bug fix in multicomponent.py

Liu-group · Jul 13, 2024 · 38d852d · 38d852d
1 parent 4e383f3
commit 38d852d
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Showing 3 changed files with 14 additions and 20 deletions.
diff --git a/autosolvate/__main__.py b/autosolvate/__main__.py
@@ -7,7 +7,7 @@
 from autosolvate.autosolvate import *
 from autosolvate.generatetrajs import *
 from autosolvate.clustergen import *
-# from autosolvate.FFmetalcomplex import *
+from autosolvate.FFmetalcomplex import *
 from autosolvate.multicomponent import *
 
 ## Main function

diff --git a/autosolvate/multicomponent.py b/autosolvate/multicomponent.py
@@ -454,7 +454,6 @@ def create_parser_multicomponent():
     parser.add_argument('-a', '--amberhome',       type=str,                   help='path to the AMBER molecular dynamics package root directory')
     return parser
 
-
 def startmulticomponent(args):
     r"""
     Wrap function that parses command line options for autosolvate multicomponent module,
@@ -514,8 +513,6 @@ def startmulticomponent(args):
     data = correct_keyword(data)
     check_inputs(data)
 
-    json.dump(data, open("/home/fren5/AutoSolvate-update/autosolvate.json", "w"), indent=4)
-    json.dump(data, open("autosolvate.json", "w"), indent=4)
     global WORKING_DIR
     WORKING_DIR = os.getcwd()
     startmulticomponent_fromdata(data)

diff --git a/docs/tutorial_multicomponent.rst b/docs/tutorial_multicomponent.rst
@@ -44,28 +44,25 @@ naphthalene_neutral.xyz:
 
 acetonitrile.pdb:
 ::
-   COMPND      Acetonitrile
-   ATOM      1  N1  SLV     1      14.182  11.288  13.720
-   ATOM      2  C2  SLV     1      13.673  12.188  13.299
-   ATOM      3  C3  SLV     1      13.153  13.383  12.698
-   ATOM      4  H4  SLV     1      13.342  13.429  11.678
-   ATOM      5  H5  SLV     1      12.069  13.440  12.762
-   ATOM      6  H6  SLV     1      13.602  14.242  13.212
-   TER 
-
+   ATOM      1  N1  ACE     1      14.182  11.288  13.720  1.00  0.00
+   ATOM      2  C2  ACE     1      13.673  12.188  13.299  1.00  0.00
+   ATOM      3  C3  ACE     1      13.153  13.383  12.698  1.00  0.00
+   ATOM      4  H4  ACE     1      13.342  13.429  11.678  1.00  0.00
+   ATOM      5  H5  ACE     1      12.069  13.440  12.762  1.00  0.00
+   ATOM      6  H6  ACE     1      13.602  14.242  13.212  1.00  0.00
+   TER   
+   END   
 
 .. image:: _images/tutorial5_2.png
    :width: 300
 
 water.pdb:
 :: 
-
-  COMPND      Water
-  HETATM    1  O           1       0.251  -0.360  -0.046  1.00  0.00
-  HETATM    2  H           1       0.249   0.684   0.231  1.00  0.00
-  HETATM    3  H           1       0.586  -0.954   0.791  1.00  0.00
-  TER       4              1 
-  END   
+   ATOM      1  O   WAT     1       0.251  -0.360  -0.046  1.00  0.00
+   ATOM      2  H   WAT     1       0.249   0.684   0.231  1.00  0.00
+   ATOM      3  H1  WAT     1       0.586  -0.954   0.791  1.00  0.00
+   TER   
+   END
 
 .. note::