import io
import os
import sys
from datetime import datetime
from past.utils import old_div
import numpy
import PIL
import schrodinger.ui.qt.structure2d as structure2d
from schrodinger.Qt import QtCore
from schrodinger.Qt import QtGui
from schrodinger.Qt import QtWidgets
from schrodinger.Qt.QtCore import QBuffer
from schrodinger.Qt.QtCore import QIODevice
from schrodinger.Qt.QtCore import QRect
from schrodinger.Qt.QtCore import QSize
from schrodinger.Qt.QtCore import Qt
from schrodinger.Qt.QtGui import QColor
from schrodinger.Qt.QtGui import QImage
from schrodinger.Qt.QtGui import QPainter
from schrodinger.Qt.QtGui import QPicture
# Import everything from rl_helper for backward compatibility, since rl_helper
# was spun off from report_helper
from .rl_helper import reportlab
from .rl_helper import rlcolors
from .rl_helper import rlcanvas
from .rl_helper import platypus
from .rl_helper import inch
from .rl_helper import styles
from .rl_helper import HeaderStyle
from .rl_helper import ParaStyle
from .rl_helper import gray
from .rl_helper import colors
from .rl_helper import blackColorMap
from .rl_helper import new_page
from .rl_helper import add_vtable
from .rl_helper import add_table
from .rl_helper import add_and_parse_SMILES
from .rl_helper import add_spacer
from .rl_helper import get_image
from .rl_helper import report_add_ms_logo
from .rl_helper import report_add_logo
from .rl_helper import header
from .rl_helper import get_pargph
from .rl_helper import pargph
from .rl_helper import aspectScale
from .rl_helper import NumberedCanvas
[docs]def replica_name(n):
if n < 26:
return chr(ord('A') + n)
else:
return replica_name(old_div(n, 26) - 1) + replica_name(n % 26)
[docs]def change_plot_colors(axis,
spines=True,
ticks=True,
labels=True,
polar=False,
label_size=8):
gr = '#888888'
if ticks:
axis.tick_params(axis='x', colors=gr, labelsize=label_size)
axis.tick_params(axis='y', colors=gr, labelsize=label_size)
if spines:
types = ['top', 'bottom', 'right', 'left']
if polar:
types = ['polar']
for s in types:
axis.spines[s].set_color(gr)
if labels:
axis.yaxis.label.set_color(gr)
axis.xaxis.label.set_color(gr)
[docs]def load_gui():
app = QtWidgets.QApplication.instance()
if not app:
app = QtWidgets.QApplication(sys.argv)
return app
[docs]def generate_ligand_2d_placeholder(filename, natoms):
qpic = QPicture()
painter = QPainter(qpic)
txt = "Molecule too big\n to render in 2D."
brect = painter.drawText(0, 0, 200, 200, QtCore.Qt.AlignCenter, txt)
painter.end()
qpic.setBoundingRect(brect)
# Convert the QPicture into QImage:
img = QImage(QtCore.QSize(200, 200), QImage.Format_ARGB32)
img.fill(0) # Initialize with zeros to overwrite garbage values
painter2 = QtGui.QPainter()
painter2.begin(img)
painter2.drawPicture(0, 0, qpic)
painter2.end()
img.save(filename)
[docs]def generate_aligned_2d_ligand_pair(fn_list, ct1, ct2, aligned_core):
"""
Given two ligands, try to generate a 2d-plot where they're aligned.
"""
from .depictor import Depictor
from .depictor import get_aligned_chmmol_from_ct
chmmol0, chmmol1 = get_aligned_chmmol_from_ct(ct1, ct2, aligned_core[0],
aligned_core[1], [], [])
chmmol_list = [chmmol0, chmmol1]
depictor = Depictor()
depictor.setCoorGenMode(False)
for fn, lig in zip(fn_list, chmmol_list):
depictor.mol2image(lig, fn)
[docs]def generate_ligand_2d_image(filename,
ligand_st=None,
scene=None,
crop=True,
ret_size=False):
''' given a scene, or a ligand st, output the 2d image'''
# if ligand is greater than 100 heavy atoms just return a
# placeholder
if ligand_st:
atom_heavy = len(
[atom for atom in ligand_st.atom if atom.atomic_number != 1])
else:
return
if atom_heavy > 100:
generate_ligand_2d_placeholder(filename, ligand_st.atom_total)
if ret_size:
return (200, 200)
return
if scene is None:
ligand_pic = structure2d.structure_item()
ligand_pic.set_structure(ligand_st)
ligand_pic.generate_picture()
scene = structure2d.structure_scene()
scene.addItem(ligand_pic)
scene.setBackgroundBrush(Qt.white)
img1 = QImage(1600, 1600, QImage.Format_ARGB32_Premultiplied)
p = QPainter(img1)
scene.render(p)
p.end()
if crop:
img1 = crop_image(img1)
img1.save(filename)
if ret_size:
return img1.size
[docs]def crop_image(image_in):
''' get rid of the white background rgb=[255,255,255]'''
#convert image to an NP array
if isinstance(image_in, QImage):
image_in = convertQimageToImage(image_in)
image_data = numpy.asarray(image_in)
# get the smallest value from RGB
image_data_bw = image_data.min(axis=2)
# get non-white rows and columns
non_empty_columns = numpy.where(image_data_bw.min(axis=0) != 255)[0]
# see if clear backckground works better
non_clear_columns = numpy.where(image_data_bw.min(axis=0) != 0)[0]
if len(non_clear_columns) < len(non_empty_columns):
non_empty_columns = non_clear_columns
non_empty_rows = numpy.where(image_data_bw.min(axis=1) != 255)[0]
if len(non_empty_columns) == 0 and len(non_empty_rows):
return image_in
cropBox = (min(non_empty_rows), max(non_empty_rows), min(non_empty_columns),
max(non_empty_columns))
image_data_new = image_data[cropBox[0]:cropBox[1] + 1, cropBox[2]:
cropBox[3] + 1, :]
image_out = PIL.Image.fromarray(image_data_new)
return image_out
[docs]def convertQimageToImage(qimg):
''' converts QImage object to PIL Image object, in order to crop'''
buffer = QBuffer()
buffer.open(QIODevice.ReadWrite)
qimg.save(buffer, "PNG")
strio = io.BytesIO()
strio.write(buffer.data())
buffer.close()
strio.seek(0)
img = PIL.Image.open(strio)
return img
[docs]def get_qcolor(hex_color):
qc = QColor()
qc.setNamedColor(hex_color)
return qc
[docs]def save_2d_annotated_img(structure_item, filename, crop=True, ret_size=False):
#img1 = QtGui.QImage(1600, 1600, QtGui.QImage.Format_ARGB32_Premultiplied)
img1 = QtGui.QImage(1200, 1200, QtGui.QImage.Format_ARGB32)
img1.fill(QtCore.Qt.white)
scene = structure2d.structure_scene()
scene.addItem(structure_item)
p = QtGui.QPainter(img1)
scene.render(p)
p.end()
if crop:
img1 = crop_image(img1)
img1.save(filename)
if ret_size:
return convertQimageToImage(img1).size