pybel.py - cinfony - Google Code

‹r136

r147

Source path: svn/ trunk/ cinfony/ pybel.py

"""
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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