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2009-09-21 Noel O'Boyle <baoilleach@gmail.com>

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* scripts/*: Copied + pasted the scripts directory from 22x as a number
	of commits were never merged.
This commit is contained in:
Noel O'Boyle
2009-09-21 11:12:00 +00:00
parent 36baf46d9e
commit afb12d1eb7
12 changed files with 737 additions and 599 deletions
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scripts/python/pybel_py3.x.py
+16 -15
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@@ -33,6 +33,7 @@ def _formatstodict(list):
broken = [(x,y.strip()) for x,y in broken]
return dict(broken)
_obconv = ob.OBConversion()
_builder = ob.OBBuilder()
informats = _formatstodict(_obconv.GetSupportedInputFormat())
"""A dictionary of supported input formats"""
outformats = _formatstodict(_obconv.GetSupportedOutputFormat())
@@ -73,7 +74,7 @@ def readfile(format, filename):
You can iterate over the molecules in a file as shown in the
following code snippet:
>>> atomtotal = 0
>>> for mol in readfile("sdf","head.sdf"):
>>> for mol in readfile("sdf", "head.sdf"):
... atomtotal += len(mol.atoms)
...
>>> print atomtotal
@@ -102,7 +103,7 @@ def readstring(format, string):
Example:
>>> input = "C1=CC=CS1"
>>> mymol = readstring("smi",input)
>>> mymol = readstring("smi", input)
>>> len(mymol.atoms)
5
"""
@@ -205,7 +206,7 @@ class Molecule(object):
@property
def atoms(self):
return [ Atom(self.OBMol.GetAtom(i+1)) for i in range(self.OBMol.NumAtoms()) ]
return [ Atom(self.OBMol.GetAtom(i+1)) for i in range(self.OBMol.NumAtoms()) ]
@property
def charge(self): return self.OBMol.GetTotalCharge()
@property
@@ -231,17 +232,17 @@ class Molecule(object):
title = property(_gettitle, _settitle)
@property
def unitcell(self):
unitcell = self.OBMol.GetData(ob.UnitCell)
if unitcell:
return ob.toUnitCell(unitcell)
else:
raise AttributeError("Molecule has no attribute 'unitcell'")
unitcell = self.OBMol.GetData(ob.UnitCell)
if unitcell:
return ob.toUnitCell(unitcell)
else:
raise AttributeError("Molecule has no attribute 'unitcell'")
@property
def _exchange(self):
if self.OBMol.HasNonZeroCoords():
return (1, self.write("mol"))
else:
return (0, self.write("can").split()[0])
if self.OBMol.HasNonZeroCoords():
return (1, self.write("mol"))
else:
return (0, self.write("can").split()[0])
def __iter__(self):
"""Iterate over the Atoms of the Molecule.
@@ -364,7 +365,7 @@ class Molecule(object):
to improve the coordinates further.
"""
forcefield = forcefield.lower()
_operations['Gen3D'].Do(self.OBMol)
_builder.Build(self.OBMol)
self.addh()
self.localopt(forcefield, steps)
@@ -526,7 +527,7 @@ class Atom(object):
@property
def coords(self):
return (self.OBAtom.GetX(), self.OBAtom.GetY(), self.OBAtom.GetZ())
return (self.OBAtom.GetX(), self.OBAtom.GetY(), self.OBAtom.GetZ())
@property
def atomicmass(self): return self.OBAtom.GetAtomicMass()
@property
@@ -607,7 +608,7 @@ class Fingerprint(object):
return ob.OBFingerprint.Tanimoto(self.fp, other.fp)
@property
def bits(self):
return _findbits(self.fp, ob.OBFingerprint.Getbitsperint())
return _findbits(self.fp, ob.OBFingerprint.Getbitsperint())
def __str__(self):
return ", ".join([str(x) for x in self.fp])