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updates

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This commit is contained in:
Marat Valiev 2012-02-10 02:26:08 +00:00
parent ca01bed956
commit c8e4bd7ea6
1 changed files with 70 additions and 20 deletions
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90
contrib/marat/nwchem-python/generic_atom.py
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@ -40,7 +40,17 @@ class GenericAtom(object):
if d:
return cls(d)
return None
@classmethod
def fromXYZrecord(cls,aline):
atomstr = string.split(aline)[0:4]
if len(atomstr) < 4:
return None
name = atomstr[0]
coord=[float(x) for x in atomstr[1:]]
return cls({"grouptag":"XYZ", "coord":coord,"name":name})
@staticmethod
def bondlength(a1,a2):
dr=a1.coord-a2.coord
@ -57,9 +67,44 @@ class GenericAtom(object):
Default values of "UNK" and "0" are used should
residue name and residue id be absent
'''
tag = self.dct.get("grouptag")
if tag is None:
resname = self.dct.get("resname","UNK").strip()
resid = str(self.dct.get("resid",0)).strip()
tag ="_".join((resname,resid))
return tag
def setGroupTag(self,tag):
'''
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
'''
self.dct["grouptag"]=tag
def resTag(self):
'''
returns that identifies res association of an atom
based on residue name and residue id (e.g. "ASP_1")
'''
resname = self.dct.get("resname","UNK").strip()
resid = str(self.dct.get("resid",0)).strip()
return "_".join((resname,resid))
tag ="_".join((resname,resid))
return tag
def setBond(self,i):
'''
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
'''
bond = self.dct.setdefault("bond",set())
bond.add(i)
def __str__(self):
return str(self.dct) + " " + str(self.coord)
@ -71,21 +116,26 @@ class GenericAtom(object):
return dr <= (a1.covRadius()+a2.covRadius())
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)
print b.coord
print b.dct
print GenericAtom.bondlength(a,b),GenericAtom.bonded(a,b)
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()
# 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)
# print b.coord
# print b.dct
# print GenericAtom.bondlength(a,b),GenericAtom.bonded(a,b)
# 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()
aline6="O1 -0.985 -1.156 1.140 0.0 0.0 "
aline5="O1 -0.985 -1.156 "
d=GenericAtom.fromXYZrecord(aline6)
print d