Ejemplo n.º 1
0
def ligand_sites_hq(selection="(all)",_self=cmd):
    cmd=_self
    ligand_sites(selection,_self)
    s = tmp_sele
    cmd.select(s,selection)
    cmd.set("surface_quality","1",selection)
    cmd.set("surface_type",0,selection)
Ejemplo n.º 2
0
def _prepare(selection,polar_contacts=None,_self=cmd):
    cmd=_self
    # this function should undo everything that is done by any preset function in this module
    # (except for coloring)
    s = tmp_sele
    cmd.select(s,selection)

    cmd.cartoon("auto",s)   
    cmd.hide("everything",s)
    
    cmd.set("two_sided_lighting",0) # global
    cmd.unset("transparency",s)
    cmd.unset("dot_normals",s)
    cmd.unset("mesh_normals",s)
    cmd.unset("surface_quality",s)
    cmd.unset("surface_type",selection)
    cmd.unset("sphere_scale",selection)
    cmd.unset_bond("stick_radius",s,s)
    cmd.unset_bond("stick_color",s,s)
    cmd.unset("cartoon_highlight_color",selection)
    cmd.unset("cartoon_fancy_helices",selection)
    cmd.unset("cartoon_smooth_loops",selection)
    cmd.unset("cartoon_flat_sheets",selection)
    cmd.unset("cartoon_side_chain_helper",selection)   
    cmd.unset("mesh_normals",s)
    cmd.unset("dot_normals",s)
    if polar_contacts == None:
        polar_contacts = _get_polar_contacts_name(s,_self)
        if polar_contacts in cmd.get_names('objects'):
            cmd.delete(polar_contacts)
Ejemplo n.º 3
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def ligand_cartoon(selection="(all)",_self=cmd):
    cmd=_self
    ligand_sites(selection,_self)
    s = tmp_sele
    cmd.select(s,selection)
    cmd.set("cartoon_side_chain_helper",1,selection)
    cmd.show("cartoon","rep ribbon")
    cmd.hide("ribbon")
    cmd.hide("surface")
Ejemplo n.º 4
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def b_factor_putty(selection="(name ca or name p)",_self=cmd):
    cmd=_self
    s = tmp_sele
    cmd.select(s,selection)
    _prepare(s,_self=cmd)
    cmd.select(s,"(name ca or name p) and ("+selection+")")
    cmd.show("cartoon",s)
    cmd.set("cartoon_flat_sheets",0,selection)
    cmd.cartoon("putty",s)
    cmd.spectrum("b",selection=s)
Ejemplo n.º 5
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def pub_solv(selection="(all)",_self=cmd):
    cmd=_self
    pretty_solv(selection,_self)
    s = tmp_sele
    cmd.select(s,selection)
    cmd.set("cartoon_smooth_loops",1,selection)
    cmd.set("cartoon_highlight_color","grey50",selection)
    cmd.set("cartoon_fancy_helices",1,selection)
    cmd.set("cartoon_flat_sheets",1,selection)
    cmd.set("cartoon_side_chain_helper",0,selection)   
    if cmd.count_atoms(s):
        cmd.zoom(s)
Ejemplo n.º 6
0
Archivo: util.py Proyecto: Almad/pymol
def colors(scheme="",_self=cmd):
    pymol=_self._pymol
    cmd=_self
    if scheme=="jmol":
        cmd.set("auto_color",0)
        cmd.set_color("hydrogen",[1.000,1.000,1.000])
        cmd.set_color("carbon",[0.567,0.567,0.567])
        cmd.set_color("nitrogen",[0.189,0.315,0.976])
        cmd.set_color("oxygen",[1.000,0.051,0.051])
        cmd.set_color("fluorine",[0.567,0.882,0.314])
        cmd.set_color("sulfur",[1.000,1.000,0.189])
        cmd.color("carbon","elem c")
        cmd.recolor()
Ejemplo n.º 7
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def x(st):
   print st
   cmd.set("raise_exceptions",0)
   valu = eval(st)
   print valu
   if cmd.is_error(valu):
      cmd.set("raise_exceptions",1)
      try:
         print eval(st)
      except pymol.CmdException:
         print "CmdException raised."
      except cmd.QuietException:
         print "QuietException raised."
Ejemplo n.º 8
0
Archivo: util.py Proyecto: Almad/pymol
def protein_vacuum_esp(selection, mode=2, border=10.0, quiet = 1, _self=cmd):
    pymol=_self._pymol
    cmd=_self

