Merge pull request #203 from rperezsoto/documentation_fixes

Fixed minor typos in the docstrings

aqme/csearch/base.py

@@ -91,7 +91,8 @@
       might be atoms, bonds, angles and dihedral. For example, a rule to keep only
       molecules with C-Pd-C atoms at 180 degrees: ['[C][Pd][C]',180].
       Special rules (--geom ['RULE_NAME']):
-        1. ['Ir_squareplanar']
+
+         1. ['Ir_squareplanar']
    bond_thres : float, default=0.2
       Threshold used to discard bonds in the geom option (+-0.2 A) 
    angle_thres : float, default=30
@@ -172,8 +173,8 @@
       Additional keywords for CREGEN (i.e. cregen_keywords='--ethr 0.02')
    xtb_keywords : str, default=None
       Define additional keywords to use in the xTB pre-optimization that are not 
-      included in -c, --uhf, -P and --input. For example: '--alpb ch2cl2 --gfn 1' 
-    crest_nrun : int, default=1
+      included in -c, --uhf, -P and --input. For example: '--alpb ch2cl2 --gfn 1'
+   crest_nrun : int, default=1
       Specify as number of runs if multiple starting points from RDKit starting points is required.
 """
 #####################################################.

aqme/qcorr.py

@@ -1,4 +1,4 @@
-"""
+r"""
 Parameters
 ----------
 
@@ -35,7 +35,7 @@
    dup_threshold : float, default=0.0001
       Energy (in hartree) used as the energy difference in E, H and G to detect 
       duplicates
-    ro_threshold : float, default=0.1
+   ro_threshold : float, default=0.1
       Rotational constant value used as the threshold to detect duplicates 
    isom_type : str, default=None
       Check for isomerization from the initial input file to the resulting 

aqme/qcorr_utils.py

@@ -171,6 +171,7 @@ def full_check(w_dir_main=os.getcwd(), destination_fullcheck="", files="*.json",
     """
     Checks that multiple calculations were done following the same protocols, including
     program and version, grid size, level of theory, dispersion and solvation model.
+    
     Parameters
     ----------
     w_dir_main : str

aqme/qdescp.py

@@ -47,7 +47,7 @@
       Performs an initial xTB geometry optimization before calculating descriptors
 
 DBSTEP descriptors
-++++++++++++++
+++++++++++++++++++
 
    dbstep_calc : bool, default=False
       Whether to add a DBSTEP calculation of buried volume when generating atomic descriptors 

docs/README.rst

@@ -1,6 +1,6 @@
 .. aqme-banner-start
 
-.. |aqme_banner| image:: ./Logos/AQME_logo.jpg
+.. |aqme_banner| image:: ../Logos/AQME_logo.jpg
 
 |aqme_banner|
 
@@ -140,6 +140,7 @@ Extra requirements if `CMIN` is used with ANI models:
    pip install ase
 
 .. code-block:: shell 
+
    pip install torch torchvision torchani
 
 Extra requirements if `QDESCP` is used with DBSTEP: