diff calc_vina_box_params.py @ 5:668c60aa4799 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"

--- a/calc_vina_box_params.py	Tue Jul 28 08:16:17 2020 -0400
+++ b/calc_vina_box_params.py	Thu Jul 22 14:04:57 2021 +0000
@@ -1,22 +1,24 @@
+import argparse
+
 import numpy as np
 from rdkit import Chem
 from rdkit.Chem import rdShapeHelpers
-import argparse
-from random import randint
+
 
 def get_mol_from_file(fname, ftype):
-    if ftype in ['mol', 'sdf']:
-        mol = Chem.MolFromMolFile(options.ligand_path)
-    elif ftype == 'pdb':
-        mol = Chem.MolFromPDBFile(options.ligand_path)
-    elif ftype == 'mol2':
-        mol = Chem.MolFromMol2File(options.ligand_path)
+    if ftype in ["mol", "sdf"]:
+        mol = Chem.MolFromMolFile(options.ligand_path, strictParsing=False, sanitize=False)
+    elif ftype == "pdb":
+        mol = Chem.MolFromPDBFile(options.ligand_path, sanitize=False)
+    elif ftype == "mol2":
+        mol = Chem.MolFromMol2File(options.ligand_path, sanitize=False)
     else:
         raise IOError
     if not mol:
         raise IOError
     return mol
 
+
 def get_params(options):
     mol = get_mol_from_file(options.ligand_path, options.ftype)
 
@@ -39,13 +41,12 @@
 
     optionalvals = ""
 
-
-    if options.seed != None:
+    if options.seed is not None:
         optionalvals += "seed = " + str(options.seed) + "\n"
-    if options.exhaustiveness != None:
+    if options.exhaustiveness is not None:
         optionalvals += "exhaustiveness = " + str(options.exhaustiveness) + "\n"
 
-    with open(options.output, 'w') as f:
+    with open(options.output, "w") as f:
         f.write(
             """
 size_x =  {}
@@ -54,30 +55,73 @@
 center_x =  {}
 center_y =  {}
 center_z =  {}
-{}""".format(box_dims[0], box_dims[1], box_dims[2], center[0], center[1], center[2], optionalvals)
+{}""".format(
+                box_dims[0],
+                box_dims[1],
+                box_dims[2],
+                center[0],
+                center[1],
+                center[2],
+                optionalvals,
+            )
         )
 
 
 if __name__ == "__main__":
-    parser = argparse.ArgumentParser(description="""
+    parser = argparse.ArgumentParser(
+        description="""
     This tool calculates a confounding box around an input ligand, and uses it to
     generate the input parameters for an autodock vina job. The output file can be fed into
-    the autodock vina tool as an alternative to creating the parameter file manually. 
-    
+    the autodock vina tool as an alternative to creating the parameter file manually.
+
     Optionally, you can include a 'buffer' in each of the x,y and z directions (in Å),
     which will be added to the confounding box in the appropriate direction.
-    """)
-    parser.add_argument('--ligand', dest='ligand_path', help='The input ligand filepath.')
-    parser.add_argument('--ftype', dest='ftype', help='Filetype of the input ligand (mol, sdf, pdb, mol2)')
-    parser.add_argument('--config', dest='output', help='The output file containing calculated params (txt)')
-    parser.add_argument('--exh', dest='exhaustiveness', type=int, help='Exhaustiveness of global search')
-    parser.add_argument('--bufx', dest='bufx', default=0, type=float, help='the buffer in the x direction '
-                                                                           '(float - in angs.)')
-    parser.add_argument('--bufy', dest='bufy', default=0, type=float, help='the buffer in the y direction '
-                                                                           '(float - in angs.)')
-    parser.add_argument('--bufz', dest='bufz', default=0, type=float, help='the buffer in the z direction '
-                                                                           '(float - in angs.)')
-    parser.add_argument('--seed', dest='seed', default=None, type=int, help='Random seed for reproducibility')
+    """
+    )
+    parser.add_argument(
+        "--ligand", dest="ligand_path", help="The input ligand filepath."
+    )
+    parser.add_argument(
+        "--ftype",
+        dest="ftype",
+        help="Filetype of the input ligand (mol, sdf, pdb, mol2)",
+    )
+    parser.add_argument(
+        "--config",
+        dest="output",
+        help="The output file containing calculated params (txt)",
+    )
+    parser.add_argument(
+        "--exh", dest="exhaustiveness", type=int, help="Exhaustiveness of global search"
+    )
+    parser.add_argument(
+        "--bufx",
+        dest="bufx",
+        default=0,
+        type=float,
+        help="the buffer in the x direction " "(float - in angs.)",
+    )
+    parser.add_argument(
+        "--bufy",
+        dest="bufy",
+        default=0,
+        type=float,
+        help="the buffer in the y direction " "(float - in angs.)",
+    )
+    parser.add_argument(
+        "--bufz",
+        dest="bufz",
+        default=0,
+        type=float,
+        help="the buffer in the z direction " "(float - in angs.)",
+    )
+    parser.add_argument(
+        "--seed",
+        dest="seed",
+        default=None,
+        type=int,
+        help="Random seed for reproducibility",
+    )
 
     options = parser.parse_args()
     get_params(options)