more sphinx things

Author: ajs99778

comp_output.py

@@ -36,15 +36,16 @@ def obj_to_dict(obj, skip_attrs=None):
 class CompOutput:
     """
     Attributes:
-        geometry    the last Geometry
-        opts        list of Geometry for each optimization steps
-        frequency   Frequency object
-        archive     a string containing the archive entry
-        energy, enthalpy, free_energy, grimme_g,
-        mass, temperature, rotational_temperature,
-        multiplicity, charge, rotational_symmetry_number
-        error, error_msg, finished,
-        gradient, E_ZPVE, ZPVE
+        
+    * geometry    the last Geometry
+    * opts        list of Geometry for each optimization steps
+    * frequency   Frequency object
+    * archive     a string containing the archive entry
+    * energy, enthalpy, free_energy, grimme_g,
+    * mass, temperature, rotational_temperature,
+    * multiplicity, charge, rotational_symmetry_number
+    * error, error_msg, finished,
+    * gradient, E_ZPVE, ZPVE
     """
 
     ELECTRONIC_ENERGY = "NRG"
@@ -159,21 +160,27 @@ def boltzmann_weights(
         v0=100,
     ):
         """
-        returns boltzmann weights
-        thermo_cos - list of CompOutput instances for thermochem corrections
-        nrg_cos - list of CompOutput to take the electronic energy from
-            order should correspond to thermo_cos
-            if not given, the energies from thermo_cos are used
-        weighting - type of energy to use for weighting
+        :param list(CompOutput) thermo_cos: list of CompOutput
+            instances for thermochem corrections
+        :param list(CompOutput) nrg_cos: list of CompOutput to
+            take the electronic energy from order should correspond
+            to thermo_cos if not given, the energies from thermo_cos
+            are used
+        :param str weighting:type of energy to use for weighting
             can be:
-                "NRG"
-                "ZPE"
-                "ENTHALPY"
-                "QHARM"
-                "QRRHO"
-                "RRHO"
-        temperature - temperature in K
-        v0 - parameter for quasi free energy corrections
+            
+                * "NRG"
+                * "ZPE"
+                * "ENTHALPY"
+                * "QHARM"
+                * "QRRHO"
+                * "RRHO"
+        
+        :param float temperature: temperature in K
+        :param float v0: parameter for quasi free energy corrections
+
+        :returns: boltzmann weights
+        :rtype: np.ndarray
         """
         if not nrg_cos:
             nrg_cos = thermo_cos
@@ -254,18 +261,18 @@ def therm_corr(self, temperature=None, v0=100, method="RRHO", pressure=1):
         for the specified cutoff frequency and temperature
         in that order (Hartrees for corrections, Eh/K for entropy)
 
