This file is indexed.

/usr/share/pyshared/ase/io/eps.py is in python-ase 3.6.0.2515-1.1.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below.

  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
import time
from math import sqrt

import numpy as np

from ase.utils import rotate
from ase.data import covalent_radii
from ase.data.colors import jmol_colors


class EPS:
    def __init__(self, atoms,
                 rotation='', show_unit_cell=False, radii=None,
                 bbox=None, colors=None, scale=20):
        self.numbers = atoms.get_atomic_numbers()
        self.colors = colors
        if colors is None:
            self.colors = jmol_colors[self.numbers]

        if radii is None:
            radii = covalent_radii[self.numbers]
        elif type(radii) is float:
            radii = covalent_radii[self.numbers] * radii
        else:
            radii = np.array(radii)

        natoms = len(atoms)

        if isinstance(rotation, str):
            rotation = rotate(rotation)

        A = atoms.get_cell()
        if show_unit_cell > 0:
            L, T, D = self.cell_to_lines(A)
            C = np.empty((2, 2, 2, 3))
            for c1 in range(2):
                for c2 in range(2):
                    for c3 in range(2):
                        C[c1, c2, c3] = np.dot([c1, c2, c3], A)
            C.shape = (8, 3)
            C = np.dot(C, rotation)  # Unit cell vertices
        else:
            L = np.empty((0, 3))
            T = None
            D = None
            C = None

        nlines = len(L)

        X = np.empty((natoms + nlines, 3))
        R = atoms.get_positions()
        X[:natoms] = R
        X[natoms:] = L

        r2 = radii**2
        for n in range(nlines):
            d = D[T[n]]
            if ((((R - L[n] - d)**2).sum(1) < r2) &
                (((R - L[n] + d)**2).sum(1) < r2)).any():
                T[n] = -1

        X = np.dot(X, rotation)
        R = X[:natoms]

        if bbox is None:
            X1 = (R - radii[:, None]).min(0)
            X2 = (R + radii[:, None]).max(0)
            if show_unit_cell == 2:
                X1 = np.minimum(X1, C.min(0))
                X2 = np.maximum(X2, C.max(0))
            M = (X1 + X2) / 2
            S = 1.05 * (X2 - X1)
            w = scale * S[0]
            if w > 500:
                w = 500
                scale = w / S[0]
            h = scale * S[1]
            offset = np.array([scale * M[0] - w / 2, scale * M[1] - h / 2, 0])
        else:
            w = (bbox[2] - bbox[0]) * scale
            h = (bbox[3] - bbox[1]) * scale
            offset = np.array([bbox[0], bbox[1], 0]) * scale

        self.w = w
        self.h = h

        X *= scale
        X -= offset

        if nlines > 0:
            D = np.dot(D, rotation)[:, :2] * scale

        if C is not None:
            C *= scale
            C -= offset

        A = np.dot(A, rotation)
        A *= scale

        self.A = A
        self.X = X
        self.D = D
        self.T = T
        self.C = C
        self.natoms = natoms
        self.d = 2 * scale * radii

    def cell_to_lines(self, A):
        nlines = 0
        nn = []
        for c in range(3):
            d = sqrt((A[c]**2).sum())
            n = max(2, int(d / 0.3))
            nn.append(n)
            nlines += 4 * n

        X = np.empty((nlines, 3))
        T = np.empty(nlines, int)
        D = np.zeros((3, 3))

        n1 = 0
        for c in range(3):
            n = nn[c]
            dd = A[c] / (4 * n - 2)
            D[c] = dd
            P = np.arange(1, 4 * n + 1, 4)[:, None] * dd
            T[n1:] = c
            for i, j in [(0, 0), (0, 1), (1, 0), (1, 1)]:
                n2 = n1 + n
                X[n1:n2] = P + i * A[(c + 1) % 3] + j * A[(c + 2) % 3]
                n1 = n2

        return X, T, D

    def write(self, filename):
        self.filename = filename
        self.write_header()
        self.write_body()
        self.write_trailer()

    def write_header(self):
        import matplotlib
        if matplotlib.__version__ <= '0.8':
            raise RuntimeError('Your version of matplotlib (%s) is too old' %
                               matplotlib.__version__)

        from matplotlib.backends.backend_ps import RendererPS, \
             GraphicsContextPS, psDefs

        self.fd = open(self.filename, 'w')
        self.fd.write('%!PS-Adobe-3.0 EPSF-3.0\n')
        self.fd.write('%%Creator: G2\n')
        self.fd.write('%%CreationDate: %s\n' % time.ctime(time.time()))
        self.fd.write('%%Orientation: portrait\n')
        bbox = (0, 0, self.w, self.h)
        self.fd.write('%%%%BoundingBox: %d %d %d %d\n' % bbox)
        self.fd.write('%%EndComments\n')

        Ndict = len(psDefs)
        self.fd.write('%%BeginProlog\n')
        self.fd.write('/mpldict %d dict def\n' % Ndict)
        self.fd.write('mpldict begin\n')
        for d in psDefs:
            d = d.strip()
            for l in d.split('\n'):
                self.fd.write(l.strip() + '\n')
        self.fd.write('%%EndProlog\n')

        self.fd.write('mpldict begin\n')
        self.fd.write('%d %d 0 0 clipbox\n' % (self.w, self.h))

        self.renderer = RendererPS(self.w, self.h, self.fd)

    def write_body(self):
        try:
            from matplotlib.path import Path
        except ImportError:
            Path = None
            from matplotlib.patches import Circle, Polygon
        else:
            from matplotlib.patches import Circle, PathPatch

        indices = self.X[:, 2].argsort()
        for a in indices:
            xy = self.X[a, :2]
            if a < self.natoms:
                r = self.d[a] / 2
                if ((xy[1] + r > 0) and (xy[1] - r < self.h) and
                    (xy[0] + r > 0) and (xy[0] - r < self.w)):
                    circle = Circle(xy, r, facecolor=self.colors[a])
                    circle.draw(self.renderer)
            else:
                a -= self.natoms
                c = self.T[a]
                if c != -1:
                    hxy = self.D[c]
                    if Path is None:
                        line = Polygon((xy + hxy, xy - hxy))
                    else:
                        line = PathPatch(Path((xy + hxy, xy - hxy)))
                    line.draw(self.renderer)

    def write_trailer(self):
        self.fd.write('end\n')
        self.fd.write('showpage\n')
        self.fd.close()


def write_eps(filename, atoms, **parameters):
    if isinstance(atoms, list):
        assert len(atoms) == 1
        atoms = atoms[0]
    EPS(atoms, **parameters).write(filename)