def __init__(self,params):
'''
Constructor uses dictionary to accept arguments
'''
if params.has_key("coords"):
coords = params["coords"]
else:
coords=[0.0,0.0,0.0]
if params.has_key("name"):
name = params["name"]
else:
name = "atom"
if params.has_key("resname"):
self.resname = params["resname"]
else:
self.resname = "UNK"
Atom.__init__(self,name,coords)
if params.has_key("resid"):
self.resid = params["resid"]
else:
self.resid = 1
if params.has_key("element"):
self.element = params["element"]
else:
if name != "atom":
self.element = AtomDictionary.elementName(name)
else:
self.element = "atom"
print "creating first atom"
aline1="ATOM 588 1HG GLU 18 -13.363 -4.163 -2.372 1.00 0.00 H"
print aline1
a = ResAtom.fromPDBrecord(aline1)
print "it should come out as this"
print a
aline2="ATOM 589 2HG GLU 18 -12.634 -3.023 -3.475 1.00 0.00 H"
print "creating second atom"
aline2="ATOM 589 2HG GLU 18 -12.634 -3.023 -3.475 1.00 0.00 H"
print aline2
b = ResAtom.fromPDBrecord(aline2)
print "it should come out as this"
print b
print "The distance between these two atoms is", Atom.bondlength(a, b)
print "PDB record for second atom with starting index 5 and resid 23"
print b.toPDBrecord(id_atom=5,id_res=23)
# PDB ATOM RECORD FORMAT
# COLUMNS DATA TYPE FIELD DEFINITION
# ------------------------------------------------------
# 1 - 6 Record name "ATOM "
# 7 - 11 Integer serial Atom serial number.
# 13 - 16 Atom name Atom name.
# 17 Character altLoc Alternate location indicator.
# 18 - 20 Residue name resName Residue name.
# 22 Character chainID Chain identifier.
# 23 - 26 Integer resSeq Residue sequence number.