Prepare the repo for opening

LICENSE

@@ -199,3 +199,7 @@
  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  See the License for the specific language governing permissions and
  limitations under the License.
+
+Files from other sources are redistributed as part of the package in the
+vermouth/redistributed directory. See vermouth/redistributed/LICENSE for the
+license of these files.

README.md

@@ -1,3 +1,79 @@
-# Martinize2: The ultimate resolution transformation tool
+# Martinize2 and vermouth: The ultimate resolution transformation tools
 
-TODO: documentation
+Martinize2 is a rewrite of [Martinize]. It is aimed at producing
+coarse-grained structures and topologies from an atomistic structure. Martinize
+is primarily developed for the [Martini] coarse-grained force field and the
+[Gromacs] simulation engine. However the architecture of the program will
+allow us to support a broader range of force fields and simulation engines in
+the future.
+
+Vermouth (for VERsatile, MOdular, and Universal Tranformation Helper) is the
+python library that powers Martinize2. It allows to describe and apply
+transformation on molecular structures and topologies using graph algorithms.
+
+## Disclaimer
+
+**Both Martinize2 and vermouth are at a prototype stage. DO NOT USE IN
+PRODUCTION.**
+
+## Installation
+
+Martinize2 and vermouth require python 3.4 or greater. They can be installed
+using the `pip` command:
+
+ pip install git+https://github.com/jbarnoud/martinize2.git#vermouth
+
+The behavior of the `pip` command can vary depending of the specificity of your
+python installation. See the [documentation on installing a python
+package][pipdoc] to learn more.
+
+## Basic usage
+
+Installing Martinize2 and vermouth with `pip` adds the `martinize2` program to
+the research PATH. You can see the available option of the program by running:
+
+ martinize2 -h
+
+At the moment, martinize2 tries to reproduce the interface of the original
+Martinize. You can find explanations on how to use Martinize on the [Martini
+tutorials]; in most cases, replacing calls to `martinize.py` by calls to
+`martinize2` should produce similar results.
+
+The documentation of the vermouth python library will come soon.
+
+## License
+
+Martinize2 and vermouth are distributed under the Apache 2.0 license.
+
+ Copyright 2018 University of Groningen
+
+ Licensed under the Apache License, Version 2.0 (the "License");
+ you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
+
+ http:https://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+
+The [full text of the license][license] is available in the source repository.
+
+## Contributions
+
+The development of Martinize2 and vermouth is done on [github]. Contributions
+are welcome as [bug reports] and [pull requests]. Note however that the
+decision of whether or not contributions can give authorship on the resulting
+academic paper is left to our sole discretion.
+
+[Martinize]: https://github.com/Tsjerk/Martinize
+[Martini]: http:https://cgmartini.nl
+[Martini tutorials]: http:https://cgmartini.nl/index.php/tutorials-general-introduction-gmx5
+[Gromacs]: http:https://www.gromacs.org
+[pipdoc]: https://packaging.python.org/tutorials/installing-packages/#installing-packages
+[license]: https://github.com/jbarnoud/martinize2/blob/master/LICENSE
+[github]: https://github.com/jbarnoud/martinize2
+[bug reports]: https://github.com/jbarnoud/martinize2/issues
+[pull requests]: https://github.com/jbarnoud/martinize2/pulls

embed_test.py → bin/embed_test.py

@@ -1,12 +1,26 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
+# Copyright 2018 University of Groningen
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http:https://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 """
 Created on Wed Aug 30 13:07:14 2017
 
 @author: peterkroon
 """
 
-from martinize2 import *
+from vermouth import *
 import networkx as nx
 import numpy as np
 import scipy.sparse.csgraph as ssc

entry_api.py → bin/martinize2

@@ -1,4 +1,19 @@
+#!/usr/bin/env python3
 # -*- coding: utf-8 -*-
+# Copyright 2018 University of Groningen
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http:https://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 """
 High level API for Martinize2
 """
@@ -7,9 +22,9 @@
 from pathlib import Path
 import os
 import numpy as np
-import martinize2 as m2
-from martinize2.forcefield import find_force_fields, FORCE_FIELDS
-from martinize2 import DATA_PATH
+import vermouth
+from vermouth.forcefield import find_force_fields, FORCE_FIELDS
+from vermouth import DATA_PATH
 import itertools
 import operator
 import textwrap
@@ -117,12 +132,12 @@ def read_system(path):
 
