Fixed a bug that avoided charging one atom

The cif file inputted needs to end in a newline. If not, things go awry.

eqeq.py

@@ -5,7 +5,7 @@
 2. to enable scaling of simulations to millions of structures.
 """
 from ctypes import cdll, c_char_p, c_int, c_double, c_float
-import json
+import json_formatter as json
 import os
 import sys
 
@@ -37,7 +37,7 @@ def run(structure, input_type="cif", output_type="cif", l=1.2, h_i0=-2.0,
         input_type: (Optional) Specifies input type. Can be anything supported
             by openbabel, as well as "json"
         output_type: (Optional) Specifies the output type. Currently, options
-            are "cif", "mol", "pdb", "car", "json", "object", and "files". The
+            are "cif", "mol", "pdb", "car", "json", "list", and "files". The
             first four return modified chemical data formats, "object" returns
             a Python object, "json" is that object serialized, and "files"
             saves files of all possible output types.
@@ -63,23 +63,26 @@ def run(structure, input_type="cif", output_type="cif", l=1.2, h_i0=-2.0,
     """
     # Error handling on string params. Should spare users some annoyance.
     o, m = output_type.lower(), method.lower()
-    if o not in ["cif", "pdb", "car", "mol", "json", "object", "files"]:
+    if o not in ["cif", "pdb", "car", "mol", "json", "list", "files"]:
         raise NotImplementedError("Output format '%s' is not supported!" % o)
     if m not in ["direct", "nonperiodic", "ewald"]:
         raise NotImplementedError("Method '%s' is not supported!" % m)
     # If linked to openbabel, use it to handle json interconversion externally
     if input_type != "cif":
         structure = format_converter.convert(structure, input_type, "cif")
     # Calls libeqeq.so's run method, returning a string of data
-    result = eqeq.run(structure, output_type, l, h_i0, charge_precision,
-                      method, m_r, m_k, eta, ionization_data_path,
-                      charge_data_path)
+    result = eqeq.run(structure, ("json" if output_type == "list" else
+                      output_type), l, h_i0, charge_precision, method, m_r,
+                      m_k, eta, ionization_data_path, charge_data_path)
+    if output_type == "list":
+        return json.loads(result)
     # This option appends atoms in json/object data with a "charge" attribute
-    if output_type in ["json", "object"]:
+    if output_type == "json":
         obj = format_converter.convert(structure, "cif", "object")
-        for atom, charge in zip(obj["atoms"], json.loads(result)):
+        result = json.loads(result)
+        for atom, charge in zip(obj["atoms"], result):
             atom["charge"] = charge
-        result = obj if output_type == "object" else json.dumps(obj)
+        result = json.dumps(obj)
     return result
 
 

format_converter.py

@@ -110,7 +110,7 @@ def json_to_cif(mof):
                      % tuple([atom["element"], i, atom["element"]] +
                      cartesian_to_fractional(atom["location"], va, vb, vc))
                      for i, atom in enumerate(mof["atoms"]))
-    return cif
+    return cif + "\n"
 
 
 def get_angle(first_vector, second_vector):

main.cpp

@@ -218,7 +218,7 @@ char *run(const char *data, const char *outputType, double _lambda, float _hI0,
         outString = OutputMOLData();
     } else if (type.compare("car") == 0) {
         outString = OutputCARData();
-    } else if (type.compare("json") == 0 || type.compare("object") == 0) {
+    } else if (type.compare("json") == 0) {
         outString = OutputJSONData();
     } else {
         cerr << "Output type \"" << outputType << "\" not supported!" << endl;
@@ -974,10 +974,10 @@ string OutputPDBData() {
 string OutputJSONData() {
     ostringstream stringStream;
     stringStream << "[";
-    for (int i = 0; i < numAtoms; i++) {
+    for (int i = 0; i < numAtoms - 1; i++) {
         stringStream << Q[i] << ",";
     }
-    stringStream << Q[numAtoms] << "]";
+    stringStream << Q[numAtoms - 1] << "]";
     return stringStream.str();
 }
 /*****************************************************************************/