/dports/science/py-pymol/pymol-open-source-2.4.0/examples/devel/ |
H A D | importing.py | 22 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 …]
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H A D | my_ext_gui.py | 23 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 …]
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H A D | link_demo.py | 8 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)
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/dports/science/py-pymol/pymol-open-source-2.4.0/layerCTest/ |
H A D | Test_Result.cpp | 3 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 …]
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H A D | Test_zstring_view.cpp | 11 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 …]
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H A D | Test_cache_ptr.cpp | 5 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 …]
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H A D | Test_copyable_ptr.cpp | 5 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 …]
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H A D | Test_type_traits.cpp | 8 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));
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H A D | Test_Util.cpp | 11 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"));
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/dports/science/py-pymol/pymol-open-source-2.4.0/modules/pymol/ |
H A D | gui.py | 17 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 …]
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H A D | commanding.py | 36 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 …]
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H A D | editing.py | 21 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 …]
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/dports/science/py-pymol/pymol-open-source-2.4.0/layer3/ |
H A D | Executive.h | 200 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 …]
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H A D | Editor.h | 65 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);
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H A D | ExecutivePython.cpp | 9 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 …]
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/dports/science/py-pymol/pymol-open-source-2.4.0/modules/pmg_tk/ |
H A D | PyMOLMapLoad.py | 8 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 …]
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/dports/science/py-pymol/pymol-open-source-2.4.0/ |
H A D | PACKAGING | 14 - <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
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/dports/science/py-pymol/pymol-open-source-2.4.0/modules/pmg_qt/ |
H A D | pymol_gl_widget.py | 6 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 …]
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/dports/science/py-pymol/pymol-open-source-2.4.0/modules/pymol/wizard/ |
H A D | charge.py | 4 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 …]
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H A D | annotation.py | 3 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
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/dports/science/py-pymol/pymol-open-source-2.4.0/layer2/ |
H A D | ObjectMesh.h | 31 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);
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H A D | ObjectGadgetRamp.h | 36 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,
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H A D | ObjectSlice.h | 51 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;
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/dports/science/py-pymol/pymol-open-source-2.4.0/test/inp/ |
H A D | B06.py | 10 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):
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/dports/science/py-pymol/pymol-open-source-2.4.0/data/chempy/sidechains/ |
H A D | generate1.py | 10 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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