grid depict functions added.

CGRtools/algorithms/depict.py

@@ -84,15 +84,22 @@ def depict(self, *, embedding=False):
 
         svg = [f'<svg width="{width:.2f}cm" height="{height:.2f}cm" '
                f'viewBox="{viewbox_x:.2f} {viewbox_y:.2f} {width:.2f} '
-               f'{height:.2f}" xmlns="http://www.w3.org/2000/svg" version="1.1">\n  <g>']
+               f'{height:.2f}" xmlns="http://www.w3.org/2000/svg" version="1.1">']
+        svg.extend(self._graph_svg(atoms, bonds, masks, viewbox_x, viewbox_y, width, height))
+        svg.append('</svg>')
+        return '\n'.join(svg)
 
+    @classmethod
+    def _graph_svg(cls, atoms, bonds, masks, viewbox_x, viewbox_y, width, height):
+        config = cls._render_config
+        svg = ['  <g>']
         if bonds:
             if masks:
                 uid = str(uuid4())
                 svg.append(f'    <defs>\n      <mask id="mask-{uid}">\n'
                            f'        <rect x="{viewbox_x:.2f}" y="{viewbox_y:.2f}" '
                            f'width="{width:.2f}" height="{height:.2f}" fill="white"/>')
-                svg.extend(self._masks_svg(masks))
+                svg.extend(cls._masks_svg(masks))
                 svg.append('      </mask>\n    </defs>\n'
                            f'    <g fill="none" stroke="{config["bond_color"]}" '
                            f'stroke-width="{config["bond_width"]:.2f}"  mask="url(#mask-{uid})">')
@@ -109,9 +116,8 @@ def depict(self, *, embedding=False):
             svg.append('    <g font-family="monospace">')
             svg.extend(atoms)
             svg.append('    </g>')
-
-        svg.append('  </g>\n</svg>')
-        return '\n'.join(svg)
+        svg.append('  </g>')
+        return svg
 
     @classmethod
     def _masks_svg(cls, masks):
@@ -504,31 +510,7 @@ def depict(self):
             svg.append('  </g>')
 
         for atoms, bonds, masks in zip(r_atoms, r_bonds, r_masks):
-            svg.append('  <g>')
-            if bonds:
-                if masks:
-                    uid = str(uuid4())
-                    svg.append(f'    <defs>\n      <mask id="mask-{uid}">\n'
-                               f'        <rect x="{viewbox_x:.2f}" y="{viewbox_y:.2f}" '
-                               f'width="{width:.2f}" height="{height:.2f}" fill="white"/>')
-                    svg.extend(Depict._masks_svg(masks))
-                    svg.append('      </mask>\n    </defs>\n'
-                               f'    <g fill="none" stroke="{config["bond_color"]}" '
-                               f'stroke-width="{config["bond_width"]:.2f}"  mask="url(#mask-{uid})">')
-                    if len(bonds) == 1:  # SVG BUG adhoc
-                        svg.append(f'      <line x1="{viewbox_x:.2f}" y1="{viewbox_y:.2f}" '
-                                   f'x2="{viewbox_x + width:.2f}" y2="{viewbox_y:.2f}" stroke="none"/>')
-                else:
-                    svg.append(f'    <g fill="none" stroke="{config["bond_color"]}" '
-                               f'stroke-width="{config["bond_width"]:.2f}">')
-                svg.extend(bonds)
-                svg.append('    </g>')
-
-            if atoms:
-                svg.append('    <g font-family="monospace">')
-                svg.extend(atoms)
-                svg.append('    </g>')
-            svg.append('  </g>')
+            svg.extend(Depict._graph_svg(atoms, bonds, masks, viewbox_x, viewbox_y, width, height))
         svg.append('</svg>')
         return '\n'.join(svg)
 

CGRtools/utils/__init__.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 #
-#  Copyright 2019, 2020 Ramil Nugmanov <nougmanoff@protonmail.com>
+#  Copyright 2019-2021 Ramil Nugmanov <nougmanoff@protonmail.com>
 #  This file is part of CGRtools.
 #
 #  CGRtools is free software; you can redistribute it and/or modify
@@ -18,9 +18,10 @@
 #
 from importlib.util import find_spec
 from .functional_groups import functional_groups
+from .grid import grid_depict
 
