Update utils/helpers.py

utils/helpers.py

@@ -82,7 +82,7 @@ def get_all_protein_resids(pdb_file):
     Returns
     -------
     resids : numpy.ndarray
-        Array of protein resids old -> new
+        indexes of ca atoms
 
     """
     try:
@@ -104,7 +104,7 @@ def get_all_metalbinding_resids(pdb_file):
     Returns
     -------
     resids : numpy.ndarray
-        id of resids that are metal binding
+        indexes of name CA that are metal binding
 
     """
 
@@ -115,10 +115,35 @@ def get_all_metalbinding_resids(pdb_file):
     prot.filter("protein")
     return prot.get(
         "index",
-        sel="name CA and resid 94 96 119"
-        #sel="name CA and resname HIS HID HIE HIP CYS CYX GLU GLH GLN ASP ASH ASN GLN MET",
+        sel="name CA and resname HIS HID HIE HIP CYS CYX GLU GLH GLN ASP ASH ASN GLN MET",
     )
 
+def get_all_resids_from_list(pdb_file, resids):
+    """Return all metal binding residues from a pdb file
+
+    Parameters
+    ----------
+    pdb_file : str
+        Path to pdb file
+    resids : list
+        id of resids that are metal binding
+
+    Returns
+    -------
+    resids : numpy.ndarray
+        indexes of name CA resids 
+
+    """
+
+    try:
+        prot = Molecule(pdb_file)
+    except:
+        exit("could not read file")
+    prot.filter("protein")
+    return prot.get(
+        "index",
+        sel=f"name CA and resid {resids}",
+    )
 
 def compute_average_p_fast(point, cutoff=1):
     """Using KDTree find the closest gridpoints