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added groupTag method

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This commit is contained in:
Marat Valiev 2012-02-09 17:54:26 +00:00
parent 67b17744fc
commit 2b248abe39
1 changed files with 20 additions and 2 deletions
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22
contrib/marat/nwchem-python/GenericAtom.py
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@ -49,7 +49,22 @@ class GenericAtom(object):
def covRadius(self):
name = self.dct["name"]
return AtomParams.covRadius(name)
def groupTag(self):
'''
returns that identifies group association of an atom
based on residue name and residue id (e.g. "ASP_1")
Default values of "UNK" and "0" are used should
residue name and residue id be absent
'''
resname = self.dct.get("resname","UNK").strip()
resid = str(self.dct.get("resid",0)).strip()
return "_".join((resname,resid))
def __str__(self):
return str(self.dct) + " " + str(self.coord)
@staticmethod
def bonded(a1,a2):
dr = linalg.norm(a1.coord-a2.coord)
@ -59,8 +74,10 @@ if __name__ == '__main__':
aline1="ATOM 588 1HG GLU 18 -13.363 -4.163 -2.372 1.00 0.00 H"
aline2="ATOM 1 I1 IO3 1 -1.555 -0.350 0.333 1.39 I"
aline3="ATOM 2 O1 IO3 1 -0.985 -1.156 1.840 -0.80 O"
aline4="ATOM 2 O1 -0.985 -1.156 1.840 -0.80 O"
a=GenericAtom.fromPDBrecord(aline2)
print a.groupTag()
print a.coord
print a.dct
b=GenericAtom.fromPDBrecord(aline3)
@ -70,4 +87,5 @@ if __name__ == '__main__':
print a.covRadius()+b.covRadius()
c=GenericAtom.fromPDBrecord(aline1)
print GenericAtom.bondlength(a,c),GenericAtom.bonded(a,c)
c=GenericAtom.fromPDBrecord(aline4)
print c.groupTag()