diff --git a/.pylintrc b/.pylintrc
new file mode 100644
index 00000000..1b194584
--- /dev/null
+++ b/.pylintrc
@@ -0,0 +1,533 @@
+[MASTER]
+
+# A comma-separated list of package or module names from where C extensions may
+# be loaded. Extensions are loading into the active Python interpreter and may
+# run arbitrary code
+extension-pkg-whitelist=
+
+# Add files or directories to the blacklist. They should be base names, not
+# paths.
+ignore=CVS,redistributed
+
+# Add files or directories matching the regex patterns to the blacklist. The
+# regex matches against base names, not paths.
+ignore-patterns=
+
+# Python code to execute, usually for sys.path manipulation such as
+# pygtk.require().
+#init-hook=
+
+# Use multiple processes to speed up Pylint.
+jobs=0
+
+# List of plugins (as comma separated values of python modules names) to load,
+# usually to register additional checkers.
+load-plugins=
+
+# Pickle collected data for later comparisons.
+persistent=yes
+
+# Specify a configuration file.
+#rcfile=
+
+# When enabled, pylint would attempt to guess common misconfiguration and emit
+# user-friendly hints instead of false-positive error messages
+suggestion-mode=yes
+
+# Allow loading of arbitrary C extensions. Extensions are imported into the
+# active Python interpreter and may run arbitrary code.
+unsafe-load-any-extension=no
+
+
+[MESSAGES CONTROL]
+
+# Only show warnings with the listed confidence levels. Leave empty to show
+# all. Valid levels: HIGH, INFERENCE, INFERENCE_FAILURE, UNDEFINED
+confidence=
+
+# Disable the message, report, category or checker with the given id(s). You
+# can either give multiple identifiers separated by comma (,) or put this
+# option multiple times (only on the command line, not in the configuration
+# file where it should appear only once).You can also use "--disable=all" to
+# disable everything first and then reenable specific checks. For example, if
+# you want to run only the similarities checker, you can use "--disable=all
+# --enable=similarities". If you want to run only the classes checker, but have
+# no Warning level messages displayed, use"--disable=all --enable=classes
+# --disable=W"
+disable=print-statement,
+        parameter-unpacking,
+        unpacking-in-except,
+        old-raise-syntax,
+        backtick,
+        long-suffix,
+        old-ne-operator,
+        old-octal-literal,
+        import-star-module-level,
+        non-ascii-bytes-literal,
+        raw-checker-failed,
+        bad-inline-option,
+        locally-disabled,
+        locally-enabled,
+        file-ignored,
+        suppressed-message,
+        useless-suppression,
+        deprecated-pragma,
+        apply-builtin,
+        basestring-builtin,
+        buffer-builtin,
+        cmp-builtin,
+        coerce-builtin,
+        execfile-builtin,
+        file-builtin,
+        long-builtin,
+        raw_input-builtin,
+        reduce-builtin,
+        standarderror-builtin,
+        unicode-builtin,
+        xrange-builtin,
+        coerce-method,
+        delslice-method,
+        getslice-method,
+        setslice-method,
+        no-absolute-import,
+        old-division,
+        dict-iter-method,
+        dict-view-method,
+        next-method-called,
+        metaclass-assignment,
+        indexing-exception,
+        raising-string,
+        reload-builtin,
+        oct-method,
+        hex-method,
+        nonzero-method,
+        cmp-method,
+        input-builtin,
+        round-builtin,
+        intern-builtin,
+        unichr-builtin,
+        map-builtin-not-iterating,
+        zip-builtin-not-iterating,
+        range-builtin-not-iterating,
+        filter-builtin-not-iterating,
+        using-cmp-argument,
+        eq-without-hash,
+        div-method,
+        idiv-method,
+        rdiv-method,
+        exception-message-attribute,
+        invalid-str-codec,
+        sys-max-int,
+        bad-python3-import,
+        deprecated-string-function,
+        deprecated-str-translate-call,
+        deprecated-itertools-function,
+        deprecated-types-field,
+        next-method-defined,
+        dict-items-not-iterating,
+        dict-keys-not-iterating,
+        dict-values-not-iterating
+
+# Enable the message, report, category or checker with the given id(s). You can
+# either give multiple identifier separated by comma (,) or put this option
+# multiple time (only on the command line, not in the configuration file where
+# it should appear only once). See also the "--disable" option for examples.
+enable=c-extension-no-member
+
+
+[REPORTS]
+
+# Python expression which should return a note less than 10 (10 is the highest
+# note). You have access to the variables errors warning, statement which
+# respectively contain the number of errors / warnings messages and the total
+# number of statements analyzed. This is used by the global evaluation report
+# (RP0004).
+evaluation=10.0 - ((float(5 * error + warning + refactor + convention) / statement) * 10)
+
+# Template used to display messages. This is a python new-style format string
+# used to format the message information. See doc for all details
+#msg-template=
+
+# Set the output format. Available formats are text, parseable, colorized, json
+# and msvs (visual studio).You can also give a reporter class, eg
+# mypackage.mymodule.MyReporterClass.
+output-format=text
+
+# Tells whether to display a full report or only the messages
+reports=no
+
+# Activate the evaluation score.
+score=yes
+
+
+[REFACTORING]
+
+# Maximum number of nested blocks for function / method body
+max-nested-blocks=5
+
+# Complete name of functions that never returns. When checking for
+# inconsistent-return-statements if a never returning function is called then
+# it will be considered as an explicit return statement and no message will be
+# printed.
+never-returning-functions=optparse.Values,sys.exit
+
+
+[LOGGING]
+
