description text you would like to add to the rotamer '
+                                                           'library. can be a string or a file')
+parser.add_argument('-r', '--reference',  default=None, help='Reference text you would like to add to the rotamer '
+                                                             'library can be a string or a file.')
 
 args = parser.parse_args()
 
 
 def main():
 
+    adding_metadata = ((args.description is not None) or
+                       (args.comment is not None) or
+                       (args.reference is not None))
+
+    if adding_metadata and len(args.files_names) > 1:
+        raise RuntimeError("You can only add descriptions, comments, or references when updating one library at a time")
+
+    description = check_textfile(args.description)
+    comment = check_textfile(args.comment)
+    reference = check_textfile(args.reference)
 
     for filename in args.files_names:
 
         if filename.endswith('_rotlib.npz'):
             shutil.copy(filename, filename + '.bku')
-            data = get_data(filename)
+            data = get_data(filename, description, comment, reference)
             np.savez(filename, **data)
 
-
         elif filename.endswith('_drotlib.zip'):
             shutil.copy(filename, filename + '.bku')
             libname = filename[:-12]
@@ -43,11 +59,11 @@ def main():
                             np.save(f'{libname}_csts.npy', csts)
                     elif f[-12] == 'A':
                         with archive.open(f) as of:
-                            libA = get_data(of)
+                            libA = get_data(of, description, comment, reference)
                             np.savez(f'{libname}A_rotlib.npz', **libA)
                     elif f[-12] == 'B':
                         with archive.open(f) as of:
-                            libB = get_data(of)
+                            libB = get_data(of, description, comment, reference)
                             np.savez(f'{libname}B_rotlib.npz', **libB)
 
             with zipfile.ZipFile(f'{libname}_drotlib.zip', mode='w') as archive:
@@ -146,4 +162,17 @@ def get_data_1_2(filename):
 
     return data
 
+def check_textfile(file):
+
+    if Path(str(file)).exists():
+
+        with open(file, 'r') as f:
+            lines = f.readlines()
+
+        lines = "\n".join(lines)
+    else:
+        lines = file
+
+    return lines
+
 main()

src/chilife/chilife.py

@@ -1185,40 +1185,54 @@ def safe_save(file: Union[str, Path], data: dict, backup: dict):
 
 
 def _print_monofunc(files):
-    print(f"{'monofunctional' + ':':^60}")
-    print("-" * 60)
+    maxw = max([len(file.stem) for file in files]) - 6
+    wrapper = textwrap.TextWrapper(width=80, subsequent_indent=" "*(maxw + 3),
+                                   replace_whitespace=False, drop_whitespace=False)
+
+    print(f"{'monofunctional' + ':':^80}")
+    print("-" * 80)
 
     for file in files:
         with np.load(file, allow_pickle=True) as f:
             for key in f.keys():
-                resname = f['resname']
+                resname = file.stem
+                if resname.endswith('_rotlib'):
+                    resname = resname[:-len('_rotlib')]
                 if 'description' in f:
                     descr = f['description']
                 else:
                     descr = "No description"
 
-        print(f'{resname:<8} : {descr}')
-    print("-" * 60)
+        print("\n".join(wrapper.wrap(f'{resname:<{maxw}} : {descr}')))
+    print("-" * 80)
 
 
 def _print_bifunc(files):
-    print(f"{'bifunctional' + ':':^60}")
-    print("-" * 60)
+
+    maxw = max([len(file.stem) for file in files]) - 7
+    wrapper = textwrap.TextWrapper(width=80, subsequent_indent=" "*(maxw + 3),
+                                   replace_whitespace=False, drop_whitespace=False)
+
+
+    print(f"{'bifunctional' + ':':^80}")
+    print("-" * 80)
 
     for file in files:
         with zipfile.ZipFile(file, 'r') as archive:
             name = archive.namelist()[0]
-            resname = name[:3]
+            resname = file.stem
             context = name[3:6]
+            if resname.endswith('_drotlib'):
+                resname = resname[:-len('_drotlib')]
             with archive.open(name) as of:
                 with np.load(of, allow_pickle=True) as f:
                     if 'description' in f:
                         descr = f['description']
                     else:
                         descr = "No description"
 
-        print(f'{resname:<4}{context:<4} : {descr}')
-    print("-" * 60)
+        print("\n".join(wrapper.wrap(f'{resname:<{maxw}} : {descr} in the {context} context')))
+    print("-" * 80)
 
 
 def list_available_rotlibs():
@@ -1238,22 +1252,22 @@ def list_available_rotlibs():
         bifunctional = tuple(dpath.glob('*_drotlib.zip'))
         if len(monofunctional) + len(bifunctional) > 0:
 
-            print("*" * 60)
-            print(f"*{f'Rotlibs in {dname}':^58}*")
+            print("*" * 80)
+            print(f"*{f'Rotlibs in {dname}':^78}*")
             if 'user' in dname:
-                print(f'*{dname.name:^58}*')
-            print("*" * 60)
+                print(f'*{dname.name:^78}*')
+            print("*" * 80)
 
             if len(monofunctional) > 0 : _print_monofunc(monofunctional)
             if len(bifunctional) > 0 : _print_bifunc(bifunctional)
 
     print()
-    print("*" * 60)
-    print(f"*{'DUNBRACK ROTLIBS':^58}*")
-    print(f"*{'ARG, ASN, ASP, CSY, GLN, GLU, HIS, ILE, LEU, LYS, MET,':^58}*")
-    print(f"*{'PHE, PRO, SER, THR, TRP, TYR, VAL':^58}*")
-    print(f"*{'(no ALA, GLY}':^58}*")
-    print("*" * 60)
+    print("*" * 80)
+    print(f"*{'DUNBRACK ROTLIBS':^78}*")
+    print(f"*{'ARG, ASN, ASP, CSY, GLN, GLU, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER,':^78}*")
+    print(f"*{'THR, TRP, TYR, VAL':^78}*")
+    print(f"*{'(no ALA, GLY}':^78}*")
+    print("*" * 80)
 
 
 def add_rotlib_dir(directory: Union[Path, str]) -> None: