File: jchem.py

package info (click to toggle)
cinfony 1.2-1
  • links: PTS, VCS
  • area: main
  • in suites: buster, jessie, jessie-kfreebsd, stretch
  • size: 880 kB
  • sloc: python: 2,964; makefile: 6
file content (661 lines) | stat: -rw-r--r-- 21,832 bytes parent folder | download | duplicates (3)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
#-*. coding: utf-8 -*-
## Copyright (c) 2012, Adrià Cereto-Massagué, Noel O'Boyle
## All rights reserved.
##
##  This file is part of Cinfony.
##  The contents are covered by the terms of the BSD license
##  which is included in the file LICENSE_BSD.txt.

"""
jchem - A Cinfony module for accessing ChemAxon's JChem from CPython and Jython

Global variables:
  chemaxon - the underlying JChem Java library
  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 os
from glob import glob

if sys.platform[:4] == "java":
    classpath = []
    if 'JCHEMDIR' in os.environ:
        assert os.path.isdir(os.path.join(os.environ['JCHEMDIR'], 'lib'))
        for jar in glob(os.path.join(os.path.join(os.environ['JCHEMDIR'],'lib'), '*.jar')):
            classpath.append(jar)

if sys.platform[:4] == "java" or sys.platform[:3] == "cli":
    import sys
    sys.path = classpath + sys.path
    import java, javax
    import chemaxon
    from chemaxon.util import MolHandler
    #Exceptions are handled differently in jpype and jython. We need to wrap them:
    MolExportException = chemaxon.marvin.io.MolExportException
    MolFormatException = chemaxon.formats.MolFormatException
else:
    from jpype import *

    if not isJVMStarted():
        _jvm = os.environ['JPYPE_JVM']
        if _jvm[0] == '"': # Remove trailing quotes
            _jvm = _jvm[1:-1]
        _cp = os.pathsep.join(os.environ.get('CLASSPATH', '').split(os.pathsep))
        startJVM(_jvm, "-Djava.class.path=" + _cp)

    chemaxon = JPackage("chemaxon")
    MolHandler = chemaxon.util.MolHandler
    try:
        _testmol = MolHandler()
    except TypeError:
        raise ImportError, "jchem.jar file cannot be found."

    # Exception wrappers for JPype
    MolExportException = JavaException
    MolFormatException = JavaException

_descset = set(['HAcc', 'HDon', 'Heavy', 'LogD', 'LogP', 'Mass', 'TPSA'])
_descset.update(dir(chemaxon.descriptors.scalars))
descs = [cls for cls in _descset if hasattr(getattr(chemaxon.descriptors.scalars, cls),'generate') and cls != 'LogD'] + ['RotatableBondsCount']
"""A list of supported descriptors"""
fps = ['ecfp']
"""A list of supported fingerprint types"""
forcefields = ["mmff94"]
"""A list of supported forcefields"""

informats = {
    'smi': "SMILES"
    ,'cxsmi': "ChemAxon exntended SMILES"
    ,'mol': "MDL MOL"
    ,'sdf': "MDL SDF"
    ,'inchi': "InChI"
    ,'cml': "Chemical Markup Language"
    , 'mrv':'Marvin Documents'
    , 'skc':'ISIS/Draw sketch file'
    , 'cdx':'ChemDraw sketch file'
    , 'cdxml':'ChemDraw sketch file'
    , "name":"Common name"
    , "peptide":"Aminoacid sequence"
    , "sybyl":"Tripos SYBYL"
    , "pdb":"PDB"
    , "xyz":"XYZ"
    , 'cube':'Gaussian cube'
    , 'gout':'Gaussian output format'
    }
"""A dictionary of supported input formats"""

outformats = {
    'smi': "SMILES"
    ,'cxsmi': "ChemAxon exntended SMILES"
    ,'mol': "MDL MOL"
    ,'sdf': "MDL SDF"
    ,'inchi': "InChI"
    ,'inchikey': "InChIKey"
    ,'cml': "CML"
    , 'mrv':'Marvin Documents'
    , 'skc':'ISIS/Draw sketch file'
    , 'cdx':'ChemDraw sketch file'
    , 'cdxml':'ChemDraw sketch file'
    , "name":"Common name"
    , "peptide":"Aminoacid sequence"
    , "sybyl":"Tripos SYBYL"
    , "pdb":"PDB"
    , "xyz":"XYZ"
    , 'cube':'Gaussian cube'
    , 'gjf':'Gaussian input format'
    }
"""A dictionary of supported output formats"""