+# Logging modules to check that the string format arguments are in logging
+# function parameter format
+logging-modules=logging
+
+
+[SIMILARITIES]
+
+# Ignore comments when computing similarities.
+ignore-comments=yes
+
+# Ignore docstrings when computing similarities.
+ignore-docstrings=yes
+
+# Ignore imports when computing similarities.
+ignore-imports=no
+
+# Minimum lines number of a similarity.
+min-similarity-lines=4
+
+
+[VARIABLES]
+
+# List of additional names supposed to be defined in builtins. Remember that
+# you should avoid to define new builtins when possible.
+additional-builtins=
+
+# Tells whether unused global variables should be treated as a violation.
+allow-global-unused-variables=yes
+
+# List of strings which can identify a callback function by name. A callback
+# name must start or end with one of those strings.
+callbacks=cb_,
+          _cb
+
+# A regular expression matching the name of dummy variables (i.e. expectedly
+# not used).
+dummy-variables-rgx=_+$|(_[a-zA-Z0-9_]*[a-zA-Z0-9]+?$)|dummy|^ignored_|^unused_
+
+# Argument names that match this expression will be ignored. Default to name
+# with leading underscore
+ignored-argument-names=_.*|^ignored_|^unused_
+
+# Tells whether we should check for unused import in __init__ files.
+init-import=no
+
+# List of qualified module names which can have objects that can redefine
+# builtins.
+redefining-builtins-modules=six.moves,past.builtins,future.builtins
+
+
+[BASIC]
+
+# Naming style matching correct argument names
+argument-naming-style=snake_case
+
+# Regular expression matching correct argument names. Overrides argument-
+# naming-style
+#argument-rgx=
+
+# Naming style matching correct attribute names
+attr-naming-style=snake_case
+
+# Regular expression matching correct attribute names. Overrides attr-naming-
+# style
+#attr-rgx=
+
+# Bad variable names which should always be refused, separated by a comma
+bad-names=foo,
+          bar,
+          baz,
+          toto,
+          tutu,
+          tata
+
+# Naming style matching correct class attribute names
+class-attribute-naming-style=snake_case
+
+# Regular expression matching correct class attribute names. Overrides class-
+# attribute-naming-style
+#class-attribute-rgx=
+
+# Naming style matching correct class names
+class-naming-style=PascalCase
+
+# Regular expression matching correct class names. Overrides class-naming-style
+#class-rgx=
+
+# Naming style matching correct constant names
+const-naming-style=UPPER_CASE
+
+# Regular expression matching correct constant names. Overrides const-naming-
+# style
+#const-rgx=
+
+# Minimum line length for functions/classes that require docstrings, shorter
+# ones are exempt.
+docstring-min-length=-1
+
+# Naming style matching correct function names
+function-naming-style=snake_case
+
+# Regular expression matching correct function names. Overrides function-
+# naming-style
+#function-rgx=
+
+# Good variable names which should always be accepted, separated by a comma
+good-names=_
+
+# Include a hint for the correct naming format with invalid-name
+include-naming-hint=no
+
+# Naming style matching correct inline iteration names
+inlinevar-naming-style=snake_case
+
+# Regular expression matching correct inline iteration names. Overrides
+# inlinevar-naming-style
+#inlinevar-rgx=
+
+# Naming style matching correct method names
+method-naming-style=snake_case
+
+# Regular expression matching correct method names. Overrides method-naming-
+# style
+#method-rgx=
+
+# Naming style matching correct module names
+module-naming-style=snake_case
+
+# Regular expression matching correct module names. Overrides module-naming-
+# style
+#module-rgx=
+
+# Colon-delimited sets of names that determine each other's naming style when
+# the name regexes allow several styles.
+name-group=
+
+# Regular expression which should only match function or class names that do
+# not require a docstring.
+no-docstring-rgx=^_
+
+# List of decorators that produce properties, such as abc.abstractproperty. Add
+# to this list to register other decorators that produce valid properties.
+property-classes=abc.abstractproperty
+
+# Naming style matching correct variable names
+variable-naming-style=snake_case
+
+# Regular expression matching correct variable names. Overrides variable-
+# naming-style
+#variable-rgx=
+
+
+[SPELLING]
+
+# Limits count of emitted suggestions for spelling mistakes
+max-spelling-suggestions=4
+
+# Spelling dictionary name. Available dictionaries: none. To make it working
+# install python-enchant package.
+spelling-dict=
+
+# List of comma separated words that should not be checked.
+spelling-ignore-words=
+
+# A path to a file that contains private dictionary; one word per line.
+spelling-private-dict-file=
+
+# Tells whether to store unknown words to indicated private dictionary in
+# --spelling-private-dict-file option instead of raising a message.
+spelling-store-unknown-words=no
+
+
+[MISCELLANEOUS]
+
+# List of note tags to take in consideration, separated by a comma.
+notes=FIXME,
+      XXX,
+      TODO
+
+
+[FORMAT]
+
+# Expected format of line ending, e.g. empty (any line ending), LF or CRLF.
+expected-line-ending-format=
+
+# Regexp for a line that is allowed to be longer than the limit.
+ignore-long-lines=^\s*(# )?<?https?://\S+>?$
+
+# Number of spaces of indent required inside a hanging  or continued line.
+indent-after-paren=4
+
+# String used as indentation unit. This is usually "    " (4 spaces) or "\t" (1
+# tab).
+indent-string='    '
+
+# Maximum number of characters on a single line.
+max-line-length=100
+
+# Maximum number of lines in a module
+max-module-lines=1000
+
+# List of optional constructs for which whitespace checking is disabled. `dict-
+# separator` is used to allow tabulation in dicts, etc.: {1  : 1,\n222: 2}.
+# `trailing-comma` allows a space between comma and closing bracket: (a, ).
+# `empty-line` allows space-only lines.