    if ((string.split(selection)!=[selection]) or
         selection not in cmd.get_names('objects')):
        print " Error: must provide an object name"
        raise cmd.QuietException
    obj_name = selection + "_e_chg"
    map_name = selection + "_e_map"
    pot_name = selection + "_e_pot"
    cmd.disable(selection)
    cmd.delete(obj_name)
    cmd.delete(map_name)
    cmd.delete(pot_name)
    cmd.create(obj_name,"((polymer and ("+selection+
               ") and (not resn A+C+T+G+U)) or ((bymol (polymer and ("+
               selection+"))) and resn NME+NHE+ACE)) and (not hydro)")
         # try to just get protein...

    protein_assign_charges_and_radii(obj_name,_self=_self)
        
    ext = cmd.get_extent(obj_name)
    max_length = max(abs(ext[0][0] - ext[1][0]),abs(ext[0][1] - ext[1][1]),abs(ext[0][2]-ext[1][2])) + 2*border

    # compute an grid with a maximum dimension of 50, with 10 A borders around molecule, and a 1.0 A minimum grid

    sep = max_length/50.0
    if sep<1.0: sep = 1.0
    print " Util: Calculating electrostatic potential..."
    if mode==0: # absolute, no cutoff
        cmd.map_new(map_name,"coulomb",sep,obj_name,border)
    elif mode==1: # neutral, no cutoff
        cmd.map_new(map_name,"coulomb_neutral",sep,obj_name,border)
    else: # local, with cutoff
        cmd.map_new(map_name,"coulomb_local",sep,obj_name,border)      
        