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

    Required parameters:
       format - Ignored, but needed for compatibility with other cinfony
                modules and also good for readability
       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
    """
    if not os.path.isfile(filename):
        raise IOError, "No such file: '%s'" % filename
    if not format in outformats:
        raise ValueError("%s is not a recognised JChem format" % format)
    try:
        mi = chemaxon.formats.MolImporter(filename)
        mol = mi.read()
        while mol:
            mol.aromatize()
            yield Molecule(mol)
            mol = mi.read()
    except chemaxon.formats.MolFormatException:
        raise ValueError("%s is not a recognised JChem format" % format)

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

    Required parameters:
       format - Ignored, but needed for compatibility with other cinfony
                modules and also good for readability
       string

    Example:
    >>> input = "C1=CC=CS1"
    >>> mymol = readstring("smi", input)
    >>> len(mymol.atoms)
    5
    """
    format = format.lower()
    if format not in informats:
        raise ValueError("%s is not a recognised JChem format" % format)
    try:
        mh = MolHandler(string)
        return Molecule(mh.molecule)
    except MolFormatException, ex:
        if sys.platform[:4] != "java":
            #Jpype exception
            ex = ex.message()
            raise IOError, ex
        else:
            raise IOError("Problem reading the supplied string")

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

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

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

    Methods:
       write(molecule)
       close()
    """
    def __init__(self, format, filename, overwrite=False):
        if ':' in format:
            format,  options = format.split(':')
            if options:
                options = ':' + options
        else:
            options = ''
        self.format = format.lower()
        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
        if format in ("smi", 'cxsmi'):
            if not options:
                options = ':a-H'
            out = chemaxon.formats.MolExporter.exportToFormat(self.Molecule,format +'les:a-H')
        try:
            self._writer = chemaxon.formats.MolExporter(filename, format + options)
        except MolExportException,  e:
            raise ValueError(e)
        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."
        self._writer.write(molecule.Molecule)
        self.total += 1

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

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

    Required parameters:
       Molecule -- a JChem Molecule or any type of cinfony Molecule

    Attributes:
       atoms, data, exactmass, formula, molwt, title

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

    The underlying JChem Molecule can be accessed using the attribute:
       Molecule
    The associated JChem MolHandler can be accessed using the attribute:
       MolHandler
    """
    _cinfony = True

    def __init__(self, Molecule):

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

        self.Molecule = Molecule
        self.MolHandler = chemaxon.util.MolHandler(self.Molecule)
        self.MolHandler.aromatize()

    @property
    def atoms(self): return [Atom(atom) for atom in self.Molecule.atomArray]
    @property
    def data(self): return MoleculeData(self)
    @property
    def formula(self): return self.MolHandler.calcMolFormula()
    @property
    def exactmass(self):
        return self.MolHandler.calcMolWeightInDouble()
    @property
    def molwt(self):
        return self.MolHandler.calcMolWeight()
    def _gettitle(self): return self.Molecule.getName()
    def _settitle(self, val): self.Molecule.setName(val)
    title = property(_gettitle, _settitle)
    @property
    def _exchange(self):
        if self.Molecule.dim > 1:
            return (1, self.write("mol"))
        else:
            return (0, self.write("smi"))

    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 __str__(self):
        return self.write()

    def addh(self):
        """Add hydrogens."""
        self.MolHandler.addHydrogens()

    def removeh(self):
        """Remove hydrogens."""
        self.MolHandler.removeHydrogens()

