예제 #1
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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)
예제 #2
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def simple(selection="(all)", _self=cmd):
    cmd = _self
    s = tmp_sele
    cmd.select(s, selection)
    _prepare(s, _self=cmd)
    util.cbc(s, _self=cmd)
    cmd.show("ribbon", s)
    cmd.show(
        "lines", "(byres ((" + s + " & r. CYS+CYX & n. SG) & bound_to (" + s +
        " & r. CYS+CYX & n. SG))) & n. CA+CB+SG")
    # try to show what covalent ligands are connected to...
    cmd.show("sticks", "(" + lig_sele + " and (" + s + ")) extend 2")
    cmd.show(
        "sticks", "byres ((" + lig_sele + " and (" + s +
        ") and not resn ACE+NAC+NME+NH2) extend 1)")
    cmd.hide("sticks", "(" + s + ") and ((not rep sticks) extend 1)")
    cmd.show("sticks", "(" + lig_sele + " and (" + s + ")) extend 2")
    # color by atom if lines or sticks are shown
    util.cnc("(( rep lines or rep sticks or (" + lig_and_solv_sele +
             ")) and (" + s + "))",
             _self=cmd)
    cmd.show("nonbonded", "(" + lig_and_solv_sele + " and (" + s + "))")
    cmd.show("lines", "(" + lig_and_solv_sele + " and (" + s + "))")
    if cmd.count_atoms(s):
        cmd.zoom(s)
    cmd.delete(s)
예제 #3
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파일: m4x.py 프로젝트: Almad/pymol
def toggle_zooms(mode=-1):
    global zooms
    if mode<0:
        zooms = not zooms
    else:
        zooms = mode
    if zooms:
        cmd.zoom(m4x_ligands,2)
    else:
        cmd.zoom("m4x_aligned")
예제 #4
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파일: m4x.py 프로젝트: jchodera/pymol
def toggle_zooms(mode=-1):
    global zooms
    if mode < 0:
        zooms = not zooms
    else:
        zooms = mode
    if zooms:
        cmd.zoom(m4x_ligands, 2)
    else:
        cmd.zoom("m4x_aligned")
예제 #5
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파일: preset.py 프로젝트: aghozlane/pymol
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)
예제 #6
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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)
예제 #7
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def ligands(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 + ")")

        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("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("nonbonded", 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()
예제 #8
0
파일: preset.py 프로젝트: evonove/pymol
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)
예제 #9
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파일: preset.py 프로젝트: aghozlane/pymol
def simple(selection="(all)",_self=cmd):
    cmd=_self
    s = tmp_sele
    cmd.select(s,selection)
    _prepare(s,_self=cmd)
    util.cbc(s,_self=cmd)
    cmd.show("ribbon",s)
    cmd.show("lines","(byres (("+s+" & r. CYS+CYX & n. SG) & bound_to ("+s+" & r. CYS+CYX & n. SG))) & n. CA+CB+SG")
    # try to show what covalent ligands are connected to...
    cmd.show("sticks","("+lig_sele+" and ("+s+")) extend 2")
    cmd.show("sticks","byres (("+lig_sele+" and ("+s+") and not resn ACE+NAC+NME+NH2) extend 1)")
    cmd.hide("sticks","("+s+") and ((not rep sticks) extend 1)")
    cmd.show("sticks","("+lig_sele+" and ("+s+")) extend 2")
    # color by atom if lines or sticks are shown
    util.cnc("(( rep lines or rep sticks or ("+lig_and_solv_sele+")) and ("+s+"))",_self=cmd)
    cmd.show("nonbonded","("+lig_and_solv_sele+" and ("+s+"))")
    cmd.show("lines","("+lig_and_solv_sele+" and ("+s+"))")
    if cmd.count_atoms(s):
        cmd.zoom(s)
    cmd.delete(s)
예제 #10
0
파일: preset.py 프로젝트: aghozlane/pymol
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)
예제 #11
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파일: m4x.py 프로젝트: 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)
예제 #12
0
파일: m4x.py 프로젝트: jchodera/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)