From f37e24b3dbd9a183fb497cbe89a4355e878b2c15 Mon Sep 17 00:00:00 2001
From: qzhu2017 <alecfans@gmail.com>
Date: Sun, 7 Apr 2024 21:05:27 -0400
Subject: [PATCH] fix reading Cl-

---
 doc/Usage.rst      | 20 ++++++++------------
 pyxtal/__init__.py |  2 +-
 pyxtal/molecule.py |  4 +++-
 pyxtal/version.py  |  2 +-
 4 files changed, 13 insertions(+), 15 deletions(-)

diff --git a/doc/Usage.rst b/doc/Usage.rst
index b48f2245..5da202e7 100644
--- a/doc/Usage.rst
+++ b/doc/Usage.rst
@@ -625,13 +625,13 @@ O atoms.
     Group: Pnnm (58)
       7.8758,   7.9794,   5.6139,  90.0000,  90.0000,  90.0000, orthorhombic
     Wyckoff sites:
-    	Al @ [ 0.0000  0.0000  0.2418], WP [4e] Site [..2]
-    	Al @ [ 0.1294  0.6392  0.0000], WP [4g] Site [..m]
-    	Si @ [ 0.2458  0.2522  0.0000], WP [4g] Site [..m]
-    	 O @ [ 0.4241  0.3636  0.0000], WP [4g] Site [..m]
-    	 O @ [ 0.5538  0.2648  0.0000], WP [4g] Site [..m]
-    	 O @ [ 0.0000  0.5000  0.6057], WP [4f] Site [..2]
-    	 O @ [ 0.8809  0.5970  0.0786], WP [8h] Site [1]
+    Al @ [ 0.0000  0.0000  0.2418], WP [4e] Site [..2]
+    Al @ [ 0.1294  0.6392  0.0000], WP [4g] Site [..m]
+    Si @ [ 0.2458  0.2522  0.0000], WP [4g] Site [..m]
+    O @ [ 0.4241  0.3636  0.0000], WP [4g] Site [..m]
+    O @ [ 0.5538  0.2648  0.0000], WP [4g] Site [..m]
+    O @ [ 0.0000  0.5000  0.6057], WP [4f] Site [..2]
+    O @ [ 0.8809  0.5970  0.0786], WP [8h] Site [1]
 
 
 Similarly, PyXtal allows the user to pre-assign the partial information (e.g.,
@@ -788,7 +788,7 @@ Database
 --------------------------------
 
 For molecular crystals, PyXtal provides a
-`db <pyxtal.db.html>`_ class to handle store the database with additional information related to the Cambridge Crystallographic Database. **This function requires the access of `CSD Python-api <https://downloads.ccdc.cam.ac.uk/documentation/API/index.html>`.**
+`db <pyxtal.db.html>`_ class to handle store the database with additional information related to the Cambridge Crystallographic Database. **This function requires the access of `CSD Python-api <https://downloads.ccdc.cam.ac.uk/documentation/API/index.html>`_.**
 
 To create a new database file (e.g., `test.db`),
 
@@ -826,8 +826,6 @@ To update some information,
 
 .. code-block:: Python
 
-::
-
     from pyxtal.db import database
     db = database('test.db')
     db.add_from_code('XATJOT')
@@ -849,8 +847,6 @@ To access the pyxtal structure
 
 .. code-block:: Python
 
-::
-
     from pyxtal.db import database
     db = database('test.db')
     xtal = db.get_pyxtal('XATJOT')
diff --git a/pyxtal/__init__.py b/pyxtal/__init__.py
index 5f326328..37c0449e 100644
--- a/pyxtal/__init__.py
+++ b/pyxtal/__init__.py
@@ -2846,7 +2846,7 @@ def from_CSD(self, csd_code):
             smi = entry.molecule.smiles
             if smi is None:
                 raise CSDError("No smile from CSD")
-            elif len(smi) > 250:
+            elif len(smi) > 350:
                 raise CSDError("long smile {:s}".format(smi))
             else:
                 if Chem.MolFromSmiles(smi) is None:
diff --git a/pyxtal/molecule.py b/pyxtal/molecule.py
index 95a40654..36b80eeb 100644
--- a/pyxtal/molecule.py
+++ b/pyxtal/molecule.py
@@ -289,7 +289,9 @@ def __init__(self,
         self.tols_matrix = self.get_tols_matrix()
         xyz = self.mol.cart_coords
         self.reset_positions(xyz-self.get_center(xyz))
-        if self.smile is not None: ori, _, self.reflect = self.get_orientation(xyz)
+        if self.smile is not None and self.smile not in ["Cl-", "F-", "Br-", "I-", "Li+", "Na+"]:
+            #print(self.smile)
+            ori, _, self.reflect = self.get_orientation(xyz)
 
     def __str__(self):
         return '[' + self.name + ']'
diff --git a/pyxtal/version.py b/pyxtal/version.py
index 364e7bae..7bbb2ef5 100644
--- a/pyxtal/version.py
+++ b/pyxtal/version.py
@@ -1 +1 @@
-__version__ = "0.6.4"
+__version__ = "0.6.5"