Update to be consistent with vmd-python interface

Eigenstate · Eigenstate · commit 8e334768ce4a · 2017-05-19T10:44:44.000-07:00
diff --git a/Dabble/builder.py b/Dabble/builder.py
@@ -27,17 +27,7 @@
 import os
 import tempfile
 
-try:
-# Pylint hates vmd
-# pylint: disable=import-error, unused-import
-    import vmd
-    import molecule
-    import trans
-    from atomsel import atomsel
-# pylint: enable=import-error, unused-import
-except ImportError:
-    from vmd import atomsel, molecule, trans
-    atomsel = atomsel.atomsel
+from vmd import atomsel, molecule, trans
 
 from Dabble import fileutils
 from Dabble import molutils
diff --git a/Dabble/fileutils.py b/Dabble/fileutils.py
@@ -24,16 +24,7 @@
 import os
 import tempfile
 
-try:
-# pylint: disable=import-error, unused-import
-    import vmd
-    import molecule
-    from atomsel import atomsel
-# pylint: enable=import-error, unused-import
-except ImportError:
-    from vmd import molecule, atomsel
-    atomsel = atomsel.atomsel
-
+from vmd import molecule, atomsel
 from Dabble.param import AmberWriter, CharmmWriter
 
 #++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
@@ -244,14 +235,14 @@ def write_final_system(out_fmt, out_name, molid, **kwargs):
 
         temp_mol = molecule.load('mae', mae_name)
         write_psf_name = mae_name.replace('.mae', '')
-        writer = AmberWriter(molid=temp_mol,
-                             tmp_dir=kwargs['tmp_dir'],
-                             forcefield=kwargs['forcefield'],
-                             lipid_sel=kwargs.get('lipid_sel'),
-                             hmr=kwargs.get('hmassrepartition'),
-                             extra_topos=tops,
-                             extra_params=pars)
-        writer.write(write_psf_name)
+        writeit = AmberWriter(molid=temp_mol,
+                              tmp_dir=kwargs['tmp_dir'],
+                              forcefield=kwargs['forcefield'],
+                              lipid_sel=kwargs.get('lipid_sel'),
+                              hmr=kwargs.get('hmassrepartition'),
+                              extra_topos=tops,
+                              extra_params=pars)
+        writeit.write(write_psf_name)
 
     return out_name
 
@@ -335,7 +326,8 @@ def check_out_type(value, forcefield, hmr=False):
         out_fmt = 'dms'
     elif ext == 'psf' and "charmm" in forcefield:
         out_fmt = 'charmm'
-    elif ext == 'prmtop' and forcefield in ["amber","charmm","charmm36","charmm36m"]:
+    elif ext == 'prmtop' and forcefield in ["amber", "charmm",
+                                            "charmm36", "charmm36m"]:
         out_fmt = 'amber'
     else:
         raise ValueError("%s is an unsupported format with %s forcefield"
diff --git a/Dabble/molutils.py b/Dabble/molutils.py
@@ -21,19 +21,10 @@
 """
 
 from __future__ import print_function
-import numpy as np
 import os
 import tempfile
-
-try:
-# pylint: disable=import-error, unused-import
-    import vmd
-    import molecule
-    from atomsel import atomsel
-# pylint: enable=import-error
-except ImportError:
-    from vmd import molecule, atomsel
-    atomsel = atomsel.atomsel
+import numpy as np
+from vmd import molecule, atomsel
 
 from Dabble import fileutils
 # pylint: disable=no-member
@@ -595,4 +586,3 @@ def num_lipids_remaining(molid, lipid_sel):
     return np.unique(atomsel_remaining(molid, lipid_sel).get('fragment')).size
 