+no-space-check=trailing-comma,
+               dict-separator
+
+# Allow the body of a class to be on the same line as the declaration if body
+# contains single statement.
+single-line-class-stmt=no
+
+# Allow the body of an if to be on the same line as the test if there is no
+# else.
+single-line-if-stmt=no
+
+
+[TYPECHECK]
+
+# List of decorators that produce context managers, such as
+# contextlib.contextmanager. Add to this list to register other decorators that
+# produce valid context managers.
+contextmanager-decorators=contextlib.contextmanager
+
+# List of members which are set dynamically and missed by pylint inference
+# system, and so shouldn't trigger E1101 when accessed. Python regular
+# expressions are accepted.
+generated-members=
+
+# Tells whether missing members accessed in mixin class should be ignored. A
+# mixin class is detected if its name ends with "mixin" (case insensitive).
+ignore-mixin-members=yes
+
+# This flag controls whether pylint should warn about no-member and similar
+# checks whenever an opaque object is returned when inferring. The inference
+# can return multiple potential results while evaluating a Python object, but
+# some branches might not be evaluated, which results in partial inference. In
+# that case, it might be useful to still emit no-member and other checks for
+# the rest of the inferred objects.
+ignore-on-opaque-inference=yes
+
+# List of class names for which member attributes should not be checked (useful
+# for classes with dynamically set attributes). This supports the use of
+# qualified names.
+ignored-classes=optparse.Values,thread._local,_thread._local
+
+# List of module names for which member attributes should not be checked
+# (useful for modules/projects where namespaces are manipulated during runtime
+# and thus existing member attributes cannot be deduced by static analysis. It
+# supports qualified module names, as well as Unix pattern matching.
+ignored-modules=
+
+# Show a hint with possible names when a member name was not found. The aspect
+# of finding the hint is based on edit distance.
+missing-member-hint=yes
+
+# The minimum edit distance a name should have in order to be considered a
+# similar match for a missing member name.
+missing-member-hint-distance=1
+
+# The total number of similar names that should be taken in consideration when
+# showing a hint for a missing member.
+missing-member-max-choices=1
+
+
+[IMPORTS]
+
+# Allow wildcard imports from modules that define __all__.
+allow-wildcard-with-all=no
+
+# Analyse import fallback blocks. This can be used to support both Python 2 and
+# 3 compatible code, which means that the block might have code that exists
+# only in one or another interpreter, leading to false positives when analysed.
+analyse-fallback-blocks=no
+
+# Deprecated modules which should not be used, separated by a comma
+deprecated-modules=optparse,tkinter.tix
+
+# Create a graph of external dependencies in the given file (report RP0402 must
+# not be disabled)
+ext-import-graph=
+
+# Create a graph of every (i.e. internal and external) dependencies in the
+# given file (report RP0402 must not be disabled)
+import-graph=
+
+# Create a graph of internal dependencies in the given file (report RP0402 must
+# not be disabled)
+int-import-graph=
+
+# Force import order to recognize a module as part of the standard
+# compatibility libraries.
+known-standard-library=
+
+# Force import order to recognize a module as part of a third party library.
+known-third-party=enchant
+
+
+[DESIGN]
+
+# Maximum number of arguments for function / method
+max-args=5
+
+# Maximum number of attributes for a class (see R0902).
+max-attributes=7
+
+# Maximum number of boolean expressions in a if statement
+max-bool-expr=5
+
+# Maximum number of branch for function / method body
+max-branches=12
+
+# Maximum number of locals for function / method body
+max-locals=15
+
+# Maximum number of parents for a class (see R0901).
+max-parents=7
+
+# Maximum number of public methods for a class (see R0904).
+max-public-methods=20
+
+# Maximum number of return / yield for function / method body
+max-returns=6
+
+# Maximum number of statements in function / method body
+max-statements=50
+
+# Minimum number of public methods for a class (see R0903).
+min-public-methods=2
+
+
+[CLASSES]
+
+# List of method names used to declare (i.e. assign) instance attributes.
+defining-attr-methods=__init__,
+                      __new__
+
+# List of member names, which should be excluded from the protected access
+# warning.
+exclude-protected=_asdict,
+                  _fields,
+                  _replace,
+                  _source,
+                  _make
+
+# List of valid names for the first argument in a class method.
+valid-classmethod-first-arg=cls
+
+# List of valid names for the first argument in a metaclass class method.
+valid-metaclass-classmethod-first-arg=mcs
+
+
+[EXCEPTIONS]
+
+# Exceptions that will emit a warning when being caught. Defaults to
+# "Exception"
+overgeneral-exceptions=Exception
diff --git a/vermouth/__init__.py b/vermouth/__init__.py
index 48cbac9c..6cf6e713 100644
--- a/vermouth/__init__.py
+++ b/vermouth/__init__.py
@@ -13,12 +13,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-"""
-Created on Tue Aug 22 11:41:47 2017
-
-@author: Peter Kroon
-"""
-
 # Find the data directory once.
 try:
     import pkg_resources
diff --git a/vermouth/deferred_file.py b/vermouth/deferred_file.py
index cd332138..e5f74cd0 100644
--- a/vermouth/deferred_file.py
+++ b/vermouth/deferred_file.py
@@ -13,12 +13,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-"""
-Created on Mon Oct  9 10:04:01 2017
-
-@author: Peter Kroon
-"""
-
 import os
 import sys
 import tempfile
diff --git a/vermouth/ffinput.py b/vermouth/ffinput.py
index 5cee7ed2..30d9e23d 100644
--- a/vermouth/ffinput.py
+++ b/vermouth/ffinput.py
@@ -24,7 +24,6 @@
 