  The resulting system does not have a force field and may not have edges.
  """
- system = m2.System()
+ system = vermouth.System()
  file_extension = path.suffix.upper()[1:] # We do not keep the dot
  if file_extension in ['PDB', 'ENT']:
- m2.PDBInput().run_system(system, str(path))
+ vermouth.PDBInput().run_system(system, str(path))
  elif file_extension in ['GRO']:
- m2.GROInput().run_system(system, str(path))
+ vermouth.GROInput().run_system(system, str(path))
  else:
  raise ValueError('Unknown file extension "{}".'.format(file_extension))
  return system
@@ -142,19 +157,21 @@ def pdb_to_universal(system, delete_unknown=False):
  """
  canonicalized = system.copy()
  canonicalized.force_field = FORCE_FIELDS['universal']
- m2.MakeBonds().run_system(canonicalized)
- m2.RepairGraph(delete_unknown=delete_unknown).run_system(canonicalized)
+ vermouth.MakeBonds().run_system(canonicalized)
+ vermouth.RepairGraph(delete_unknown=delete_unknown).run_system(canonicalized)
  return canonicalized
 
 
 def martinize(system, mappings, to_ff, delete_unknown=False):
  """
  Convert a system from one force field to an other at lower resolution.
  """
- m2.DoMapping(mappings=mappings, to_ff=to_ff, delete_unknown=delete_unknown).run_system(system)
- m2.DoAverageBead().run_system(system)
- m2.ApplyBlocks().run_system(system)
- m2.DoLinks().run_system(system)
+ vermouth.DoMapping(mappings=mappings,
+ to_ff=to_ff,
+ delete_unknown=delete_unknown).run_system(system)
+ vermouth.DoAverageBead().run_system(system)
+ vermouth.ApplyBlocks().run_system(system)
+ vermouth.DoLinks().run_system(system)
  return system
 
 
@@ -175,7 +192,7 @@ def write_gmx_topology(system, top_path):
  for molidx, (molecule_type, _) in enumerate(molecule_types):
  molecule_type.moltype = 'molecule_{}'.format(molidx)
  with open('molecule_{}.itp'.format(molidx), 'w') as outfile:
- m2.gmx.itp.write_molecule_itp(molecule_type, outfile)
+ vermouth.gmx.itp.write_molecule_itp(molecule_type, outfile)
  # Reorganize the molecule type assignment to write the top file.
  # The top file "molecules" section lists the molecules in the same order
  # as in the structure and group them. To do the grouping, we associate each
@@ -230,7 +247,9 @@ def entry():
  parser.add_argument('-ff', dest='to_ff', default='martini22')
  args = parser.parse_args()
 
- known_force_fields = m2.forcefield.find_force_fields(Path(DATA_PATH) / 'force_fields')
+ known_force_fields = vermouth.forcefield.find_force_fields(
+ Path(DATA_PATH) / 'force_fields'
+ )
  known_mappings = read_mapping_directory(Path(DATA_PATH) / 'mappings')
 
  from_ff = 'universal'
@@ -259,10 +278,10 @@ def entry():
  if args.posres != 'None':
  selectors = {'All': select_all, 'Backbone': select_backbone}
  selector = selectors[args.posres]
- m2.ApplyPosres(selector, args.posres_fc).run_system(system)
+ vermouth.ApplyPosres(selector, args.posres_fc).run_system(system)
 
  # Write a PDB file.
- m2.pdb.write_pdb(system, str(args.outpath))
+ vermouth.pdb.write_pdb(system, str(args.outpath))
 
  write_gmx_topology(system, Path('topol.top'))
 

run_martinize2.py → bin/run_martinize2.py

@@ -1,12 +1,26 @@
 # -*- coding: utf-8 -*-
+# Copyright 2018 University of Groningen
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http:https://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 """
 Created on Tue Aug 22 11:48:46 2017
 
 @author: Peter Kroon
 """
 #import matplotlib.pyplot as plt
 #plt.close('all')
-from martinize2 import *
+from vermouth import *
 
 import os.path as osp