 
-__all__ = ['functional_groups']
+__all__ = ['functional_groups', 'grid_depict']
 
 
 if find_spec('rdkit'):

CGRtools/utils/functional_groups.py

@@ -16,6 +16,7 @@
 #
 #  You should have received a copy of the GNU Lesser General Public License
 #  along with this program; if not, see <https://www.gnu.org/licenses/>.
+#
 
 
 def functional_groups(molecule, limit):

CGRtools/utils/grid.py

@@ -0,0 +1,78 @@
+# -*- coding: utf-8 -*-
+#
+#  Copyright 2021 Ramil Nugmanov <nougmanoff@protonmail.com>
+#  This file is part of CGRtools.
+#
+#  CGRtools is free software; you can redistribute it and/or modify
+#  it under the terms of the GNU Lesser General Public License as published by
+#  the Free Software Foundation; either version 3 of the License, or
+#  (at your option) any later version.
+#
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+#  GNU Lesser General Public License for more details.
+#
+#  You should have received a copy of the GNU Lesser General Public License
+#  along with this program; if not, see <https://www.gnu.org/licenses/>.
+#
+from itertools import zip_longest
+from typing import List, Tuple, Union
+from ..containers import MoleculeContainer, QueryContainer, CGRContainer, QueryCGRContainer
+
+graphs = Union[MoleculeContainer, QueryContainer, CGRContainer, QueryCGRContainer]
+
+
+def grid_depict(molecules: Union[List[graphs], Tuple[graphs, ...]], cols: int = 3):
+    """
+    Depict molecules grid.
+
+    :param cols: number of molecules per row.
+    """
+    config = MoleculeContainer._render_config
+    font_size = config['font_size']
+    font125 = 1.25 * font_size
+
+    planes = []
+    render = []
+    shift_y = shift_x = 0.
+    for ms in zip_longest(*[iter(molecules)] * cols):
+        height = 0.
+        for m in ms:
+            if m is None:
+                break
+            min_y = min(y for x, y in m._plane.values())
+            max_y = max(y for x, y in m._plane.values())
+            h = max_y - min_y
+            if height < h:  # get height of row
+                height = h
+            planes.append(m._plane.copy())
+
+        # now align mols by height
+        shift_y -= height / 2. + 2.
+        max_x = 0.
+        for m in ms:
+            if m is None:
+                break
+            max_x = m._fix_plane_mean(max_x, shift_y) + 2.
+            render.append(m.depict(embedding=True)[:3])
+            if max_x > shift_x:  # get total width
+                shift_x = max_x
+        shift_y -= height / 2.
+
+    # restore planes
+    for p, m in zip(planes, molecules):
+        m._plane = p
+
+    width = shift_x + 3.0 * font_size
+    height = -shift_y + 2.5 * font_size
+    svg = [f'<svg width="{width:.2f}cm" height="{height:.2f}cm" '
+           f'viewBox="{-font125:.2f} {-font125:.2f} {width:.2f} '
+           f'{height:.2f}" xmlns="http://www.w3.org/2000/svg" version="1.1">']
+    for atoms, bonds, masks in render:
+        svg.extend(MoleculeContainer._graph_svg(atoms, bonds, masks, -font125, -font125, width, height))
+    svg.append('</svg>')
+    return '\n'.join(svg)
+
+
+__all__ = ['grid_depict']

setup.py

@@ -54,7 +54,7 @@ def finalize_options(self):
 
 setup(
     name='CGRtools',
-    version='4.1.16',
+    version='4.1.17',
     packages=['CGRtools', 'CGRtools.algorithms', 'CGRtools.algorithms.components', 'CGRtools.containers',
               'CGRtools.files', 'CGRtools.files._mdl', 'CGRtools.periodictable', 'CGRtools.periodictable.element',
               'CGRtools.utils', 'CGRtools.attributes'],