From 08c52fda09f854bb11808b105182ab67eed1cbfa Mon Sep 17 00:00:00 2001
From: James Graham <J.A.Graham@soton.ac.uk>
Date: Fri, 16 Dec 2016 12:40:24 +0000
Subject: [PATCH] Tidied functional forms code
---
pycgtool/bondset.py | 25 ++++++++++++-------------
pycgtool/functionalforms.py | 31 ++++++++++++++++++++++++++-----
test/test_functionalforms.py | 1 -
3 files changed, 38 insertions(+), 19 deletions(-)
diff --git a/pycgtool/bondset.py b/pycgtool/bondset.py
index def598f..1768c8d 100644
--- a/pycgtool/bondset.py
+++ b/pycgtool/bondset.py
@@ -115,31 +115,29 @@ class BondSet:
except AttributeError:
self._default_fc = False
+ # Setup default functional forms
functional_forms = FunctionalForms()
- self._functional_forms = {}
+ if self._default_fc:
+ default_forms = ["MartiniDefaultLength", "MartiniDefaultAngle", "MartiniDefaultDihedral"]
+ else:
+ default_forms = ["Harmonic", "CosHarmonic", "Harmonic"]
+ self._functional_forms = [None, None]
+ self._functional_forms.extend(map(lambda x: functional_forms[x], default_forms))
+
try:
self._functional_forms[2] = functional_forms[options.length_form]
except AttributeError:
- if self._default_fc:
- self._functional_forms[2] = functional_forms.MartiniDefaultLength
- else:
- self._functional_forms[2] = functional_forms.Harmonic
+ pass
try:
self._functional_forms[3] = functional_forms[options.angle_form]
except AttributeError:
- if self._default_fc:
- self._functional_forms[3] = functional_forms.MartiniDefaultAngle
- else:
- self._functional_forms[3] = functional_forms.CosHarmonic
+ pass
try:
self._functional_forms[4] = functional_forms[options.dihedral_form]
except AttributeError:
- if self._default_fc:
- self._functional_forms[4] = functional_forms.MartiniDefaultDihedral
- else:
- self._functional_forms[4] = functional_forms.Harmonic
+ pass
with CFG(filename) as cfg:
for mol in cfg:
@@ -150,6 +148,7 @@ class BondSet:
for atomlist in mol:
try:
# TODO consider best way to override default func form
+ # On per bond, or per type basis
func_form = functional_forms[atomlist[-1]]
except AttributeError:
func_form = self._functional_forms[len(atomlist)]
diff --git a/pycgtool/functionalforms.py b/pycgtool/functionalforms.py
index a3f4e83..919e425 100644
--- a/pycgtool/functionalforms.py
+++ b/pycgtool/functionalforms.py
@@ -5,10 +5,20 @@ from pycgtool.util import SimpleEnum
class FunctionalForms(object):
+ """
+ Class holding list of all defined functional forms for Boltzmann Inversion.
+
+ Creating an instance causes the Enum of functional forms to be updated with
+ all new subclasses of FunctionalForm. These may then be accessed by name,
+ either as attributes or using square brackets.
+ """
FormsEnum = SimpleEnum.enum("FormsEnum")
@classmethod
- def refresh(cls):
+ def _refresh(cls):
+ """
+ Update the functional forms Enum to include all new subclasses of FunctionalForm.
+ """
enum_dict = cls.FormsEnum.as_dict()
for subclass in FunctionalForm.__subclasses__():
name = subclass.__name__
@@ -19,6 +29,7 @@ class FunctionalForms(object):
def __init__(self, **kwargs):
self._kwargs = kwargs
+ type(self)._refresh()
def __getattr__(self, item):
return type(self).FormsEnum[item].value
@@ -37,9 +48,23 @@ class FunctionalForms(object):
class FunctionalForm(object, metaclass=abc.ABCMeta):
+ """
+ Parent class of any functional form used in Boltzmann Inversion to convert variance to a force constant.
+
+ New functional forms must define a static __call__ method.
+ """
@staticmethod
@abc.abstractstaticmethod
def __call__(mean, var, temp):
+ """
+ Calculate force constant.
+ Abstract static method to be defined by all functional forms.
+
+ :param mean: Mean of internal coordinate distribution
+ :param var: Variance of internal coordinate distribution
+ :param temp: Temperature of simulation
+ :return: Calculated force constant
+ """
pass
@@ -73,7 +98,3 @@ class MartiniDefaultDihedral(FunctionalForm):
@staticmethod
def __call__(mean, var, temp):
return 50.
-
-FunctionalForms.refresh()
-
-
diff --git a/test/test_functionalforms.py b/test/test_functionalforms.py
index 05e2147..56056e5 100644
--- a/test/test_functionalforms.py
+++ b/test/test_functionalforms.py
@@ -16,7 +16,6 @@ class FunctionalFormTest(unittest.TestCase):
@staticmethod
def __call__(mean, var, temp):
return "TestResult"
- FunctionalForms.refresh()
funcs = FunctionalForms()
self.assertIn("TestFunc", funcs)
--
GitLab