def __call__(self):
if self.name not in cmd.get_names('objects'):
import threading
threading.Thread(None, cmd.delete, args=(self.cb_name,)).start()
return
v = cmd.get_view()
if v == self.prev_v:
return
self.prev_v = v
t = v[12:15]
if self.corner:
vp = cmd.get_viewport()
R_mc = [v[0:3], v[3:6], v[6:9]]
off_c = [0.15 * v[11] * vp[0] / vp[1], 0.15 * v[11], 0.0]
if self.corner in [2,3]:
off_c[0] *= -1
if self.corner in [3,4]:
off_c[1] *= -1
off_m = cpv.transform(R_mc, off_c)
t = cpv.add(t, off_m)
z = -v[11] / 30.0
m = [z, 0, 0, 0, 0, z, 0, 0, 0, 0, z, 0, t[0] / z, t[1] / z, t[2] / z, 1]
cmd.set_object_ttt(self.name, m)
def __call__(self):
if self.name not in cmd.get_names('objects'):
import threading
threading.Thread(None, cmd.delete, args=(self.cb_name,)).start()
return
v = cmd.get_view()
if v == self.prev_v:
return
self.prev_v = v
t = v[12:15]
if self.corner:
vp = cmd.get_viewport()
R_mc = [v[0:3], v[3:6], v[6:9]]
off_c = [0.15 * v[11] * vp[0] / vp[1], 0.15 * v[11], 0.0]
if self.corner in [2,3]:
off_c[0] *= -1
if self.corner in [3,4]:
off_c[1] *= -1
off_m = cpv.transform(R_mc, off_c)
t = cpv.add(t, off_m)
z = -v[11] / 30.0
m = [z, 0, 0, t[0] / z, 0, z, 0, t[1] / z, 0, 0, z, t[2] / z, 0, 0, 0, 1]
cmd.set_object_ttt(self.name, m, homogenous=1)
def poseview(ligand='organic inorganic', protein='polymer', width=0, height=0,
filename='', exe='poseview', state=-1, quiet=1):
'''
DESCRIPTION
PoseView wrapper
http://www.biosolveit.de/poseview/
USAGE
poseview [ ligand [, protein [, width [, height [, exe [, state ]]]]]]
ARGUMENTS
ligand = string: atom selection {default: organic inorganic}
protein = string: atom selection {default: polymer}
width = int: image width {default: viewport width}
height = int: image height {default: viewport height}
filename = string: output PNG file name {default: temporary}
exe = string: path to executable {default: poseview}
SETUP
1) Put poseview executable to PATH (e.g. /usr/bin/poseview)
2) Set environment variable BIOSOLVE_LICENSE_FILE="/path/to/poseview.lic"
'''
import tempfile
import subprocess
import os
import shutil
width, height = int(width), int(height)
state, quiet = int(state), int(quiet)
if width == 0 or height == 0:
viewport = cmd.get_viewport()
if width != 0:
height = int(viewport[0] / float(width) * viewport[1])
elif height != 0:
width = int(viewport[1] / float(height) * viewport[0])
else:
width, height = viewport
exe = cmd.exp_path(exe)
tempdir = tempfile.mkdtemp()
try:
ligand_filename = os.path.join(tempdir, 'ligand.sdf')
protein_filename = os.path.join(tempdir, 'protein.pdb')
if not filename:
filename = os.path.join(tempdir, 'image.png')
cmd.save(ligand_filename, ligand, state)
cmd.save(protein_filename, protein, state)
args = [exe, '-l', ligand_filename, '-p', protein_filename, '-t', '',
'-o', filename, '-s', str(width), str(height)]
if not quiet:
print(' poseview: running...')
process = subprocess.Popen(args,
universal_newlines=True,
stderr=subprocess.STDOUT, stdout=subprocess.PIPE)
stdout, _ = process.communicate()
if not quiet:
print(stdout)
print(' poseview: done')
if filename.endswith('.png'):
cmd.load(filename)
elif not quiet:
print(' Warning: cannot load "%s" into PyMOL, unsupported file type' % (filename))
except OSError:
print(' Error: Cannot execute "%s", please provide full path to poseview executable' % (exe))
raise CmdException
finally:
shutil.rmtree(tempdir)
def testViewport(self):
v = (100, 50)
cmd.viewport(*v)
self.assertEqual(cmd.get_viewport(), v)
def poseview(ligand='organic inorganic', protein='polymer', width=0, height=0,
filename='', exe='poseview', state=-1, quiet=1):
'''
DESCRIPTION
PoseView wrapper
http://www.biosolveit.de/poseview/
USAGE
poseview [ ligand [, protein [, width [, height [, exe [, state ]]]]]]
ARGUMENTS
ligand = string: atom selection {default: organic inorganic}
protein = string: atom selection {default: polymer}
width = int: image width {default: viewport width}
height = int: image height {default: viewport height}
filename = string: output PNG file name {default: temporary}
exe = string: path to executable {default: poseview}
SETUP
1) Put poseview executable to PATH (e.g. /usr/bin/poseview)
2) Set environment variable BIOSOLVE_LICENSE_FILE="/path/to/poseview.lic"
'''
import tempfile, subprocess, os, shutil
width, height = int(width), int(height)
state, quiet = int(state), int(quiet)
if width == 0 or height == 0:
viewport = cmd.get_viewport()
if width != 0:
height = int(viewport[0] / float(width) * viewport[1])
elif height != 0:
width = int(viewport[1] / float(height) * viewport[0])
else:
width, height = viewport
exe = cmd.exp_path(exe)
tempdir = tempfile.mkdtemp()
try:
ligand_filename = os.path.join(tempdir, 'ligand.sdf')
protein_filename = os.path.join(tempdir, 'protein.pdb')
if not filename:
filename = os.path.join(tempdir, 'image.png')
cmd.save(ligand_filename, ligand, state)
cmd.save(protein_filename, protein, state)
args = [exe, '-l', ligand_filename, '-p', protein_filename, '-t', '',
'-o', filename, '-s', str(width), str(height)]
if not quiet:
print ' poseview: running...'
process = subprocess.Popen(args,
stderr=subprocess.STDOUT, stdout=subprocess.PIPE)
stdout, _ = process.communicate()
if not quiet:
print stdout
print ' poseview: done'
if filename.endswith('.png'):
cmd.load(filename)
elif not quiet:
print ' Warning: cannot load "%s" into PyMOL, unsupported file type' % (filename)
except OSError:
print ' Error: Cannot execute "%s", please provide full path to poseview executable' % (exe)
raise CmdException
finally:
shutil.rmtree(tempdir)
def testViewport(self):
v = (100,50)
cmd.viewport(*v)
self.assertEqual(cmd.get_viewport(), v)
