updated sequenceID to start from 0. updated all it's usages. Fixed bu…

…g in Molecule where writing files with MDtraj didn't delete the temp files

htmd/builder/amber.py

@@ -215,7 +215,7 @@ def build(mol, ff=None, topo=None, param=None, prefix='structure', outdir='./bui
         if len(disulfide) != 0:
             for d in disulfide:
                 # Convert to stupid amber residue numbering
-                uqseqid = sequenceID((mol.resid, mol.insertion, mol.segid)) + mol.resid[0] - 1
+                uqseqid = sequenceID((mol.resid, mol.insertion, mol.segid)) + mol.resid[0]
                 uqres1 = int(np.unique(uqseqid[mol.atomselect('segid {} and resid {}'.format(d.segid1, d.resid1))]))
                 uqres2 = int(np.unique(uqseqid[mol.atomselect('segid {} and resid {}'.format(d.segid2, d.resid2))]))
                 # Rename the CYS to CYX if there is a disulfide bond
@@ -262,7 +262,7 @@ def build(mol, ff=None, topo=None, param=None, prefix='structure', outdir='./bui
         f.write('# Adding disulfide bonds\n')
         for d in disulfide:
             # Convert to stupid amber residue numbering
-            uqseqid = sequenceID((mol.resid, mol.insertion, mol.segid)) + mol.resid[0] - 1
+            uqseqid = sequenceID((mol.resid, mol.insertion, mol.segid)) + mol.resid[0]
             uqres1 = int(np.unique(uqseqid[mol.atomselect('segid {} and resid {}'.format(d.segid1, d.resid1))]))
             uqres2 = int(np.unique(uqseqid[mol.atomselect('segid {} and resid {}'.format(d.segid2, d.resid2))]))
             f.write('bond mol.{}.SG mol.{}.SG\n'.format(uqres1, uqres2))

htmd/model.py

@@ -546,7 +546,7 @@ def viewStates(self, states=None, statetype='macro', protein=None, ligand=None,
             viewer.send('start_sscache')
 
     def _viewStatesNGL(self, states, statetype, protein, ligand, mols, numsamples, gui=False):
-        from htmd.builder.builder import sequenceID
+        from htmd.molecule.util import sequenceID
         if states is None:
             states = range(self.macronum)
         if isinstance(states, int):
@@ -568,7 +568,7 @@ def _viewStatesNGL(self, states, statetype, protein, ligand, mols, numsamples, g
             if ligand:
                 mol = ref.copy()
                 mol.remove(ligand, _logger=False)
-                mol.coords = np.atleast_3d(mol.coords[:, :, 0])
+                mol.dropFrames(keep=0)
                 mols[i].filter(ligand, _logger=False)
             mols[i].set('chain', '{}'.format(s))
             tmpcoo = mols[i].coords

htmd/molecule/molecule.py

@@ -222,6 +222,11 @@ def frame(self, value):
             raise NameError("Frame index out of range. Molecule contains {} frame(s). Frames are 0-indexed.".format(self.numFrames))
         self._frame = value
 
+    @property
+    def numResidues(self):
+        from htmd.molecule.util import sequenceID
+        return sequenceID((self.resid, self.insertion, self.chain))
+
     def insert(self, mol, index, collisions=False, coldist=1.3):
         """Insert the contents of one molecule into another at a specific index.
 
@@ -973,21 +978,27 @@ def view(self, sel=None, style=None, color=None, guessBonds=True, viewer=None, h
         self.write(xtc)
 
         # Call the specified backend
+        retval = None
         if viewer is None:
             from htmd.config import _config
             viewer = _config['viewer']
         if viewer.lower() == 'notebook':
-            return self._viewMDTraj(psf, xtc)
+            retval = self._viewMDTraj(psf, xtc)
         elif viewer.lower() == 'vmd':
             self._viewVMD(psf, xtc, viewerhandle, name, guessBonds)
+            #retval = viewerhandle
         elif viewer.lower() == 'ngl' or viewer.lower() == 'webgl':
-            return self._viewNGL(gui=gui)
+            retval = self._viewNGL(gui=gui)
         else:
+            os.remove(xtc)
+            os.remove(psf)
             raise ValueError('Unknown viewer.')
 
         # Remove temporary files
         os.remove(xtc)
         os.remove(psf)
+        if retval is not None:
+            return retval
 
     def _viewVMD(self, psf, xtc, vhandle, name, guessbonds):
         if name is None:
@@ -1186,7 +1197,7 @@ def sequence(self, oneletter=True):
         '?EEI'
 
         """
-        from htmd.builder.builder import sequenceID
+        from htmd.molecule.util import sequenceID
         prot = self.atomselect('protein')
         segs = np.unique(self.segid[prot])
         increm = sequenceID((self.resid, self.insertion, self.chain))

htmd/molecule/util.py

@@ -44,7 +44,7 @@ def molTMscore(mol, ref, selCAmol, selCAref):
     from htmd.molecule.molecule import _residueNameTable
 
     def calculateVariables(currmol):
-        res = sequenceID((currmol.resid, currmol.insertion, currmol.segid, currmol.chain)) - 1
+        res = sequenceID((currmol.resid, currmol.insertion, currmol.segid, currmol.chain))
         caidx = currmol.name == 'CA'
         res = np.unique(res)
         reslen = len(res)
@@ -144,7 +144,7 @@ def sequenceID(field, prepend=None):
     else:
         seq = np.empty(fieldlen, dtype=object)
 
-    c = int(1)
+    c = int(0)
     if prepend is None:
         seq[0] = c
     else:

htmd/projections/metricsecondarystructure.py

@@ -64,7 +64,7 @@ def _calcarrays(self, mol):
         mol = mol.copy()
         mol.filter(self.sel, _logger=False)
 
-        residues = sequenceID((mol.resid, mol.chain, mol.insertion)) - 1  # Start at 0
+        residues = sequenceID((mol.resid, mol.chain, mol.insertion))
 
         backbone = mol.atomselect('backbone')
         ca_indices = np.where(mol.name == 'CA')[0].astype(np.int32)