    cmd.ramp_new(pot_name, map_name, selection=obj_name,zero=1)
    cmd.hide("everything",obj_name)
    cmd.show("surface",obj_name)
    cmd.set("surface_color",pot_name,obj_name)
    cmd.set("surface_ramp_above_mode",1,obj_name)
Ejemplo n.º 9
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def technical(selection="(all)",_self=cmd):
    cmd=_self
    s = tmp_sele
    cmd.select(s,selection)
    polar_contacts = _get_polar_contacts_name(s,_self)
    _prepare(s,polar_contacts,_self=cmd)
    util.chainbow(s,_self=cmd)
    util.cbc("("+lig_sele+" and ("+s+"))",_self=cmd)   
    util.cbac("(("+s+") and not elem c)",_self=cmd)
    cmd.show("nonbonded",s)
    cmd.show("lines","((("+s+") and not "+lig_sele+") extend 1)")
    cmd.show("sticks","("+lig_sele+" and ("+s+"))")
    cmd.show("ribbon",s)
    cmd.dist(polar_contacts,s,s,mode=2,label=0,reset=1) # hbonds
    if polar_contacts in cmd.get_names():
        cmd.enable(polar_contacts)
        cmd.set("dash_width",1.5,polar_contacts)
        cmd.hide("labels",polar_contacts)
        cmd.show("dashes",polar_contacts)
    cmd.show("nonbonded","(("+lig_sele+"|resn hoh+wat+h2o) and ("+s+"))")
Ejemplo n.º 10
0
def pretty_solv(selection="(all)",_self=cmd):
    cmd=_self
    s = tmp_sele
    cmd.select(s,selection)
    polar_contacts = _get_polar_contacts_name(s,_self)
    _prepare(s,polar_contacts,_self=cmd)
    cmd.dss(s,preserve=1)
    cmd.cartoon("auto",s)
    cmd.show("cartoon",s)
    cmd.show("sticks","("+lig_sele+" and ("+s+"))")
    cmd.show("nb_spheres","(("+lig_sele+"|resn hoh+wat+h2o) and ("+s+"))")
    util.cbc("("+lig_sele+" and ("+s+"))",_self=cmd)
    util.cbac("("+lig_sele+" and ("+s+") and not elem c)",_self=cmd)
    cmd.spectrum("count",selection="(elem c and ("+s+") and not "+lig_sele+")")
    cmd.set("cartoon_highlight_color",-1,selection)
    cmd.set("cartoon_fancy_helices",0,selection)
    cmd.set("cartoon_smooth_loops",0,selection)
    cmd.set("cartoon_flat_sheets",1,selection)
    cmd.set("cartoon_side_chain_helper",0,selection)   
    if polar_contacts in cmd.get_names():
        cmd.disable(polar_contacts)
    if cmd.count_atoms(s):
        cmd.zoom(s)
Ejemplo n.º 11
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def ligand_sites_dots(selection="(all)",_self=cmd):
    cmd=_self
    ligand_sites(selection,_self)
    s = tmp_sele
    cmd.select(s,selection)
    cmd.show("sticks",s+" and rep lines")
    cmd.hide("lines",s+" and rep lines")
    cmd.set("surface_type","1",selection)
    cmd.set("surface_quality","1",selection)
    cmd.set("dot_normals",0,s)
Ejemplo n.º 12
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def ligand_sites_trans_hq(selection="(all)",_self=cmd):
    cmd=_self
    ligand_sites(selection,_self)
    s = tmp_sele
    cmd.select(s,selection)
    cmd.show("sticks",s+" and rep lines")
    cmd.hide("lines",s+" and rep lines")
    cmd.set("transparency","0.33",s)
    cmd.set("surface_type",0,selection)
    cmd.set("surface_quality",1,selection)
Ejemplo n.º 13
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def ligand_sites_mesh(selection="(all)",_self=cmd):
    cmd=_self
    ligand_sites(selection,_self)
    s = tmp_sele
    cmd.select(s,selection)
    cmd.show("sticks",s+" and rep lines")
    cmd.hide("lines",s+" and rep lines")
    cmd.set("surface_type","2",selection)
    cmd.set("surface_quality","0",selection)
    cmd.set("mesh_normals",0,s)
    cmd.delete(s)
Ejemplo n.º 14
0
def ligand_sites(selection="(all)",_self=cmd):
    cmd=_self
    try:
        s = tmp_sele
        cmd.select(s,selection)
        polar_contacts = _get_polar_contacts_name(s,_self)
        _prepare(s,polar_contacts,_self=cmd)
        host = "_preset_host"
        solvent = "_preset_solvent"
        near_solvent = "_preset_solvent"
        lig = "_preset_lig"
        cmd.select(host,s+" and "+prot_and_dna_sele)
        cmd.select(solvent,s+" and "+solv_sele)
        cmd.select(lig,s+" and "+lig_sele)
        cmd.select(near_solvent,s+" and ("+solvent+" within 4 of "+lig+")")
        cmd.flag("ignore",host,"clear")
        cmd.flag("ignore",lig+"|"+solvent,"set")

        util.chainbow(host,_self=cmd)
        util.cbc(lig,_self=cmd)
        util.cbac("(("+s+") and not elem c)",_self=cmd)
        cmd.hide("everything",s)
        cmd.show("ribbon",host)
        cmd.show("lines","("+s+" and byres ("+host+" within 5 of "+lig+"))")
        cmd.show("surface","("+s+" and ((rep lines expand 4) within 6 of "+lig+"))")
        cmd.set("two_sided_lighting",1) # global setting
        cmd.set("transparency",0,s)
        cmd.set("surface_quality",0,s)

        cmd.show("sticks",lig)
        cmd.show("sticks",solvent+" and neighbor "+lig)
        cmd.show("lines","("+s+" and (rep lines extend 1) and "+lig+")")

        if cmd.count_atoms(lig):
            cmd.dist(polar_contacts,host+"|"+near_solvent,lig+"|"+near_solvent,mode=2,quiet=1,label=0,reset=1) # hbonds
            if polar_contacts in cmd.get_names():
                cmd.enable(polar_contacts)
                cmd.hide("labels",polar_contacts)
                cmd.show("dashes",polar_contacts)
        else:
            cmd.delete(polar_contacts)
                