-        temperature: float, temperature in K- None will use self.temperature
-        pressure: float, pressure in atm
-        v0: float, cutoff/damping parameter for quasi G corrections
-        method: str - type of quasi treatment:
-                RRHO  - no quasi treatment
-                QRRHO - Grimme's quasi-RRHO
-                see Grimme, S. (2012), Supramolecular Binding Thermodynamics by
-                Dispersion‐Corrected Density Functional Theory. Chem. Eur. J.,
-                18: 9955-9964. (DOI: 10.1002/chem.201200497) for details
-                QHARM - Truhlar's quasi-harmonic
-                see J. Phys. Chem. B 2011, 115, 49, 14556–14562
-                (DOI: 10.1021/jp205508z) for details
+        :param float temperature: temperature in K- None will use self.temperature
+        :param float pressure: pressure in atm
+        :param float v0: float, cutoff/damping parameter for quasi G corrections
+        :param str method: type of free energy\:
+            * RRHO  - no quasi treatment
+            * QRRHO - Grimme's quasi-RRHO
+              see Grimme, S. (2012), Supramolecular Binding Thermodynamics by
+              Dispersion‐Corrected Density Functional Theory. Chem. Eur. J.,
+              18: 9955-9964. (DOI: 10.1002/chem.201200497) for details
+            * QHARM - Truhlar's quasi-harmonic
+              see J. Phys. Chem. B 2011, 115, 49, 14556–14562
+              (DOI: 10.1021/jp205508z) for details
         """
         if self.frequency is None:
             msg = "Vibrational frequencies not found, "
@@ -398,10 +405,11 @@ def therm_corr(self, temperature=None, v0=100, method="RRHO", pressure=1):
     def calc_G_corr(self, temperature=None, v0=0, method="RRHO", **kwargs):
         """
         returns quasi rrho free energy correction (Eh)
-        temperature: float, temperature; default is self.temperature
-        v0: float, parameter for quasi-rrho or quasi-harmonic entropy
-        method: str (RRHO, QRRHO, QHARM) method for treating entropy
-                see CompOutput.therm_corr for references
+        
+        :param float temperature: temperature; default is self.temperature
+        :param float v0: parameter for quasi-rrho or quasi-harmonic entropy
+        :param str method: (RRHO, QRRHO, QHARM) method for treating entropy
+            see CompOutput.therm_corr for references
         """
         Ecorr, Hcorr, Stot = self.therm_corr(temperature, v0, method, **kwargs)
         T = temperature if temperature is not None else self.temperature
@@ -412,6 +420,7 @@ def calc_G_corr(self, temperature=None, v0=0, method="RRHO", **kwargs):
     def calc_Grimme_G(self, temperature=None, v0=100, **kwargs):
         """
         returns quasi rrho free energy (Eh)
+        
         see Grimme, S. (2012), Supramolecular Binding Thermodynamics by
         Dispersion‐Corrected Density Functional Theory. Chem. Eur. J.,
         18: 9955-9964. (DOI: 10.1002/chem.201200497) for details
@@ -538,8 +547,10 @@ def follow(self, reverse=False, step=0.1):
     def compute_rot_temps(self):
         """
         sets self's 'rotational_temperature' attribute by using self.geometry
+        
         not recommended b/c atoms should be specific isotopes, but this uses
         average atomic weights
+        
         exists because older versions of ORCA don't print rotational temperatures
         """
         COM = self.geometry.COM(mass_weight=True)

component.py

@@ -26,14 +26,17 @@
 
 class Component(Geometry):
     """
+    class for parts of a Geometry (e.g. ligands)
     Attributes:
-    :name:          str
-    :comment:       str
-    :atoms:         list(Atom)
-    :other:         dict()
-    :substituents:  list(Substituent) substituents detected
-    :backbone:      list(Atom) the backbone atoms
-    :key_atoms:     list(Atom) the atoms used for mapping
+    
+    * name           str
+    * comment        str
+    * atoms          list(Atom)
+    * other          dict()
+    * substituents   list(Substituent) substituents detected
+    * backbone       list(Atom) the backbone atoms
+    * key_atoms      list(Atom) the atoms used for mapping
+    
     """
 
     AARON_LIBS = os.path.join(AARONLIB, "Ligands")
@@ -132,6 +135,7 @@ def list(
         denticity=None,
         include_ext=False,
     ):
+        """returns a list of ligand names in the library"""
         names = []
         for lib in [cls.AARON_LIBS, cls.BUILTIN]:
             if not os.path.exists(lib):
@@ -219,11 +223,13 @@ def c2_symmetric(self, to_center=None, tolerance=0.1):
     def sterimol(self, to_center=None, bisect_L=False, **kwargs):
         """
         calculate ligand sterimol parameters for the ligand
-        to_center - atom the ligand is coordinated to
-        bisect_L - L axis will bisect (or analogous for higher denticity
-                   ligands) the L-M-L angle
-                   Default - center to centroid of key atoms
-        **kwargs - arguments passed to Geometry.sterimol
+        
+        :param Atom to_center: atom the ligand is coordinated to
+        :param bool bisect_L: L axis will bisect (or analogous for higher denticity
+            ligands) the L-M-L angle
+            
+            Default - center to centroid of key atoms
+        :param kwargs: - arguments passed to Geometry.sterimol
         """
         if to_center is not None:
             center = self.find(to_center)
@@ -318,7 +324,7 @@ def detect_backbone(self, to_center=None):
         Detects backbone and substituents attached to backbone
         Will tag atoms as 'backbone' or by substituent name
 
