#-*. coding: utf-8 -*- ## Copyright (c) 2008-2012, Noel O'Boyle; 2012, Adrià Cereto-Massagué ## All rights reserved. ## ## This file is part of Cinfony. ## The contents are covered by the terms of the GPL v2 license ## which is included in the file LICENSE_GPLv2.txt. """ pybel - A Cinfony module for accessing Open Babel Global variables: ob - the underlying SWIG bindings for Open Babel 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 sys import math import os.path import tempfile if sys.platform[:4] == "java": import org.openbabel as ob import java.lang.System java.lang.System.loadLibrary("openbabel_java") _obfuncs = ob.openbabel_java _obconsts = ob.openbabel_javaConstants import javax elif sys.platform[:3] == "cli": import System import clr clr.AddReference('System.Windows.Forms') clr.AddReference('System.Drawing') from System.Windows.Forms import ( Application, DockStyle, Form, PictureBox, PictureBoxSizeMode ) from System.Drawing import Image, Size _obdotnet = os.environ["OBDOTNET"] if _obdotnet[0] == '"': # Remove trailing quotes _obdotnet = _obdotnet[1:-1] clr.AddReferenceToFileAndPath(os.path.join(_obdotnet, "OBDotNet.dll")) import OpenBabel as ob _obfuncs = ob.openbabel_csharp _obconsts = ob.openbabel_csharp else: import openbabel as ob _obfuncs = _obconsts = ob try: import Tkinter as tk import Image as PIL import ImageTk as piltk except ImportError: #pragma: no cover tk = None def _formatstodict(list): if sys.platform[:4] == "java": list = [list.get(i) for i in range(list.size())] 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() _builder = ob.OBBuilder() 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 def _getpluginnames(ptype): if sys.platform[:4] == "cli": plugins = ob.VectorString() else: plugins = ob.vectorString() ob.OBPlugin.ListAsVector(ptype, None, plugins) if sys.platform[:4] == "java": plugins = [plugins.get(i) for i in range(plugins.size())] return [x.split()[0] for x in plugins] descs = _getpluginnames("descriptors") """A list of supported descriptors""" _descdict = _getplugins(ob.OBDescriptor.FindType, descs) fps = [_x.lower() for _x in _getpluginnames("fingerprints")] """A list of supported fingerprint types""" _fingerprinters = _getplugins(ob.OBFingerprint.FindFingerprint, fps) forcefields = [_x.lower() for _x in _getpluginnames("forcefields")] """A list of supported forcefields""" _forcefields = _getplugins(ob.OBForceField.FindType, forcefields) operations = _getpluginnames("ops") """A list of supported operations""" _operations = _getplugins(ob.OBOp.FindType, operations) def readfile(format, filename, opt=None): """Iterate over the molecules in a file. Required parameters: format - see the informats variable for a list of available input formats filename Optional parameters: opt - a dictionary of format-specific options For format options with no parameters, specify the value as None. You can access the first molecule in a file using the next() method of the iterator (or the next() keyword in Python 3): mol = readfile("smi", "myfile.smi").next() # Python 2 mol = next(readfile("smi", "myfile.smi")) # Python 3 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 """ if opt == None: opt = {} obconversion = ob.OBConversion() formatok = obconversion.SetInFormat(format) for k, v in opt.items(): if v == None: obconversion.AddOption(k, obconversion.INOPTIONS) else: obconversion.AddOption(k, obconversion.INOPTIONS, str(v)) if not formatok: raise ValueError("%s is not a recognised Open Babel format" % format) if not os.path.isfile(filename): raise IOError("No such file: '%s'" % filename) def filereader(): obmol = ob.OBMol() notatend = obconversion.ReadFile(obmol,filename) while notatend: yield Molecule(obmol) obmol = ob.OBMol() notatend = obconversion.Read(obmol) return filereader() def readstring(format, string, opt=None): """Read in a molecule from a string. Required parameters: format - see the informats variable for a list of available input formats string Optional parameters: opt - a dictionary of format-specific options For format options with no parameters, specify the value as None. Example: >>> input = "C1=CC=CS1" >>> mymol = readstring("smi", input) >>> len(mymol.atoms) 5 """ if opt == None: opt = {} obmol = ob.OBMol() obconversion = ob.OBConversion() formatok = obconversion.SetInFormat(format) if not formatok: raise ValueError("%s is not a recognised Open Babel format" % format) for k, v in opt.items(): if v == None: obconversion.AddOption(k, obconversion.INOPTIONS) else: obconversion.AddOption(k, obconversion.INOPTIONS, str(v)) 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) opt -- a dictionary of format-specific options For format options with no parameters, specify the value as None. Methods: write(molecule) close() """ def __init__(self, format, filename, overwrite=False, opt=None): if opt == None: opt = {} 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 Open Babel format" % format) for k, v in opt.items(): if v == None: self.obConversion.AddOption(k, self.obConversion.OUTOPTIONS) else: self.obConversion.AddOption(k, self.obConversion.OUTOPTIONS, str(v)) 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_index = _obconsts.UnitCell if sys.platform[:3] == "cli": unitcell_index = System.UInt32(unitcell_index) unitcell = self.OBMol.GetData(unitcell_index) if unitcell: if sys.platform[:3] != "cli": return _obfuncs.toUnitCell(unitcell) else: return unitcell.Downcast[ob.OBUnitCell]() 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. """ if sys.platform[:3] == "cli": fp = ob.VectorUInt() else: fp = ob.vectorUnsignedInt() fptype = fptype.lower() 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, opt=None): """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) opt -- a dictionary of format specific options For format options with no parameters, specify the value as None. 