def make_pov(file, meta=True):
f1, f2 = file, file[:-4] + '.inc'
(header, data) = cmd.get_povray()
povfile = open(f1, 'w')
if meta: povfile.write(header)
povview = cmd.get_view()
povfile.write("""\n
// Uncomment the following lines if you have the pymolmacro.inc include file and want to use it.
/*
#include \"pymolmacro.inc\"
PYMOL_VIEW( %10.5f, %10.5f, %10.5f,
%10.5f, %10.5f, %10.5f,
%10.5f, %10.5f, %10.5f,
%10.5f, %10.5f, %10.5f,
%10.5f, %10.5f, %10.5f,
%10.5f, %10.5f, %10.5f )
*/
""" % povview)
povfile.write('#include "%s"\n\n' % f2)
povfile.close()
povfile = open(f2, 'w')
povfile.write(data)
povfile.close()
def make_pov(file):
"""
Do "run make_pov.py" from within pymol and then execute the script
with "make_pov('povray.inp')" to create the povray.inp file.
make note of the dimensions written out by this script and use the
same (or the same ratio) within povray:
e.g. output (the "vol" lines only appear if spheres are present):
PyMOL>make_pov('povray.inp')
RayRenderPOV: w 1100 h 900 f 63.349 b 102.310
RayRenderPOV: vol -17.316 17.316 -14.168
RayRenderPOV: vol 14.168 63.349 102.310
RayRenderPovRay: processed 714 graphics primitives.
Ray: total time: 0.03 sec. = 123885.9 frames/hour. (0.03 sec. accum.)
So for example, you would run povray with:
povray +Ipovray.inp +W1100 +H900
or
povray +Ipovray.inp +W550 +H450
"""
(header,data) = cmd.get_povray()
povfile=open(file,'w')
povfile.write(header)
povfile.write(data)
povfile.close()
def saveSC(self):
(pov_header, pov_body) = cmd.get_povray()
self.p = pov()
self.p.globalShaderFactory.seleShader = self.spColorShaderDict
self.p.globalImage.setFloorColor(self.bgColor)
self.p.globalImage.setFloorShader(self.optionMenu_bgShader.getvalue())
self.p.globalImage.setGlobalShader(self.optionMenu_shader.getvalue())
self.p.globalImage.setFloorShadow(self.dropShadow.get())
self.p.globalImage.setOutputWidth(int(self.varImageWidth.get()))
self.p.globalImage.setFloorAngle(self.stageAngle)
# shader settings
self.p.globalShaderFactory.colorSpace = self.optionMenu_colorSpace.getvalue()
self.p.globalShaderFactory.shaderSamples = self.shaderSamples
self.p.globalShaderFactory.phongSpec = self.phongSpec
self.p.globalShaderFactory.shinyRefl = self.shinyRefl
self.p.globalShaderFactory.glassETA = self.glassETA
if self.dofDist != -1:
self.p.globalCamera.attr['type'] = 'thinlens'
# will be used in p.parsePov
# change fdist before p.camera writing SCString
self.p.globalCamera.dofScale = self.dofDist
self.p.parsePov(''.join([pov_header, pov_body]))
self.console.set('%28s' % ('kflow.sc saved.'))
def make_pov(file, meta=True):
f1, f2 = file, file[:-4] + '.inc'
(header,data) = cmd.get_povray()
povfile = open(f1,'w')
if meta: povfile.write(header)
povview = cmd.get_view()
povfile.write("""\n
// Uncomment the following lines if you have the pymolmacro.inc include file and want to use it.
/*
#include \"pymolmacro.inc\"
PYMOL_VIEW( %10.5f, %10.5f, %10.5f,
%10.5f, %10.5f, %10.5f,
%10.5f, %10.5f, %10.5f,
%10.5f, %10.5f, %10.5f,
%10.5f, %10.5f, %10.5f,
%10.5f, %10.5f, %10.5f )
*/
""" % povview)
povfile.write('#include "%s"\n\n' % f2)
povfile.close()
povfile = open(f2,'w')
povfile.write(data)
povfile.close()
def testGetPovray(self):
cmd.fragment('gly')
cmd.show_as('sticks')
pov = cmd.get_povray()
self.assertTrue(isinstance(pov, tuple))
self.assertEqual(len(pov), 2)
self.assertTrue(pov[0].startswith('camera {direction<0.0,0.0'))
self.assertTrue(pov[1].startswith('cylinder{<'))
from pymol import cmd
import os
if not ('pept' in cmd.get_names()):
cmd.delete('all')
util.ray_shadows('heavy')
cmd.do('load $PYMOL_PATH/test/dat/pept.pdb')
cmd.do('set surface_quality=1')
cmd.do('show surface;hide lines;')
cmd.zoom('all', 10)
cmd.do('clip far,-40;show surface;hide lines;set smooth_color=1')
cmd.viewport(300, 300)
pov = cmd.get_povray()
f = open("tmp_pymol.pov", 'w')
f.write(pov[0])
f.write("#include \"colors.inc\"\n")
f.write("#include \"stones.inc\"\n")
f.write("#include \"woods.inc\"\n")
f.write(pov[1])
f.write("plane {<0,1,0.5>, -70 texture{T_Grnt10 scale 40}}\n")
f.write(
"sphere {<14,4,-132>, 7.0 pigment{color Grey} finish{reflection 1.0 metallic}}\n"
)
for x in range(-30, 30, 5):
f.write("sphere {<%6.4f,-12,-100>, 2.0 texture{P_WoodGrain1B scale 8}}\n" %
(x))
f.write("box {<-17,17,-120>,<13,15,-160> pigment {color Red}}\n")
f.close()
cmd.refresh()