-        :to_center:   the atoms connected to the metal/active center
+        :param list(Atom) to_center:   the atoms connected to the metal/active center
         """
         # we must remove any tags already made
         for a in self.atoms:
@@ -428,8 +434,9 @@ def capped_backbone(self, to_center=None, as_copy=True):
     def minimize_sub_torsion(self, geom=None, **kwargs):
         """
         rotates substituents to minimize LJ potential
-        geom: calculate LJ potential between self and another geometry-like
-              object, instead of just within self
+        
+        :param None|Geometry geom: calculate LJ potential between self and another geometry-like
+            object, instead of just within self
         """
         if geom is None:
             geom = self
@@ -458,24 +465,31 @@ def cone_angle(
     ):
         """
         returns cone angle in degrees
-        center - Atom() that this component is coordinating
-                 used as the apex of the cone
-        method (str) can be:
-            'Tolman' - Tolman cone angle for unsymmetric ligands
-                       See J. Am. Chem. Soc. 1974, 96, 1, 53–60 (DOI: 10.1021/ja00808a009)
-                       NOTE: this does not make assumptions about the geometry
-                       NOTE: only works with monodentate and bidentate ligands
-            'exact' - cone angle from Allen et. al.
-                      See Bilbrey, J.A., Kazez, A.H., Locklin, J. and Allen, W.D.
-                      (2013), Exact ligand cone angles. J. Comput. Chem., 34:
-                      1189-1197. (DOI: 10.1002/jcc.23217)
-        return_cones - return cone apex, center of base, and base radius list
-                       the sides of the cones will be 5 angstroms long
-                       for Tolman cone angles, multiple cones will be returned, one for
-                       each substituent coming off the coordinating atom
-        radii: 'bondi' - Bondi vdW radii
-               'umn'   - vdW radii from Mantina, Chamberlin, Valero, Cramer, and Truhlar
-               dict() with elements as keys and radii as values
+        
+        :param Atom center: that this component is coordinating
+            used as the apex of the cone
+        :param str method: can be:
+            * 'Tolman' - Tolman cone angle for unsymmetric ligands
+              
+              See J. Am. Chem. Soc. 1974, 96, 1, 53–60 (DOI: 10.1021/ja00808a009)
+               
+              :NOTE: this does not make assumptions about the geometry
+               
+              :NOTE: only works with monodentate and bidentate ligands
+            * 'exact' - cone angle from Allen et. al.
+              
+              See Bilbrey, J.A., Kazez, A.H., Locklin, J. and Allen, W.D.
+              (2013), Exact ligand cone angles. J. Comput. Chem., 34:
+              1189-1197. (DOI: 10.1002/jcc.23217)
+        :param bool return_cones: return cone apex, center of base, and base radius list
+            the sides of the cones will be 5 angstroms long
+            
+            for Tolman cone angles, multiple cones will be returned, one for
+            each substituent coming off the coordinating atom
+        :param str|dict radii:
+            * 'bondi' - Bondi vdW radii
+            * 'umn'   - vdW radii from Mantina, Chamberlin, Valero, Cramer, and Truhlar
+            * dict() with elements as keys and radii as values
         """
         if method.lower() == "tolman":
             CITATION = "doi:10.1021/ja00808a009"
@@ -907,11 +921,12 @@ def solid_angle(
     ):
         """
         calculate the solid angle of a ligand
-        center - atoms or point to denote the center of the sphere
-        radii - "umn", "bondi", or a dictionary with elements as
+        
+        :param Atom center: atoms or point to denote the center of the sphere
+        :param str|dict radii: "umn", "bondi", or a dictionary with elements as
             the keys and radii as the values
-        grid - number of points in lebedev grid
-        return_solid_cone - return solid ligand cone angle (degrees)
+        :param int grid: number of points in lebedev grid
+        :param bool return_solid_cone: return solid ligand cone angle (degrees)
             instead of solid angle (steradians)
         """
         # we calculate the solid angle by projecting each atom's