 import collections
 import copy
-import math
 import numbers
 import json
 from .molecule import (
@@ -33,8 +32,6 @@
     Choice, NotDefinedOrNot,
     ParamDistance, ParamAngle, ParamDihedral, ParamDihedralPhase,
 )
-import networkx as nx
-import copy
 
 VALUE_PREDICATES = {
     'not': NotDefinedOrNot,
@@ -55,7 +52,7 @@ def _tokenize(line):
     An interaction line is any uncommented and non empty line that follows a
     section header about an interaction type. Such a line is composed of the
     following parts:
-    
+
     * a list of atoms involved in the interaction,
     * an optional delimiter that indicates the end of the atom list,
     * a list of parameters for the interaction.
@@ -218,7 +215,7 @@ def _substitute_macros(line, macros):
         end = start + len(macro_value)
     return line
 
-        
+
 def _some_atoms_left(tokens, atoms, natoms):
     if tokens and tokens[0] == '--':
         tokens.popleft()
@@ -285,7 +282,7 @@ def _treat_block_interaction_atoms(atoms, context, section):
                 msg = ('Atom names in blocks cannot be prefixed with + or -. '
                        'The name "{}", used in section "{}" of the block "{}" '
                        'is not valid in a block.')
-                raise IOError(msg.format(reference, section, block.name))
+                raise IOError(msg.format(reference, section, context.name))
 
