Change dist name from lie_topology to mdstudio_topology

README.md

@@ -1 +1 @@
-# lie_topology
+# mdstudio_topology

lie_topology/__main__.py → mdstudio_topology/__main__.py

@@ -3,24 +3,24 @@
 import yaml
 
 
-from lie_topology.molecule.molecule import Molecule
-from lie_topology.molecule.blueprint import Blueprint
-from lie_topology.molecule.structure import Structure
-from lie_topology.parsers.cnfParser import ParseCnf
-from lie_topology.parsers.pdbParser import ParsePdb
-from lie_topology.parsers.groParser import ParseGro
-from lie_topology.parsers.sdfParser import ParseSdf
-from lie_topology.parsers.mol2Parser import ParseMol2
-from lie_topology.parsers.mdtopParser import ParseMdtop
-from lie_topology.parsers.mdmtbParser import ParseMDMtb
+from mdstudio_topology.molecule.molecule import Molecule
+from mdstudio_topology.molecule.blueprint import Blueprint
+from mdstudio_topology.molecule.structure import Structure
+from mdstudio_topology.parsers.cnfParser import ParseCnf
+from mdstudio_topology.parsers.pdbParser import ParsePdb
+from mdstudio_topology.parsers.groParser import ParseGro
+from mdstudio_topology.parsers.sdfParser import ParseSdf
+from mdstudio_topology.parsers.mol2Parser import ParseMol2
+from mdstudio_topology.parsers.mdtopParser import ParseMdtop
+from mdstudio_topology.parsers.mdmtbParser import ParseMDMtb
 
-from lie_topology.utilities.make_topology import MakeSequence
+from mdstudio_topology.utilities.make_topology import MakeSequence
 
-from lie_topology.writers.cnfWriter import WriteCnf
-from lie_topology.writers.gromosTopologyWriter import WriteGromosTopology
+from mdstudio_topology.writers.cnfWriter import WriteCnf
+from mdstudio_topology.writers.gromosTopologyWriter import WriteGromosTopology
 
-from lie_topology.forcefield.physconst import PhysicalConstants
-from lie_topology.molecule.crystal import BoxVectorsToLattice, LatticeToBoxVectors
+from mdstudio_topology.forcefield.physconst import PhysicalConstants
+from mdstudio_topology.molecule.crystal import BoxVectorsToLattice, LatticeToBoxVectors
 
 
 def WriteSimJson( forcefield, coordinates ):
@@ -108,15 +108,15 @@ def main():
 def main():
     
     # test atom schema
-    with open("lie_topology/schemas/resources/atom.v1.json", 'r') as ifs:
+    with open("mdstudio_topology/schemas/resources/atom.v1.json", 'r') as ifs:
 
         schema = json.load(ifs)
 
         test_atom = { "uid" : "a1", "name" : "CA", "position" : [1.0, 2.0, 3.0] }
 
         jsonschema.validate( test_atom, schema)
 
-    with open("lie_topology/schemas/resources/bond.v1.json", 'r') as ifs:
+    with open("mdstudio_topology/schemas/resources/bond.v1.json", 'r') as ifs:
 
         schema = json.load(ifs)
 
@@ -127,7 +127,7 @@ def main():
 """
 
 from mdstudio.runner import main
-from lie_topology.application import TopologyComponent
+from mdstudio_topology.application import TopologyComponent
 
 if __name__ == '__main__':
-    main(TopologyComponent)
+    main(TopologyComponent)

lie_topology/application.py → mdstudio_topology/application.py

@@ -70,7 +70,5 @@ def is_debug(self):
 
         self.log.info('debug_sytem {sys:s}', sys=str(response["system"]))
 
-
     def report_delay(self, direction, delay):
         self.log.info('{direction:>20} delay: {delay:>8.2f} ms', direction=direction, delay=delay.total_seconds() * 1000)
-

lie_topology/core/group.py → mdstudio_topology/core/group.py

@@ -2,7 +2,7 @@
 
 from collections import OrderedDict
 
-from lie_topology.core.molecule import Molecule
+from mdstudio_topology.core.molecule import Molecule
 
 class Group(object):
 

lie_topology/core/molecule.py → mdstudio_topology/core/molecule.py

@@ -2,7 +2,7 @@
 
 from collections import OrderedDict
 
-from lie_topology.core.atom import Atom
+from mdstudio_topology.core.atom import Atom
 
 class Molecule(object):
 

lie_topology/core/system.py → mdstudio_topology/core/system.py

@@ -2,8 +2,8 @@
 
 from collections import OrderedDict
 
-from lie_topology.core.group import Group
-from lie_topology.core.uuid import UUIDGenerator
+from mdstudio_topology.core.group import Group
+from mdstudio_topology.core.uuid import UUIDGenerator
 
 class System(object):
 

lie_topology/data/md_top/54a7mtb_to_aatop.py → mdstudio_topology/data/md_top/54a7mtb_to_aatop.py

