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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,169 @@ | ||
| """Script to update the database for the lattice parameter search""" | ||
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| __author__ = "Adam Simpkin" | ||
| __date__ = "28 Apr 2017" | ||
| __version__ = "0.1" | ||
|
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| import cctbx.crystal | ||
| import cctbx.uctbx | ||
| import cPickle | ||
| import numpy | ||
| import os | ||
| import urllib | ||
|
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| import simbad.constants | ||
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| class _LatticeParameters(object): | ||
| """A basic lattice parameter sorting class""" | ||
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| __slots__ = ('pdb_code', 'a', 'b', 'c', 'alpha', 'beta', 'gamma', 'space_group') | ||
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| def __init__(self, pdb_code, a, b, c, alpha, beta, gamma, space_group): | ||
| self.pdb_code = pdb_code | ||
| self.a = a | ||
| self.b = b | ||
| self.c = c | ||
| self.alpha = alpha | ||
| self.beta = beta | ||
| self.gamma = gamma | ||
| self.space_group = space_group | ||
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| def __repr__(self): | ||
| return "{0}(pdb_code={1} a={2} b={3} c={4} alpha={5}, beta={6}, gamma={7}, space_group={8}".format( | ||
| self.__class__.__name__, self.pdb_code, self.a, self.b, self.c, | ||
| self.alpha, self.beta, self.gamma, self.space_group) | ||
|
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| def _as_dict(self): | ||
| """Convert the :obj:`_LatticeParameterScore <simbad.lattice.search._LatticeParameterScore>` | ||
| object to a dictionary""" | ||
| dictionary = {} | ||
| for k in self.__slots__: | ||
| dictionary[k] = getattr(self, k) | ||
| return dictionary | ||
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|
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| def custom_report(): | ||
| """Create a custom report from the PDB and returns a :obj: _LatticeParameters containing | ||
| the pdb code, lattice parameters and space group for every structure in the PDBs""" | ||
|
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| link = 'http://www.rcsb.org/pdb/rest/customReport.csv?pdbids=*&customReportColumns=lengthOfUnitCellLatticeA,' \ | ||
| 'lengthOfUnitCellLatticeB,lengthOfUnitCellLatticeC,unitCellAngleAlpha,unitCellAngleBeta,unitCellAngleGamma,' \ | ||
| 'spaceGroup&format=csv&service=wsfile' | ||
|
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| urllib.urlretrieve(link, os.path.join(os.getcwd(), 'results.csv')) | ||
|
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| results = [] | ||
| with open(os.path.join(os.getcwd(), 'results.csv'), 'r') as f: | ||
| for line in f: | ||
| if line.startswith('structureId'): | ||
| continue | ||
| else: | ||
| try: | ||
| tmp = line.split('","') | ||
| pdb_code = tmp[0][1:] | ||
| a = float(tmp[1]) | ||
| b = float(tmp[2]) | ||
| c = float(tmp[3]) | ||
| alpha = float(tmp[4]) | ||
| beta = float(tmp[5]) | ||
| gamma = float(tmp[6]) | ||
| space_group = tmp[7][:-2] | ||
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| data = _LatticeParameters(pdb_code, a, b, c, alpha, beta, gamma, space_group) | ||
| results.append(data) | ||
| except ValueError: | ||
| pass | ||
|
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| os.unlink(os.path.join(os.getcwd(), 'results.csv')) | ||
|
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| return results | ||
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| def calculate_niggli_cell(unit_cell, space_group): | ||
| """Calculate the parameters of the Niggli cell | ||
| Parameters | ||
| ---------- | ||
| unit_cell : list, tuple | ||
| The parameters of the unit cell | ||
| space_group : str | ||
| The space group | ||
| Returns | ||
| ------- | ||
| list | ||
| The Niggli cell parameters | ||
| """ | ||
|
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| unit_cell = cctbx.uctbx.unit_cell(unit_cell) | ||
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| xs = cctbx.crystal.symmetry( | ||
| unit_cell=unit_cell, | ||
| space_group=space_group | ||
| ) | ||
| niggli_cell = xs.change_basis(xs.change_of_basis_op_to_niggli_cell()).unit_cell() | ||
| niggli_cell = numpy.array(eval(str(niggli_cell))).tolist() | ||
| return niggli_cell | ||
|
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| def create_niggli_cell_db(crystal_data): | ||
| """Generate a new database for the lattice parameter search, overwrites old file""" | ||
|
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| # pickle_file = 'niggli_database.cpk' | ||
| pickle_file = simbad.constants.SIMBAD_LATTICE_DB | ||
| names = [] | ||
| lattice_pars = [] | ||
|
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| for i, c in enumerate(crystal_data): | ||
| unit_cell = ' '.join(str(p) for p in [c.a, c.b, c.c, c.alpha, c.beta, c.gamma]) | ||
|
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| if c.space_group.replace(' ', '') == "A1": | ||
| space_group = "P1" | ||
| elif c.space_group.replace(' ', '') == "B2": | ||
| space_group = "B112" | ||
| elif c.space_group.replace(' ', '') == "C1211": | ||
| space_group = "C2" | ||
| elif c.space_group.replace(' ', '') == "F422": | ||
| space_group = "I422" | ||
| elif c.space_group.replace(' ', '') == "I21": | ||
| space_group = "I2" | ||
| elif c.space_group.replace(' ', '') == "I1211": | ||
| space_group = "I2" | ||
| elif c.space_group.replace(' ', '') == "P21212A": | ||
| space_group = "P212121" | ||
| elif c.space_group.replace(' ', '') == "R3": | ||
| space_group = "R3:R" | ||
| elif c.space_group.replace(' ', '') == "C4212": | ||
| space_group = "P422" | ||
| else: | ||
| space_group = c.space_group | ||
|
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| try: | ||
| niggli_cell = calculate_niggli_cell(unit_cell, space_group) | ||
| except AssertionError: | ||
| pass | ||
| except ValueError: | ||
| pass | ||
| except RuntimeError: | ||
| pass | ||
|
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| if niggli_cell: | ||
| vals = numpy.array(niggli_cell) | ||
| if len(vals) == 6: | ||
| lattice_pars.append(vals) | ||
| names.append(c.pdb_code) | ||
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| print "Total files loaded = {0}".format(i) | ||
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| database = [names, lattice_pars] | ||
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| cPickle.dump(database, open(pickle_file, "w")) | ||
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| return | ||
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| if __name__ == "__main__": | ||
| results = custom_report() | ||
| create_niggli_cell_db(results) |
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