Finish fluctmatch-3.3.5

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 3.3.4
+current_version = 3.3.5
 commit = True
 tag = True
 

README.rst

@@ -44,9 +44,9 @@ Overview
     :alt: PyPI Package latest release
     :target: https://pypi.python.org/pypi/fluctmatch
 
-.. |commits-since| image:: https://img.shields.io/github/commits-since/tclick/python-fluctmatch/v3.3.4.svg
+.. |commits-since| image:: https://img.shields.io/github/commits-since/tclick/python-fluctmatch/v3.3.5.svg
     :alt: Commits since latest release
-    :target: https://github.com/tclick/python-fluctmatch/compare/v3.3.4...master
+    :target: https://github.com/tclick/python-fluctmatch/compare/v3.3.5...master
 
 .. |wheel| image:: https://img.shields.io/pypi/wheel/fluctmatch.svg
     :alt: PyPI Wheel

docs/conf.py

@@ -26,7 +26,7 @@
 year = u'2014-2017'
 author = u'Timothy Click'
 copyright = '{0}, {1}'.format(year, author)
-version = release = u'3.3.4'
+version = release = u'3.3.5'
 
 pygments_style = 'trac'
 templates_path = ['.']

setup.py

@@ -45,7 +45,7 @@ def read(*names, **kwargs):
 
 setup(
     name="fluctmatch",
-    version="3.3.4",
+    version="3.3.5",
     license="BSD license",
     description="Elastic network model using fluctuation matching.",
     long_description="%s\n%s" % (

src/fluctmatch/__init__.py

@@ -24,7 +24,7 @@
 
 import logging
 
-__version__ = "3.3.4"
+__version__ = "3.3.5"
 
 _MODELS = dict()
 _DESCRIBE = dict()

src/fluctmatch/commands/cmd_splittraj.py

@@ -113,7 +113,7 @@
     metavar="LOG",
     show_default=True,
     default="splittraj.log",
-    type=click.Path(exists=False, file_okay=True, resolve_path=True),
+    type=click.Path(exists=False, file_okay=True, resolve_path=False),
     help="Log file",
 )
 @click.option(
@@ -177,7 +177,7 @@ def cli(program, toppar, topology, trajectory, data, index, outfile, logfile,
             },
             "file": {
                 "class": "logging.FileHandler",
-                "filename": logfile,
+                "filename": path.join(os.getcwd(), logfile),
                 "level": "INFO",
                 "mode": "w",
                 "formatter": "detailed",

src/fluctmatch/commands/cmd_table_convert.py

@@ -114,7 +114,7 @@ def cli(logfile, top1, top2, coord, table, outfile):
             },
             "file": {
                 "class": "logging.FileHandler",
-                "filename": logfile,
+                "filename": path.join(os.getcwd(), logfile),
                 "level": "INFO",
                 "mode": "w",
                 "formatter": "detailed",
@@ -130,7 +130,10 @@ def cli(logfile, top1, top2, coord, table, outfile):
     cg = mda.Universe(top1, coord)
     fluctmatch = mda.Universe(top2, coord)
     convert = dict(zip(fluctmatch.atoms.names, cg.atoms.names))
-    resnames = dict(zip(cg.residues.resnums, cg.residues.resnames))
+    resnames = pd.DataFrame.from_records(
+        zip(cg.residues.segids, cg.residues.resnums, cg.residues.resnames),
+        columns=["segid", "res", "resn"]
+    ).set_index(["segid", "res"])
 
     with open(table, "rb") as tbl:
         logger.info("Loading {}.".format(table))
@@ -147,10 +150,14 @@ def cli(logfile, top1, top2, coord, table, outfile):
     constants["J"] = constants["J"].apply(lambda x: convert[x])
 
     # Create lists of corresponding residues
-    constants["resnI"] = constants["resI"].apply(
-        lambda x: resnames[x]).to_frame()
-    constants["resnJ"] = constants["resJ"].apply(
-        lambda x: resnames[x]).to_frame()
+    columns = ["segidI", "resI", "segidJ", "resJ"]
+    resnI = []
+    resnJ = []
+    for segidI, resI, segidJ, resJ in constants[columns].values:
+        resnI.append(resnames.loc[(segidI, resI),])
+        resnJ.append(resnames.loc[(segidJ, resJ),])
+    constants["resnI"] = pd.concat(resnI).values
+    constants["resnJ"] = pd.concat(resnJ).values
 
     # Concatenate the columns
     cols = ["segidI", "resI", "resnI", "I", "segidJ", "resJ", "resnJ", "J"]