diff --git a/aqme/csearch/base.py b/aqme/csearch/base.py index 0fab2b22..ac4b88a4 100644 --- a/aqme/csearch/base.py +++ b/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. """ #####################################################. diff --git a/aqme/qcorr.py b/aqme/qcorr.py index 6c2371a8..e9eea2d0 100644 --- a/aqme/qcorr.py +++ b/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 diff --git a/aqme/qcorr_utils.py b/aqme/qcorr_utils.py index 09c3030e..e6f9d9b3 100644 --- a/aqme/qcorr_utils.py +++ b/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 diff --git a/aqme/qdescp.py b/aqme/qdescp.py index 6d42194a..a126995b 100644 --- a/aqme/qdescp.py +++ b/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 diff --git a/docs/README.rst b/docs/README.rst index 410b767e..1bec4380 100644 --- a/docs/README.rst +++ b/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: