Add Python charge scripts. First example xtb GFN2 charges

avogadro/calc/chargemodel.cpp

@@ -57,7 +57,7 @@ Array<double> ChargeModel::potentials(Core::Molecule& mol,
   return potentials;
 }
 
-void ChargeModel::appendError(const std::string& errorString, bool newLine)
+void ChargeModel::appendError(const std::string& errorString, bool newLine) const
 {
   m_error += errorString;
   if (newLine)

avogadro/calc/chargemodel.h

@@ -109,10 +109,10 @@ class AVOGADROCALC_EXPORT ChargeModel
    * @param errorString The error to be added.
    * @param newLine Add a new line after the error string?
    */
-  void appendError(const std::string& errorString, bool newLine = true);
+  void appendError(const std::string& errorString, bool newLine = true) const;
 
 private:
-  std::string m_error;
+  mutable std::string m_error;
 
   float m_dielectric;
 };

avogadro/qtplugins/CMakeLists.txt

@@ -96,7 +96,6 @@ add_subdirectory(applycolors)
 add_subdirectory(bondcentrictool)
 add_subdirectory(bonding)
 add_subdirectory(cartoons)
-add_subdirectory(commandscripts)
 add_subdirectory(coordinateeditor)
 add_subdirectory(copypaste)
 add_subdirectory(crystal)
@@ -147,8 +146,12 @@ endif()
 add_subdirectory(apbs)
 add_subdirectory(cp2kinput)
 add_subdirectory(gamessinput)
+
+# script plugins (input generators, etc.)
+add_subdirectory(commandscripts)
 add_subdirectory(quantuminput)
 add_subdirectory(scriptfileformats)
+add_subdirectory(scriptcharges)
 
 if(USE_LIBARCHIVE)
   add_subdirectory(plugindownloader)
@@ -160,18 +163,20 @@ endif()
 
 # The scene plugins
 add_subdirectory(ballandstick)
-add_subdirectory(licorice)
-add_subdirectory(vanderwaals)
-add_subdirectory(wireframe)
+add_subdirectory(closecontacts)
 add_subdirectory(force)
+add_subdirectory(licorice)
 add_subdirectory(meshes)
-add_subdirectory(closecontacts)
 add_subdirectory(noncovalent)
+add_subdirectory(vanderwaals)
+add_subdirectory(vanderwaalsao)
+add_subdirectory(wireframe)
 if (USE_OPENGL)
   # needs some raw OpenGL code
   add_subdirectory(overlayaxes)
 endif()
-add_subdirectory(vanderwaalsao)
+
+# other optional plugins
 if (USE_PROTOCALL)
   add_subdirectory(clientserver)
 endif()

avogadro/qtplugins/scriptcharges/CMakeLists.txt

@@ -0,0 +1,23 @@
+set(scriptcharges_srcs
+  scriptchargemodel.cpp
+  scriptcharges.cpp
+)
+
+avogadro_plugin(ScriptCharges
+  "Scriptable electrostatics models"
+  ExtensionPlugin
+  scriptcharges.h
+  ScriptCharges
+  "${scriptcharges_srcs}"
+  ""
+)
+
+target_link_libraries(ScriptCharges PRIVATE AvogadroCalc )
+
+# Bundled format scripts:
+set(charge_scripts
+  chargeScripts/xtb.py
+)
+
+install(PROGRAMS ${charge_scripts}
+  DESTINATION "${INSTALL_LIBRARY_DIR}/avogadro2/scripts/charges/")

avogadro/qtplugins/scriptcharges/chargeScripts/xtb.py

@@ -0,0 +1,100 @@
+#  This source file is part of the Avogadro project.
+#  This source code is released under the 3-Clause BSD License, (see "LICENSE").
+
+import argparse
+import json
+import sys
+import os
+from shutil import which
+import tempfile
+import subprocess
+
+
+def getMetaData():
+    # before we return metadata, make sure xtb is in the path
+    if which("xtb") is None:
+        return {}  # Avogadro will ignore us now
+
+    metaData = {}
+    metaData["inputFormat"] = "xyz"  # could be other formats, but this is fine
+    metaData["identifier"] = "GFN2"
+    metaData["name"] = "GFN2"
+    metaData["description"] = "Calculate atomic partial charges using GFN2 and xtb"
+    metaData["charges"] = True
+    metaData["potential"] = False
+    metaData["elements"] = "1-86"  # up to Radon
+    return metaData
+
+
+def charges():
+    # Avogadro will send us the sdf file as stdin
+    # we need to write it to a temporary file
+
+    # get the whole sdf file
+    xyz = sys.stdin.read()
+
+    fd, name = tempfile.mkstemp(".xyz")
+    os.write(fd, xyz.encode())
+    os.close(fd)
+
+    # run xtb
+    xtb = which("xtb")
+    if xtb is None:  # we check again
+        return ""
+
+    # for now, ignore the output itself
+    tempdir = tempfile.mkdtemp()
+    output = subprocess.run(
+        [xtb, name], stdout=subprocess.PIPE, cwd=tempdir, check=True
+    )
+    # instead we read the "charges" file
+    result = ""
+    with open(tempdir + "/" + "charges", "r", encoding="utf-8") as f:
+        result = f.read()
+
+    # try to cleanup the temporary files
+    os.remove(name)
+    for filename in os.listdir(tempdir):
+        try:
+            os.remove(tempdir + "/" + filename)
+        except:
+            continue
+    # and try to cleanup the directory
+    try:
+        os.rmdir(tempdir)
+    except:
+        pass
+
+    # write the charges to stdout
+    return result
+
+
+def potential():
+    # at the moment, xtb doesn't have a good way to do this
+    # and the method shouldn't be called anyway
+
+    # if your plugin has a potential, you can return it here
+    # .. you'll get JSON with the file and the set of points
+    #   e.g. { "xyz" : "xyz file contents", "points" : [ x,y,z, x,y,z, ... ] }
+    #    or  { "sdf" : "sdf file contents", "points" : [ x,y,z, x,y,z, ... ] }
+    # .. and you print the list of potentials to stdout
+    return ""
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser("GFN2 partial charges")
+    parser.add_argument("--display-name", action="store_true")
+    parser.add_argument("--metadata", action="store_true")
+    parser.add_argument("--charges", action="store_true")
+    parser.add_argument("--potential", action="store_true")
+    parser.add_argument("--lang", nargs="?", default="en")
+    args = vars(parser.parse_args())
+
+    if args["metadata"]:
+        print(json.dumps(getMetaData()))
+    elif args["display_name"]:
+        print(getMetaData()["name"])
+    elif args["charges"]:
+        print(charges())
+    elif args["potential"]:
+        print(potential())