From d4d32ad4b3bce355807b80134f949c0a31949cda Mon Sep 17 00:00:00 2001
From: James Graham <J.A.Graham@soton.ac.uk>
Date: Wed, 4 May 2016 14:25:22 +0100
Subject: [PATCH] Added documentation RST files to repo Added some more doc
strings
---
doc/source/index.rst | 2 +-
doc/source/modules.rst | 7 +++++++
doc/source/pycgtool.bondset.rst | 7 +++++++
doc/source/pycgtool.forcefield.rst | 7 +++++++
doc/source/pycgtool.frame.rst | 7 +++++++
doc/source/pycgtool.interface.rst | 7 +++++++
doc/source/pycgtool.mapping.rst | 7 +++++++
doc/source/pycgtool.parsers.cfg.rst | 7 +++++++
doc/source/pycgtool.parsers.rst | 17 ++++++++++++++++
doc/source/pycgtool.rst | 30 ++++++++++++++++++++++++++++
doc/source/pycgtool.util.rst | 7 +++++++
doc/source/pycgtool.warnings.rst | 7 +++++++
pycgtool.py | 2 +-
pycgtool/bondset.py | 31 +++++++++++++++++++++++++++++
pycgtool/interface.py | 16 +++++++++++++++
15 files changed, 159 insertions(+), 2 deletions(-)
create mode 100644 doc/source/modules.rst
create mode 100644 doc/source/pycgtool.bondset.rst
create mode 100644 doc/source/pycgtool.forcefield.rst
create mode 100644 doc/source/pycgtool.frame.rst
create mode 100644 doc/source/pycgtool.interface.rst
create mode 100644 doc/source/pycgtool.mapping.rst
create mode 100644 doc/source/pycgtool.parsers.cfg.rst
create mode 100644 doc/source/pycgtool.parsers.rst
create mode 100644 doc/source/pycgtool.rst
create mode 100644 doc/source/pycgtool.util.rst
create mode 100644 doc/source/pycgtool.warnings.rst
diff --git a/doc/source/index.rst b/doc/source/index.rst
index 0eb5352..f9d409e 100644
--- a/doc/source/index.rst
+++ b/doc/source/index.rst
@@ -13,7 +13,7 @@ Contents:
members
-Indices and tables
+Indexes
==================
* :ref:`genindex`
diff --git a/doc/source/modules.rst b/doc/source/modules.rst
new file mode 100644
index 0000000..cb57cae
--- /dev/null
+++ b/doc/source/modules.rst
@@ -0,0 +1,7 @@
+pycgtool
+========
+
+.. toctree::
+ :maxdepth: 4
+
+ pycgtool
diff --git a/doc/source/pycgtool.bondset.rst b/doc/source/pycgtool.bondset.rst
new file mode 100644
index 0000000..6d1777e
--- /dev/null
+++ b/doc/source/pycgtool.bondset.rst
@@ -0,0 +1,7 @@
+pycgtool.bondset module
+=======================
+
+.. automodule:: pycgtool.bondset
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/doc/source/pycgtool.forcefield.rst b/doc/source/pycgtool.forcefield.rst
new file mode 100644
index 0000000..a25ef72
--- /dev/null
+++ b/doc/source/pycgtool.forcefield.rst
@@ -0,0 +1,7 @@
+pycgtool.forcefield module
+==========================
+
+.. automodule:: pycgtool.forcefield
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/doc/source/pycgtool.frame.rst b/doc/source/pycgtool.frame.rst
new file mode 100644
index 0000000..f231e7f
--- /dev/null
+++ b/doc/source/pycgtool.frame.rst
@@ -0,0 +1,7 @@
+pycgtool.frame module
+=====================
+
+.. automodule:: pycgtool.frame
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/doc/source/pycgtool.interface.rst b/doc/source/pycgtool.interface.rst
new file mode 100644
index 0000000..a724d24
--- /dev/null
+++ b/doc/source/pycgtool.interface.rst
@@ -0,0 +1,7 @@
+pycgtool.interface module
+=========================
+
+.. automodule:: pycgtool.interface
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/doc/source/pycgtool.mapping.rst b/doc/source/pycgtool.mapping.rst
new file mode 100644
index 0000000..7beba67
--- /dev/null
+++ b/doc/source/pycgtool.mapping.rst
@@ -0,0 +1,7 @@
+pycgtool.mapping module
+=======================
+
+.. automodule:: pycgtool.mapping
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/doc/source/pycgtool.parsers.cfg.rst b/doc/source/pycgtool.parsers.cfg.rst
new file mode 100644
index 0000000..07faee1
--- /dev/null
+++ b/doc/source/pycgtool.parsers.cfg.rst
@@ -0,0 +1,7 @@
+pycgtool.parsers.cfg module
+===========================
+
+.. automodule:: pycgtool.parsers.cfg
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/doc/source/pycgtool.parsers.rst b/doc/source/pycgtool.parsers.rst
new file mode 100644
index 0000000..e1fea8b
--- /dev/null
+++ b/doc/source/pycgtool.parsers.rst
@@ -0,0 +1,17 @@
+pycgtool.parsers package
+========================
+
+Submodules
+----------
+
+.. toctree::
+
+ pycgtool.parsers.cfg
+
+Module contents
+---------------
+
+.. automodule:: pycgtool.parsers
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/doc/source/pycgtool.rst b/doc/source/pycgtool.rst
new file mode 100644
index 0000000..3375064
--- /dev/null
+++ b/doc/source/pycgtool.rst
@@ -0,0 +1,30 @@
+pycgtool package
+================
+
+Subpackages
+-----------
+
+.. toctree::
+
+ pycgtool.parsers
+
+Submodules
+----------
+
+.. toctree::
