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"""
pybel - A Cinfony module for accessing OpenBabel from CPython

Global variables:
ob - the underlying SWIG bindings for OpenBabel
informats - a dictionary of supported input formats
outformats - a dictionary of supported output formats
descs - a list of supported descriptors
fps - a list of supported fingerprint types
forcefields - a list of supported forcefields
"""

import math
import os.path
import tempfile
import openbabel as ob

try:
import oasa
import oasa.cairo_out
except ImportError: #pragma: no cover
oasa = None

try:
import Tkinter as tk
import Image as PIL
import ImageTk as piltk
except ImportError: #pragma: no cover
tk = None

def _formatstodict(list):
broken = [x.replace("[Read-only]", "").replace("[Write-only]","").split(" -- ") for x in list]
broken = [(x,y.strip()) for x,y in broken]
return dict(broken)
_obconv = ob.OBConversion()
informats = _formatstodict(_obconv.GetSupportedInputFormat())
"""A dictionary of supported input formats"""
outformats = _formatstodict(_obconv.GetSupportedOutputFormat())
"""A dictionary of supported output formats"""

def _getplugins(findplugin, names):
plugins = dict([(x, findplugin(x)) for x in names if findplugin(x)])
return plugins

descs = ['LogP', 'MR', 'TPSA']
"""A list of supported descriptors"""
_descdict = _getplugins(ob.OBDescriptor.FindType, descs)
fps = ['FP2', 'FP3', 'FP4']
"""A list of supported fingerprint types"""
_fingerprinters = _getplugins(ob.OBFingerprint.FindFingerprint, fps)
forcefields = ['uff', 'mmff94', 'ghemical']
"""A list of supported forcefields"""
_forcefields = _getplugins(ob.OBForceField.FindType, forcefields)
operations = ['Gen3D']
"""A list of supported operations"""
_operations = _getplugins(ob.OBOp.FindType, operations)

def readfile(format, filename):
"""Iterate over the molecules in a file.

Required parameters:
format - see the informats variable for a list of available
input formats
filename

You can access the first molecule in a file using the next() method
of the iterator:
mol = readfile("smi", "myfile.smi").next()

You can make a list of the molecules in a file using:
mols = list(readfile("smi", "myfile.smi"))

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"):
... atomtotal += len(mol.atoms)
...
>>> print atomtotal
43
"""
obconversion = ob.OBConversion()
formatok = obconversion.SetInFormat(format)
if not formatok:
raise ValueError("%s is not a recognised OpenBabel format" % format)
if not os.path.isfile(filename):
raise IOError("No such file: '%s'" % filename)
obmol = ob.OBMol()
notatend = obconversion.ReadFile(obmol,filename)
while notatend:
yield Molecule(obmol)
obmol = ob.OBMol()
notatend = obconversion.Read(obmol)

def readstring(format, string):
"""Read in a molecule from a string.

Required parameters:
format - see the informats variable for a list of available
input formats
string

Example:
>>> input = "C1=CC=CS1"
>>> mymol = readstring("smi", input)
>>> len(mymol.atoms)
5
"""
obmol = ob.OBMol()
obconversion = ob.OBConversion()

formatok = obconversion.SetInFormat(format)
if not formatok:
raise ValueError("%s is not a recognised OpenBabel format" % format)

success = obconversion.ReadString(obmol, string)
if not success:
raise IOError("Failed to convert '%s' to format '%s'" % (
string, format))
return Molecule(obmol)

class Outputfile(object):
"""Represent a file to which *output* is to be sent.

Although it's possible to write a single molecule to a file by
calling the write() method of a molecule, if multiple molecules
are to be written to the same file you should use the Outputfile
class.

Required parameters:
format - see the outformats variable for a list of available
output formats
filename

Optional parameters:
overwrite -- if the output file already exists, should it
be overwritten? (default is False)

Methods:
write(molecule)
close()
"""
def __init__(self, format, filename, overwrite=False):
self.format = format
self.filename = filename
if not overwrite and os.path.isfile(self.filename):
raise IOError("%s already exists. Use 'overwrite=True' to overwrite it." % self.filename)
self.obConversion = ob.OBConversion()
formatok = self.obConversion.SetOutFormat(self.format)
if not formatok:
raise ValueError("%s is not a recognised OpenBabel format" % format)
self.total = 0 # The total number of molecules written to the file

def write(self, molecule):
"""Write a molecule to the output file.

Required parameters:
molecule
"""
if not self.filename:
raise IOError("Outputfile instance is closed.")

if self.total==0:
self.obConversion.WriteFile(molecule.OBMol, self.filename)
else:
self.obConversion.Write(molecule.OBMol)
self.total += 1

def close(self):
"""Close the Outputfile to further writing."""
self.obConversion.CloseOutFile()
self.filename = None

class Molecule(object):
"""Represent a Pybel Molecule.

Required parameter:
OBMol -- an Open Babel OBMol or any type of cinfony Molecule

Attributes:
atoms, charge, conformers, data, dim, energy, exactmass, formula,
molwt, spin, sssr, title, unitcell.
(refer to the Open Babel library documentation for more info).

Methods:
addh(), calcfp(), calcdesc(), draw(), localopt(), make3D(), removeh(),
write()

The underlying Open Babel molecule can be accessed using the attribute:
OBMol
"""
_cinfony = True

def __init__(self, OBMol):

if hasattr(OBMol, "_cinfony"):
a, b = OBMol._exchange
if a == 0:
mol = readstring("smi", b)
else:
mol = readstring("mol", b)
OBMol = mol.OBMol

self.OBMol = OBMol

@property
def atoms(self):
return [ Atom(self.OBMol.GetAtom(i+1)) for i in range(self.OBMol.NumAtoms()) ]
@property
def charge(self): return self.OBMol.GetTotalCharge()
@property
def conformers(self): return self.OBMol.GetConformers()
@property
def data(self): return MoleculeData(self.OBMol)
@property
def dim(self): return self.OBMol.GetDimension()
@property
def energy(self): return self.OBMol.GetEnergy()
@property
def exactmass(self): return self.OBMol.GetExactMass()
@property
def formula(self): return self.OBMol.GetFormula()
@property
def molwt(self): return self.OBMol.GetMolWt()
@property
def spin(self): return self.OBMol.GetTotalSpinMultiplicity()
@property
def sssr(self): return self.OBMol.GetSSSR()
def _gettitle(self): return self.OBMol.GetTitle()
def _settitle(self, val): self.OBMol.SetTitle(val)
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'")
@property
def _exchange(self):
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.

This allows constructions such as the following:
for atom in mymol:
print atom
"""
return iter(self.atoms)

def calcdesc(self, descnames=[]):
"""Calculate descriptor values.

Optional parameter:
descnames -- a list of names of descriptors

If descnames is not specified, all available descriptors are
calculated. See the descs variable for a list of available
descriptors.
"""
if not descnames:
descnames = descs
ans = {}
for descname in descnames:
try:
desc = _descdict[descname]
except KeyError:
raise ValueError("%s is not a recognised Open Babel descriptor type" % descname)
ans[descname] = desc.Predict(self.OBMol)
return ans

def calcfp(self, fptype="FP2"):
"""Calculate a molecular fingerprint.

Optional parameters:
fptype -- the fingerprint type (default is "FP2"). See the
fps variable for a list of of available fingerprint
types.
"""
fp = ob.vectorUnsignedInt()
try:
fingerprinter = _fingerprinters[fptype]
except KeyError:
raise ValueError("%s is not a recognised Open Babel Fingerprint type" % fptype)
fingerprinter.GetFingerprint(self.OBMol, fp)
return Fingerprint(fp)

def write(self, format="smi", filename=None, overwrite=False):
"""Write the molecule to a file or return a string.

Optional parameters:
format -- see the informats variable for a list of available
output formats (default is "smi")
filename -- default is None
overwite -- if the output file already exists, should it
be overwritten? (default is False)

If a filename is specified, the result is written to a file.
Otherwise, a string is returned containing the result.

To write multiple molecules to the same file you should use
the Outputfile class.
"""
obconversion = ob.OBConversion()
formatok = obconversion.SetOutFormat(format)
if not formatok:
raise ValueError("%s is not a recognised OpenBabel format" % format)

if filename:
if not overwrite and os.path.isfile(filename):
raise IOError("%s already exists. Use 'overwrite=True' to overwrite it." % filename)
obconversion.WriteFile(self.OBMol,filename)
obconversion.CloseOutFile()
else:
return obconversion.WriteString(self.OBMol)

def localopt(self, forcefield="mmff94", steps=500):
"""Locally optimize the coordinates.

Optional parameters:
forcefield -- default is "mmff94". See the forcefields variable
for a list of available forcefields.
steps -- default is 500

If the molecule does not have any coordinates, make3D() is
called before the optimization. Note that the molecule needs
to have explicit hydrogens. If not, call addh().
"""
forcefield = forcefield.lower()
if self.dim != 3:
self.make3D(forcefield)
ff = _forcefields[forcefield]
success = ff.Setup(self.OBMol)
if not success:
return
ff.SteepestDescent(steps)
ff.GetCoordinates(self.OBMol)

## def globalopt(self, forcefield="MMFF94", steps=1000):
## if not (self.OBMol.Has2D() or self.OBMol.Has3D()):
## self.make3D()
## self.localopt(forcefield, 250)
## ff = _forcefields[forcefield]
## numrots = self.OBMol.NumRotors()
## if numrots > 0:
## ff.WeightedRotorSearch(numrots, int(math.log(numrots + 1) * steps))
## ff.GetCoordinates(self.OBMol)

def make3D(self, forcefield = "mmff94", steps = 50):
"""Generate 3D coordinates.

Optional parameters:
forcefield -- default is "mmff94". See the forcefields variable
for a list of available forcefields.
steps -- default is 50

Once coordinates are generated, hydrogens are added and a quick
local optimization is carried out with 50 steps and the
MMFF94 forcefield. Call localopt() if you want
to improve the coordinates further.
"""
forcefield = forcefield.lower()
_operations['Gen3D'].Do(self.OBMol)
self.addh()
self.localopt(forcefield, steps)

def addh(self):
"""Add hydrogens."""
self.OBMol.AddHydrogens()

def removeh(self):
"""Remove hydrogens."""
self.OBMol.DeleteHydrogens()

def __str__(self):
return self.write()

def draw(self, show=True, filename=None, update=False, usecoords=False):
"""Create a 2D depiction of the molecule.

Optional parameters:
show -- display on screen (default is True)
filename -- write to file (default is None)
update -- update the coordinates of the atoms to those
determined by the structure diagram generator
(default is False)
usecoords -- don't calculate 2D coordinates, just use
the current coordinates (default is False)

OASA is used for 2D coordinate generation and depiction. Tkinter and
Python Imaging Library are required for image display.
"""
etab = ob.OBElementTable()

if not oasa:
errormessage = ("OASA not found, but is required for 2D structure "
"generation and depiction. OASA is part of BKChem. "
"See installation instructions for more "
"information.")
raise ImportError(errormessage)
mol = oasa.molecule()
for atom in self.atoms:
v = mol.create_vertex()
v.symbol = etab.GetSymbol(atom.atomicnum)
v.charge = atom.formalcharge
if usecoords:
v.x, v.y, v.z = atom.coords[0] * 30., atom.coords[1] * 30., 0.0
mol.add_vertex(v)

for bond in ob.OBMolBondIter(self.OBMol):
e = mol.create_edge()
e.order = bond.GetBO()
if bond.IsHash():
e.type = "h"
elif bond.IsWedge():
e.type = "w"
mol.add_edge(bond.GetBeginAtomIdx() - 1,
bond.GetEndAtomIdx() - 1,
e)
# I'm sure there's a more elegant way to do the following, but here goes...
# let's set the stereochemistry around double bonds
self.write("can") # Perceive UP/DOWNness
for bond in ob.OBMolBondIter(self.OBMol):
ends = bond.GetBeginAtomIdx(), bond.GetEndAtomIdx()
if bond.GetBO() == 2:
stereobonds = [[b for b in ob.OBAtomBondIter(self.OBMol.GetAtom(x)) if b.GetIdx() != bond.GetIdx() and (b.IsUp() or b.IsDown())]
for x in ends]
if stereobonds[0] and stereobonds[1]: # Needs to be defined at either end
if stereobonds[0][0].IsUp() == stereobonds[1][0].IsUp():
# Either both up or both down
stereo = oasa.stereochemistry.cis_trans_stereochemistry.SAME_SIDE
else:
stereo = oasa.stereochemistry.cis_trans_stereochemistry.OPPOSITE_SIDE
atomids = [(b[0].GetBeginAtomIdx(), b[0].GetEndAtomIdx()) for b in stereobonds]
extremes = []
for id, end in zip(ends, atomids):
if end[0] == id:
extremes.append(end[1])
else:
extremes.append(end[0])
center = mol.get_edge_between(mol.atoms[ends[0] - 1], mol.atoms[ends[1] - 1])
st = oasa.stereochemistry.cis_trans_stereochemistry(
center = center, value = stereo,
references = (mol.atoms[extremes[0] - 1], mol.atoms[ends[0] - 1],
mol.atoms[ends[1] - 1], mol.atoms[extremes[1] - 1]))
mol.add_stereochemistry(st)

mol.remove_unimportant_hydrogens()
if not usecoords:
oasa.coords_generator.calculate_coords(mol, bond_length=30)
if update:
newcoords = [(v.x / 30., v.y / 30., 0.0) for v in mol.vertices]
for atom, newcoord in zip(ob.OBMolAtomIter(self.OBMol), newcoords):
atom.SetVector(*newcoord)
if filename or show:
maxx = max([v.x for v in mol.vertices])
minx = min([v.x for v in mol.vertices])
maxy = max([v.y for v in mol.vertices])
miny = min([v.y for v in mol.vertices])
maxcoord = max(maxx - minx, maxy - miny)
fontsize = 16
bondwidth = 6
linewidth = 2
if maxcoord > 270: # 300 - margin * 2
for v in mol.vertices:
v.x *= 270. / maxcoord
v.y *= 270. / maxcoord
fontsize *= math.sqrt(270. / maxcoord)
bondwidth *= math.sqrt(270. / maxcoord)
linewidth *= math.sqrt(270. / maxcoord)
if filename:
filedes = None
else:
filedes, filename = tempfile.mkstemp()

canvas = oasa.cairo_out.cairo_out()
canvas.show_hydrogens_on_hetero = True
canvas.font_size = fontsize
canvas.bond_width = bondwidth
canvas.line_width = linewidth
canvas.mol_to_cairo(mol, filename)
if show:
if not tk:
errormessage = ("Tkinter or Python Imaging "
"Library not found, but is required for image "
"display. See installation instructions for "
"more information.")
raise ImportError(errormessage)
root = tk.Tk()
root.title((hasattr(self, "title") and self.title)
or self.__str__().rstrip())
frame = tk.Frame(root, colormap="new", visual='truecolor').pack()
image = PIL.open(filename)
imagedata = piltk.PhotoImage(image)
label = tk.Label(frame, image=imagedata).pack()
quitbutton = tk.Button(root, text="Close", command=root.destroy).pack(fill=tk.X)
root.mainloop()
if filedes:
os.close(filedes)
os.remove(filename)

class Atom(object):
"""Represent a Pybel atom.

Required parameter:
OBAtom -- an Open Babel OBAtom

Attributes:
atomicmass, atomicnum, cidx, coords, coordidx, exactmass,
formalcharge, heavyvalence, heterovalence, hyb, idx,
implicitvalence, isotope, partialcharge, spin, type,
valence, vector.

(refer to the Open Babel library documentation for more info).

The original Open Babel atom can be accessed using the attribute:
OBAtom
"""

def __init__(self, OBAtom):
self.OBAtom = OBAtom

@property
def coords(self):
return (self.OBAtom.GetX(), self.OBAtom.GetY(), self.OBAtom.GetZ())
@property
def atomicmass(self): return self.OBAtom.GetAtomicMass()
@property
def atomicnum(self): return self.OBAtom.GetAtomicNum()
@property
def cidx(self): return self.OBAtom.GetCIdx()
@property
def coordidx(self): return self.OBAtom.GetCoordinateIdx()
@property
def exactmass(self): return self.OBAtom.GetExactMass()
@property
def formalcharge(self): return self.OBAtom.GetFormalCharge()
@property
def heavyvalence(self): return self.OBAtom.GetHvyValence()
@property
def heterovalence(self): return self.OBAtom.GetHeteroValence()
@property
def hyb(self): return self.OBAtom.GetHyb()
@property
def idx(self): return self.OBAtom.GetIdx()
@property
def implicitvalence(self): return self.OBAtom.GetImplicitValence()
@property
def isotope(self): return self.OBAtom.GetIsotope()
@property
def partialcharge(self): return self.OBAtom.GetPartialCharge()
@property
def spin(self): return self.OBAtom.GetSpinMultiplicity()
@property
def type(self): return self.OBAtom.GetType()
@property
def valence(self): return self.OBAtom.GetValence()
@property
def vector(self): return self.OBAtom.GetVector()

def __str__(self):
c = self.coords
return "Atom: %d (%.2f %.2f %.2f)" % (self.atomicnum, c[0], c[1], c[2])

def _findbits(fp, bitsperint):
"""Find which bits are set in a list/vector.

This function is used by the Fingerprint class.

>>> _findbits([13, 71], 8)
[1, 3, 4, 9, 10, 11, 15]
"""
ans = []
start = 1
for x in fp:
i = start
while x > 0:
if x % 2:
ans.append(i)
x >>= 1
i += 1
start += bitsperint
return ans

class Fingerprint(object):
"""A Molecular Fingerprint.