 #++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-
diff --git a/Dabble/param/amber.py b/Dabble/param/amber.py
@@ -30,16 +30,7 @@
 import warnings
 from subprocess import check_output
 from pkg_resources import resource_filename
-
-try:
-# pylint: disable=import-error, unused-import
-    import vmd
-    import molecule
-    from atomsel import atomsel
-# pylint: enable=import-error, unused-import
-except ImportError:
-    from vmd import molecule, atomsel
-    atomsel = atomsel.atomsel
+from vmd import molecule, atomsel
 
 from networkx.drawing.nx_pydot import write_dot
 from parmed.tools import chamber, parmout, HMassRepartition, checkValidity
diff --git a/Dabble/param/ambermatcher.py b/Dabble/param/ambermatcher.py
@@ -30,15 +30,7 @@
 from networkx.algorithms import isomorphism
 from networkx.drawing.nx_pydot import write_dot
 from pkg_resources import resource_filename
-
-try:
-# pylint: disable=import-error, unused-import
-    import vmd
-    from atomsel import atomsel
-# pylint: enable=import-error, unused-import
-except ImportError:
-    from vmd import atomsel
-    atomsel = atomsel.atomsel
+from vmd import atomsel
 
 from . import MoleculeMatcher
 logger = logging.getLogger(__name__) # pylint: disable=invalid-name
diff --git a/Dabble/param/charmm.py b/Dabble/param/charmm.py
@@ -26,17 +26,7 @@
 import os
 import tempfile
 from pkg_resources import resource_filename
-
-try:
-# pylint: disable=import-error, unused-import
-    import vmd
-    import molecule
-    from atomsel import atomsel
-    from VMD import evaltcl
-# pylint: enable=import-error, unused-import
-except ImportError:
-    from vmd import atomsel, evaltcl, molecule
-    atomsel = atomsel.atomsel
+from vmd import atomsel, evaltcl, molecule
 
 from Dabble.param import CharmmMatcher
 
@@ -81,8 +71,7 @@ class CharmmWriter(object):
 
     #==========================================================================
 
-    def __init__(self, tmp_dir, molid, lipid_sel="lipid", extra_topos=None,
-                 override_defaults=False):
+    def __init__(self, tmp_dir, molid, lipid_sel="lipid", **kwargs):
 
         # Create TCL temp file and directory
         self.tmp_dir = tmp_dir
@@ -93,7 +82,7 @@ def __init__(self, tmp_dir, molid, lipid_sel="lipid", extra_topos=None,
         self.molid = molid
         self.psf_name = ""
         # Default parameter sets
-        if override_defaults:
+        if kwargs.get("override_defaults", False):
             self.topologies = []
         else:
             self.topologies = [
@@ -112,8 +101,8 @@ def __init__(self, tmp_dir, molid, lipid_sel="lipid", extra_topos=None,
                                                        os.path.join("charmm_parameters",
                                                                     top))
 
-        if extra_topos:
-            self.topologies.extend(extra_topos)
+        if kwargs.get("extra_topos"):
+            self.topologies.extend(kwargs.get("extra_topos"))
 
         # Initialize graph matcher with topologies we know about
         self.matcher = CharmmMatcher(self.topologies)
diff --git a/Dabble/param/charmmmatcher.py b/Dabble/param/charmmmatcher.py
@@ -27,15 +27,7 @@
 import networkx as nx
 from networkx.drawing.nx_pydot import write_dot
 from networkx.algorithms import isomorphism
-
-try:
-# pylint: disable=import-error, unused-import
-    import vmd
-    from atomsel import atomsel
-# pylint: enable=import-error, unused-import
-except ImportError:
-    from vmd import atomsel
-    atomsel = atomsel.atomsel
+from vmd import atomsel
 
 from . import MoleculeMatcher
 logger = logging.getLogger(__name__) # pylint: disable=invalid-name
diff --git a/Dabble/param/moleculematcher.py b/Dabble/param/moleculematcher.py
@@ -29,14 +29,7 @@
 
 import networkx as nx
 from networkx.algorithms import isomorphism
-try:
-# pylint: disable=import-error, unused-import
-    import vmd
-    from atomsel import atomsel
-# pylint: enable=import-error, unused-import
-except ImportError:
-    from vmd import atomsel
-    atomsel = atomsel.atomsel
+from vmd import atomsel
 
 logger = logging.getLogger(__name__) # pylint: disable=invalid-name
 
diff --git a/convert_step5_to_dabble.py b/convert_step5_to_dabble.py
@@ -6,15 +6,9 @@
 
 from __future__ import print_function
 import os
-try:
-    import vmd
-    import molecule
-    from atomsel import atomsel
-except ModuleNotFoundError:
-    from vmd import atomsel, molecule
-    atomsel = atomsel.atomsel
-
-thedir = os.path.abspath(raw_input("Which directory contains step5_assembly.{psf,crd}? > "))
+from vmd import atomsel, molecule
+
+thedir = os.path.abspath(input("Which directory contains step5_assembly.{psf,crd}? > "))
 if not os.path.isdir(thedir):
     raise ValueError("%s not a valid directory" % thedir)
 
