add findSurfaceCharge.py

Author: tcwarner

findSurfaceCharge.py

@@ -0,0 +1,150 @@
+from __future__ import print_function
+from pymol import cmd
+
+
+def findSurfaceAtoms(selection="all",cutoff=2.5):
+    """
+    Adapted from Jason Vertrees https://pymolwiki.org/index.php/FindSurfaceResidues
+DESCRIPTION
+
+    Finds those atoms on the surface of a protein
+    that have at least 'cutoff' exposed A**2 surface area.
+
+USAGE
+
+    findSurfaceAtoms [ selection, [ cutoff ]]
+
+SEE ALSO
+
+    findSurfaceResidues
+    """
+    cutoff = float(cutoff)
+
+    tmpObj = cmd.get_unused_name("_tmp")
+    cmd.create(tmpObj, "(" + selection + ") and polymer", zoom=0)
+
+    cmd.set("dot_solvent", 1, tmpObj)
+    cmd.get_area(selection=tmpObj, load_b=1)
+
+    # threshold on what one considers an "exposed" atom (in A**2):
+    cmd.remove(tmpObj + " and b < " + str(cutoff))
+
+    selName = cmd.get_unused_name("exposed_atm_")
+
+    cmd.select(selName, "(" + selection + ") in " + tmpObj)
+
+    cmd.delete(tmpObj)
+
+    return selName
+
+
+def _findSurfaceChargeImpl(selection, pH, folded, cutoff):
+
+    def get_exposed_residues(selection,cutoff):
+        cutoff = float(cutoff)
+
+
+        selName = findSurfaceAtoms(selection, cutoff)
+
+        tempExposed = set()
+        cmd.iterate(selName, "tempExposed.add((resv,oneletter))", space=locals())
+        cmd.delete(selName)
+
+        tempExposed=sorted(tempExposed) #list of exposed residues
+        exposed=[]
+        for res in tempExposed:
+                exposed.append(res[1]+str(res[0]))
+
+        return exposed
+
+    if folded:
+        exposed = get_exposed_residues(selection,cutoff)
+    else:
+        exposed = get_exposed_residues(selection,0)
+
+    pH=float(pH)
+
+    #gets all charged amino acids on the surface
+    exposedAtms=""
+    K=0
+    R=0
+    D=0
+    H=0
+    E=0
+
+    for r in exposed:
+        amino=r[0]
+        if amino not in "KRDHE":
+            continue
+        elif amino=='K':
+            K+=1
+        elif amino=='R':
+            R+=1
+        elif amino=='D':
+            D+=1
+        elif amino=="H":
+            H+=1
+        elif amino=='E':
+            E+=1
+        exposedAtms+=amino
+        chargedAA=amino
+
+
+    kCharge= 1 / (1 + 10 ** (pH - 10.54))
+    rCharge= 1 / (1 + 10 ** (pH - 12.48))
+    dCharge= -(1 / (1 + 10 ** (4.07 - pH)))
+    eCharge= -(1 / (1 + 10 ** (3.90 - pH)))
+    hCharge= 1 / (1 + 10 ** (pH - 6.04))
+
+    charge=kCharge*K+rCharge*R+hCharge*H+dCharge*D+eCharge*E
+    charge=round(charge,2)
+    if charge>0:
+        chargetx="+"+str(charge)
+    else:
+        chargetx=str(charge)
+
+    if folded:
+        print ("Exposed charged residues: " +str(exposedAtms))
+        print ("The expected surface charge of " + selection +" at pH " + str(pH) +" is: " +chargetx)
+
+    else:
+        print ("Charged residues: "+str(exposedAtms))
+        print ("The expected charge of denatured " + selection +" at pH " +str(pH) +" is: " +chargetx)
+    return (selection, chargetx)
+
+
+def findSurfaceCharge(selection="", pH=7.0, folded=True, cutoff=2.5):
+    """
+DESCRIPTION
+
+    Calculates a surface charge at entered pH. Also allows for the charge of an unfolded protein to be calculated.
+
+USAGE
+
+    findSurfaceCharge [pH, [folded, [selection ,[cutoff]]]]
+
+ARGUMENTS
+
+    pH = The pH value to estimate a surface charge at
+
+    folded = Whether the protein is folded (True) or denatured (False)
+
+    selection = string: object or selection in which to find exposed
+        residues {default: empty string - all objects}
+
+    cutoff = float: cutoff of what is exposed or not {default: 2.5 Ang**2}
+
+RETURNS
+
+    A printout of the estimated surface charge at a given pH
+
+    """
+    if not selection:
+        for obj in cmd.get_names():
+            _findSurfaceChargeImpl(obj, pH, folded, cutoff)
+    else:
+        _findSurfaceChargeImpl(selection, pH, folded, cutoff)
+
+
+cmd.extend("findSurfaceAtoms", findSurfaceAtoms)
+cmd.extend("findSurfaceCharge", findSurfaceCharge)