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added residue determination for XYZ files

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This commit is contained in:
Marat Valiev 2012-02-10 02:25:06 +00:00
parent 38eb9a0089
commit 228b8620e9
1 changed files with 60 additions and 7 deletions
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67
contrib/marat/nwchem-python/my_system.py
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@ -43,7 +43,22 @@ class MySystem(object):
a=GenericAtom.fromPDBrecord(line)
cls.AddAtom(a)
return cls
@classmethod
def fromXYZfile(cls,filename):
'''
alternative constructor from PDB file
'''
cls = MySystem()
fp = open(str(filename),'r')
for line in fp.readlines():
a=GenericAtom.fromXYZrecord(line)
if a is not None:
cls.AddAtom(a)
return cls
def toPDBfile(self):
for residue in self.residues.itervalues():
print residue
@ -52,16 +67,51 @@ class MySystem(object):
self.atoms.append(a1)
rmap = self.residues
tag = a1.groupTag()
# print tag
if tag not in rmap:
# print "tag not found"
rmap[tag]=GenericResidue()
rmap[tag].AddAtom(a1)
def connectAtoms(self):
for i in range(len(self.atoms)):
for j in range(i+1,len(self.atoms)):
a1=self.atoms[i]
a2=self.atoms[j]
if GenericAtom.bonded(a1, a2):
a1.setBond(j)
a2.setBond(i)
for a in self.atoms:
print a
def groupAtoms(self):
rmap = self.residues
ir = 0
for i in range(len(self.atoms)):
a1=self.atoms[i]
if a1.groupTag()!="XYZ":
continue
ir = ir +1
# tag = '{:0>3}'.format(ir)
tag="00"+str(ir)
tag=tag[-3:]
a1.setGroupTag(tag)
rmap[tag]=GenericResidue()
rmap[tag].AddAtom(a1)
rmap["XYZ"].delAtom(a1)
for j in range(i+1,len(self.atoms)):
a2=self.atoms[j]
if GenericAtom.bonded(a1, a2):
a2.setGroupTag(tag)
rmap[tag].AddAtom(a2)
rmap["XYZ"].delAtom(a2)
del rmap["XYZ"]
for a in self.atoms:
print a
def info(self):
for residue in self.residues.itervalues():
print residue
for tag,res in self.residues.iteritems():
print tag
print res
if __name__ == '__main__':
# sim0 = MySystem("test")
@ -80,7 +130,10 @@ if __name__ == '__main__':
# a = ResAtom.fromPDBrecord(aline2)
# sim0.AddAtom(a)
#
sim1 = MySystem.fromPDBfile("test.pdb")
sim1 = MySystem.fromXYZfile("test.xyz")
print sim1.residues["XYZ"]
# sim1.connectAtoms()
sim1.groupAtoms()
sim1.info()
# sim1 = MySystem.fromPDBfile("test.pdb")
#