fixed 0.1.6 merge conflicts

.gitignore

@@ -41,7 +41,7 @@ output/*/index.html
 # Sphinx
 docs/_build
 
-# 
+#
 *.itp
 *.top
 *.log
@@ -57,3 +57,5 @@ test/systems/8*
 test/systems/9*
 test/systems/archive
 .DS_Store
+
+*sublime-project

HISTORY.rst

@@ -22,7 +22,7 @@ History
 0.1.3 (2013-09-16)
 ++++++++++++++++++
 
-* The conversion part wa rewritten to make it more flexible.
+* The conversion part was rewritten to make it more flexible.
 * Cholestrol test is now passed.
 
 

README.md

@@ -18,11 +18,10 @@ reverse conversion of GROMACS topologies to NAMD is planned an will be implement
 
 
 ### Current stage
-PyTopol is currently in *alpha stage*. The results for several
-systems are shown below which are encouraging. However, before using it for
-production simulations, more testing is needed.
 
-Current version is 0.1.5. All 0.1.x versions will be considered alpha.
+Current version is 0.1.6.
+
+All 0.1.x versions will be considered **alpha**. See the results for the current tests below.
 
 
 ### Feedback
@@ -36,17 +35,14 @@ PyTopol is licensed under [GNU GPLv3](http://www.gnu.org/licenses/gpl.html).
 
 ## Quickstart
 
-[How to install PyTopol](https://github.com/resal81/PyTopol/wiki/PyTopol-Installation).
-
-[How to use psf2top.py](https://github.com/resal81/PyTopol/wiki/psf2top-Usage).
-
-[Comparison of NAMD and GROMACS for converted PSF topologies](https://github.com/resal81/PyTopol/wiki/psf2top-Tests).
+#### Installation
+[How to install PyTopol](https://github.com/resal81/PyTopol/wiki/PyTopol-Installation)
 
-## Summary of test results
 
-#### psf2top.py
+#### PSF to GROMACS topology conversion
+[How to use psf2top.py](https://github.com/resal81/PyTopol/wiki/psf2top-Usage)
 
