New command: delete_states

Delete states from multistate objects. Currently only supports
non-discrete molecular objects.

layer2/ObjectMolecule.cpp

@@ -11208,6 +11208,31 @@ int ObjectMoleculeSetStateOrder(ObjectMolecule * I, int * order, int len) {
   return false;
 }
 
+/*========================================================================*/
+pymol::Result<> ObjectMoleculeDeleteStates(ObjectMolecule* I, const std::vector<int>& states)
+{
+  auto& CSet = I->CSet;
+
+  // first pass, check for invalid states
+  for (auto state : states) {
+    if (state < 0 || state >= I->NCSet) {
+      auto msg = pymol::string_format("Invalid state index: %d", state);
+      I->G->Feedback->addColored(msg.c_str(), FB_Errors);
+      return {};
+    }
+  }
+
+  // second pass, delete states
+  for (auto it = states.rbegin(); it != states.rend(); ++it) {
+    int state = *it;
+    DeleteP(CSet[state]);
+    CSet.erase(state, 1);
+  }
+  I->NCSet -= states.size();
+  CSet.resize(I->NCSet);
+  return {};
+}
+
 /*========================================================================*/
 ObjectMolecule::~ObjectMolecule()
 {

layer2/ObjectMolecule.h

@@ -308,6 +308,14 @@ int ObjectMoleculeCheckFullStateSelection(ObjectMolecule * I, int sele, int stat
 
 int ObjectMoleculeSetStateOrder(ObjectMolecule * I, int * order, int len);
 
+/**
+ * @brief Deletes a CoordSet/State from a molecule object
+ * @param I ObjectMolecule
+ * @param states state indices (0-based)
+ * @note This function only works on non-discrete molecular objects
+ */
+pymol::Result<> ObjectMoleculeDeleteStates(ObjectMolecule* I, const std::vector<int>& state);
+
 int ObjectMoleculeAddPseudoatom(ObjectMolecule * I, int sele_index, const char *name,
                                 const char *resn, const char *resi, const char *chain,
                                 const char *segi, const char *elem, float vdw,

layer3/Executive.cpp

@@ -14278,6 +14278,30 @@ pymol::Result<std::vector<DiscardedRec>> ExecutiveDelete(PyMOLGlobals * G, pymol
   return discardedRecs;
 }
 
+pymol::Result<> ExecutiveDeleteStates(
+    PyMOLGlobals* G, std::string_view name, const std::vector<int>& states)
+{
+  for (auto& rec : ExecutiveGetSpecRecsFromPattern(G, name.data())) {
+    if (rec.type != cExecObject) {
+      continue;
+    }
+    auto* obj = rec.obj;
+    if (obj->type != cObjectMolecule) {
+      continue;
+    }
+    auto* mol = static_cast<ObjectMolecule*>(obj);
+    if (mol->DiscreteFlag) {
+      G->Feedback->addColored(
+          "Error: Cannot delete states from discrete objects.\n", FB_Warnings);
+      continue;
+    }
+    ObjectMoleculeDeleteStates(mol, states);
+  }
+  SceneChanged(G);
+  ExecutiveInvalidatePanelList(G);
+  return {};
+}
+
 void ExecutiveReAddSpec(PyMOLGlobals* G, std::vector<DiscardedRec>& specs)
 {
   auto I = G->Executive;

layer3/Executive.h

@@ -341,6 +341,16 @@ pymol::CObject** ExecutiveFindObjectsByType(PyMOLGlobals * G, int objType);
 int ExecutiveIterateObject(PyMOLGlobals * G, pymol::CObject ** obj, void **hidden);
 pymol::Result<std::vector<DiscardedRec>> ExecutiveDelete(PyMOLGlobals * G, pymol::zstring_view nameView, bool save = false);
 
+/**
+ * @brief Deletes states from an object
+ * @param name name of the object
+ * @param states list of states to be deleted (0-based, must be sorted and
+ * unique)
+ * @note Currently only works on non-discrete molecular objects
+ */
+pymol::Result<> ExecutiveDeleteStates(
+    PyMOLGlobals* G, std::string_view name, const std::vector<int>& states);
+
 /**
  * @brief Unregisters the specification record from PyMOL
  * @param rec specification record to be purged/removed

layer4/Cmd.cpp

@@ -5178,6 +5178,20 @@ static PyObject *CmdDelete(PyObject * self, PyObject * args)
   return APISuccess();
 }
 