        cmd.show("nb_spheres",lig+"|"+host+"|"+near_solvent)
        if cmd.count_atoms(lig):
            cmd.zoom(lig,3)
        cmd.delete(host)
        cmd.delete(solvent)
        cmd.delete(near_solvent)
        cmd.delete(lig)
    except:
        traceback.print_exc()
    cmd.delete(s)
Ejemplo n.º 15
0
def ball_and_stick(selection="(all)",mode=1,_self=cmd):
    cmd=_self
    s = tmp_sele
    cmd.select(s,selection)
    _prepare(s,_self=cmd)
    if mode == 1:
        cmd.hide("everything",s)
        cmd.set_bond("stick_color","white",s,s)
        cmd.set_bond("stick_radius","0.14",s,s)
        cmd.set("sphere_scale","0.25",s)
        cmd.show("sticks",s)
        cmd.show("spheres",s)
    elif mode == 2:
        cmd.hide("everything",s)
        cmd.set_bond("stick_color","white",s,s)
        cmd.set_bond("stick_radius","-0.14",s,s)
        cmd.set("stick_ball","1")
        cmd.set("stick_ball_ratio",-1.0)
        cmd.set("stick_ball_color","atomic")
        cmd.show("sticks",s)
Ejemplo n.º 16
0
Archivo: m4x.py Proyecto: Almad/pymol
def setup_contexts(context_info):   # Author: Warren DeLano
    (list,dict) = context_info[0:2]
    key_list = [
        'F1','F2','F3','F4','F5','F6','F7','F8','F9','F10', #,'F11','F12',
        'SHFT-F1','SHFT-F2','SHFT-F3','SHFT-F4','SHFT-F5','SHFT-F6','SHFT-F7',
        'SHFT-F8','SHFT-F9','SHFT-F10']# ,'SHFT-F11','SHFT-F12']
    doc_list = ["Keys"]
    zoom_context = 1
    global labels
    labels = 1
    if len(key_list):
        key = key_list.pop(0)
        cmd.set_key(key,toggle_labels)
        doc_list.append(key+": Toggle Dist")        
    if len(key_list):
        key = key_list.pop(0)
        cmd.set_key(key,lambda :(cmd.zoom(),toggle_labels(0)))
        doc_list.append(key+": Zoom All")
    
    for a in list:
        water = a+"_water"
        ligand = a+"_ligand"
        site = a+"_site"
        hbond = a+"_hbond"
        name_list = dict[a]
        zoom_list = []
        if water in name_list:
            cmd.show("nonbonded",water)
            util.cbac(water)
            zoom_list.append(water)
        if ligand in name_list:
            cmd.show("sticks",ligand)
            cmd.hide("cartoon",ligand)
            util.cbag(ligand)
            zoom_list.append(ligand)
        if site in name_list:
            cmd.show("sticks",site)
            util.cbac(site)
            zoom_list.append(site)
            # replace cartoon with explicit atoms for "site" atoms
            cmd.hide("cartoon",site)
            cmd.show("sticks","(byres (neighbor ("+site+" and name c))) and name n+ca")
            cmd.show("sticks","(byres (neighbor ("+site+" and name n))) and name c+ca+o")
        if len(zoom_list):
            if len(key_list):
                key = key_list.pop(0)
                zoom_str = string.join(zoom_list,' or ')
                if zoom_context == 1:
                    zoom_context = zoom_str
                elif zoom_context not in (0,1):
                    zoom_context = 0
                cmd.set_key(key,lambda x=zoom_str:(cmd.zoom(x)))
                mo = re.search("_([^_]+)$",a)
                if mo:
                    cont_name = mo.groups()[0]
                else:
                    cont_name = a
                doc_list.append(key+": Zoom "+cont_name)
                
        if hbond in name_list:
            cmd.show("dashes",hbond)
            cmd.show("labels",hbond)

