Added PDBGC functionality, minor bugfixes.

Added the funcionality of writing out a PDB structure with group
contributions added in the B-factor field (q_calc.py gc ... --pdbgc asd.pdb)
Changed the output of GCs - sorted by numeric index (not string index).

Minor bug in read_prm fixed (error in raising an error).
Double init of logger in q_calc and q_automapper removed.

packages/Qpyl/common.py

@@ -36,7 +36,7 @@
 logger = logging.getLogger(__name__)
 
 
-__version__ = "0.5.7"
+__version__ = "0.5.8"
 
 
 class SpecialFormatter(logging.Formatter):

packages/Qpyl/core/qparameter.py

@@ -134,9 +134,8 @@ def read_prm(self, parm_fn):
                         key, value = line.split()
                     except ValueError:
                         raise QPrmError("Malformed key/value pair in "
-                                        "[options] section of parm file: "
-                                        "{line}"
-                                        .format(line))
+                                        "[options] section of parm file: {}"
+                                        "".format(line))
                     self.options[key] = value
 
 

packages/Qpyl/qgroupcontrib.py

@@ -242,7 +242,8 @@ def calcall(self):
 
         # iterate through each residue and calculate
         # means and stdevs
-        for res_key in sorted(gcs.keys()):
+        # (sort by residue index)
+        for res_key in sorted(gcs.keys(), key=lambda x: int(x.split(".")[0])):
             rc = gcs[res_key]
             resid, resname = res_key.split(".")
             # get mean and stdev
@@ -522,5 +523,29 @@ def plotdata(self):
         return plots
 
 
+    def get_pdbgc(self):
+        """Return the pdb structure (string) with added GC values.
 
-
+        Fill the 'Temperature factor' fields with the calculated GC values,
+        and return the whole pdb structure in string format.
+        """
+        resids, _, _, _, _, els, _ = self.gcs_stats.get_columns()
+        gcs = dict(zip(resids, els))
+        pdb = []
+        for mol in self._pdb_qstruct.molecules:
+            for res in mol.residues:
+                for atom in res.atoms:
+                    x, y, z = atom.coordinates
+                    try:
+                        gc = gcs[atom.residue.index]
+                    except KeyError:
+                        gc = 0
+                    finally:
+                        pdb.append("ATOM  {:>5d} {:<4s} {:3s}  {:>4d}    "\
+                                "{:>8.3f}{:>8.3f}{:>8.3f}{:>6}{:>6.2f}"\
+                                "".format(atom.index, atom.name,
+                                          atom.residue.name,
+                                          atom.residue.index,
+                                          x, y, z, "", gc))
+            pdb.append("GAP")
+        return "\n".join(pdb)

qscripts-cli/q_automapper.py

@@ -55,9 +55,6 @@
 from Qpyl.qmapping import QMapper, QMapperError
 from Qpyl.common import backup_file, init_logger
 
-logger = init_logger('Qpyl')
-
-
 def main():
     logger = init_logger('Qpyl')
 

qscripts-cli/q_calc.py

@@ -36,8 +36,6 @@
 from Qpyl import plotdata
 from Qpyl.common import backup_file, init_logger
 
-logger = init_logger('Qpyl')
-
 def gc(args):
 
     if not os.path.lexists(args.pdb):
@@ -158,6 +156,14 @@ def gc(args):
     print "Wrote '{}'... (q_plot.py is your "\
           "friend)".format(fn_out)
 
+    # writeout the pdbgc if requested
+    if args.pdbgc_out:
+        backup = backup_file(args.pdbgc_out)
+        if backup:
+            print "# Backed up '{}' to '{}'".format(args.pdbgc_out, backup)
+        open(args.pdbgc_out, 'w').write(qgc.get_pdbgc())
+        print "Wrote '{}'... (use Pymol/Chimera/VMD and color by B-factor)"\
+            "".format(args.pdbgc_out)
 
 
 def main():
@@ -233,6 +239,12 @@ def main():
                                 "".format(QScfg.get("files", "calcs_log")),
                            default=QScfg.get("files", "calcs_log"))
 
+    gc_optarg.add_argument("--pdbgc", dest="pdbgc_out",
+                           help="Output filename of PDB structure file "
+                                "with group contributions in place of the "
+                                "B-factor. Default=Don't output.",
+                           default=None)
+
     gc_optarg.add_argument("--writeout", action="store_true", default=False,
                            help="Write out QCalc inputs and outputs."
                                 "Default=Don't")