From 5b04798ecf6faa8ba91df6ca607884cbbdc3e816 Mon Sep 17 00:00:00 2001
From: James Graham <J.A.Graham@soton.ac.uk>
Date: Fri, 16 Dec 2016 15:33:09 +0000
Subject: [PATCH] CFG parser use OrderedDict Small amounts of tidying elsewhere
---
data/atom_masses.json | 7 ++++---
doc/source/tutorial.rst | 2 +-
pycgtool/frame.py | 2 +-
pycgtool/mapping.py | 14 +++++++++-----
pycgtool/parsers/cfg.py | 25 ++++++++-----------------
5 files changed, 23 insertions(+), 27 deletions(-)
diff --git a/data/atom_masses.json b/data/atom_masses.json
index e344c37..cea07cf 100644
--- a/data/atom_masses.json
+++ b/data/atom_masses.json
@@ -1,7 +1,8 @@
{
+ "H": 1.0080,
"C": 12.0110,
- "O": 15.9994,
"N": 14.0067,
- "H": 1.0080,
- "P": 30.9738
+ "O": 15.9994,
+ "P": 30.9738,
+ "S": 32.0600
}
diff --git a/doc/source/tutorial.rst b/doc/source/tutorial.rst
index c7f83e1..af620ff 100644
--- a/doc/source/tutorial.rst
+++ b/doc/source/tutorial.rst
@@ -2,7 +2,7 @@ PyCGTOOL Tutorial
=================
This tutorial follows the complete process of parametrising a new molecule within the MARTINI forcefield, covering aspects of mapping design, model generation and model validation.
-PyCGTOOL is used at multiple stages, showing its use in several different situations
+PyCGTOOL is used at multiple stages, showing its use in several different situations.
All files required to follow this tutorial are present in the ``doc/tutorial_files`` directory.
The molecule chosen as a target for this parametrisation is the :math:`\beta_1` antagonist atenolol.
diff --git a/pycgtool/frame.py b/pycgtool/frame.py
index 3a6191b..b7a959b 100644
--- a/pycgtool/frame.py
+++ b/pycgtool/frame.py
@@ -358,7 +358,7 @@ class Frame:
atoms = []
for res in self.residues:
for atom in res:
- atoms.append(repr(atom.coords))
+ atoms.append(repr(atom))
rep += "\n".join(atoms)
return rep
diff --git a/pycgtool/mapping.py b/pycgtool/mapping.py
index 0a6794e..64abd39 100644
--- a/pycgtool/mapping.py
+++ b/pycgtool/mapping.py
@@ -84,7 +84,6 @@ class Mapping:
:return: Instance of Mapping
"""
self._mappings = {}
-
self._map_center = options.map_center
self._masses_are_set = False
@@ -127,6 +126,8 @@ class Mapping:
else:
bead.charge += atoms[atom][0]
+ self._masses_are_set = True
+
def __len__(self):
return len(self._mappings)
@@ -153,7 +154,6 @@ class Mapping:
if bead.mass == 0:
mass_array = np.zeros((len(bead.atoms), 1), dtype=np.float32)
for i, atom in enumerate(bead.atoms):
- mass = 0
try:
mass = mass_dict[atom[:2]]
except KeyError:
@@ -185,6 +185,7 @@ class Mapping:
cgframe.name = name
missing_mappings = set()
+ cg_bead_num = 1
for aares in aa_residues:
try:
@@ -196,12 +197,15 @@ class Mapping:
continue
cgres = Residue(name=aares.name, num=aares.num)
- cgres.atoms = [Atom(name=bead.name, type=bead.type, charge=bead.charge, mass=bead.mass) for bead in molmap]
+ cgres.atoms = [Atom(name=bmap.name, 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
bead.charge = bmap.charge
bead.mass = bmap.mass
+ bead.num = cg_bead_num
+
+ cg_bead_num += 1
cgframe.add_residue(cgres)
cgframe.natoms += len(cgres)
@@ -229,7 +233,7 @@ class Mapping:
cgframe.box = frame.box
select_predicate = lambda res: res.name in self._mappings and not (exclude is not None and res.name in exclude)
- aa_residues = (aares for aares in frame if select_predicate(aares))
+ aa_residues = filter(select_predicate, frame)
for aares, cgres in zip(aa_residues, cgframe):
molmap = self._mappings[aares.name]
@@ -249,7 +253,7 @@ class Mapping:
return cgframe
-@numba.jit(nopython=True)
+@numba.jit
def calc_coords_weight(ref_coords, coords, box, weights):
"""
Calculate the coordinates of a single CG bead from weighted component atom coordinates.
diff --git a/pycgtool/parsers/cfg.py b/pycgtool/parsers/cfg.py
index 9e4d452..87695b3 100644
--- a/pycgtool/parsers/cfg.py
+++ b/pycgtool/parsers/cfg.py
@@ -5,6 +5,8 @@ Format is based upon GROMACS .itp files but does not support nesting of sections
"""
import os
+from collections import OrderedDict
+
class Section:
"""
@@ -48,7 +50,7 @@ class CFG:
Contains a dictionary of Sections.
"""
- __slots__ = ["filename", "_sections", "_section_names", "_iter_section"]
+ __slots__ = ["filename", "_sections"]
def __init__(self, filename=None, allow_duplicate=False):
"""
@@ -59,13 +61,12 @@ class CFG:
:return: Instance of CFG
"""
self.filename = filename
- self._sections = {}
- self._section_names = []
+ self._sections = OrderedDict()
with open(self.filename) as f:
curr_section = None
for line in f:
- line = line.strip(" \t\n")
+ line = line.strip()
if not line or line.startswith(";"):
continue
@@ -73,14 +74,12 @@ class CFG:
cfg2 = CFG(os.path.join(os.path.dirname(self.filename),
line.split()[1]))
self._sections.update(cfg2._sections)
- self._section_names += cfg2._section_names
continue
elif line.startswith("["):
curr_section = line.strip("[ ]")
if curr_section in self._sections and not allow_duplicate:
raise DuplicateSectionError(curr_section, self.filename)
- self._section_names.append(curr_section)
self._sections[curr_section] = Section(name=curr_section)
continue
@@ -94,21 +93,13 @@ class CFG:
pass
def __len__(self):
- return len(self._section_names)
+ return len(self._sections)
def __iter__(self):
- self._iter_section = -1
- return self
-
- def __next__(self):
- self._iter_section += 1
- if self._iter_section >= len(self._section_names):
- raise StopIteration
- sec = self._section_names[self._iter_section]
- return self._sections[sec]
+ return iter(self._sections.values())
def __contains__(self, item):
- return item in self._section_names
+ return item in self._sections
def __getitem__(self, item):
return self._sections[item]
--
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