+static PyObject *CmdDeleteStates(PyObject * self, PyObject * args)
+{
+  PyMOLGlobals* G = nullptr;
+  const char* objName;
+  PyObject* statesPyList;
+  API_SETUP_ARGS(G, self, args, "OsO", &self, &objName, &statesPyList);
+  std::vector<int> states;
+  PConvFromPyObject(G, statesPyList, states);
+  API_ASSERT(APIEnterNotModal(G));
+  auto result = ExecutiveDeleteStates(G, objName, states);
+  APIExit(G);
+  return APIResult(G, result);
+}
+
 static PyObject *CmdCartoon(PyObject * self, PyObject * args)
 {
   PyMOLGlobals *G = nullptr;
@@ -6275,6 +6289,7 @@ static PyMethodDef Cmd_methods[] = {
   {"del_colorection", CmdDelColorection, METH_VARARGS},
   {"fake_drag", CmdFakeDrag, METH_VARARGS},
   {"delete", CmdDelete, METH_VARARGS},
+  {"delete_states", CmdDeleteStates, METH_VARARGS},
   {"dirty", CmdDirty, METH_VARARGS},
   {"dirty_wizard", CmdDirtyWizard, METH_VARARGS},
   {"dihedral", CmdDihedral, METH_VARARGS},

modules/pymol/api.py

@@ -66,6 +66,7 @@
       async_,             \
       cls,                \
       delete,             \
+      delete_states,      \
       do,                 \
       log,                \
       log_close,          \

modules/pymol/commanding.py

@@ -528,6 +528,7 @@ def delete(name, *, _self=cmd):
 SEE ALSO
 
     remove
+    delete_states
         '''
         r = DEFAULT_ERROR
         try:
@@ -538,6 +539,63 @@ def delete(name, *, _self=cmd):
         if _self._raising(r,_self): raise pymol.CmdException
         return r
 
+    def delete_states(name: str, states: str, *, _self=cmd):
+        '''
+DESCRIPTION
+
+USAGE
+
+    delete_states name, states
+
+ARGUMENTS
+
+    name = name(s) of object(s), supports wildcards (*)
+
+    states = string: space separated list of state numbers or ranges
+
+EXAMPLES
+
+    delete_state 1nmr, 1-5     # delete states 1 to 5 from 1nmr
+    delete_state *, 1-3 10-40  # deletes states 1 to 3 and 10 to 40 from all applicable objects
+
+PYMOL API
+
+    cmd.delete_states(string name = object-name, string states = states string)
+
+SEE ALSO
+
+    delete
+        '''
+
+        def get_state_list(states_str):
+            output=[]
+            input_str = re.sub(r"\s"," ", states_str)
+            input_str = input_str.replace("-"," -")
+            input_str = input_str.replace("- ","-")
+            input_str = input_str.strip().split()
+
+            last = -1
+            for x in input_str:
+                if not x.isdigit():
+                    if x.startswith("-"):
+                        direction = 1
+                        current = last
+                        last = int(x[1:]) - 1
+                        if last < current:
+                            direction = -1
+                        while current != last:
+                            current += direction
+                            output.append(str(current))
+                else:
+                    val = int(x) - 1
+                    output.append(str(val))
+                    last = val
+            return output
+
+        with _self.lockcm:
+            output = get_state_list(states)
+            states_list = sorted(set(map(int, output)))
+            return _cmd.delete_states(_self._COb, name, states_list)
 
     class Selection(str):
         pass

modules/pymol/keywords.py

@@ -59,6 +59,7 @@ def get_command_keywords(self_cmd=cmd):
         'create'        : [ self_cmd.create            , 0 , 0 , ''  , parsing.LEGACY ],
         'decline'       : [ self_cmd.decline           , 0 , 0 , ''  , parsing.STRICT ],
         'delete'        : [ self_cmd.delete            , 0 , 0 , ''  , parsing.STRICT ],
+        'delete_states' : [ self_cmd.delete_states     , 0 , 0 , ''  , parsing.STRICT ],
         'def'           : [ self_cmd.python_help       , 0 , 0 , ''  , parsing.PYTHON ],
         'del'           : [ self_cmd.python_help       , 0 , 0 , ''  , parsing.PYTHON ],
         'deprotect'     : [ self_cmd.deprotect         , 0 , 0 , ''  , parsing.STRICT ],

testing/tests/api/commanding.py

@@ -37,6 +37,12 @@ def testDelete(self):
         cmd.delete('m1 m2')
         self.assertEqual(cmd.get_names(), ['m3'])
 
+    def testDeleteStates(self):
+        cmd.pseudoatom('m1', state=10)
+        self.assertEqual(cmd.count_states('m1'), 10)
+        cmd.delete_states('m1', '4-8')
+        self.assertEqual(cmd.count_states('m1'), 5)
+
     def testDo(self):
         # tested with other methods
         pass