os.system("x-povray +Itmp_pymol.pov +Otmp_pymol.png +W300 +H300 +A")
def render(self, renderType):
#cmd.do('save t.pov')
#print 'image width: %d' % (int(self.varImageWidth.get()))
#print 'drop shadow: %s' % self.dropShadow.get()
#print 'bg color: %s' % (self.bgColor)
#print 'stage angle: %d' % (self.stageAngle)
#print 'molecule shader: %s' % self.optionMenu_shader.getvalue()
#print 'background shader: %s' % self.optionMenu_bgShader.getvalue()
try:
os.unlink('kflow.sc')
os.unlink('output.png')
except:
#traceback.print_exc()
pass
(pov_header, pov_body) = cmd.get_povray()
self.p = pov()
self.p.globalShaderFactory.seleShader = self.spColorShaderDict
self.p.globalImage.setFloorColor(self.bgColor)
self.p.globalImage.setFloorShader(self.optionMenu_bgShader.getvalue())
self.p.globalImage.setGlobalShader(self.optionMenu_shader.getvalue())
self.p.globalImage.setFloorShadow(self.dropShadow.get())
# shader settings
self.p.globalShaderFactory.colorSpace = self.optionMenu_colorSpace.getvalue()
self.p.globalShaderFactory.shaderSamples = self.shaderSamples
self.p.globalShaderFactory.phongSpec = self.phongSpec
self.p.globalShaderFactory.shinyRefl = self.shinyRefl
self.p.globalShaderFactory.glassETA = self.glassETA
if renderType == '':
self.console.set('%28s' % ('Full Render'))
self.p.globalImage.setOutputWidth(int(self.varImageWidth.get()))
else:
self.console.set('%28s' % ('Render IPR'))
self.p.globalImage.setOutputWidth(800)
self.p.globalImage.setFloorAngle(self.stageAngle)
if self.dofDist != -1:
self.p.globalCamera.attr['type'] = 'thinlens'
# will be used in p.parsePov
# change fdist before p.camera writing SCString
self.p.globalCamera.dofScale = self.dofDist
self.p.parsePov(''.join([pov_header, pov_body]))
sunflowpath = os.path.expanduser('~')+'/kflow.jar'
#print sunflowpath
if os.path.isfile(sunflowpath) != True:
self.getSunflow(sunflowpath)
path_java='\"'+sunflowpath.replace('\\', '/')+'\"'
cmd_args = '%s -v 0 -o output.png kflow.sc' % (renderType)
print 'Start rendering ...'
p=subprocess.Popen('java -jar '+path_java+' '+cmd_args, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
while True:
out = p.stdout.read(1)
if out == '' and p.poll() != None:
break
if out!='':
sys.stdout.write(out)
sys.stdout.flush()
from pymol import cmd
import os
if not ('pept' in cmd.get_names()):
cmd.delete('all')
util.ray_shadows('heavy')
cmd.do('load $PYMOL_PATH/test/dat/pept.pdb')
cmd.do('set surface_quality=1')
cmd.do('show surface;hide lines;')
cmd.zoom('all',10)
cmd.do('clip far,-40;show surface;hide lines;set smooth_color=1')
cmd.viewport(300,300)
pov = cmd.get_povray()
f=open("tmp_pymol.pov",'w')
f.write(pov[0])
f.write("#include \"colors.inc\"\n");
f.write("#include \"stones.inc\"\n");
f.write("#include \"woods.inc\"\n");
f.write(pov[1])
f.write("plane {<0,1,0.5>, -70 texture{T_Grnt10 scale 40}}\n");
f.write("sphere {<14,4,-132>, 7.0 pigment{color Grey} finish{reflection 1.0 metallic}}\n");
for x in range(-30,30,5):
f.write("sphere {<%6.4f,-12,-100>, 2.0 texture{P_WoodGrain1B scale 8}}\n"%(x))
f.write("box {<-17,17,-120>,<13,15,-160> pigment {color Red}}\n")
f.close()
cmd.refresh()
os.system("x-povray +Itmp_pymol.pov +Otmp_pymol.png +W300 +H300 +A")
cmd.load_png('tmp_pymol.png')
def make_pov(file):
(header, data) = cmd.get_povray()
povfile = open(file, 'w')
povfile.write(header)
povfile.write(data)
povfile.close()
def make_pov(file): (header,data) = cmd.get_povray() povfile=open(file,'w') povfile.write(header) povfile.write(data) povfile.close()
cmd.space("cmyk")
cmd.bg_color(color="white")
cmd.load('4hea_vis_res.pdb')
cmd.load('6rfr_vis_res.pdb')
cmd.load('refined_cav.pdb')
cmd.load('6rfr_UQ9_realigned.pdb')
cmd.hide(representation="everything", selection="all")
cmd.show(representation="mesh", selection="refined_cav")
cmd.show(representation="sticks", selection="4hea_vis_res")
cmd.show(representation="spheres", selection="6rfr_UQ9_realigned")
cmd.show(representation="sticks", selection="6rfr_vis_res")
cmd.do('color cyan, 6rfr_UQ9_realigned and name C*')
cmd.do('color cyan, 6rfr_vis_res and name C*')
cmd.do('color pink, 4hea_vis_res and name c*')
cmd.do('color pink, refined_cav')
cmd.zoom("all", complete=1)
cmd.rotate("z", angle=90)
cmd.rotate("x", angle=90)
pov_file = open('pymol_scene_no_hydrogens_tyr_marker_set.pov', 'w')
for part in cmd.get_povray():
pov_file.write(part)
pov_file.close()
cmd.quit()