diff --git a/get_restraint_mask.py b/get_restraint_mask.py
@@ -23,12 +23,7 @@
 
 """
 from __future__ import print_function
-try:
-    import vmd, molecule
-    from atomsel import atomsel
-except ImportError:
-    from vmd import atomsel, molecule
-    atomsel = atomsel.atomsel
+from vmd import atomsel, molecule
 
 import itertools
 import readline
diff --git a/test/3NOB/test_3nob.py b/test/3NOB/test_3nob.py
@@ -1,13 +1,7 @@
 # Tests writing amber format with amber parameters
 # Special isopeptide bond between two residues
-import pytest
-import subprocess, os
-try:
-    import vmd, molecule
-    from atomsel import atomsel
-except ImportError:
-    from vmd import atomsel, molecule
-    atomsel = atomsel.atomsel
+import os
+from vmd import atomsel, molecule
 
 dir = os.path.dirname(__file__)
 #==============================================================================
diff --git a/test/arrestin_po4_cyp/test_arrestin_cyp.py b/test/arrestin_po4_cyp/test_arrestin_cyp.py
@@ -1,6 +1,5 @@
 # Tests covalently bonded ligand
-import pytest
-import subprocess, os
+import os
 
 dir = os.path.dirname(__file__) + "/"
 
@@ -12,13 +11,7 @@ def test_covalent_ligand_patches(tmpdir):
     hydrogen atom should be renamed in the palmitoylcysteine.
     Also tests for detection of phosphorylations on amino acids.
     """
-    try:
-        import vmd, molecule
-        from atomsel import atomsel
-    except ImportError:
-        from vmd import atomsel, molecule
-        atomsel = atomsel.atomsel
-
+    from vmd import atomsel, molecule
     from Dabble.param import CharmmWriter
 
     # Parameterize with charmm parameters
diff --git a/test/b2ar_multiligand/test_b2ar_alp_multiligand.py b/test/b2ar_multiligand/test_b2ar_alp_multiligand.py
@@ -1,6 +1,5 @@
 # Tests multiple ligands
-import pytest
-import subprocess, os
+import os
 
 dir = os.path.dirname(__file__) + "/"
 
@@ -9,13 +8,7 @@
 def test_multiligand_building(tmpdir):
     """
     Solvates and membranes a system with multiple ligands """
-    try:
-        import vmd, molecule
-        from atomsel import atomsel
-    except ImportError:
-        from vmd import atomsel, molecule
-        atomsel = atomsel.atomsel
-
+    from vmd import atomsel, molecule
     from Dabble import DabbleBuilder
 
     # Build the system
@@ -47,13 +40,7 @@ def test_multiligand_parameterizing(tmpdir):
     """
     Checks the parameterization of a system with multiple ligands
     """
-    try:
-        import vmd, molecule
-        from atomsel import atomsel
-    except ImportError:
-        from vmd import atomsel, molecule
-        atomsel = atomsel.atomsel
-
+    from vmd import atomsel, molecule
     from Dabble.param import CharmmWriter
 
     # Parameterize the multiple ligand system with charmm parameters
@@ -83,11 +70,7 @@ def test_multiligand_charmm36m(tmpdir):
     """
     Checks parameterization with charmm36m forcefield
     """
-    try:
-        import vmd, molecule
-    except ImportError:
-        from vmd import molecule
-
+    from vmd import molecule
     from Dabble.param import AmberWriter
 
     p = str(tmpdir.mkdir("charmm36m"))
diff --git a/test/graph_ligand/test_graph_ligand.py b/test/graph_ligand/test_graph_ligand.py
diff --git a/test/lsd/test_lsd.py b/test/lsd/test_lsd.py
diff --git a/test/moleculematcher/test_matcher.py b/test/moleculematcher/test_matcher.py
diff --git a/test/relaxin/test_relaxin.py b/test/relaxin/test_relaxin.py
diff --git a/test/rho_c_tail/test_rho_tail.py b/test/rho_c_tail/test_rho_tail.py
