From ddaf27dea83985a6e52308ba13f456c653652069 Mon Sep 17 00:00:00 2001
From: Oliver Beckstein <orbeckst@gmail.com>
Date: Tue, 10 Jun 2014 14:12:24 -0700
Subject: [PATCH] run.single() to run a propka calculation without script

- can pass a single pdffile (or stream(!))
- added options lib.loadOptions() to pass opt string
---
 propka/lib.py |  8 ++++++--
 propka/run.py | 18 ++++++++++++++++++
 2 files changed, 24 insertions(+), 2 deletions(-)

diff --git a/propka/lib.py b/propka/lib.py
index caa62ff..88f2ba9 100644
--- a/propka/lib.py
+++ b/propka/lib.py
@@ -107,7 +107,7 @@ def make_combination(combis, interaction):
 
 
 
-def loadOptions():
+def loadOptions(*args):
     """
     load the arguments parser with options
     """
@@ -166,7 +166,11 @@ def loadOptions():
 
 
     # parsing and returning options and arguments
-    options, args = parser.parse_args()
+    if len(args) == 0:
+        # command line
+        options, args = parser.parse_args()
+    else:
+        options, args = parser.parse_args(list(args))
 
     # adding specified filenames to arguments
     if options.filenames:
diff --git a/propka/run.py b/propka/run.py
index 867a000..7eb13a5 100644
--- a/propka/run.py
+++ b/propka/run.py
@@ -13,3 +13,21 @@ def main():
         my_molecule = propka.molecular_container.Molecular_container(pdbfile, options)
         my_molecule.calculate_pka()
         my_molecule.write_pka()
+
+def single(pdbfile, optargs=None):
+    """Run a single PROPKA calculation using *pdbfile* as input.
+
+    Commandline options can be passed as a **list** in *optargs*.
+
+    .. rubric:: Example
+
+    ::
+       single("protein.pdb", optargs=["--mutation=N25R/N181D", "-v", "--pH=7.2"])
+    """
+    optargs = optargs if optargs is not None else []
+    options, ignored_pdbfiles = propka.lib.loadOptions(*optargs)
+
+    my_molecule = propka.molecular_container.Molecular_container(pdbfile, options)
+    my_molecule.calculate_pka()
+    my_molecule.write_pka()
+    return my_molecule