enhanced contact detection

PyPDB/PyPDB.py

@@ -2084,21 +2084,70 @@ class residue(atmList):
 				return True
 		return False
 
-	def contact(self, res2, dist = 4.):
+	def contact(self, res2, dist = 4., what = "All", what_return = "info"):
 		"""
 		PDB.contact: return true or false depending on the distance between the atoms.
-		@param what : the atom name (CA, CB)
 		@param dist : the threshold to detect contacts
+		@param what : "All", "BBBB", "BBSC", "SCSC"
+		@param what_info : "info", or the atom name for distance (CA, CB)
 		@return     : an array of the contactMap
 		"""
 		for atm in self:
+			if what != "All":
+				isBB = atm.atmName() in BBATMS
 			x1, y1, z1 = atm.xyz()
+
 			for atm2 in res2:
 				x2, y2, z2 = atm2.xyz()
+				if what != "All":
+					isBB2 = atm2.atmName() in BBATMS
+				if (what == "SCSC") and (isBB or isBB2):
+					continue
+				if (what == "BBBB") and ((not isBB) or (not isBB2)):
+					continue
+				if (what == "BBSC") and ( ((isBB) and (isBB2)) or ((not isBB) and (not isBB2))):
+					continue
+				if (what == "notBBBB") and ( ((isBB) and (isBB2))):
+					continue
+				# water is 2.8 (diameter)
 				aDist = distance(x1, y1, z1, x2, y2, z2)
-				if aDist < dist:
-					return True
-		return False
+				r1 = 0.8 # 1.6 # C
+				elem  = atm.atmName()[0]
+				if elem == "N":
+					r1 = 0.9 # 1.5
+				if elem == "O":
+					r1 = 0.73 # 1.4
+				if elem == "S":
+					r1 = 1.04 # 1.85
+				if elem == "H":
+					r1 = 0.37 # 1.2
+				r2 = 0.8 # 1.6 # C
+				elem2 = atm2.atmName()[0]
+				if elem2 == "N":
+					r2 = 0.9 # 1.5
+				if elem2 == "O":
+					r2 = 0.73 # 1.4
+				if elem2 == "S":
+					r2 = 1.04 # 1.85
+				if elem2 == "H":
+					r2 = 0.37 # 1.2
+								
+				if aDist - r1 - r2 < dist:
+						if what_return == "info":
+							# print(what, atm.atmName(), atm.resNum(), r1, isBB, atm2.atmName(), atm2.resNum(), r2, isBB2, aDist)
+							return True
+						else:
+							ca1 = self.findAtm(atmName = what_return)
+							ca2 = res2.findAtm(atmName = what_return)
+							# print(what_return, ca1.atmName(), ca2.atmName())
+							if (ca1 != None) and (ca2 != None):
+								x1, y1, z1 = ca1.xyz()
+								x2, y2, z2 = ca2.xyz()
+								# print("distance calculated")
+								return distance(x1, y1, z1, x2, y2, z2)
+		if what_return == "info":                             
+			return False
+		return None
 
 
 ## ========================================
@@ -4972,6 +5021,20 @@ x[0:2]
 					return True
 		return False
 
+	def intraContacts(self, dist = 4., what = "All"):
+		"""
+		what is one of All, SCSC, BBBB or BBSC
+		"""
+		for res in range(0,len(self)):
+			for res2 in range(res+2, len(self)):
+				if self[res].contact(self[res2], dist = dist, what = what, what_return = "info"):
+					# print("%s %s %s %s %s" % (self.id, \
+					# 	self[res].rName(), self[res].rNum(), self[res2].rName(), self[res2].rNum()))
+					print("%s %s %s %s %s %f" % (self.id, \
+						self[res].rName(), self[res].rNum(), self[res2].rName(), self[res2].rNum(), \
+						self[res].contact(self[res2], dist = dist, what = what, what_return = "CA")))
+		return False
+
 	def contactMap(self, what = "CA", dist = 11.):
 		"""
 		PDB.contactMap: return an internal  contact map based on