-**Table 1**. Summary of the rmsd of potential terms between GROMACS 4.6.3 and NAMD 2.9. Single and double correspond to the single and double-precision versions of GROMCAS. Energies are in kcal/mol.
+**Table 1**. Summary of the rmsd of potential energy terms between GROMACS 4.6.3 and NAMD 2.9 (kcal/mol). Single and double correspond to the single and double-precision versions of GROMCAS.
 
 ```
 --------------------------  -----------------  -----------------

pytopol/__init__.py

@@ -3,4 +3,4 @@
 
 __author__ = 'Reza Salari'
 __email__ = '[email protected]'
-__version__ = '0.1.5'
+__version__ = '0.1.6'

pytopol/parsers/blocks.py

@@ -11,8 +11,12 @@ def __init__(self):
         self.impropertypes    = []
         self.cmaptypes        = []
         self.interactiontypes = []
+        self.pairtypes        = []
+        self.constrainttypes  = []
         self.forcefield=  None
 
+        self.information = {} # like 'atomtypes': self.atomtypes
+
 
 
 class Molecule(object):
@@ -26,8 +30,17 @@ def __init__(self):
         self.angles    = []
         self.dihedrals = []
         self.impropers = []
+
         self.cmaps     = []
         self.pairs     = []
+        self.exclusion_numb = None  # 0, 1, 2, ..
+        self.exclusions = []
+        self.settles    = []
+        self.constraints= []
+
+        self.information = {}  # like 'atoms': self.atoms
+
+        self.name = None
 
         self._anumb_to_atom = {}
 
@@ -105,7 +118,7 @@ class Atom(object):
         altlocs = list,
         atomtype= str,
         radius  = float,
-        charge  = radius,
+        charge  = float,
         mass    = float,
         chain   = str,
         resname = str,
@@ -130,50 +143,6 @@ def get_atomtype(self):
             return False
 
 
-
-class Bond:
-    def __init__(self):
-        self.atom1 = None
-        self.atom2 = None
-
-class Angle:
-    def __init__(self):
-        self.atom1 = None
-        self.atom2 = None
-        self.atom3 = None
-
-class Dihedral:
-    def __init__(self):
-        self.atom1 = None
-        self.atom2 = None
-        self.atom3 = None
-        self.atom4 = None
-
-class Improper:
-    def __init__(self):
-        self.atom1 = None
-        self.atom2 = None
-        self.atom3 = None
-        self.atom4 = None
-
-class CMap:
-    def __init__(self):
-        self.atom1 = None
-        self.atom2 = None
-        self.atom3 = None
-        self.atom4 = None
-        self.atom5 = None
-        self.atom6 = None
-        self.atom7 = None
-        self.atom8 = None
-
-class Pair:
-    def __init__(self):
-        self.atom1 = None
-        self.atom2 = None
-
-
-
 class Param:
     def convert(self, reqformat):
         assert reqformat in ('charmm', 'gromacs')
@@ -242,9 +211,18 @@ def convert(self, reqformat):
 
         elif isinstance(self, ImproperType):
             if reqformat == 'gromacs' and self.format == 'charmm':
-                self.gromacs['param']['kpsi'] = self.charmm['param']['kpsi'] * 2 * 4.184
-                self.gromacs['param']['psi0'] = self.charmm['param']['psi0']
+                for imp in self.charmm['param']:
+                    convimp = {}
+                    convimp['kpsi']  = imp['kpsi'] * 2 * 4.184
+                    convimp['psi0']  = imp['psi0']
+                    if imp.get('n', False):
+                        convimp['n']     = imp['n']
+                    self.gromacs['param'].append(convimp)
                 self.gromacs['func'] = 2
+
+                # self.gromacs['param']['kpsi'] = self.charmm['param']['kpsi'] * 2 * 4.184
+                # self.gromacs['param']['psi0'] = self.charmm['param']['psi0']
+                # self.gromacs['func'] = 2
             else:
                 raise NotImplementedError
 
@@ -261,8 +239,12 @@ def convert(self, reqformat):
 
         elif isinstance(self, InteractionType):
             if reqformat == 'gromacs' and self.format == 'charmm':
-                self.gromacs['param']['lje'] = abs(self.charmm['param']['lje']) * 4.184
-                self.gromacs['param']['ljl'] = self.charmm['param']['ljl'] * 0.1 /  (2**(1.0/6.0))   # no *2
+                if self.charmm['param']['lje'] is not None:
+                    self.gromacs['param']['lje'] = abs(self.charmm['param']['lje']) * 4.184
+                    self.gromacs['param']['ljl'] = self.charmm['param']['ljl'] * 0.1 /  (2**(1.0/6.0))   # no *2
+                else:
+                    self.gromacs['param']['lje'] = None
+                    self.gromacs['param']['ljl'] = None
 
                 if self.charmm['param']['lje14'] is not None:
                     self.gromacs['param']['lje14'] = abs(self.charmm['param']['lje14']) * 4.184
@@ -293,31 +275,47 @@ class BondType(Param):
     def __init__(self, format):
         assert format in ('charmm', 'gromacs')
         self.format = format
+
+
+        self.atom1 = None
+        self.atom2 = None
+
         self.atype1 = None
         self.atype2 = None
 
         self.charmm = {'param': {'kb':None, 'b0':None} }
-        self.gromacs= {'param': {}, 'func':None}
+        self.gromacs= {'param': {'kb':None, 'b0':None}, 'func':None}
 
 
 class AngleType(Param):
     def __init__(self, format):
         assert format in ('charmm', 'gromacs')
         self.format = format
 
+
+        self.atom1 = None
+        self.atom2 = None
+        self.atom3 = None
+
         self.atype1 = None
         self.atype2 = None
         self.atype3 = None
 
         self.charmm = {'param':{'ktetha':None, 'tetha0':None, 'kub':None, 's0':None} }
-        self.gromacs= {'param':{}}
+        self.gromacs= {'param':{'ktetha':None, 'tetha0':None, 'kub':None, 's0':None}, 'func':None}
 
 
 class DihedralType(Param):
     def __init__(self, format):
         assert format in ('charmm', 'gromacs')
         self.format = format
 
+
+        self.atom1 = None
+        self.atom2 = None
+        self.atom3 = None
+        self.atom4 = None
+
         self.atype1 = None
         self.atype2 = None
         self.atype3 = None
@@ -337,15 +335,24 @@ def __init__(self, format):
         self.atype3 = None
         self.atype4 = None
 
-        self.charmm = {'param': {'kpsi': None, 'psi0':None} }
-        self.gromacs= {'param':{}, 'func':None}
+        self.charmm = {'param':[]}
+        self.gromacs= {'param':[], 'func': None}  # {'kpsi': None, 'psi0':None}
 
 
 class CMapType(Param):
     def __init__(self, format):
         assert format in ('charmm', 'gromacs')
         self.format = format
 
+        self.atom1 = None
+        self.atom2 = None
+        self.atom3 = None
+        self.atom4 = None
+        self.atom5 = None
+        self.atom6 = None
+        self.atom7 = None
+        self.atom8 = None
+
         self.atype1 = None
         self.atype2 = None
         self.atype3 = None
@@ -364,9 +371,37 @@ def __init__(self, format):
         assert format in ('charmm', 'gromacs')
         self.format = format
 
+        self.atom1  = None
+        self.atom2  = None
+
         self.atype1 = None
         self.atype2 = None
 
         self.charmm = {'param': {'lje':None, 'ljl':None, 'lje14':None, 'ljl14':None} }
-        self.gromacs= {'param': {'lje':None, 'ljl':None, 'lje14':None, 'ljl14':None} }
+        self.gromacs= {'param': {'lje':None, 'ljl':None, 'lje14':None, 'ljl14':None}, 'func':None }
+
 
+class SettleType(Param):
+    def __init__(self, format):
+        assert format in ('gromacs',)
+        self.atom = None
+        self.dOH  = None
+        self.dHH  = None
+
+class ConstraintType(Param):
+    def __init__(self, format):
+        assert format in ('gromacs',)
+
+        self.atom1 = None
+        self.atom2 = None
+
+        self.atype1 = None
+        self.atype2 = None
+
+        self.gromacs= {'param': {'b0':None}, 'func':None}
+
+
+class Exclusion:
+    def __init__(self):
+        self.main_atom  = None
+        self.other_atoms = []

pytopol/parsers/charmmpar.py

@@ -444,8 +444,14 @@ def add_params_to_system(self, system, panic_on_missing_param=True):
                 newimp.atype3 = at3
                 newimp.atype4 = at4
 
-                newimp.charmm['param']['kpsi'] = kpsi
-                newimp.charmm['param']['psi0'] = psi0
+                # newimp.charmm['param']['kpsi'] = kpsi
+                # newimp.charmm['param']['psi0'] = psi0
+
+                m = {}
+                m['kpsi'] = kpsi
+                m['psi0'] = psi0
+
+                newimp.charmm['param'].append(m)
 
                 system.impropertypes.append(newimp)