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")