Required parameters:
fingerprint -- a vector calculated by OBFingerprint.FindFingerprint()

Attributes:
fp -- the underlying fingerprint object
bits -- a list of bits set in the Fingerprint

Methods:
The "|" operator can be used to calculate the Tanimoto coeff. For example,
given two Fingerprints 'a', and 'b', the Tanimoto coefficient is given by:
tanimoto = a | b
"""
def __init__(self, fingerprint):
self.fp = fingerprint
def __or__(self, other):
return ob.OBFingerprint.Tanimoto(self.fp, other.fp)
@property
def bits(self):
return _findbits(self.fp, ob.OBFingerprint.Getbitsperint())
def __str__(self):
return ", ".join([str(x) for x in self.fp])

class Smarts(object):
"""A Smarts Pattern Matcher

Required parameters:
smartspattern

Methods:
findall(molecule)

Example:
>>> mol = readstring("smi","CCN(CC)CC") # triethylamine
>>> smarts = Smarts("[#6][#6]") # Matches an ethyl group
>>> print smarts.findall(mol)
[(1, 2), (4, 5), (6, 7)]

The numbers returned are the indices (starting from 1) of the atoms
that match the SMARTS pattern. In this case, there are three matches
for each of the three ethyl groups in the molecule.
"""
def __init__(self,smartspattern):
"""Initialise with a SMARTS pattern."""
self.obsmarts = ob.OBSmartsPattern()
success = self.obsmarts.Init(smartspattern)
if not success:
raise IOError("Invalid SMARTS pattern")
def findall(self,molecule):
"""Find all matches of the SMARTS pattern to a particular molecule.

Required parameters:
molecule
"""
self.obsmarts.Match(molecule.OBMol)
return [x for x in self.obsmarts.GetUMapList()]

class MoleculeData(object):
"""Store molecule data in a dictionary-type object

Required parameters:
obmol -- an Open Babel OBMol

Methods and accessor methods are like those of a dictionary except
that the data is retrieved on-the-fly from the underlying OBMol.

Example:
>>> mol = readfile("sdf", 'head.sdf').next()
>>> data = mol.data
>>> print data
{'Comment': 'CORINA 2.61 0041 25.10.2001', 'NSC': '1'}
>>> print len(data), data.keys(), data.has_key("NSC")
2 ['Comment', 'NSC'] True
>>> print data['Comment']
CORINA 2.61 0041 25.10.2001
>>> data['Comment'] = 'This is a new comment'
>>> for k,v in data.iteritems():
... print k, "-->", v
Comment --> This is a new comment
NSC --> 1
>>> del data['NSC']
>>> print len(data), data.keys(), data.has_key("NSC")
1 ['Comment'] False
"""
def __init__(self, obmol):
self._mol = obmol
def _data(self):
return [ob.toPairData(x) for x in self._mol.GetData() if x.GetDataType()==ob.PairData or x.GetDataType()==ob.CommentData]
def _testforkey(self, key):
if not key in self:
raise KeyError("'%s'" % key)
def keys(self):
return [x.GetAttribute() for x in self._data()]
def values(self):
return [x.GetValue() for x in self._data()]
def items(self):
return zip(self.keys(), self.values())
def __iter__(self):
return iter(self.keys())
def iteritems(self):
return iter(self.items())
def __len__(self):
return len(self._data())
def __contains__(self, key):
return self._mol.HasData(key)
def __delitem__(self, key):
self._testforkey(key)
self._mol.DeleteData(self._mol.GetData(key))
def clear(self):
for key in self:
del self[key]
def has_key(self, key):
return key in self
def update(self, dictionary):
for k, v in dictionary.iteritems():
self[k] = v
def __getitem__(self, key):
self._testforkey(key)
return ob.toPairData(self._mol.GetData(key)).GetValue()
def __setitem__(self, key, value):
if key in self:
pairdata = ob.toPairData(self._mol.GetData(key))
pairdata.SetValue(str(value))
else:
pairdata = ob.OBPairData()
pairdata.SetAttribute(key)
pairdata.SetValue(str(value))
self._mol.CloneData(pairdata)
def __repr__(self):
return dict(self.iteritems()).__repr__()

if __name__=="__main__": #pragma: no cover
import doctest
doctest.testmod(verbose=True)
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Change log

r145 by baoilleach on Feb 18, 2009   Diff
Synching with OBPybel.
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Older revisions

r136 by baoilleach on Oct 04, 2008   Diff
Fixed bug reported by Björn Grüning
and investigated by Tim. Needed to
check status of ff.Setup before
continuing.
r122 by baoilleach on Aug 06, 2008   Diff
Updating docstrings.
r121 by baoilleach on Aug 06, 2008   Diff
Update docstrings
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