From c638290de2a113481d97537610035905a1e7e07b Mon Sep 17 00:00:00 2001
From: James Graham <J.A.Graham@soton.ac.uk>
Date: Tue, 11 Apr 2017 15:45:20 +0100
Subject: [PATCH] Make certain parameters to __init__ functions required where
this makes sense
---
pycgtool/bondset.py | 8 ++++----
pycgtool/frame.py | 12 +++++++++++-
pycgtool/mapping.py | 26 +++++++++++++-------------
test/test_frame.py | 6 +++---
4 files changed, 31 insertions(+), 21 deletions(-)
diff --git a/pycgtool/bondset.py b/pycgtool/bondset.py
index 972e053..0ce9e97 100644
--- a/pycgtool/bondset.py
+++ b/pycgtool/bondset.py
@@ -33,13 +33,13 @@ class Bond:
"""
__slots__ = ["atoms", "atom_numbers", "values", "eqm", "fconst", "_func_form"]
- def __init__(self, atoms=None, atom_numbers=None, func_form=None):
+ def __init__(self, atoms, atom_numbers=None, func_form=None):
"""
Create a single bond definition.
- :param atoms: List of atom names defining the bond
- :param atom_numbers: List of atom numbers defining the bond
- :return: Instance of Bond
+ :param List[str] atoms: List of atom names defining the bond
+ :param List[int] atom_numbers: List of atom numbers defining the bond
+ :param func_form: Functional form to use for Boltzmann Inversion
"""
self.atoms = atoms
self.atom_numbers = atom_numbers
diff --git a/pycgtool/frame.py b/pycgtool/frame.py
index b61d6c8..d8877a9 100644
--- a/pycgtool/frame.py
+++ b/pycgtool/frame.py
@@ -37,7 +37,17 @@ class Atom:
"""
__slots__ = ["name", "num", "type", "mass", "charge", "coords"]
- def __init__(self, name=None, num=None, type=None, mass=None, charge=None, coords=None):
+ def __init__(self, name, num, type=None, mass=None, charge=None, coords=None):
+ """
+ Create an atom.
+
+ :param str name: The name of the atom
+ :param int num: The atom number
+ :param str type: The atom type
+ :param float mass: The mass of the atom
+ :param float charge: The charge of the atom
+ :param coords: The coordinates of the atom
+ """
self.name = name
self.num = num
self.type = type
diff --git a/pycgtool/mapping.py b/pycgtool/mapping.py
index e566c45..437103e 100644
--- a/pycgtool/mapping.py
+++ b/pycgtool/mapping.py
@@ -29,18 +29,18 @@ class BeadMap(Atom):
"""
__slots__ = ["name", "type", "atoms", "charge", "mass", "weights", "weights_dict"]
- def __init__(self, name=None, type=None, atoms=None, charge=0, mass=0):
+ def __init__(self, name, num, type=None, atoms=None, charge=0, mass=0):
"""
- Create a single bead mapping
-
- :param name: The name of the bead
- :param type: The bead type
- :param atoms: The atom names from which the bead is made up
- :param charge: The net charge on the bead
- :param mass: The total bead mass
- :return: Instance of BeadMap
+ Create a single bead mapping.
+
+ :param str name: The name of the bead
+ :param int num: The number of the bead
+ :param str type: The bead type
+ :param List[str] atoms: The atom names from which the bead is made up
+ :param float charge: The net charge on the bead
+ :param float mass: The total bead mass
"""
- Atom.__init__(self, name=name, type=type, charge=charge, mass=mass)
+ Atom.__init__(self, name, num, type=type, charge=charge, mass=mass)
self.atoms = atoms
# NB: Mass weights are added in Mapping.__init__ if an itp file is provided
self.weights_dict = {"geom": np.array([[1. / len(atoms)] for _ in atoms], dtype=np.float32),
@@ -92,7 +92,7 @@ class Mapping:
self._mappings[mol_name] = []
self._manual_charges[mol_name] = False
molmap = self._mappings[mol_name]
- for name, typ, first, *atoms in mol_section:
+ for i, (name, typ, first, *atoms) in enumerate(mol_section):
charge = 0
try:
# Allow optional charge in mapping file
@@ -101,7 +101,7 @@ class Mapping:
except ValueError:
atoms.insert(0, first)
assert atoms, "Bead {0} specification contains no atoms".format(name)
- newbead = BeadMap(name=name, type=typ, atoms=atoms, charge=charge)
+ newbead = BeadMap(name, i, type=typ, atoms=atoms, charge=charge)
molmap.append(newbead)
# TODO this only works with one moleculetype in one itp - extend this
@@ -202,7 +202,7 @@ class Mapping:
continue
cgres = Residue(name=aares.name, num=aares.num)
- cgres.atoms = [Atom(name=bmap.name, type=bmap.type, charge=bmap.charge, mass=bmap.mass, coords=np.zeros(3)) for bmap in molmap]
+ cgres.atoms = [Atom(bmap.name, bmap.num, type=bmap.type, charge=bmap.charge, mass=bmap.mass, coords=np.zeros(3)) for bmap in molmap]
for i, (bead, bmap) in enumerate(zip(cgres, molmap)):
cgres.name_to_num[bead.name] = i
diff --git a/test/test_frame.py b/test/test_frame.py
index 4e95882..cd6a01f 100644
--- a/test/test_frame.py
+++ b/test/test_frame.py
@@ -22,13 +22,13 @@ class AtomTest(unittest.TestCase):
self.assertEqual("Type", atom.type)
def test_atom_add_missing_data(self):
- atom1 = Atom(name="Name", num=0, type="Type")
- atom2 = Atom(mass=1)
+ atom1 = Atom("Name1", 0, type="Type")
+ atom2 = Atom("Name2", 0, mass=1)
with self.assertRaises(AssertionError):
atom1.add_missing_data(atom2)
- atom2 = Atom(name="Name", num=0, mass=1)
+ atom2 = Atom("Name1", 0, mass=1)
atom1.add_missing_data(atom2)
self.assertEqual(1, atom1.mass)
--
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