        
    cmd.wizard("fedora",doc_list)
    if zoom_context not in (0,1):
        cmd.zoom(zoom_context)
    toggle_labels(0)
#    cmd.feedback("enable","python","output")
    cmd.feedback("enable","objectmolecule","results")
    cmd.feedback("disable","selector","actions")
    cmd.feedback("disable","scene","actions")
    cmd.set("internal_feedback",1)
    cmd.set("internal_prompt",0)
Ejemplo n.º 17
0
Archivo: m4x.py Proyecto: Almad/pymol
def setup_alignment_contexts(context_info):   # Author: Warren DeLano
    (list,dict) = context_info[0:2]
    doc_list = ['\888Legend:']
    obj_name_dict = {}
    for a in list:
        sf = string.find(a,"_")
        if sf>=0:
            object_name = a[0:sf]
            if not obj_name_dict.has_key(object_name):
                obj_name_dict[object_name] = 1
                col_index = cmd.get_object_color_index(object_name)
                if col_index>=0:
                    col_tup = cmd.get_color_tuple(col_index)
                    if is_tuple(col_tup):
                        col_int = map(lambda x:int(x*9+0.49999),col_tup)
                        col_str = string.join(map(lambda x:chr(ord('0')+x),col_int),'')
                        doc_list.append("\\"+col_str+object_name+"\\---")
                    
    key_list = [
        'F1','F2','F3','F4','F5','F6','F7','F8','F9','F10', #,'F11','F12',
        'SHFT-F1','SHFT-F2','SHFT-F3','SHFT-F4','SHFT-F5','SHFT-F6','SHFT-F7',
        'SHFT-F8','SHFT-F9','SHFT-F10']# ,'SHFT-F11','SHFT-F12']
    doc_list.append("")
    doc_list.append("\\888Toggles:")
    zoom_context = 1
                                  
    global labels,ligands,waters,sites,cgos,zooms,dashes
    labels = 1
    ligands = 1
    waters = 1
    sites = 1
    cgos = 0
    zooms = 0
    dashes = 1
    global m4x_sites,m4x_ligands,m4x_waters
    m4x_sites = "m4x_sites"
    m4x_ligands = "m4x_ligands"
    m4x_waters = "m4x_waters"

    cmd.select(m4x_sites,"none")
    cmd.select(m4x_ligands,"none")
    cmd.select(m4x_waters,"none")   
    if len(key_list):
        key = key_list.pop(0)
        cmd.set_key(key,toggle_zooms)
        doc_list.append(key+": Zoom")
    if len(key_list):
        key = key_list.pop(0)
        cmd.set_key(key,toggle_sites)
        doc_list.append(key+": Sites")        
    if len(key_list):
        key = key_list.pop(0)
        cmd.set_key(key,toggle_waters)
        doc_list.append(key+": Waters")        
    if len(key_list):
        key = key_list.pop(0)
        cmd.set_key(key,toggle_dashes)
        doc_list.append(key+": H-Bonds")        
    if len(key_list):
        key = key_list.pop(0)
        cmd.set_key(key,toggle_cgos)
        doc_list.append(key+": Fits")        
    if len(key_list):
        key = key_list.pop(0)
        cmd.set_key(key,toggle_ligands)
        doc_list.append(key+": Ligands")        
    if len(key_list):
        key = key_list.pop(0)
        cmd.set_key(key,toggle_labels)
        doc_list.append(key+": HB-Dists")        
    
