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/dports/science/py-pymol/pymol-open-source-2.4.0/examples/devel/
H A Dimporting.py22 import pymol
36 pymol.cmd.rock()
37 pymol.cmd.turn("x",180)
40 pymol.cmd.orient()
41 pymol.cmd.turn("y",85)
42 pymol.cmd.zoom("all",20)
50 pymol.cmd.window("hide")
53 pymol.cmd.window("show")
55 pymol.cmd.window("hide")
58 pymol.cmd.window("show")
[all …]
H A Dmy_ext_gui.py23 def run(pymol): argument
34 pymol.cmd.set("sweep_mode",3)
35 pymol.cmd.rock()
36 pymol.cmd.turn("x",180)
37 pymol.cmd.load("$TUT/1hpv.pdb")
38 pymol.preset.pretty("1hpv")
39 pymol.cmd.orient()
40 pymol.cmd.turn("y",85)
41 pymol.cmd.zoom("all",20)
43 pymol.cmd.show("sticks","organic")
[all …]
H A Dlink_demo.py8 import pymol
9 from pymol.wizard import Wizard
10 from pymol import cmd, util
11 import pymol
31 pymol.stored.link = ''
33 if len(pymol.stored.link):
34 webbrowser.open(pymol.stored.link)
/dports/science/py-pymol/pymol-open-source-2.4.0/layerCTest/
H A DTest_Result.cpp3 using namespace pymol::test;
6 pymol::Result<int> sum(int i, int j) in sum()
24 pymol::Result<pymol::common_type_t<T, U>> sum(T i, U j) in sum()
41 pymol::Result<int> sumError(int i, int j) in sumError()
43 return pymol::Error{"Values cannot be summed."}; in sumError()
57 static pymol::Result<> returnEmptyBrackets() in returnEmptyBrackets()
70 auto error1 = pymol::Error();
72 auto error2 = pymol::Error::make<pymol::Error::QUIET>();
73 REQUIRE(error2.code() == pymol::Error::QUIET);
79 pymol::Result<int> result1 = pymol::Error::QUIET;
[all …]
H A DTest_zstring_view.cpp11 using namespace pymol::test;
20 pymol::zstring_view v1(s1);
29 pymol::zstring_view v2(v1);
81 pymol::zstring_view v1 = nullsafe1;
91 pymol::zstring_view v1 = "foobar";
92 pymol::zstring_view v2 = v1;
111 std::set<pymol::zstring_view> set1;
114 pymol::zstring_view v1 =
188 pymol::zstring_view v1("foobar");
230 pymol::zstring_view v1;
[all …]
H A DTest_cache_ptr.cpp5 using namespace pymol::test;
9 pymol::cache_ptr<int> p1;
29 pymol::cache_ptr<int> p1;
32 pymol::cache_ptr<int> p2(p1);
41 pymol::cache_ptr<int> p2(p1);
49 pymol::cache_ptr<int> p1;
52 pymol::cache_ptr<int> p2;
62 pymol::cache_ptr<int> p2;
71 pymol::cache_ptr<int> p1;
74 pymol::cache_ptr<int> p2;
[all …]
H A DTest_copyable_ptr.cpp5 using namespace pymol::test;
9 pymol::copyable_ptr<int> p1;
29 pymol::copyable_ptr<int> p1;
32 pymol::copyable_ptr<int> p2(p1);
41 pymol::copyable_ptr<int> p2(p1);
51 pymol::copyable_ptr<int> p1;
54 pymol::copyable_ptr<int> p2;
64 pymol::copyable_ptr<int> p2;
73 pymol::copyable_ptr<int> p1;
76 pymol::copyable_ptr<int> p2;
[all …]
H A DTest_type_traits.cpp8 auto shaped = pymol::reshape<3>(flat);
15 REQUIRE(pymol::equal(shaped[0], shaped[0] + 3, flat + 0));
16 REQUIRE(pymol::equal(shaped[1], shaped[1] + 3, flat + 3));
22 const float* flat = pymol::flatten(shaped);
23 REQUIRE(pymol::equal(shaped[0], shaped[0] + 3, flat + 0));
24 REQUIRE(pymol::equal(shaped[1], shaped[1] + 3, flat + 3));
26 float* flat_from_ptr = pymol::flatten(shaped_ptr);
27 REQUIRE(pymol::equal(flat, flat + 6, flat_from_ptr));
H A DTest_Util.cpp11 auto str = pymol::join_to_string("Hello ", 42, ch);
17 auto str = pymol::string_format("%s %d!", "Hello", 42);
20 auto str2 = pymol::string_format("%s %d!", std::string("Hello"), 42);
23 auto str3 = pymol::string_format("");
26 auto str4 = pymol::string_format("%s %d!", "ThisStringWillNotBeSmallStringOptimized", 42);
67 REQUIRE(pymol::starts_with(str, "_H"));
70 REQUIRE(pymol::starts_with(str2, "_J"));