+
+ pycgtool.bondset
+ pycgtool.forcefield
+ pycgtool.frame
+ pycgtool.interface
+ pycgtool.mapping
+ pycgtool.util
+ pycgtool.warnings
+
+Module contents
+---------------
+
+.. automodule:: pycgtool
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/doc/source/pycgtool.util.rst b/doc/source/pycgtool.util.rst
new file mode 100644
index 0000000..973651b
--- /dev/null
+++ b/doc/source/pycgtool.util.rst
@@ -0,0 +1,7 @@
+pycgtool.util module
+====================
+
+.. automodule:: pycgtool.util
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/doc/source/pycgtool.warnings.rst b/doc/source/pycgtool.warnings.rst
new file mode 100644
index 0000000..cc5e32b
--- /dev/null
+++ b/doc/source/pycgtool.warnings.rst
@@ -0,0 +1,7 @@
+pycgtool.warnings module
+========================
+
+.. automodule:: pycgtool.warnings
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/pycgtool.py b/pycgtool.py
index c14f0f9..0e9695e 100755
--- a/pycgtool.py
+++ b/pycgtool.py
@@ -13,7 +13,7 @@ def main(args, config):
"""
Main function of the program PyCGTOOL.
- Performs the complete AA->CG mapping and outputs a GROMACS forcefield directory.
+ Performs the complete AA->CG mapping and outputs a files dependent on given input.
:param args: Arguments from argparse
:param config: Configuration dictionary
diff --git a/pycgtool/bondset.py b/pycgtool/bondset.py
index f6c3381..e678bd4 100644
--- a/pycgtool/bondset.py
+++ b/pycgtool/bondset.py
@@ -128,15 +128,35 @@ class BondSet:
self._create_angles(mol.name, options.generate_dihedrals)
def get_bond_lengths(self, mol, with_constr=False):
+ """
+ Return list of all bond lengths in molecule. May include constraints.
+
+ :param mol: Molecule name to return bonds for
+ :param with_constr: Include constraints?
+ :return: List of bonds
+ """
if with_constr:
return [bond for bond in self._molecules[mol] if len(bond.atoms) == 2]
else:
return [bond for bond in self._molecules[mol] if len(bond.atoms) == 2 and bond.fconst < self._fconst_constr_threshold]
def get_bond_length_constraints(self, mol):
+ """
+ Return list of all bond length constraints in molecule.
+
+ :param mol: Molecule name to return bonds for
+ :return: List of bonds
+ """
return [bond for bond in self._molecules[mol] if len(bond.atoms) == 2 and bond.fconst >= self._fconst_constr_threshold]
def get_bond_angles(self, mol, exclude_triangle=True):
+ """
+ Return list of all bond angles in molecule.
+
+ :param mol: Molecule name to return bonds for
+ :param exclude_triangle: Exclude angles that are part of a triangle?
+ :return: List of bonds
+ """
angles = [bond for bond in self._molecules[mol] if len(bond.atoms) == 3]
if exclude_triangle:
@@ -154,6 +174,12 @@ class BondSet:
return angles
def get_bond_dihedrals(self, mol):
+ """
+ Return list of all bond dihedrals in molecule.
+
+ :param mol: Molecule name to return bonds for
+ :return: List of bonds
+ """
return [bond for bond in self._molecules[mol] if len(bond.atoms) == 4]
def _create_angles(self, mol, gen_dihedrals=False):
@@ -326,6 +352,11 @@ class BondSet:
angle_default_fc=self._angle_default_fc)
def dump_values(self, target_number=100000):
+ """
+ Output measured bond values to files for length, angles and dihedrals.
+
+ :param target_number: Approx number of sample measurements to output. If None, all samples will be output
+ """
def transpose(bond_list):
"""
Transpose a list of bonds containing values and slice to provide target number of rows.
diff --git a/pycgtool/interface.py b/pycgtool/interface.py
index de10647..97ba5a7 100644
--- a/pycgtool/interface.py
+++ b/pycgtool/interface.py
@@ -1,3 +1,6 @@
+"""
+This module contains classes for interaction at the terminal.
+"""
import collections
import curses
import curses.textpad
@@ -7,8 +10,16 @@ import time
class Options:
"""
Class to hold program options not specified at the initial command line.
+
+ Values can be queried by indexing as a dictionary or by attribute. Iterable.
"""
def __init__(self, default, args=None):
+ """
+ Create Options instance from iterable of keys and default values.
+
+ :param default: Iterable of key, default value pairs (e.g. list of tuples)
+ :param args: Optional program arguments from Argparse, will be displayed in interactive mode
+ """
self._dict = collections.OrderedDict()
for key, val in default:
try:
@@ -221,6 +232,11 @@ class Progress:
return self
def __next__(self):
+ """
+ Allow iteration over Progress while testing prewhile and postwhile conditions.
+
+ :return: Iteration number
+ """
if self._postwhile is not None and self._its > 0 and not self._postwhile():
self._stop()
--
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