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. """ if opt == None: opt = {} obconversion = ob.OBConversion() formatok = obconversion.SetOutFormat(format) if not formatok: raise ValueError("%s is not a recognised Open Babel format" % format) for k, v in opt.items(): if v == None: obconversion.AddOption(k, obconversion.OUTOPTIONS) else: obconversion.AddOption(k, obconversion.OUTOPTIONS, str(v)) 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() _builder.Build(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) Tkinter and Python Imaging Library are required for image display. """ obconversion = ob.OBConversion() formatok = obconversion.SetOutFormat("_png2") if not formatok: errormessage = ("PNG depiction support not found. You should compile " "Open Babel with support for Cairo. See installation " "instructions for more information.") raise ImportError(errormessage) # Need to copy to avoid removing hydrogens from self workingmol = Molecule(ob.OBMol(self.OBMol)) workingmol.removeh() if not usecoords: _operations['gen2D'].Do(workingmol.OBMol) if update == True: if workingmol.OBMol.NumAtoms() != self.OBMol.NumAtoms(): errormessage = ("It is not possible to update the original molecule " "with the calculated coordinates, as the original " "molecule contains explicit hydrogens for which no " "coordinates have been calculated.") raise RuntimeError(errormessage) else: for i in range(workingmol.OBMol.NumAtoms()): self.OBMol.GetAtom(i + 1).SetVector(workingmol.OBMol.GetAtom(i + 1).GetVector()) if filename: filedes = None else: if sys.platform[:3] == "cli" and show: errormessage = ("It is only possible to show the molecule if you " "provide a filename. The reason for this is that I kept " "having problems when using temporary files.") raise RuntimeError(errormessage) filedes, filename = tempfile.mkstemp() workingmol.write("_png2", filename=filename, overwrite=True) if show: if sys.platform[:4] == "java": image = javax.imageio.ImageIO.read(java.io.File(filename)) frame = javax.swing.JFrame(visible=1) frame.getContentPane().add(javax.swing.JLabel(javax.swing.ImageIcon(image))) frame.setSize(300,300) frame.setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE) frame.show() elif sys.platform[:3] == "cli": form = _MyForm() form.setup(filename, self.title) Application.Run(form) else: 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 if sys.platform[:4] == "java": fp = [fp.get(i) for i in range(fp.size())] 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): fp = self.fp if sys.platform[:4] == "java": fp = [self.fp.get(i) for i in range(self.fp.size())] return ", ".join([str(x) for x in 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) vector = self.obsmarts.GetUMapList() if sys.platform[:4] == "java": vector = [vector.get(i) for i in range(vector.size())] return list(vector) 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() # Python 2 >>> # mol = next(readfile("sdf", 'head.sdf')) # Python 3 >>> 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.items(): ... 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): data = self._mol.GetData() if sys.platform[:4] == "java": data = [data.get(i) for i in range(data.size())] answer = [x for x in data if x.GetDataType()==_obconsts.PairData or x.GetDataType()==_obconsts.CommentData] if sys.platform[:3] != "cli": answer = [_obfuncs.toPairData(x) for x in answer] return answer 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 iter(zip(self.keys(), self.values())) def __iter__(self): return iter(self.keys()) def iteritems(self): # Can remove for Python 3 return 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.items(): self[k] = v def __getitem__(self, key): self._testforkey(key) answer = self._mol.GetData(key) if sys.platform[:3] != "cli": answer = _obfuncs.toPairData(answer) return answer.GetValue() def __setitem__(self, key, value): if key in self: if sys.platform[:3] != "cli": pairdata = _obfuncs.toPairData(self._mol.GetData(key)) else: pairdata = self._mol.GetData(key).Downcast[ob.OBPairData]() 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.items()).__repr__() if sys.platform[:3] == "cli": class _MyForm(Form): def __init__(self): Form.__init__(self) def setup(self, filename, title): # adjust the form's client area size to the picture self.ClientSize = Size(300, 300) self.Text = title self.filename = filename self.image = Image.FromFile(self.filename) pictureBox = PictureBox() # this will fit the image to the form pictureBox.SizeMode = PictureBoxSizeMode.StretchImage pictureBox.Image = self.image # fit the picture box to the frame pictureBox.Dock = DockStyle.Fill self.Controls.Add(pictureBox) self.Show() if __name__=="__main__": #pragma: no cover import doctest doctest.testmod(verbose=True)