73 REQUIRE(!pymol::starts_with(str2, "F"));
/dports/science/py-pymol/pymol-open-source-2.4.0/modules/pymol/
H A Dgui.py17 import pymol
24 if pymol._ext_gui is None:
26 return pymol._ext_gui
50 pymol = _self._pymol
51 if pymol._ext_gui is not None:
62 pymol = _self._pymol
63 if pymol._ext_gui is not None:
76 pymol = _self._pymol
77 if pymol._ext_gui is not None:
88 pymol = _self._pymol
[all …]
H A Dcommanding.py36 import pymol
118 pymol=_self._pymol
120 pymol._log_file = QueueFile(filename)
125 if hasattr(pymol,"_log_file"):
128 del pymol._log_file
145 pymol._log_file = None
211 pymol=_self._pymol
213 if hasattr(pymol,"_log_file"):
214 if pymol._log_file is not None:
215 pymol._log_file.close()
[all …]
H A Dediting.py21 import pymol
54 if _self._raising(r,_self): raise pymol.CmdException
70 if _self._raising(r,_self): raise pymol.CmdException
960 import pymol.wizard.dragging
1234 raise pymol.CmdException
1631 raise pymol.CmdException
1745 raise pymol.CmdException
1791 raise pymol.CmdException
2078 raise pymol.CmdException
2120 raise pymol.CmdException
[all …]
/dports/science/py-pymol/pymol-open-source-2.4.0/layer3/
H A DExecutive.h200 pymol::Result<> ExecutiveLoad(
225 pymol::Result<> ExecutivePseudoatom(PyMOLGlobals* G, pymol::zstring_view object_name,
252 pymol::Result<> ExecutiveAddBondByIndices(PyMOLGlobals* G, pymol::zstring_view oname,
358 pymol::Result<pymol::vla<float>> ExecutiveRMSStates(
362 pymol::Result<> ExecutiveReset(PyMOLGlobals*, pymol::zstring_view);
400 pymol::Result<> ExecutiveMove(
406 pymol::Result<> ExecutiveCopy(
522 pymol::Result<bool>
544 const char* src_name, pymol::vla<float> range, pymol::vla<float> color,
672 pymol::Result<> ExecutiveClip(PyMOLGlobals* G, pymol::zstring_view clipStr);
[all …]
H A DEditor.h65 pymol::Result<> EditorReplace(PyMOLGlobals* G, const char* elem, int geom,
67 pymol::Result<> EditorAttach(PyMOLGlobals* G, const char* elem, int geom,
69 pymol::Result<> EditorRemove(PyMOLGlobals * G, int hydrogen, int quiet);
70 pymol::Result<> EditorHFill(PyMOLGlobals * G, int quiet=1);
71 pymol::Result<> EditorHFix(PyMOLGlobals * G, const char *sele, int quiet);
72 pymol::Result<> EditorCycleValence(PyMOLGlobals * G, int quiet=1);
77 pymol::Result<> EditorSelect(PyMOLGlobals* G, const char* s0, const char* s1,
79 pymol::Result<> EditorTorsion(PyMOLGlobals * G, float angle);
80 pymol::Result<> EditorInvert(PyMOLGlobals * G, int quiet);
H A DExecutivePython.cpp9 pymol::Result<> ExecutiveLoadObject(PyMOLGlobals* G, in ExecutiveLoadObject()
156 pymol::Result<> ExecutiveSetRawAlignment(PyMOLGlobals* G, in ExecutiveSetRawAlignment()
157 pymol::zstring_view alnname, PyObject* raw, pymol::zstring_view guidename, in ExecutiveSetRawAlignment()
167 return pymol::make_error("alignment must be list"); in ExecutiveSetRawAlignment()
172 pymol::vla<int> align_vla(n_cols * 3); in ExecutiveSetRawAlignment()
179 return pymol::make_error("columns must be list"); in ExecutiveSetRawAlignment()
191 return pymol::make_error("indices must be (str, int)"); in ExecutiveSetRawAlignment()
197 return pymol::make_error("object ", model, " not found"); in ExecutiveSetRawAlignment()
238 pymol::Result<float> ExecutiveFitPairs( in ExecutiveFitPairs()
243 return pymol::make_error("No selections provided"); in ExecutiveFitPairs()
[all …]
/dports/science/py-pymol/pymol-open-source-2.4.0/modules/pmg_tk/
H A DPyMOLMapLoad.py8 import pymol
9 from pymol import headering
229 helpText = pymol.cmd.map_generate.__doc__
259 pfx = pymol.cmd.get_unused_name(pfx)
