/usr/lib/python2.7/dist-packages/csb/apps/bfit.py is in python-csb 1.2.3+dfsg-3.
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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 | """
Python application for robust structure superposition of two structures.
bfit models non-rigid displacements in protein ensembles with outlier-tolerant
probability distributions.
"""
import numpy
import csb.apps
import csb.bio.utils
from csb.bio.io.wwpdb import LegacyStructureParser
from csb.bio.sequence import SequenceAlignment
class ExitCodes(csb.apps.ExitCodes):
IO_ERROR = 2
INPUT_ERROR = 3
class AppRunner(csb.apps.AppRunner):
@property
def target(self):
return BFitApp
def command_line(self):
cmd = csb.apps.ArgHandler(self.program, __doc__)
# Input structures
cmd.add_positional_argument('pdb1', str,
'full path to the first structure')
cmd.add_positional_argument('pdb2', str,
'full path to the second structure')
# Optional arguments
cmd.add_scalar_option('chain1', 'c', str,
'Chain of the first structure',
default='A')
cmd.add_scalar_option('chain2', 'd', str,
'Chain of the second structure',
default='A')
cmd.add_scalar_option('scalemixture', 's', str,
'Scale mixture distribution',
default='student',
choices=['student', 'k'])
cmd.add_scalar_option('alignment', 'a', str,
'Alignment in fasta format defining equivalent positions\n'
+ 'Assumes that chain1 is the first sequence of '
+ 'the alignment and chain2 the second sequence')
cmd.add_scalar_option('outfile', 'o', str,
'file to which the rotated second ' +
'structure will be written',
default='bfit.pdb')
cmd.add_scalar_option('niter', 'n', int,
'Number of optimization steps',
default=200)
cmd.add_boolean_option('em', None,
'Use the EM algorithm for optimsation',
default = False)
return cmd
class BFitApp(csb.apps.Application):
"""
Python application for robust structure superposition of two protein structures
"""
def main(self):
try:
parser = LegacyStructureParser(self.args.pdb1)
r = parser.parse()
parser = LegacyStructureParser(self.args.pdb2)
m = parser.parse()
except IOError as e:
self.exit('PDB file parsing failed\n' + str(e.value), ExitCodes.IO_ERROR)
X = numpy.array(r[self.args.chain1].get_coordinates(['CA'], True))
Y = numpy.array(m[self.args.chain2].get_coordinates(['CA'], True))
if self.args.alignment is not None:
align = SequenceAlignment.parse(file(self.args.alignment).read())
align = align[:2, :]
matches = []
for i in range(1, align.length + 1):
if not align.gap_at(i):
matches.append([align.columns[i][0].rank - 1,
align.columns[i][1].rank - 1])
matches = numpy.array(matches)
X = X[matches[:, 0], :]
Y = Y[matches[:, 1], :]
if len(X) != len(Y):
self.exit('Structures are of different lengths,' +
' please specify an alignment',
ExitCodes.INPUT_ERROR)
R, t = csb.bio.utils.bfit(X, Y, self.args.niter,
self.args.scalemixture, self.args.em)
m.transform(R, t)
m.to_pdb(self.args.outfile)
def main():
AppRunner().run()
if __name__ == '__main__':
main()
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