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91 lines
2.6 KiB
Python
91 lines
2.6 KiB
Python
'''
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Created on Feb 7, 2012
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@author: marat
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'''
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import sys
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from pdbrecord import PDBAtomRecord
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from numpy import array,linalg
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from atom_params import *
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class GenericAtom(object):
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'''
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classdocs
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'''
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def __init__(self,d):
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'''
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Constructor
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'''
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self.dct = d
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if d:
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if type(d) is not type({}):
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print("wrong type ", type(d))
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print("expecting", type({}))
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sys.exit(1)
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else:
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self.dct = d
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try:
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self.coord=array(self.dct.pop("coord"))
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except:
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self.coord=None
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@classmethod
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def fromPDBrecord(cls,buf):
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'''
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alternative constructor from PDB record
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'''
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d=PDBAtomRecord.dct(buf)
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if d:
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return cls(d)
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return None
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@staticmethod
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def bondlength(a1,a2):
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dr=a1.coord-a2.coord
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return linalg.norm(dr)
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def covRadius(self):
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name = self.dct["name"]
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return AtomParams.covRadius(name)
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def groupTag(self):
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'''
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returns that identifies group association of an atom
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based on residue name and residue id (e.g. "ASP_1")
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Default values of "UNK" and "0" are used should
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residue name and residue id be absent
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'''
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resname = self.dct.get("resname","UNK").strip()
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resid = str(self.dct.get("resid",0)).strip()
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return "_".join((resname,resid))
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def __str__(self):
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return str(self.dct) + " " + str(self.coord)
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@staticmethod
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def bonded(a1,a2):
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dr = linalg.norm(a1.coord-a2.coord)
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return dr <= (a1.covRadius()+a2.covRadius())
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if __name__ == '__main__':
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aline1="ATOM 588 1HG GLU 18 -13.363 -4.163 -2.372 1.00 0.00 H"
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aline2="ATOM 1 I1 IO3 1 -1.555 -0.350 0.333 1.39 I"
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aline3="ATOM 2 O1 IO3 1 -0.985 -1.156 1.840 -0.80 O"
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aline4="ATOM 2 O1 -0.985 -1.156 1.840 -0.80 O"
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a=GenericAtom.fromPDBrecord(aline2)
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print(a.groupTag())
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print(a.coord)
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print(a.dct)
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b=GenericAtom.fromPDBrecord(aline3)
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print(b.coord)
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print(b.dct)
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print(GenericAtom.bondlength(a,b),GenericAtom.bonded(a,b))
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print(a.covRadius()+b.covRadius())
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c=GenericAtom.fromPDBrecord(aline1)
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print(GenericAtom.bondlength(a,c),GenericAtom.bonded(a,c))
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c=GenericAtom.fromPDBrecord(aline4)
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print(c.groupTag())
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