config.py

@@ -85,11 +85,14 @@
 class Config(configparser.ConfigParser):
     """
     Reads configuration information from INI files found at:
+        
         $QCHASM/AaronTools/config.ini
         $AARONLIB/config.ini
         ./config.ini or /path/to/file supplied during initialization
+    
     Access to configuration information available using dictionary notation.
         eg: self[`section_name`][`option_name`] returns `option_value`
+    
     See help(configparser.ConfigParser) for more information
     """
 
@@ -216,8 +219,10 @@ def __init__(
     def get(self, section, option, *, junk="_ ", max_junk=1, **kwargs):
         """
         see ConfigParser.get for details
+        
         junk are characters that are not important in the option name
         max_junk - number of allowed junk characters
+        
         e.g. junk="_" with max_junk=1 when looking for
         'empirical dispersion' will match 'empirical_dispersion'
         """
@@ -397,8 +402,11 @@ def _parse_changes(self):
     def parse_functions(self):
         """
         Evaluates functions supplied in configuration file
+        
         Functions indicated by "%{...}"
+        
         Pulls in values of options indicated by $option_name
+        
         Eg:
             ppn = 4
             memory = %{ $ppn * 2 }GB --> memory = 8GB
@@ -493,20 +501,25 @@ def _read_config(self, infile, quiet, skip_user_default):
     def get_other_kwargs(self, section="Theory"):
         """
         Returns dict() that can be unpacked and passed to Geometry.write along with a theory
+        
         Example:
-        [Theory]
-        route = pop NBORead
-                opt MaxCycle=1000, NoEigenTest
-        end_of_file = $nbo RESONANCE NBOSUM E2PERT=0.0 NLMO BNDIDX $end
+            
+            [Theory]
+            route = pop NBORead
+                    opt MaxCycle=1000, NoEigenTest
+            end_of_file = $nbo RESONANCE NBOSUM E2PERT=0.0 NLMO BNDIDX $end
 
         this adds opt(MaxCycle=1000,NoEigenTest) pop=NBORead to the route with any other
         pop or opt options being added by the job type
 
         'two-layer' options can also be specified as a python dictionary
+        
         the following is equivalent to the above example:
-        [Theory]
-        route = {"pop":["NBORead"], "opt":["MaxCycle=1000", NoEigenTest"]}
-        end_of_file = $nbo RESONANCE NBOSUM E2PERT=0.0 NLMO BNDIDX $end
+            
+            [Theory]
+            route = {"pop":["NBORead"], "opt":["MaxCycle=1000", NoEigenTest"]}
+            end_of_file = $nbo RESONANCE NBOSUM E2PERT=0.0 NLMO BNDIDX $end
+        
         """
         # these need to be dicts
         two_layer = [
@@ -1060,6 +1073,7 @@ def _parse_includes(self, section=None):
         """
         Moves option values from subsections into parent section
         Eg:
+        
             [HPC]
             include = Wheeler
             ppn = 12
@@ -1107,11 +1121,13 @@ def _parse_includes(self, section=None):
     def as_dict(self, spec=None, skip=None):
         """
         Forms a metadata spec dictionary from configuration info
-        :spec: (dict) if given, append key/vals to that dict
-        :skip: (list) skip storing stuff according to (section, option) or attrs
-               section, option, and attrs are strings that can be regex (full match only)
-               eg: skip=[("Job", ".*"), "conformer"] will skip everything in the Job
-               section and the Config.conformer attribute
+        
+        :param dict spec: if given, append key/vals to that dict
+        :param list skip: skip storing stuff according to (section, option) or attrs
+            section, option, and attrs are strings that can be regex (full match only)
+            
+            eg: skip=[("Job", ".*"), "conformer"] will skip everything in the Job
+            section and the Config.conformer attribute
         """
         if spec is None:
             spec = {}