[WIP] Makes Pylint happier

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

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

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:

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
  ))
 
 

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

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

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

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

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)
 
 

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

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

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

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

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