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final version

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This commit is contained in:
Marat Valiev 2012-02-09 02:51:58 +00:00
parent e03dc3bb7f
commit 362e5fc0dc
1 changed files with 27 additions and 21 deletions
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48
contrib/marat/nwchem-python/pdbrecord.py
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@ -6,28 +6,32 @@ Created on Feb 7, 2012
class PDBAtomRecord(object):
'''
class PDBAtomRecord parses ATOM or HETATM line in PDB file.
It can only properly handle ATOM or HETATM records.
Before getting individual fields one should test
whether the record is atom based using PDBAtomRecord.test() method.
Perhaps the best way to use this class at this point is to generate
dictionary using PDBAtomRecord.dict(aline1)
Class PDBAtomRecord processes ATOM or HETATM line in PDB file.
For all other records None value will be returned.
PDBAtomRecord.test is used to verify PDB line is of ATOM or HETATM type.
PDBAtomRecord.dct will return all available records in a dictionary with the keys
indicated below
'''
# Dictionary for column locations (see at the end for more info)
irec=dict(record=[0,6],atomid=[6,11],name=[12,16],resname=[17,20],
resid=[22,26],coord=[30,54],element=[76,78])
# Dictionary for types of fields
atype=dict(record="string",atomid="int",name="string",resname="string",
resid="int",coord="float array",element="string")
def __init__(self):
'''
Constructor
'''
pass
# def __init__(self):
# '''
# Constructor
# '''
# pass
@staticmethod
def field(name,buf):
'''
returns value of the "name" field in the provided "buf" buffer
always returns None value if buffer is not of ATOM or HETATM type
'''
# print inspect.getsource(PDBAtomRecord.fieldName)
if not PDBAtomRecord.test(buf):
return None
@ -59,7 +63,10 @@ class PDBAtomRecord(object):
return value
@staticmethod
def dict(buf):
def dct(buf):
'''
returns all the available fields in a dictionary
'''
if not PDBAtomRecord.test(buf):
return None
@ -73,11 +80,10 @@ class PDBAtomRecord(object):
@staticmethod
def test(buf):
'''
tests whether buffer is of ATOM or HETATM type
'''
return buf[0:6] in ("ATOM ","HETATM")
def __str__(self):
return self.buf
if __name__ == '__main__':
@ -87,10 +93,10 @@ if __name__ == '__main__':
print PDBAtomRecord.field("name",'')
print PDBAtomRecord.field("name",aline3)
print PDBAtomRecord.dict(aline1)
print PDBAtomRecord.dict(aline2)
print PDBAtomRecord.dict(aline3)
print PDBAtomRecord.dict('')
print PDBAtomRecord.dct(aline1)
print PDBAtomRecord.dct(aline2)
print PDBAtomRecord.dct(aline3)
print PDBAtomRecord.dct('')
# 1 - 6 Record name "ATOM "