@@ -29,15 +29,15 @@
 import json
 import numpy as np
 
-from lie_topology.common.tokenizer          import Tokenizer
-from lie_topology.common.exception          import LieTopologyException
-from lie_topology.molecule.molecule         import Molecule
-from lie_topology.molecule.bond             import Bond
-from lie_topology.molecule.angle            import Angle
-from lie_topology.molecule.dihedral         import Dihedral
-from lie_topology.molecule.improper         import Improper
-from lie_topology.molecule.vsite            import InPlaneSite
-from lie_topology.molecule.reference        import AtomReference
+from mdstudio_topology.common.tokenizer          import Tokenizer
+from mdstudio_topology.common.exception          import LieTopologyException
+from mdstudio_topology.molecule.molecule         import Molecule
+from mdstudio_topology.molecule.bond             import Bond
+from mdstudio_topology.molecule.angle            import Angle
+from mdstudio_topology.molecule.dihedral         import Dihedral
+from mdstudio_topology.molecule.improper         import Improper
+from mdstudio_topology.molecule.vsite            import InPlaneSite
+from mdstudio_topology.molecule.reference        import AtomReference
 
 def _GenAatopRef( solute, index ):
 

lie_topology/parsers/cnfParser.py → mdstudio_topology/parsers/cnfParser.py

@@ -30,11 +30,11 @@
 
 from copy import deepcopy
 
-from lie_topology.core.tokenizer import Tokenizer
-from lie_topology.core.structure import Structure, Time
-from lie_topology.core.topology  import Topology
-from lie_topology.core.crystal   import Lattice
-from lie_topology.core.group     import Group
+from mdstudio_topology.core.tokenizer import Tokenizer
+from mdstudio_topology.core.structure import Structure, Time
+from mdstudio_topology.core.topology  import Topology
+from mdstudio_topology.core.crystal   import Lattice
+from mdstudio_topology.core.group     import Group
 
 def _AppendTopological( activeTopology, resNum, resName, atomName, atomNum ):
 

mdstudio_topology/parsers/topology/__init__.py

@@ -0,0 +1 @@
+from mdstudio_topology.parsers.topology.read_mdtop import read_mdtop

lie_topology/parsers/topology/read_mdtop.py → mdstudio_topology/parsers/topology/read_mdtop.py

@@ -1,7 +1,7 @@
 
 from lie_graph import GraphAxis
-from lie_topology.core.io.yaml.yaml_ext import ordered_load
-from lie_topology.core.topology.nodes import TopologyNode
+from mdstudio_topology.core.io.yaml.yaml_ext import ordered_load
+from mdstudio_topology.core.topology.nodes import TopologyNode
 
 def read_meta_data(ff_definitions, ff_graph):
 

settings.yml

@@ -1,3 +1,3 @@
 static:
   vendor: mdgroup
-  component: lie_topology
+  component: mdstudio_topology

setup.py

@@ -1,11 +1,11 @@
 #! /usr/bin/env python
 # -*- coding: utf-8 -*-
 
-# package: lie_docking
+# package: mdstudio_topology
 # file: setup.py
 #
-# Part of ‘lie_docking’, a package providing molecular docking functionality
-# for the LIEStudio package.
+# Part of ‘mdstudio_topology’, a package providing component wrapping
+# topology parsers and writers for theMDStudio package.
 #
 # Copyright © 2018 K.M.Visscher, VU University Amsterdam, the Netherlands
 #
@@ -24,20 +24,20 @@
 
 from setuptools import setup, find_packages
 
-distribution_name = 'lie_topology'
+distribution_name = 'mdstudio_topology'
 
 setup(
     name=distribution_name,
     version=0.1,
     description='MDStudio component wrapping topology parsers and writers',
     author='Koen M. Visscher, VU University, Amsterdam, The Netherlands',
     author_email=['[email protected]'],
-    url='https://github.com/MD-Studio/lie_topology.git',
+    url='https://github.com/MD-Studio/MDStudio_topology.git',
     license='Apache Software License 2.0',
-    keywords='MDStudio molecular simulation',
+    keywords='MDStudio molecular simulation topology',
     platforms=['Any'],
     packages=find_packages(),
-    package_data={'lie_topology': ['data/*']},
+    package_data={'mdstudio_topology': ['data/*']},
     py_modules=[distribution_name],
     install_requires=['mdstudio', 'numpy','lie_graph'],
     include_package_data=False,

tests/__main__.py

@@ -4,7 +4,7 @@
 from lie_graph import GraphAxis
 from enum import Enum
 
-from lie_topology.parsers.topology import read_mdtop
+from mdstudio_topology.parsers.topology import read_mdtop
 
 class NodeType(Enum):
     Atom     = 1
@@ -20,7 +20,7 @@ class EdgeType(Enum):
 
 def verify_graph():
 
-    print('running debug version of lie_topology')
+    print('running debug version of mdstudio_topology')
     system = GraphAxis()
 
     # testing a molecule graph setup