 
 def _split_node_key(key):
@@ -296,6 +293,7 @@ def _split_node_key(key):
         raise IOError('A node key cannot be empty.')
 
     # If the atom name is prefixed, we can get the order.
+    prefix_end = 0  # Make sure prefix_end is defined even if key is empty
     for prefix_end, char in enumerate(key):
         if char not in '+-><*':
             break
@@ -320,7 +318,7 @@ def _split_node_key(key):
 def _get_order_and_prefix_from_attributes(attributes):
     prefix_from_attributes = ''
     order_from_attributes = None
-    Sequence = collections.Sequence
+    Sequence = collections.Sequence  # pylint: disable=invalid-name
     if attributes.get('order') is not None:
         order = attributes['order']
         order_from_attributes = order
@@ -707,7 +705,7 @@ def _parse_patterns(tokens, context, context_type):
     context.patterns.append(atoms)
 
 
-def _parse_variables(tokens, force_field):
+def _parse_variables(tokens, force_field, section):
     if len(tokens) > 2:
         raise IOError('Unexpected column in section "{}".'.format(section))
     elif len(tokens) < 2:
@@ -724,6 +722,16 @@ def _parse_features(tokens, context, context_type):
 
 
 def read_ff(lines, force_field):
+    """
+    Read a .ff file and update the force field with its content.
+
+    Parameters
+    ----------
+    lines
+        Iterable on the file lines to read.
+    force_field: vermouth.ForceField
+        The force field to update.
+    """
     interactions_natoms = {
         'bonds': 2,
         'angles': 3,
@@ -808,7 +816,7 @@ def read_ff(lines, force_field):
                 if context is not None:
                     raise IOError('The [variables] section must be defined '
                                   'before the blocks and the links.')
-                _parse_variables(tokens, force_field)
+                _parse_variables(tokens, force_field, section)
             elif tokens[0] == '#meta':
                 _parse_meta(tokens, context, context_type, section)
             else:
diff --git a/vermouth/forcefield.py b/vermouth/forcefield.py
index 2a6b8008..83bb4502 100644
--- a/vermouth/forcefield.py
+++ b/vermouth/forcefield.py
@@ -14,7 +14,6 @@
 
 import itertools
 from glob import glob
-from pathlib import Path
 import os
 from .gmx.rtp import read_rtp
 from .ffinput import read_ff
@@ -24,6 +23,19 @@
 
 
 class ForceField(object):
+    """
+    Description of a force field.
+
+    Attributes
+    ----------
+    blocks: dict
+    links: list
+    modifications: list
+    renamed_residues: dict
+    name: str
+    variables: dict
+    reference_graphs: dict
+    """
     def __init__(self, directory):
         self.blocks = {}
         self.links = []
@@ -34,6 +46,12 @@ def __init__(self, directory):
         self.read_from(directory)
 
     def read_from(self, directory):
+        """
+        Populate or update the force field from a directory.
+
+        The provided directory must contain a subdirectory with the same name
+        as the force field.
+        """
         source_files = iter_force_field_files(directory)
         for source in source_files:
             extension = os.path.splitext(source)[-1]
@@ -69,14 +87,35 @@ def has_feature(self, feature):
         bool
         """
         return feature in self.features
-        
+
 
 def find_force_fields(directory, force_fields=None):
     """
-    Find all the force fields in the given directory.
+    Read all the force fields in the given directory.
 
     A force field is defined as a directory that contains at least one RTP
     file. The name of the force field is the base name of the directory.
+
+    If the force field argument is not ``None``, then it must be a dictionary
+    with force field names as keys and instances of :class:`ForceField` as
+    values. The force fields in the dictionary will be updated if force fields
+    with the same names are found in the directory.
+
+    Parameters
+    ----------
+    directory: pathlib.Path or str
+        The path to the directory containing the force fields.
+    force_fields: dict (optional)
+        A dictionary of force fields to update.
+
+    Returns
+    -------
+    dict
+        A dictionary of force fields read or updated. Keys are force field
+        names as strings, and values are instances of :class:`ForceField`. If a
+        dictionary was provided as the "force_fields" argument, then the
+        returned dictionary is the same instance as the one provided but with
+        updated content.
     """
     if force_fields is None:
         force_fields = {}
@@ -99,10 +138,13 @@ def find_force_fields(directory, force_fields=None):
     return force_fields
 
 
-def iter_force_field_files(directory, parsers=FORCE_FIELD_PARSERS):
+def iter_force_field_files(directory, extensions=FORCE_FIELD_PARSERS.keys()):
+    """
+    Returns a generator over the path of all the force field files in the directory.
+    """
     return itertools.chain(*(
         glob(os.path.join(directory, '*' + extension))
-        for extension in parsers
+        for extension in extensions
     ))
 
 
diff --git a/vermouth/geometry.py b/vermouth/geometry.py
index 41ffadae..727590ae 100644
--- a/vermouth/geometry.py
+++ b/vermouth/geometry.py
@@ -49,7 +49,7 @@ def distance_matrix(coordinates_a, coordinates_b):
     )
 
 
-def angle(vectorBA, vectorBC):
+def angle(vector_ba, vector_bc):
     """
     Calculate the angle in radians between two vectors.
 
@@ -61,8 +61,8 @@ def angle(vectorBA, vectorBC):
 
     It returns the angle between BA and BC.
     """
-    nominator = np.dot(vectorBA, vectorBC)
-    denominator = np.linalg.norm(vectorBA) * np.linalg.norm(vectorBC)
+    nominator = np.dot(vector_ba, vector_bc)
+    denominator = np.linalg.norm(vector_ba) * np.linalg.norm(vector_bc)
     cosine = nominator / denominator
     # Floating errors at the limits may cause issues.
     cosine = np.clip(cosine, -1, 1)
@@ -84,13 +84,13 @@ def dihedral(coordinates):
     float
         The calculated angle between -pi and +pi.
     """
-    vectorAB = coordinates[1, :] - coordinates[0, :]
-    vectorBC = coordinates[2, :] - coordinates[1, :]
-    vectorCD = coordinates[3, :] - coordinates[2, :]
-    normalABC = np.cross(vectorAB, vectorBC)
-    normalBCD = np.cross(vectorBC, vectorCD)
-    psin = np.dot(normalABC, vectorCD) * np.linalg.norm(vectorBC)
-    pcos = np.dot(normalABC, normalBCD)
+    vector_ab = coordinates[1, :] - coordinates[0, :]
+    vector_bc = coordinates[2, :] - coordinates[1, :]
+    vector_cd = coordinates[3, :] - coordinates[2, :]
+    normal_abc = np.cross(vector_ab, vector_bc)
+    normal_bcd = np.cross(vector_bc, vector_cd)
+    psin = np.dot(normal_abc, vector_cd) * np.linalg.norm(vector_bc)
+    pcos = np.dot(normal_abc, normal_bcd)
     return np.arctan2(psin, pcos)
 
 
@@ -114,10 +114,10 @@ def dihedral_phase(coordinates):
     dihedral
         Calculate a dihedral angle.
     """
-    angle = dihedral(coordinates)
-    angle -= np.pi
-    if angle > np.pi:
-        angle -= 2 * np.pi
-    if angle < -np.pi:
-        angle += 2 * np.pi
-    return angle
+    dihedral_angle = dihedral(coordinates)
+    dihedral_angle -= np.pi
+    if dihedral_angle > np.pi:
+        dihedral_angle -= 2 * np.pi
+    if dihedral_angle < -np.pi:
+        dihedral_angle += 2 * np.pi
+    return dihedral_angle
diff --git a/vermouth/gmx/__init__.py b/vermouth/gmx/__init__.py
index f68c9050..0f9f2edd 100644
--- a/vermouth/gmx/__init__.py
+++ b/vermouth/gmx/__init__.py
@@ -13,12 +13,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-"""
-Created on Tue Aug 22 11:42:17 2017
-
-@author: Peter Kroon
-"""
-
 from .gro import read_gro, write_gro
 from .itp import write_molecule_itp
 from .rtp import read_rtp
diff --git a/vermouth/gmx/gro.py b/vermouth/gmx/gro.py
index 8e02e8cf..7f03922d 100644
--- a/vermouth/gmx/gro.py
+++ b/vermouth/gmx/gro.py
@@ -13,11 +13,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-"""
-Created on Tue Aug 22 11:34:12 2017
-
-@author: Peter Kroon
-"""
 from ..molecule import Molecule
 from ..utils import first_alpha
 from ..truncating_formatter import TruncFormatter
diff --git a/vermouth/graph_utils.py b/vermouth/graph_utils.py
index 2271b3da..b07fc392 100644
--- a/vermouth/graph_utils.py
+++ b/vermouth/graph_utils.py
@@ -14,11 +14,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-"""
-Created on Tue Oct 10 10:51:03 2017
-
-@author: peterkroon
-"""
 from collections import defaultdict
 import itertools
 import networkx as nx
diff --git a/vermouth/map_input.py b/vermouth/map_input.py
index ce3e85cb..d352bd57 100644
--- a/vermouth/map_input.py
+++ b/vermouth/map_input.py
@@ -183,9 +183,13 @@ def read_mapping_directory(directory):
             except IOError:
                 raise IOError('An error occured while reading "{}".'.format(path))
         for from_ff in all_from_ff:
+            to_ff = None
             for to_ff in all_to_ff:
                 mappings[from_ff][to_ff][name] = (mapping, weights, extra)
-            mappings[from_ff][to_ff] = dict(mappings[from_ff][to_ff])
+            if to_ff is not None:
+                # If all_to_ff is empty, then to_ff will not be redefined by
+                # the above for loop.
+                mappings[from_ff][to_ff] = dict(mappings[from_ff][to_ff])
     return dict(mappings)
 
 
diff --git a/vermouth/molecule.py b/vermouth/molecule.py
index dd0c35e9..33a80196 100644
--- a/vermouth/molecule.py
+++ b/vermouth/molecule.py
@@ -13,12 +13,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-"""
-Created on Thu Sep 14 10:58:04 2017
-
-@author: Peter Kroon
-"""
-
 from collections import defaultdict, OrderedDict, namedtuple
 import copy
 from functools import partial
diff --git a/vermouth/pdb/__init__.py b/vermouth/pdb/__init__.py
index 717a1394..38a5642d 100644
--- a/vermouth/pdb/__init__.py
+++ b/vermouth/pdb/__init__.py
@@ -13,10 +13,4 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-"""
-Created on Tue Aug 22 11:42:42 2017
-
-@author: Peter Kroon
-"""
-
 from .pdb import read_pdb, write_pdb
diff --git a/vermouth/pdb/pdb.py b/vermouth/pdb/pdb.py
index b66be791..7f1bb29c 100644
--- a/vermouth/pdb/pdb.py
+++ b/vermouth/pdb/pdb.py
@@ -13,11 +13,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-"""
-Created on Tue Aug 22 11:33:07 2017
-
-@author: Peter Kroon
-"""
 from ..molecule import Molecule
 from ..utils import first_alpha, distance
 from ..truncating_formatter import TruncFormatter
diff --git a/vermouth/processors/__init__.py b/vermouth/processors/__init__.py
index 877b5ff1..077d3312 100644
--- a/vermouth/processors/__init__.py
+++ b/vermouth/processors/__init__.py
@@ -14,12 +14,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-"""
-Created on Wed Oct  4 10:45:54 2017
-
-@author: peterkroon
-"""
-
 from .gro_reader import GROInput
 from .make_bonds import MakeBonds
 from .pdb_reader import PDBInput
diff --git a/vermouth/processors/apply_blocks.py b/vermouth/processors/apply_blocks.py
index cd2f79b7..12aa5d56 100644
--- a/vermouth/processors/apply_blocks.py
+++ b/vermouth/processors/apply_blocks.py
@@ -14,11 +14,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-"""
-Created on Fri Oct 27 14:39:20 2017
-
-@author: peterkroon
-"""
 from ..gmx import read_rtp
 