286 except pymol.CmdException as e:
295 skin = pymol._ext_gui.skin
297 pymol.cmd.set("suspend_updates", 1)
301 pymol.cmd.isosurface(pymol.cmd.get_unused_name(r+"-srf"),
310 pymol.cmd.color("red", meshName)
322 pymol.cmd.color("blue", surfName)
[all …]
/dports/science/py-pymol/pymol-open-source-2.4.0/
H A DPACKAGING14 - <pymol python module> + "/pymol_path"
16 "modules/pymol/__init__.py"
17 - sys.prefix + "/share/pymol"
25 == pymol package ==
27 modules/pymol -> /usr/lib/pythonX.X/site-packages/pymol
31 == pymol-data package ==
33 scripts -> /usr/share/pymol/scripts (RUNTIME REQUIREMENT)
34 data -> /usr/share/pymol/data (RUNTIME REQUIREMENT)
37 python setup.py install --pymol-path=/usr/share/pymol
/dports/science/py-pymol/pymol-open-source-2.4.0/modules/pmg_qt/
H A Dpymol_gl_widget.py6 import pymol
8 from pymol.Qt import QtCore
9 from pymol.Qt import QtGui
10 from pymol.Qt import QtWidgets
17 from pymol._cmd import glViewport
27 from pymol.Qt import QtOpenGL
81 self.pymol = PyMOL()
82 self.pymol.start()
83 self.cmd = self.pymol.cmd
198 self.pymol.draw()
[all …]
/dports/science/py-pymol/pymol-open-source-2.4.0/modules/pymol/wizard/
H A Dcharge.py4 from pymol.wizard import Wizard
5 from pymol import cmd
6 import pymol
128 pymol.stored.charge = 0
162 pymol.stored.charge=self.partial_charge
173 pymol.stored.chg_dict = {}
184 pymol.stored.valid_atoms = []
188 for a in pymol.stored.valid_atoms:
224 pymol.stored.charge=self.partial_charge
245 pymol.stored.charge=self.partial_charge
[all …]
H A Dannotation.py3 from pymol.wizard import Wizard
4 from pymol import cmd
5 import pymol
23 pymol = self.cmd._pymol
24 if hasattr(pymol.session,'annotation'):
25 anno_dict = pymol.session.annotation
45 pymol=_self._pymol
59 if not hasattr(pymol.session,'annotation'):
60 pymol.session.annotation = {}
65 pymol.session.annotation[object] = state_dict
/dports/science/py-pymol/pymol-open-source-2.4.0/layer2/
H A DObjectMesh.h31 pymol::vla<int> N;
35 pymol::vla<float> V;
45 pymol::vla<float> AtomVertex;
49 pymol::cache_ptr<CGO> UnitCellCGO;
52 pymol::copyable_ptr<Isofield> Field;
54 pymol::cache_ptr<CGO> shaderCGO;
55 pymol::cache_ptr<CGO> shaderUnitCellCGO;
60 pymol::vla<ObjectMeshState> State;
89 pymol::Result<float> ObjectMeshGetLevel(ObjectMesh * I, int state);
H A DObjectGadgetRamp.h36 pymol::vla<float> Level;
37 pymol::vla<float> LevelTmp;
38 pymol::vla<float> Color;
82 pymol::vla<float>&& level_vla,
83 pymol::vla<float>&& color_vla,
91 pymol::vla<float>&& level_vla,
92 pymol::vla<float>&& color_vla,
H A DObjectSlice.h51 pymol::vla<float> values;
52 pymol::vla<float> points;
53 pymol::vla<int> flags;
54 pymol::vla<float> colors;
55 pymol::vla<float> normals;
58 pymol::vla<int> strips;
60 pymol::cache_ptr<CGO> shaderCGO;
/dports/science/py-pymol/pymol-open-source-2.4.0/test/inp/
H A DB06.py10 from pymol import cmd
12 import pymol
17 pymol.run = 1
19 cmd.set_key('F1',lambda p=pymol:(setattr(p,'run',0)))
20 cmd.set_key('F2',lambda p=pymol:(setattr(p,'run',1)))
35 getattr(pymol.preset,cur_rep)('pdb')
48 while(pymol.run==0):
/dports/science/py-pymol/pymol-open-source-2.4.0/data/chempy/sidechains/
H A Dgenerate1.py10 from pymol import cmd
12 import pymol
13 from pymol import cmd
32 pymol.stored.list = []
34 candi_list = pymol.stored.list
64 pymol.stored.list=[]
66 termi_list = pymol.stored.list
86 resn = pymol.stored.resn
90 pymol.stored.names = []
93 name_list.append(tuple(pymol.stored.names))

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