    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.
        """
        if ':' in format:
            format,  options = format.split(':')
            if options:
                options = ':' + options
        else:
            options = ''
        format = format.lower()
        if format not in outformats:
            raise ValueError("%s is not a recognised format" % format)

        if filename is not None and not overwrite and os.path.isfile(filename):
            raise IOError, "%s already exists. Use 'overwrite=True' to overwrite it." % filename

        if format in ("smi", 'cxsmi'):
            if not options:
                options = ':a-H'
            out = chemaxon.formats.MolExporter.exportToFormat(self.Molecule,format +'les' + options)
        elif format == 'inchikey':
            out = chemaxon.formats.MolExporter.exportToFormat(self.Molecule,'inchikey').replace('InChIKey=', '')
        else:
            out = chemaxon.formats.MolExporter.exportToFormat(self.Molecule,format + options)
            if format == 'inchi':
                out = out.split('AuxInfo=')[0]
        if filename:
            output = open(filename, "w")
            print >> output, out
            output.close()
            return
        else:
            return out


    def calcfp(self, fp="ecfp"):
        """Calculate a molecular fingerprint.

        Optional parameters:
           fptype -- the fingerprint type (default is "daylight"). See the
                     fps variable for a list of of available fingerprint
                     types.
        """
        fp = fp.lower()
        if fp in fps:
            if fp == 'ecfp':
                fp = chemaxon.descriptors.ECFP(ECFPConfiguration)
                fp.generate(self.Molecule)
        else:
            raise ValueError, "%s is not a recognised fingerprint type" % fp
        return Fingerprint(fp)

    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:
            if descname not in descs:
                raise ValueError, "%s is not a recognised descriptor type" % descname
            if descname == 'RotatableBondsCount':
                ta = chemaxon.calculations.TopologyAnalyser()
                ta.setMolecule(self.Molecule)
                ans[descname] = ta.rotatableBondCount()
            else:
                desc = getattr(chemaxon.descriptors.scalars, descname)('')
                desc.generate(self.Molecule)
                ans[descname] = desc.toFloatArray()[0]
        return ans

    def make3D(self):
        """Generate 3D coordinates.

        Hydrogens are added, and a low energy conformer is found
        using the MMFF94 forcefield.
        """
        self.addh()
        cp = chemaxon.marvin.calculations.ConformerPlugin()
        cp.setMolecule(self.Molecule)
        cp.setLowestEnergyConformerCalculation(True)
        cp.setMMFF94Optimization(True)
        success = cp.run()
        optmol = cp.getMMFF94OptimizedStrucutre()
        self.Molecule = optmol
        self.MolHandler = chemaxon.util.MolHandler(self.Molecule)
        self.MolHandler.aromatize()

    def draw(self, show=True, filename=None, update=False,
             usecoords=False):
        """Create a 2D depiction of the molecule.
        """
        if not usecoords:
            molecule = self.Molecule.clone()
            molecule.setDim(0)
        else:
            molecule = self.Molecule
        if update:
            myMolecule = readstring("mol", Molecule(molecule).write("mol"))
            self.Molecule = myMolecule.Molecule
            self.MolHandler = myMolecule.MolHandler
        bytearray = chemaxon.formats.MolExporter.exportToBinFormat(molecule, 'png')
        if filename:
            of = java.io.FileOutputStream(filename)
            of.write(bytearray)
            of.close()
        if show:
            source = java.io.ByteArrayInputStream(bytearray)
            reader = javax.imageio.ImageIO.getImageReadersByFormatName('png').next()
            iis = javax.imageio.ImageIO.createImageInputStream(source)
            reader.setInput(iis, True)
            param = reader.getDefaultReadParam()
            image = reader.read(0, param)
            frame = javax.swing.JFrame()
            imageIcon = javax.swing.ImageIcon(image)
            label = javax.swing.JLabel()
            label.setIcon(imageIcon)
            frame.getContentPane().add(label, java.awt.BorderLayout.CENTER)
            frame.pack()
            frame.setVisible(True)
            frame.show()


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

    Required parameters:
       fingerprint -- a vector calculated by one of the fingerprint methods

    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 1 - self.fp.getTanimoto(other.fp)
    def __getattr__(self, attr):
        if attr == "bits":
            # Create a bits attribute on-the-fly
            bs = self.fp.toBitSet()
            bits = [-1]
            while True:
                setbit = bs.nextSetBit(bits[-1] + 1)
                if setbit == -1:
                    break
                bits.append(setbit)
            return bits[1:] # Leave out the initial '-1'
        else:
            raise AttributeError, "Fingerprint has no attribute %s" % attr
    def __str__(self):
        return ", ".join([str(x) for x in self.fp.toIntArray()])

class Atom(object):
    """Represent an Atom.

    Required parameters:
       Atom -- a JChem Atom

    Attributes:
       atomicnum, coords, formalcharge

    The original JChem Atom can be accessed using the attribute:
       Atom
    """

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

    @property
    def atomicnum(self): return self.Atom.getAtno()
    @property
    def coords(self):
            return (self.Atom.x, self.Atom.y, self.Atom.z)
    @property
    def formalcharge(self):
        return self.Atom.charge

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

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

    Required parameters:
       smartspattern

    Methods:
       findall()

    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)]
    """
    def __init__(self, smartspattern):
        """Initialise with a SMARTS pattern."""
        self.search = chemaxon.sss.search.MolSearch()
        smarts = MolHandler(smartspattern)
        smarts.setQueryMode(True)
        smarts.aromatize()
        self.search.setQuery(smarts.molecule)

    def findall(self, molecule):
        """Find all matches of the SMARTS pattern to a particular molecule.

        Required parameters:
           molecule
        """
        self.search.setTarget(molecule.Molecule)
        match = self.search.findAll()
        result = []
        for i in xrange(len(match)):
            result.append(tuple([n+1 for n in match[i]]))
        return result

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

    Required parameters:
      Molecule -- a JChem Molecule

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

    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, Molecule):
        self._data = Molecule.Molecule.properties()
    def _testforkey(self, key):
        if not key in self:
            raise KeyError, "'%s'" % key
    def keys(self):
        return list(self._data.keys)
    def values(self):
        return [self[k] for k in self._data.keys]
    def items(self):
        return [(k, self[k]) for k in self._data.keys]
    def __iter__(self):
        return iter(self.keys())
    def iteritems(self):
        return iter(self.items())
    def __len__(self):
        return len(self._data.keys)
    def __contains__(self, key):
        return key in self.keys()
    def __delitem__(self, key):
        self._testforkey(key)
        self._data.setString(key, None)
    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 self._data.get(key).propValue
    def __setitem__(self, key, value):
        self._data.setString(key, str(value))
    def __repr__(self):
        return dict(self.iteritems()).__repr__()

ECFPConfiguration = """<?xml version="1.0" encoding="UTF-8"?>
<ECFPConfiguration Version="0.1">

    <Parameters Length="1024" Diameter="4" Counts="no"/>

    <IdentifierConfiguration>
        <!-- Default atom properties (switched on by Value=1) -->
        <Property Name="AtomicNumber" Value="1"/>
        <Property Name="HeavyNeighborCount" Value="1"/>
        <Property Name="HCount" Value="1"/>
        <Property Name="FormalCharge" Value="1"/>
        <Property Name="IsRingAtom" Value="1"/>

        <!-- Other built-in atom properties (switched off by Value=0) -->
        <Property Name="ConnectionCount" Value="0"/>
        <Property Name="Valence" Value="0"/>
        <Property Name="Mass" Value="0"/>
        <Property Name="MassNumber" Value="0"/>
        <Property Name="HasAromaticBond" Value="0"/>
        <Property Name="IsTerminalAtom" Value="0"/>
        <Property Name="IsStereoAtom" Value="0"/>
    </IdentifierConfiguration>

    <StandardizerConfiguration Version="0.1">
        <Actions>
            <Action ID="aromatize" Act="aromatize"/>
            <RemoveExplicitH ID="RemoveExplicitH" Groups="target"/>
        </Actions>
    </StandardizerConfiguration>

    <ScreeningConfiguration>
        <ParametrizedMetrics>
            <ParametrizedMetric Name="Tanimoto" ActiveFamily="Generic" Metric="Tanimoto" Threshold="0.5"/>
            <ParametrizedMetric Name="Euclidean" ActiveFamily="Generic" Metric="Euclidean" Threshold="10"/>
        </ParametrizedMetrics>
    </ScreeningConfiguration>

</ECFPConfiguration>
"""

if __name__=="__main__": #pragma: no cover
    mol = readstring("smi", "CC(=O)Cl")
    mol.title = u"Adrià"
    mol.draw()

    for mol in readfile("sdf", "head.sdf"):
        pass