    for a in list:
        include_flag = 0
        water = a+"_water"
        ligand = a+"_ligand"
        site = a+"_site"
        hbond = a+"_hbond"
        if cmd.count_atoms(site):
            if cmd.count_atoms(site+" & m4x_aligned"):
                include_flag = 1
        if cmd.count_atoms(ligand):
            if cmd.count_atoms(ligand+" & m4x_nearby"):
                include_flag = 1
        if include_flag:
            name_list = dict[a]
            if water in name_list:
                cmd.select(m4x_waters,m4x_waters+"|"+water)
            if ligand in name_list:
                cmd.select(m4x_ligands,m4x_ligands+"|"+ligand)
            if site in name_list:
                cmd.select(m4x_sites,m4x_sites+"|"+site+
                "|((byres (neighbor ("+site+" and name c))) and name n+ca)"+
                "|((byres (neighbor ("+site+" and name n))) and name c+ca+o)")
    cmd.wizard("fedora",doc_list)
    toggle_cgos(1)
    toggle_labels(0)
    toggle_dashes(0)
    toggle_ligands(1)
    toggle_sites(0)
    toggle_waters(0)
    toggle_cgos(1)
    cmd.deselect()
#    cmd.feedback("enable","python","output")
    cmd.feedback("enable","objectmolecule","results")
    cmd.set("internal_feedback",1)
    cmd.set("internal_prompt",0)
    cmd.feedback("disable","selector","actions")
    cmd.feedback("disable","scene","actions")
Ejemplo n.º 18
0
Archivo: util.py Proyecto: Almad/pymol
def ray_shadows(mode,_self=cmd):
    pymol=_self._pymol
    cmd=_self
    # adjustment factors for new lighting model in 0.99
    reflect_scale = 0.5
    direct_scale = 1.8
    gamma_scale = 1/1.3
    ambient_scale = 1.16
    if mode=='none':
        cmd.set('ray_shadows',0)
    else:
        cmd.set('ray_shadows',1)
    if mode=='light': 
        cmd.set('light_count',2)
        cmd.set("light","[-0.4,-0.4,-1.0]")
        cmd.set('ambient',0.14)
        cmd.set('direct',0.65)
        cmd.set('reflect',0.25)
        cmd.set('shininess',40)
        cmd.set('power',1.0)
        cmd.set('specular_intensity',0.5)
        cmd.set('spec_direct',0)
        cmd.set('spec_count',-1)
        cmd.set('ray_shadow_decay_factor',0)
    elif mode=='matte':
        cmd.set('light_count',4)
        cmd.set("light","[-0.4,-0.4,-1.0]")
        cmd.set("light2","[-0.3,-0.4,-1.0]")
        cmd.set("light3","[-0.3,-0.3,-1.0]")
        cmd.set("light4","[-0.4,-0.3,-1.0]")
        cmd.set('ambient',0.14)
        cmd.set('direct',0.45)
        cmd.set('reflect',0.45)
        cmd.set('shininess',25)
        cmd.set('power',1.25)
        cmd.set('spec_count',-1)                
        cmd.set('specular_intensity',0.2)
        cmd.set('spec_direct',0)
        cmd.set('ray_shadow_decay_factor',0)
    elif mode=='soft':
        cmd.set('light_count',10)
        cmd.set("light","[-0.4,-0.4,-1.0]")
        cmd.set("light2","[-0.3,-0.4,-1.0]")
        cmd.set("light3","[-0.3,-0.3,-1.0]")
        cmd.set("light4","[-0.4,-0.3,-1.0]")
        cmd.set("light5","[-0.4,-0.5,-1.0]")
        cmd.set("light6","[-0.5,-0.5,-1.0]")
        cmd.set("light7","[-0.5,-0.4,-1.0]")
        cmd.set("light8","[-0.5,-0.3,-1.0]")
        cmd.set("light9","[-0.3,-0.5,-1.0]")
        cmd.set('ambient',0.14)
        cmd.set('direct',0.40)
        cmd.set('reflect',0.50)
        cmd.set('specular_intensity',0.5)
        cmd.set('spec_count',1)
        cmd.set('shininess',55)
        cmd.set('power',1.0)
        cmd.set('spec_direct',0)        
        cmd.set('ray_shadow_decay_factor',0.1)
        cmd.set('ray_shadow_decay_range',1.8)
    elif mode=='occlusion':
        cmd.set('light_count',9)
        cmd.set("light" ,"[-0.2,-0.2,-1.0]")
        cmd.set("light2","[-0.2, 0.0,-1.0]")
        cmd.set("light3","[-0.2, 0.2,-1.0]")
        cmd.set("light4","[ 0.0, 0.2,-1.0]")
        cmd.set("light5","[ 0.2, 0.2,-1.0]")
        cmd.set("light6","[ 0.2, 0.0,-1.0]")
        cmd.set("light7","[ 0.2,-0.2,-1.0]")
        cmd.set("light8","[ 0.0,-0.2,-1.0]")
        cmd.set('ambient',0.18)
        cmd.set('direct',0.10)
        cmd.set('reflect',0.80)
        cmd.set('shininess',10)
        cmd.set('spec_count',-1)        
        cmd.set('power',1.0)
        cmd.set('specular_intensity',0)
        cmd.set('spec_direct',0.25)
        cmd.set('ray_shadow_decay_factor',0.1)
        cmd.set('ray_shadow_decay_range',5.0)
    elif mode=='medium':
        cmd.set('light_count',2)
        cmd.set("light","[-0.4,-0.4,-1.0]")
        cmd.set('ambient',0.14)
        cmd.set('direct',0.45)
        cmd.set('reflect',0.45)
        cmd.set('shininess',55)
        cmd.set('spec_count',-1)
        cmd.set('power',1.0)
        cmd.set('specular_intensity',0.5)
        cmd.set('spec_direct',0)
        cmd.set('ray_shadow_decay_factor',0)
    elif mode=='heavy':
        cmd.set('light_count',2)        
        cmd.set("light","[-0.4,-0.4,-1.0]")
        cmd.set('ambient',0.05)
        cmd.set('direct',0.20)
        cmd.set('reflect',0.85)
        cmd.set('spec_count',-1)
        cmd.set('shininess',90) 
        cmd.set('power',1.0) 
        cmd.set('specular_intensity',0.5)
        cmd.set('spec_direct',0)
        cmd.set('ray_shadow_decay_factor',0)
    elif mode=='black': # best for light backgrounds
        cmd.set('light_count',2)
        cmd.set("light","[-0.4,-0.4,-1.0]")
        cmd.set('ambient',0.001)
        cmd.set('direct',0.0)
        cmd.set('reflect',1.1)
        cmd.set('spec_count',-1)
        cmd.set('power',1.0)
        cmd.set('shininess',90)
        cmd.set('specular_intensity',0.5)
        cmd.set('spec_direct',0)
        cmd.set('ray_shadow_decay_factor',0)
Ejemplo n.º 19
0
Archivo: util.py Proyecto: Almad/pymol
def performance(mode,_self=cmd):
    pymol=_self._pymol
    cmd=_self
    mode = int(mode)
    if mode==0: # maximum quality
        cmd.set('line_smooth',1)
        cmd.set('depth_cue',1)         
        cmd.set('specular',1)
        cmd.set('surface_quality',1)
        cmd.set('stick_quality',15)
        cmd.set('sphere_quality',2)
        cmd.set('cartoon_sampling',14)
        cmd.set('ribbon_sampling',10)
        cmd.set('transparency_mode',2)
        cmd.set('stick_ball',1)
        cmd.do("rebuild")
    elif mode==33:
        cmd.set('line_smooth',1)         
        cmd.set('depth_cue',1)         
        cmd.set('specular',1)
        cmd.set('surface_quality',0)
        cmd.set('stick_quality',8)
        cmd.set('sphere_quality',1)
        cmd.set('cartoon_sampling',7)
        cmd.set('ribbon_sampling',1)
        cmd.set('transparency_mode',2)
        cmd.set('stick_ball',0)
        cmd.do("rebuild")
    elif mode==66: # good perfomance
        cmd.set('line_smooth',0)
        cmd.set('depth_cue',0)         
        cmd.set('specular',1)
        cmd.set('surface_quality',0)
        cmd.set('stick_quality',8)
        cmd.set('sphere_quality',1)
        cmd.set('cartoon_sampling',6)
        cmd.set('ribbon_sampling',1)
        cmd.set('transparency_mode',2)
        cmd.set('stick_ball',0.0)
        cmd.do("rebuild")         
    else: # maximum performance
        cmd.set('line_smooth',0)
        cmd.set('depth_cue',0)
        cmd.set('specular',0)
        cmd.set('surface_quality',-1) # new
        cmd.set('stick_quality',5)
        cmd.set('sphere_quality',0)
        cmd.set('ribbon_sampling',1)
        cmd.set('cartoon_sampling',3)
        cmd.set('transparency_mode',0)
        cmd.set('stick_ball',0.0)
        cmd.do("rebuild")