def tls_segment_recombination(self): if not hasattr(self.cpartition, "rmsd_b_mtx"): return "" rmatrix = self.cpartition.rmsd_b_mtx tbl = table.StringTableFromMatrix(rmatrix) filename = "%s_CHAIN%s_NTLS%s_RECOMBINATION.txt" % ( self.struct_id, self.chain_id, self.cpartition.num_tls_segments()) open(filename, "w").write(str(tbl)) m, n = rmatrix.shape tbl = table.StringTable(m + 1, n + 1, '<td></td>') ## label top and left table margins for i, tls in enumerate(self.cpartition.iter_tls_segments()): tbl[i + 1, 0] = '<td style="background-color:%s">%s</td>' % ( tls.color.rgbs, tls.display_label()) tbl[0, i + 1] = tbl[i + 1, 0] ## recombination values ## determine min/max values for coloring min_rmsd_b = rmatrix[0, 0] max_rmsd_b = rmatrix[0, 0] for i in xrange(m): for j in xrange(n): min_rmsd_b = min(min_rmsd_b, rmatrix[i, j]) max_rmsd_b = max(max_rmsd_b, rmatrix[i, j]) b_range = max_rmsd_b - min_rmsd_b for i in xrange(m): for j in xrange(n): scale = (rmatrix[i, j] - min_rmsd_b) / b_range bright = 1.0 - (0.75 * scale) rgbs = misc.rgb_f2s((bright, bright, bright)) tbl[i + 1, j + 1] = '<td style="background-color:%s;padding:5px;font-size:x-small">%6.2f</td>' % ( rgbs, rmatrix[i, j]) l = [ '<table style="background-color:#bbbbff;border-width:thin;border-color:black;border-style:solid">\n' ] for i in xrange(m + 1): l.append('<tr>') for j in xrange(n + 1): l.append(tbl[i, j]) l.append('</tr>\n') l += ['</table>\n'] l2 = [ '<center>', gnuplots.FormatFigureHTML("RMSD B Values of Combined TLS Groups", captions.TLS_GROUP_RECOMBINATION, "".join(l)), '</center>' ] return "".join(l2)
def tls_segment_recombination(self): if not hasattr(self.cpartition, "rmsd_b_mtx"): return "" rmatrix = self.cpartition.rmsd_b_mtx tbl = table.StringTableFromMatrix(rmatrix) filename = "%s_CHAIN%s_NTLS%s_RECOMBINATION.txt" % ( self.struct_id, self.chain_id, self.cpartition.num_tls_segments()) open(filename, "w").write(str(tbl)) m, n = rmatrix.shape tbl = table.StringTable(m + 1, n + 1, '<td></td>') ## label top and left table margins for i, tls in enumerate(self.cpartition.iter_tls_segments()): tbl[i + 1, 0] = '<td style="background-color:%s">%s</td>' % (tls.color.rgbs, tls.display_label()) tbl[0, i + 1] = tbl[i + 1, 0] ## recombination values ## determine min/max values for coloring min_rmsd_b = rmatrix[0, 0] max_rmsd_b = rmatrix[0, 0] for i in xrange(m): for j in xrange(n): min_rmsd_b = min(min_rmsd_b, rmatrix[i, j]) max_rmsd_b = max(max_rmsd_b, rmatrix[i, j]) b_range = max_rmsd_b - min_rmsd_b for i in xrange(m): for j in xrange(n): scale = (rmatrix[i, j] - min_rmsd_b) / b_range bright = 1.0 - (0.75 * scale) rgbs = misc.rgb_f2s((bright, bright, bright)) tbl[i + 1, j + 1] = '<td style="background-color:%s;padding:5px;font-size:x-small">%6.2f</td>' % ( rgbs, rmatrix[i, j]) l = ['<table style="background-color:#bbbbff;border-width:thin;border-color:black;border-style:solid">\n'] for i in xrange(m + 1): l.append('<tr>') for j in xrange(n + 1): l.append(tbl[i, j]) l.append('</tr>\n') l += ['</table>\n'] l2 = ['<center>', gnuplots.FormatFigureHTML("RMSD B Values of Combined TLS Groups", captions.TLS_GROUP_RECOMBINATION, "".join(l)), '</center>'] return "".join(l2)
def __init__(self, index, name, rgbf, thumbnail_dir, thumbnail_size = (25, 25)): self.index = index self.name = name self.rgbf = rgbf self.rgbi = misc.rgb_f2i(rgbf) self.rgbs = misc.rgb_f2s(rgbf) self.thumbnail_dir = thumbnail_dir self.thumbnail_size = thumbnail_size self.thumbnail_path = os.path.join(thumbnail_dir, "%s.png" % (name)) img = Image.new("RGBA", thumbnail_size, self.rgbi) img.save(self.thumbnail_path, "png")
def __init__(self, index, name, rgbf, thumbnail_dir, thumbnail_size=(25, 25)): self.index = index self.name = name self.rgbf = rgbf self.rgbi = misc.rgb_f2i(rgbf) self.rgbs = misc.rgb_f2s(rgbf) self.thumbnail_dir = thumbnail_dir self.thumbnail_size = thumbnail_size self.thumbnail_path = os.path.join(thumbnail_dir, "%s.png" % (name)) img = Image.new("RGBA", thumbnail_size, self.rgbi) img.save(self.thumbnail_path, "png")