 from .processor import Processor
diff --git a/vermouth/processors/do_links.py b/vermouth/processors/do_links.py
index 06442734..317c6611 100644
--- a/vermouth/processors/do_links.py
+++ b/vermouth/processors/do_links.py
@@ -14,11 +14,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-"""
-Created on Wed Oct 25 16:00:02 2017
-
-@author: peterkroon
-"""
 from ..molecule import LinkPredicate, attributes_match, NotDefinedOrNot
 from .processor import Processor
 from ..gmx import read_rtp
diff --git a/vermouth/processors/do_mapping.py b/vermouth/processors/do_mapping.py
index e0263005..6fa9e21a 100644
--- a/vermouth/processors/do_mapping.py
+++ b/vermouth/processors/do_mapping.py
@@ -14,12 +14,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-"""
-Created on Tue Oct 10 11:11:54 2017
-
-@author: peterkroon
-"""
-
 from ..molecule import Molecule
 from .processor import Processor
 from ..utils import are_all_equal
diff --git a/vermouth/processors/gro_reader.py b/vermouth/processors/gro_reader.py
index be740783..311f398e 100644
--- a/vermouth/processors/gro_reader.py
+++ b/vermouth/processors/gro_reader.py
@@ -14,12 +14,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-"""
-Created on Wed Oct  4 10:41:10 2017
-
-@author: peterkroon
-"""
-
 from ..gmx import gro
 from .processor import Processor
 
diff --git a/vermouth/processors/make_bonds.py b/vermouth/processors/make_bonds.py
index 6bdcecb7..8d03a96e 100644
--- a/vermouth/processors/make_bonds.py
+++ b/vermouth/processors/make_bonds.py
@@ -14,12 +14,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-"""
-Created on Wed Oct  4 10:48:58 2017
-
-@author: peterkroon
-"""
-
 from .. import KDTree
 from ..molecule import Molecule
 from .processor import Processor
diff --git a/vermouth/processors/pdb_reader.py b/vermouth/processors/pdb_reader.py
index ffaa452a..20a5ba17 100644
--- a/vermouth/processors/pdb_reader.py
+++ b/vermouth/processors/pdb_reader.py
@@ -14,15 +14,10 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-"""
-Created on Wed Oct  4 10:41:10 2017
-
-@author: peterkroon
-"""
-
 from ..pdb import read_pdb
 from .processor import Processor
 
+
 class PDBInput(Processor):
     def run_system(self, system, filename):
         molecule = read_pdb(filename)
diff --git a/vermouth/processors/processor.py b/vermouth/processors/processor.py
index 11860398..5d5b0a69 100644
--- a/vermouth/processors/processor.py
+++ b/vermouth/processors/processor.py
@@ -14,11 +14,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-"""
-Created on Wed Oct  4 13:03:50 2017
-
-@author: peterkroon
-"""
 
 class Processor:
     def run_system(self, system):
diff --git a/vermouth/processors/repair_graph.py b/vermouth/processors/repair_graph.py
index e9cfe65b..2fcd036e 100644
--- a/vermouth/processors/repair_graph.py
+++ b/vermouth/processors/repair_graph.py
@@ -14,12 +14,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-"""
-Created on Thu Oct  5 10:43:19 2017
-
-@author: peterkroon
-"""
-
 from .processor import Processor
 from ..graph_utils import *
 
diff --git a/vermouth/system.py b/vermouth/system.py
index a11d3f07..015d90ba 100644
--- a/vermouth/system.py
+++ b/vermouth/system.py
@@ -14,12 +14,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-"""
-Created on Wed Oct  4 10:39:09 2017
-
-@author: peterkroon
-"""
-
 
 class System:
     def __init__(self):
diff --git a/vermouth/truncating_formatter.py b/vermouth/truncating_formatter.py
index fbe9c159..32b302d0 100644
--- a/vermouth/truncating_formatter.py
+++ b/vermouth/truncating_formatter.py
@@ -14,12 +14,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-"""
-Created on Fri Oct 20 13:53:45 2017
-
-@author: peterkroon
-"""
-
 import string
 import re
 from collections import namedtuple
diff --git a/vermouth/utils.py b/vermouth/utils.py
index e554c215..48f8a3dc 100644
--- a/vermouth/utils.py
+++ b/vermouth/utils.py
@@ -13,12 +13,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-"""
-Created on Tue Aug 22 11:38:17 2017
-
-@author: Peter Kroon
-"""
-
 import numpy as np
 
 try: