diff --git a/.travis.yml b/.travis.yml
index 94edbd1b9dc607746929142b825e81d03540195e..605deb06b39daa98a76b0c33a512bf377cbe6d13 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -92,6 +92,10 @@ install:
- export INCLUDE="$HOME/opt/include:$INCLUDE"
- export LIBRARY_PATH="$HOME/opt/lib:$LIBRARY_PATH"
- export LD_LIBRARY_PATH="$HOME/opt/lib:$LD_LIBRARY_PATH"
+ - export PYTHONPATH="$HOME/opt/lib/plumed/python:$PYTHONPATH"
+# Setting the TMPDIR in this way allegedly prevents problems with the compilation of
+#Â PLUMED + Python on macos
+ - export TMPDIR="/tmp"
# on travis, better dump stack trace in case there is an error
- export PLUMED_STACK_TRACE=yes
# build the manual, only if log contains string [makedoc]
@@ -124,6 +128,16 @@ install:
- if test "$MAKEDOC" == yes ; then sudo apt-get install -y doxygen-latex ; fi
# install lcov
- if test "$MAKEDOC" == yes ; then ./.travis/install.lcov v1.13 ; fi
+# install numpy and cython for python interface
+ - if test "$TRAVIS_OS_NAME" == "linux" ; then wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh ; fi
+ - if test "$TRAVIS_OS_NAME" == "osx" ; then wget https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh ; fi
+ - bash miniconda.sh -b -p $HOME/miniconda
+ - export PATH="$HOME/miniconda/bin:$PATH"
+ - hash -r
+ - conda config --set always_yes yes --set changeps1 no
+ - conda update -q conda
+ - conda create -q -n test-environment python=3.6 numpy Cython
+ - source activate test-environment
# then replace doxygen with the desided version
# I use 1.8.10 instead of 1.8.11 since it looks like 1.8.11 have troubles with
# non case sensitive files (it writes capitalized filenames)
diff --git a/Makefile b/Makefile
index 7be10652df3890c81a10f56ed13952a9d775d74e..4aba51e1054ad1d998830e1a47955194fb230253 100644
--- a/Makefile
+++ b/Makefile
@@ -8,7 +8,7 @@ endif
SRCDIRS := src test
-SUBDIRS := $(SRCDIRS) user-doc developer-doc regtest macports vim astyle
+SUBDIRS := $(SRCDIRS) user-doc developer-doc regtest macports vim astyle python
SUBDIRSCLEAN:=$(addsuffix .clean,$(SUBDIRS))
@@ -20,6 +20,7 @@ ifdef GCCDEP
all:
$(MAKE) lib
$(MAKE) -C vim
+ $(MAKE) -C python
# target useful for macports
# it builds the code then the documentation
diff --git a/configure b/configure
index 3e7320705a548a07f0c0cc198b670edf717711b2..971a7188e8dedef4a2c608f90c3eb9e66a6cf7bd 100755
--- a/configure
+++ b/configure
@@ -632,6 +632,8 @@ doxygen
make_doc
readelf
LD
+cython
+py
OPENMP_CXXFLAGS
EGREP
GREP
@@ -724,6 +726,7 @@ enable_xdrfile
enable_boost_graph
enable_boost_serialization
enable_fftw
+enable_python
enable_openmp
'
ac_precious_vars='build_alias
@@ -1395,6 +1398,7 @@ Optional Features:
--enable-boost_serialization
enable search for boost serialization, default: no
--enable-fftw enable search for fftw, default: no
+ --enable-python enable search for python, default: yes
--disable-openmp do not use OpenMP
Some influential environment variables:
@@ -2957,6 +2961,24 @@ fi
+python=
+# Check whether --enable-python was given.
+if test "${enable_python+set}" = set; then :
+ enableval=$enable_python; case "${enableval}" in
+ (yes) python=true ;;
+ (no) python=false ;;
+ (*) as_fn_error $? "wrong argument to --enable-python" "$LINENO" 5 ;;
+ esac
+else
+ case "yes" in
+ (yes) python=true ;;
+ (no) python=false ;;
+ esac
+
+fi
+
+
+
@@ -7546,6 +7568,89 @@ fi
fi
+if test $python == true ; then
+ # Extract the first word of "python", so it can be a program name with args.
+set dummy python; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_py+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$py"; then
+ ac_cv_prog_py="$py" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ ac_cv_prog_py="found"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+py=$ac_cv_prog_py
+if test -n "$py"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $py" >&5
+$as_echo "$py" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ # Extract the first word of "cython", so it can be a program name with args.
+set dummy cython; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_cython+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$cython"; then
+ ac_cv_prog_cython="$cython" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ ac_cv_prog_cython="found"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+cython=$ac_cv_prog_cython
+if test -n "$cython"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $cython" >&5
+$as_echo "$cython" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ if test "$py" == found && test "$cython" == found ; then
+ $as_echo "#define __PLUMED_HAS_PYTHON 1" >>confdefs.h
+
+ else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cannot enable python" >&5
+$as_echo "$as_me: WARNING: cannot enable python" >&2;}
+ fi
+fi
diff --git a/configure.ac b/configure.ac
index 708bc405cf01643650bc6fa0c933d21e62f3d087..5b580c56cf82d4ae2d4bd5198cac14758675a4ef 100644
--- a/configure.ac
+++ b/configure.ac
@@ -249,6 +249,7 @@ PLUMED_CONFIG_ENABLE([xdrfile],[search for xdrfile],[yes])
PLUMED_CONFIG_ENABLE([boost_graph],[search for boost graph],[no])
PLUMED_CONFIG_ENABLE([boost_serialization],[search for boost serialization],[no])
PLUMED_CONFIG_ENABLE([fftw],[search for fftw],[no])
+PLUMED_CONFIG_ENABLE([python],[search for python],[yes])
AC_ARG_VAR(SOEXT,[extension of dynamic libraries (so/dylib)])
AC_ARG_VAR(STATIC_LIBS,[variables that should be linked statically directly to MD code - configure will add here -ldl if necessary ])
@@ -585,6 +586,15 @@ fi
if test $zlib == true ; then
PLUMED_CHECK_PACKAGE([zlib.h],[gzopen],[__PLUMED_HAS_ZLIB],[z])
fi
+if test $python == true ; then
+ AC_CHECK_PROG([py],[python],[found])
+ AC_CHECK_PROG([cython],[cython],[found])
+ if test "$py" == found && test "$cython" == found ; then
+ AC_DEFINE([__PLUMED_HAS_PYTHON])
+ else
+ AC_MSG_WARN([cannot enable python])
+ fi
+fi
if test $gsl == true ; then
found=ko
diff --git a/python/.gitignore b/python/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..bac163535e27198d4ed639a1ca80a0d3aed5b2ab
--- /dev/null
+++ b/python/.gitignore
@@ -0,0 +1,9 @@
+/*
+# in this directory, only accept source, Makefile and README
+!/.gitignore
+!/*.pxd
+!/*.py
+!/*.pyx
+!/Makefile
+!/README
+!/module.type
diff --git a/python/Makefile b/python/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..0877e8893eb3e9940627a34c28b3694a30316df9
--- /dev/null
+++ b/python/Makefile
@@ -0,0 +1,34 @@
+# include the machine dependent configuration
+ifneq ($(MAKECMDGOALS),clean)
+ -include ../Makefile.conf
+endif
+
+.PHONY: all clean install
+
+plumed_compiled := $(wildcard ../src/lib/plumed)
+
+ifeq ($(strip $(plumed_compiled)),)
+
+all:
+ @echo You must compile plumed before building the cython interface
+
+else
+
+ifneq (,$(findstring __PLUMED_HAS_PYTHON,$(CPPFLAGS)))
+
+all:
+ @echo Building python interface for PLUMED
+ python buildPythonInterface.py build_ext -i
+
+else
+
+all:
+ @echo Did not find __PLUMED_HAS_PYTHON
+ @echo $(CPPFLAGS)
+
+endif
+
+endif
+
+clean:
+ rm -fr *.so plumed.cpp build
diff --git a/python/buildPythonInterface.py b/python/buildPythonInterface.py
new file mode 100644
index 0000000000000000000000000000000000000000..72e853f6985197cde1b55e31b270781df2a5378e
--- /dev/null
+++ b/python/buildPythonInterface.py
@@ -0,0 +1,79 @@
+#/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+# Copyright (c) 2011-2016 The plumed team
+# (see the PEOPLE file at the root of the distribution for a list of names)
+#
+# See http://www.plumed.org for more information.
+#
+# This file is part of plumed, version 2.
+#
+# plumed is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# plumed is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with plumed. If not, see <http://www.gnu.org/licenses/>.
+#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#
+# This python routine builds an interface between plumed and python using cython
+#
+from distutils.core import setup
+from distutils.extension import Extension
+from Cython.Build import cythonize
+import numpy
+import subprocess
+import os
+
+# Function for checking if PLUMED is in path
+def is_exe(fpath):
+ return os.path.isfile(fpath) and os.access(fpath, os.X_OK)
+
+# Check if PLUMED is in PATH
+plumedexe = '../src/lib/plumed'
+for path in os.environ["PATH"].split(os.pathsep):
+ path = path.strip('"')
+ exe_file = os.path.join(path, 'plumed')
+ if is_exe(exe_file) :
+ plumedexe=exe_file
+ break
+
+#Â Get information on where plumed headers and libraries are installed and the version number
+print( "Plumedexe is " + plumedexe )
+plumedroot = subprocess.check_output([plumedexe, 'info', '--root']).decode("utf-8").strip("\n")
+print( "Creating interface for plumed version in " + plumedroot )
+plumedhead = subprocess.check_output([plumedexe, 'info', '--include-dir']).decode("utf-8").strip("\n") + "/plumed/wrapper/"
+print( "Using headers in " + plumedhead )
+plumedversion = subprocess.check_output([plumedexe, 'info', '--version']).decode("utf-8")
+print( "Version number for this plumed is " + plumedversion )
+# Get list containing all config variables so we can extract information on compilers to use during cython build
+plumedconfig = subprocess.check_output([plumedexe, 'info', '--configuration']).decode("utf-8").split("\n")
+
+for line in plumedconfig :
+ if "CC=" in line : os.environ["CC"] = line.replace("CC=","").replace("\n","")
+ if "CXX=" in line : os.environ["CXX"] = line.replace("CXX=","").replace("\n","")
+ if "LDSO=" in line : os.environ["LDSHARED"] = line.replace("LDSO=","").replace("\n","")
+
+print( "Building interface using CC=" + os.environ["CC"] + " , CXX=" + os.environ["CXX"] + " and LDSHARED=" + os.environ["LDSHARED"] )
+
+setup(
+ name='plumed',
+ version=plumedversion,
+ description='Python interface to PLUMED',
+ author='Gareth A. Tribello',
+ author_email='plumed-users@googlegroups.com',
+ url='http://www.plumed.org',
+ ext_modules = cythonize([
+ Extension( name="plumed",
+ sources=["plumed.pyx"],
+ library_dirs=[plumedroot, plumedroot + "/src/lib/"],
+ libraries=["plumed"],
+ language="c++",
+ include_dirs=[plumedhead, numpy.get_include()]
+ )
+ ])
+)
diff --git a/python/cplumed.pxd b/python/cplumed.pxd
new file mode 100644
index 0000000000000000000000000000000000000000..e0f58c121983ed2d84a1a29adf904953c1f12180
--- /dev/null
+++ b/python/cplumed.pxd
@@ -0,0 +1,29 @@
+#/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+# Copyright (c) 2011-2016 The plumed team
+# (see the PEOPLE file at the root of the distribution for a list of names)
+#
+# See http://www.plumed.org for more information.
+#
+# This file is part of plumed, version 2.
+#
+# plumed is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# plumed is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with plumed. If not, see <http://www.gnu.org/licenses/>.
+#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#
+# This create cython wrappers to the main bits of the PLUMED libraray
+#
+cdef extern from "Plumed.h" :
+ ctypedef struct plumed:
+ pass
+ plumed plumed_create()
+ void plumed_cmd(plumed p, const char*key, const void*val) except +
diff --git a/python/plumed.pyx b/python/plumed.pyx
new file mode 100644
index 0000000000000000000000000000000000000000..de2767157b241f3cddd5ac9adfd6a8786666b163
--- /dev/null
+++ b/python/plumed.pyx
@@ -0,0 +1,80 @@
+#/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+# Copyright (c) 2011-2016 The plumed team
+# (see the PEOPLE file at the root of the distribution for a list of names)
+#
+# See http://www.plumed.org for more information.
+#
+# This file is part of plumed, version 2.
+#
+# plumed is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# plumed is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with plumed. If not, see <http://www.gnu.org/licenses/>.
+#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#
+# This is a cython wrapper for the main parts of the PLUMED interface - the constructor and cmd
+# The main purpose of this is to convert the python types to C types that PLUMED understands
+#
+
+cimport cplumed # This imports information from pxd file - including contents of this file here causes name clashes
+import numpy as np
+cimport numpy as np
+
+cdef class Plumed:
+ cdef cplumed.plumed c_plumed
+ def __cinit__(self):
+ self.c_plumed = cplumed.plumed_create() #new cplumed.Plumed()
+ cdef int pres = 8
+ cplumed.plumed_cmd(self.c_plumed, "setRealPrecision", <void*>&pres )
+ def __dealloc__(self):
+ pass
+ #del self.c_plumed
+
+ def cmd_ndarray_real(self, ckey, val):
+ cdef double [:] abuffer = val.ravel()
+ cplumed.plumed_cmd(self.c_plumed, ckey, <void*>&abuffer[0])
+ def cmd_ndarray_int(self, ckey, val):
+ cdef long [:] abuffer = val.ravel()
+ cplumed.plumed_cmd(self.c_plumed, ckey, <void*>&abuffer[0])
+ cdef cmd_float(self, ckey, double val ):
+ cplumed.plumed_cmd(self.c_plumed, ckey, <void*>&val )
+ cdef cmd_int(self, ckey, int val):
+ cplumed.plumed_cmd(self.c_plumed, ckey, <void*>&val)
+
+ def cmd( self, key, val=None ):
+ cdef bytes py_bytes = key.encode()
+ cdef char* ckey = py_bytes
+ cdef char* cval
+ cdef np.int_t[:] ibuffer
+ cdef np.float64_t[:] dbuffer
+ if val is None :
+ cplumed.plumed_cmd( self.c_plumed, ckey, NULL )
+ elif isinstance(val, (int,long) ):
+ if key=="getDataRank" :
+ raise ValueError("when using cmd with getDataRank option value must a size one ndarray")
+ self.cmd_int(ckey, val)
+ elif isinstance(val, float ) :
+ if key=="getBias" :
+ raise ValueError("when using cmd with getBias option value must be a size one ndarray")
+ self.cmd_float(ckey, val)
+ elif isinstance(val, np.ndarray) :
+ if( val.dtype=="float64" ):
+ self.cmd_ndarray_real(ckey, val)
+ elif( val.dtype=="int64" ) :
+ self.cmd_ndarray_int(ckey, val)
+ else :
+ raise ValueError("ndarrys should be float64 or int64")
+ elif isinstance(val, basestring ) :
+ py_bytes = val.encode()
+ cval = py_bytes
+ cplumed.plumed_cmd( self.c_plumed, ckey, <void*>cval )
+ else :
+ raise ValueError("Unknown value type ({})".format(str(type(val))))
diff --git a/regtest/.gitignore b/regtest/.gitignore
index a19e9d680d5318bfc20d10bb29c17e1a434c58b6..6e747a7ce991b8a50154b8d2ab3e8796377d3f77 100644
--- a/regtest/.gitignore
+++ b/regtest/.gitignore
@@ -12,6 +12,7 @@
!/drr
!/mapping
!/multicolvar
+!/python
!/secondarystructure
!/trajectories
!/scripts
diff --git a/regtest/python/Makefile b/regtest/python/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..42480767ae852294cf2d7269ac5a1c16064d1849
--- /dev/null
+++ b/regtest/python/Makefile
@@ -0,0 +1,2 @@
+include ../scripts/module.make
+
diff --git a/regtest/python/rt-protein/Makefile b/regtest/python/rt-protein/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/python/rt-protein/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/python/rt-protein/colvar.ref b/regtest/python/rt-protein/colvar.ref
new file mode 100644
index 0000000000000000000000000000000000000000..2749c867608d9faec8a9b4890a22c9d46f3337d2
--- /dev/null
+++ b/regtest/python/rt-protein/colvar.ref
@@ -0,0 +1,75 @@
+#! FIELDS time t1 t2 t3 t4 t5 t6 t7 t8 t9 t10 t11 t12 t13 t14 t15 t16 t17 t18 t19 t20 t21 t22 t23 t24 t25 t26 t27 t28 t29 t30 t31 t32
+#! SET min_t1 -pi
+#! SET max_t1 pi
+#! SET min_t2 -pi
+#! SET max_t2 pi
+#! SET min_t3 -pi
+#! SET max_t3 pi
+#! SET min_t4 -pi
+#! SET max_t4 pi
+#! SET min_t5 -pi
+#! SET max_t5 pi
+#! SET min_t6 -pi
+#! SET max_t6 pi
+#! SET min_t7 -pi
+#! SET max_t7 pi
+#! SET min_t8 -pi
+#! SET max_t8 pi
+#! SET min_t9 -pi
+#! SET max_t9 pi
+#! SET min_t10 -pi
+#! SET max_t10 pi
+#! SET min_t11 -pi
+#! SET max_t11 pi
+#! SET min_t12 -pi
+#! SET max_t12 pi
+#! SET min_t13 -pi
+#! SET max_t13 pi
+#! SET min_t14 -pi
+#! SET max_t14 pi
+#! SET min_t15 -pi
+#! SET max_t15 pi
+#! SET min_t16 -pi
+#! SET max_t16 pi
+#! SET min_t17 -pi
+#! SET max_t17 pi
+#! SET min_t18 -pi
+#! SET max_t18 pi
+#! SET min_t19 -pi
+#! SET max_t19 pi
+#! SET min_t20 -pi
+#! SET max_t20 pi
+#! SET min_t21 -pi
+#! SET max_t21 pi
+#! SET min_t22 -pi
+#! SET max_t22 pi
+#! SET min_t23 -pi
+#! SET max_t23 pi
+#! SET min_t24 -pi
+#! SET max_t24 pi
+#! SET min_t25 -pi
+#! SET max_t25 pi
+#! SET min_t26 -pi
+#! SET max_t26 pi
+#! SET min_t27 -pi
+#! SET max_t27 pi
+#! SET min_t28 -pi
+#! SET max_t28 pi
+#! SET min_t29 -pi
+#! SET max_t29 pi
+#! SET min_t30 -pi
+#! SET max_t30 pi
+#! SET min_t31 -pi
+#! SET max_t31 pi
+#! SET min_t32 -pi
+#! SET max_t32 pi
+ 0.000000 2.6673 -2.6079 -2.5276 2.5020 -1.3261 3.0525 -1.8084 -0.0736 -1.3280 2.6118 -2.0303 1.8183 -1.3815 -0.2169 -1.2568 -0.7685 -1.7450 -0.3744 1.2239 0.8575 -2.4660 2.6198 -1.8094 2.9244 -1.5597 2.8624 -1.1022 2.1081 -2.0835 0.6224 -2.1615 2.7653
+ 1.000000 2.6673 -2.6079 -2.5276 2.5020 -1.3261 3.0525 -1.8084 -0.0736 -1.3280 2.6118 -2.0303 1.8183 -1.3815 -0.2169 -1.2568 -0.7685 -1.7450 -0.3744 1.2239 0.8575 -2.4660 2.6198 -1.8094 2.9244 -1.5597 2.8624 -1.1022 2.1081 -2.0835 0.6224 -2.1615 2.7653
+ 2.000000 -0.9673 2.4119 -2.2418 2.7803 -2.3131 2.3876 -2.3286 2.3327 -1.4141 2.2393 -2.2142 2.2270 -0.9976 -0.3431 -1.0938 -0.3082 -2.2269 -0.2595 0.7807 0.4861 -2.3900 2.7449 -1.4376 2.1693 -2.3192 2.6746 -1.2204 2.4187 -1.4845 -0.1224 -2.6383 -0.5531
+ 3.000000 -1.3798 2.7585 -2.3505 2.3231 -2.4228 2.7527 -2.5022 2.4132 -1.0556 2.2403 -2.4706 2.7123 -1.4820 0.2169 -1.1392 -0.7251 -2.1587 -0.0695 1.0791 0.9229 -2.8680 2.8393 -1.0979 2.0346 -2.1888 2.3545 -1.0655 2.3049 -1.3419 0.0942 -1.1673 2.3807
+ 4.000000 1.2920 -0.7003 -2.5882 2.4760 -2.4540 2.3686 -1.4398 2.6403 -2.4205 2.0865 -1.3307 1.4736 -1.0424 -0.1993 -1.4950 -0.1059 -2.4983 -0.1105 1.0443 0.4840 -1.7222 2.4065 -1.7269 2.3143 -2.2191 2.3508 -1.1054 2.6893 -1.3528 -0.5495 -2.7595 2.9670
+ 5.000000 1.8599 -3.1274 -1.3579 2.4524 -1.9912 2.8062 -2.0123 2.1368 -1.4832 2.4309 -2.0781 2.1238 -1.3223 -0.0961 -1.5850 -0.3327 -1.9738 -0.3105 1.0355 0.7932 -2.2536 2.8352 -1.7773 2.2652 -2.0858 2.6194 -1.2476 2.5713 -1.3721 -0.3135 -2.7986 -0.5437
+ 6.000000 -1.5246 -0.2344 -2.7770 2.3525 -2.2150 2.7121 -2.1907 2.7251 -2.1034 2.8239 -2.4138 1.7869 -0.8552 -0.6065 -1.0890 -0.4862 -1.9182 -0.1710 1.1336 0.3106 -1.7386 2.5118 -1.6340 2.4873 -2.3121 2.5220 -1.2814 2.6471 -1.2469 -0.4013 -1.5424 0.0513
+ 7.000000 1.3204 2.6070 -2.5673 -3.0655 -2.0904 2.3325 -2.5554 2.6183 -1.8992 2.6116 -1.9680 2.2707 -1.3625 -0.6381 -1.3566 -0.0505 -2.2325 -0.1415 0.9845 0.5160 -1.8538 2.8091 -2.1497 2.1461 -2.3947 2.5541 -2.3627 2.4673 -1.6932 1.0496 -2.6498 2.5858
+ 8.000000 -1.0771 -3.0455 -2.5817 2.8269 -1.8861 2.3354 -2.7105 2.4447 -1.6689 2.7067 -2.4288 2.1654 -1.3553 -0.4675 -1.2710 -0.4276 -2.2087 0.0495 0.9547 0.9757 -2.3635 2.8981 -1.8110 2.6522 -2.4328 2.3552 -2.2381 2.1866 -1.0044 -0.3137 -2.0097 0.1108
+ 9.000000 1.3122 -0.2812 -1.5467 2.8023 -1.4313 2.3505 -2.4359 2.5426 -1.8438 2.8783 -2.6368 1.9558 -1.2627 -0.5596 -1.0455 -0.2465 -2.1349 -0.1464 0.9422 0.2845 -1.7008 2.9339 -2.1567 2.6516 -2.4158 2.1019 -1.7146 2.0221 -1.2844 0.3707 -1.1716 2.6711
diff --git a/regtest/python/rt-protein/config b/regtest/python/rt-protein/config
new file mode 100644
index 0000000000000000000000000000000000000000..57dff95f9f3629a7e1f75f1cac2d52021a23fade
--- /dev/null
+++ b/regtest/python/rt-protein/config
@@ -0,0 +1,4 @@
+plumed_needs=python
+# this is to test a different name
+arg="./python-script.py"
+extra_files="../../trajectories/trajectory.xyz"
diff --git a/regtest/python/rt-protein/logfile.reference b/regtest/python/rt-protein/logfile.reference
new file mode 100644
index 0000000000000000000000000000000000000000..c46dd449a1c7f036f0bd523c4556990040b7c858
--- /dev/null
+++ b/regtest/python/rt-protein/logfile.reference
@@ -0,0 +1,10 @@
+RUNNING ANALYSIS FOR STEP 0
+RUNNING ANALYSIS FOR STEP 1
+RUNNING ANALYSIS FOR STEP 2
+RUNNING ANALYSIS FOR STEP 3
+RUNNING ANALYSIS FOR STEP 4
+RUNNING ANALYSIS FOR STEP 5
+RUNNING ANALYSIS FOR STEP 6
+RUNNING ANALYSIS FOR STEP 7
+RUNNING ANALYSIS FOR STEP 8
+RUNNING ANALYSIS FOR STEP 9
diff --git a/regtest/python/rt-protein/python-script.py b/regtest/python/rt-protein/python-script.py
new file mode 100644
index 0000000000000000000000000000000000000000..88edd6abb29a3f064ec997dba45fd922c6955fb4
--- /dev/null
+++ b/regtest/python/rt-protein/python-script.py
@@ -0,0 +1,149 @@
+# The numbers calculated by the following python script are compared with those output from this PLUMED input
+#
+# MOLINFO STRUCTURE=template.pdb
+# t1: TORSION ATOMS=@phi-2
+# t2: TORSION ATOMS=@psi-2
+# t3: TORSION ATOMS=@phi-3
+# t4: TORSION ATOMS=@psi-3
+# t5: TORSION ATOMS=@phi-4
+# t6: TORSION ATOMS=@psi-4
+# t7: TORSION ATOMS=@phi-5
+# t8: TORSION ATOMS=@psi-5
+# t9: TORSION ATOMS=@phi-6
+# t10: TORSION ATOMS=@psi-6
+# t11: TORSION ATOMS=@phi-7
+# t12: TORSION ATOMS=@psi-7
+# t13: TORSION ATOMS=@phi-8
+# t14: TORSION ATOMS=@psi-8
+# t15: TORSION ATOMS=@phi-9
+# t16: TORSION ATOMS=@psi-9
+# t17: TORSION ATOMS=@phi-10
+# t18: TORSION ATOMS=@psi-10
+# t19: TORSION ATOMS=@phi-11
+# t20: TORSION ATOMS=@psi-11
+# t21: TORSION ATOMS=@phi-12
+# t22: TORSION ATOMS=@psi-12
+# t23: TORSION ATOMS=@phi-13
+# t24: TORSION ATOMS=@psi-13
+# t25: TORSION ATOMS=@phi-14
+# t26: TORSION ATOMS=@psi-14
+# t27: TORSION ATOMS=@phi-15
+# t28: TORSION ATOMS=@psi-15
+# t29: TORSION ATOMS=@phi-16
+# t30: TORSION ATOMS=@psi-16
+# t31: TORSION ATOMS=@phi-17
+# t32: TORSION ATOMS=@psi-17
+#
+# PRINT ARG=t1,t2,t3,t4,t5,t6,t7,t8,t9,t10,t11,t12,t13,t14,t15,t16,t17,t18,t19,t20,t21,t22,t23,t24,t25,t26,t27,t28,t29,t30,t31,t32 FILE=colvar.ref FMT=%8.4f
+
+import numpy as np
+import plumed
+
+def read_xyz(filename):
+ xyz = open(filename)
+ n_atoms = int(xyz.readline())
+ title, trajectory = xyz.readline(), []
+ while True :
+ atom_type, coordinates = np.zeros(n_atoms).astype(str), np.zeros([n_atoms,3])
+ for i in range(0,n_atoms) :
+ line = xyz.readline()
+ atom,x,y,z = line.split()
+ atom_type[i]=atom
+ coordinates[i,:]=np.array([x,y,z],dtype=np.float64)
+ trajectory.append( coordinates )
+ nextline = xyz.readline()
+ if( nextline=="" ) : break
+ c_atoms = int(nextline)
+ if( c_atoms!=n_atoms ) : break
+ title = xyz.readline()
+ xyz.close()
+ return trajectory
+
+def create_plumed_var( p, name, command ):
+ p.cmd("readInputLine", name + ": " + command )
+ shape = np.zeros( 1, dtype=np.int_ )
+ p.cmd("getDataRank " + name, shape )
+ data = np.zeros((1))
+ p.cmd("setMemoryForData " + name, data )
+ return data
+
+# Output to four decimal places only
+np.set_printoptions(precision=4)
+# Read trajectory
+traj = read_xyz("traj.xyz")
+num_frames = len(traj)
+num_atoms = traj[0].shape[0]
+
+# Create arrays for stuff
+box=np.diag(12.41642*np.ones(3,dtype=np.float64))
+virial=np.zeros((3,3),dtype=np.float64)
+masses=np.ones(num_atoms,dtype=np.float64)
+forces=np.random.rand(num_atoms,3)
+charges=np.zeros(num_atoms,dtype=np.float64)
+
+# Create PLUMED object and read input
+p = plumed.Plumed()
+p.cmd("setMDEngine","python")
+p.cmd("setTimestep", 1.)
+p.cmd("setKbT", 1.)
+p.cmd("setNatoms",num_atoms)
+p.cmd("setLogFile","test.log")
+p.cmd("init")
+p.cmd("readInputLine","MOLINFO STRUCTURE=template.pdb")
+t1 = create_plumed_var( p, "t1", "TORSION ATOMS=@phi-2" )
+t2 = create_plumed_var( p, "t2", "TORSION ATOMS=@psi-2" )
+t3 = create_plumed_var( p, "t3", "TORSION ATOMS=@phi-3" )
+t4 = create_plumed_var( p, "t4", "TORSION ATOMS=@psi-3" )
+t5 = create_plumed_var( p, "t5", "TORSION ATOMS=@phi-4" )
+t6 = create_plumed_var( p, "t6", "TORSION ATOMS=@psi-4" )
+t7 = create_plumed_var( p, "t7", "TORSION ATOMS=@phi-5" )
+t8 = create_plumed_var( p, "t8", "TORSION ATOMS=@psi-5" )
+t9 = create_plumed_var( p, "t9", "TORSION ATOMS=@phi-6" )
+t10 = create_plumed_var( p, "t10", "TORSION ATOMS=@psi-6" )
+t11 = create_plumed_var( p, "t11", "TORSION ATOMS=@phi-7" )
+t12 = create_plumed_var( p, "t12", "TORSION ATOMS=@psi-7" )
+t13 = create_plumed_var( p, "t13", "TORSION ATOMS=@phi-8" )
+t14 = create_plumed_var( p, "t14", "TORSION ATOMS=@psi-8" )
+t15 = create_plumed_var( p, "t15", "TORSION ATOMS=@phi-9" )
+t16 = create_plumed_var( p, "t16", "TORSION ATOMS=@psi-9" )
+t17 = create_plumed_var( p, "t17", "TORSION ATOMS=@phi-10" )
+t18 = create_plumed_var( p, "t18", "TORSION ATOMS=@psi-10" )
+t19 = create_plumed_var( p, "t19", "TORSION ATOMS=@phi-11" )
+t20 = create_plumed_var( p, "t20", "TORSION ATOMS=@psi-11" )
+t21 = create_plumed_var( p, "t21", "TORSION ATOMS=@phi-12" )
+t22 = create_plumed_var( p, "t22", "TORSION ATOMS=@psi-12" )
+t23 = create_plumed_var( p, "t23", "TORSION ATOMS=@phi-13" )
+t24 = create_plumed_var( p, "t24", "TORSION ATOMS=@psi-13" )
+t25 = create_plumed_var( p, "t25", "TORSION ATOMS=@phi-14" )
+t26 = create_plumed_var( p, "t26", "TORSION ATOMS=@psi-14" )
+t27 = create_plumed_var( p, "t27", "TORSION ATOMS=@phi-15" )
+t28 = create_plumed_var( p, "t28", "TORSION ATOMS=@psi-15" )
+t29 = create_plumed_var( p, "t29", "TORSION ATOMS=@phi-16" )
+t30 = create_plumed_var( p, "t30", "TORSION ATOMS=@psi-16" )
+t31 = create_plumed_var( p, "t31", "TORSION ATOMS=@phi-17" )
+t32 = create_plumed_var( p, "t32", "TORSION ATOMS=@psi-17" )
+
+# Read in the correct answers that were calculated directly using PLUMED
+correct_torsions = np.loadtxt("colvar.ref")
+# Open an output file
+of = open("logfile", "w+")
+
+# Now analyze the trajectory
+for step in range(0,num_frames) :
+ of.write("RUNNING ANALYSIS FOR STEP " + str(step) + "\n" )
+ p.cmd("setStep",step )
+ p.cmd("setBox",box )
+ p.cmd("setMasses", masses )
+ p.cmd("setCharges", charges )
+ p.cmd("setPositions", traj[step])
+ p.cmd("setForces", forces )
+ p.cmd("setVirial", virial )
+ p.cmd("calc")
+ bias = np.zeros((1),dtype=np.float64)
+ p.cmd("getBias", bias )
+ variables = np.array([t1,t2,t3,t4,t5,t6,t7,t8,t9,t10,t11,t12,t13,t14,t15,t16,t17,t18,t19,t20,t21,t22,t23,t24,t25,t26,t27,t28,t29,t30,t31,t32]).ravel()
+ zeros = variables - correct_torsions[step,1:]
+ for data in zeros :
+ if abs(data)>1E-4 : of.write("MISMATCH BETWEEN VALUE FROM PLUMED AND VALUE FROM PYTHON")
+
+of.close()
diff --git a/regtest/python/rt-protein/template.pdb b/regtest/python/rt-protein/template.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..d6c5b487d1362c1c0634baa8f1f8fbadd1785f96
--- /dev/null
+++ b/regtest/python/rt-protein/template.pdb
@@ -0,0 +1,258 @@
+CRYST1 54.082 55.003 54.078 90.00 90.00 90.00 P 1 1
+ATOM 1 HH31 ACE X 1 18.200 28.300 38.920 1.01 0.00
+ATOM 2 CH3 ACE X 1 19.200 28.640 38.660 12.01 0.00
+ATOM 3 HH32 ACE X 1 19.800 28.800 39.560 1.01 0.00
+ATOM 4 HH33 ACE X 1 19.260 29.480 37.940 1.01 0.00
+ATOM 5 C ACE X 1 19.940 27.420 38.000 12.01 0.00
+ATOM 6 O ACE X 1 19.260 26.460 37.780 16.00 0.00
+ATOM 7 N GLY X 2 21.180 27.540 37.660 14.01 0.00
+ATOM 8 H GLY X 2 21.620 28.380 38.000 1.01 0.00
+ATOM 9 CA GLY X 2 21.860 26.700 36.720 12.01 0.00
+ATOM 10 HA1 GLY X 2 22.220 25.740 37.100 1.01 0.00
+ATOM 11 HA2 GLY X 2 21.140 26.460 35.940 1.01 0.00
+ATOM 12 C GLY X 2 23.020 27.380 36.020 12.01 0.00
+ATOM 13 O GLY X 2 23.580 28.360 36.460 16.00 0.00
+ATOM 14 N GLU X 3 23.260 26.960 34.800 14.01 0.00
+ATOM 15 H GLU X 3 22.780 26.180 34.400 1.01 0.00
+ATOM 16 CA GLU X 3 24.380 27.480 33.960 12.01 0.00
+ATOM 17 HA GLU X 3 24.560 28.520 34.200 1.01 0.00
+ATOM 18 CB GLU X 3 25.580 26.560 34.280 12.01 0.00
+ATOM 19 HB1 GLU X 3 25.640 26.340 35.340 1.01 0.00
+ATOM 20 HB2 GLU X 3 25.400 25.620 33.760 1.01 0.00
+ATOM 21 CG GLU X 3 26.860 27.220 33.760 12.01 0.00
+ATOM 22 HG1 GLU X 3 26.740 27.400 32.700 1.01 0.00
+ATOM 23 HG2 GLU X 3 27.040 28.160 34.260 1.01 0.00
+ATOM 24 CD GLU X 3 28.020 26.240 33.960 12.01 0.00
+ATOM 25 OE1 GLU X 3 28.580 26.180 35.060 16.00 0.00
+ATOM 26 OE2 GLU X 3 28.340 25.460 33.100 16.00 0.00
+ATOM 27 C GLU X 3 23.920 27.520 32.500 12.01 0.00
+ATOM 28 O GLU X 3 23.320 26.540 32.080 16.00 0.00
+ATOM 29 N TRP X 4 24.300 28.520 31.640 14.01 0.00
+ATOM 30 H TRP X 4 24.900 29.220 32.060 1.01 0.00
+ATOM 31 CA TRP X 4 24.140 28.600 30.160 12.01 0.00
+ATOM 32 HA TRP X 4 23.180 28.120 29.920 1.01 0.00
+ATOM 33 CB TRP X 4 24.060 30.080 29.800 12.01 0.00
+ATOM 34 HB1 TRP X 4 25.040 30.580 29.760 1.01 0.00
+ATOM 35 HB2 TRP X 4 23.600 30.140 28.820 1.01 0.00
+ATOM 36 CG TRP X 4 23.100 30.900 30.600 12.01 0.00
+ATOM 37 CD1 TRP X 4 23.420 32.100 31.160 12.01 0.00
+ATOM 38 HD1 TRP X 4 24.400 32.520 30.980 1.01 0.00
+ATOM 39 NE1 TRP X 4 22.400 32.480 32.000 14.01 0.00
+ATOM 40 HE1 TRP X 4 22.340 33.380 32.460 1.01 0.00
+ATOM 41 CE2 TRP X 4 21.360 31.680 31.720 12.01 0.00
+ATOM 42 CZ2 TRP X 4 20.060 31.700 32.240 12.01 0.00
+ATOM 43 HZ2 TRP X 4 19.760 32.500 32.880 1.01 0.00
+ATOM 44 CH2 TRP X 4 19.160 30.740 31.760 12.01 0.00
+ATOM 45 HH2 TRP X 4 18.140 30.800 32.100 1.01 0.00
+ATOM 46 CZ3 TRP X 4 19.500 29.740 30.800 12.01 0.00
+ATOM 47 HZ3 TRP X 4 18.820 29.000 30.400 1.01 0.00
+ATOM 48 CE3 TRP X 4 20.820 29.720 30.340 12.01 0.00
+ATOM 49 HE3 TRP X 4 21.160 29.000 29.600 1.01 0.00
+ATOM 50 CD2 TRP X 4 21.800 30.640 30.880 12.01 0.00
+ATOM 51 C TRP X 4 25.140 27.720 29.320 12.01 0.00
+ATOM 52 O TRP X 4 26.160 27.320 29.800 16.00 0.00
+ATOM 53 N THR X 5 24.940 27.700 28.000 14.01 0.00
+ATOM 54 H THR X 5 24.020 27.860 27.640 1.01 0.00
+ATOM 55 CA THR X 5 25.960 27.380 26.960 12.01 0.00
+ATOM 56 HA THR X 5 26.800 26.860 27.420 1.01 0.00
+ATOM 57 CB THR X 5 25.340 26.340 26.040 12.01 0.00
+ATOM 58 HB THR X 5 26.020 26.080 25.220 1.01 0.00
+ATOM 59 CG2 THR X 5 25.080 25.000 26.720 12.01 0.00
+ATOM 60 HG21 THR X 5 24.820 24.320 25.900 1.01 0.00
+ATOM 61 HG22 THR X 5 26.040 24.740 27.160 1.01 0.00
+ATOM 62 HG23 THR X 5 24.300 25.140 27.480 1.01 0.00
+ATOM 63 OG1 THR X 5 24.100 26.780 25.600 16.00 0.00
+ATOM 64 HG1 THR X 5 23.880 26.680 24.660 1.01 0.00
+ATOM 65 C THR X 5 26.540 28.580 26.180 12.01 0.00
+ATOM 66 O THR X 5 27.360 28.340 25.280 16.00 0.00
+ATOM 67 N TYR X 6 26.080 29.800 26.380 14.01 0.00
+ATOM 68 H TYR X 6 25.280 29.900 26.980 1.01 0.00
+ATOM 69 CA TYR X 6 26.500 30.960 25.620 12.01 0.00
+ATOM 70 HA TYR X 6 26.640 30.580 24.600 1.01 0.00
+ATOM 71 CB TYR X 6 25.460 32.060 25.820 12.01 0.00
+ATOM 72 HB1 TYR X 6 24.540 31.620 25.440 1.01 0.00
+ATOM 73 HB2 TYR X 6 25.300 32.200 26.880 1.01 0.00
+ATOM 74 CG TYR X 6 25.720 33.340 25.140 12.01 0.00
+ATOM 75 CD1 TYR X 6 25.760 33.500 23.740 12.01 0.00
+ATOM 76 HD1 TYR X 6 25.560 32.600 23.180 1.01 0.00
+ATOM 77 CE1 TYR X 6 25.940 34.720 23.100 12.01 0.00
+ATOM 78 HE1 TYR X 6 25.860 34.780 22.020 1.01 0.00
+ATOM 79 CZ TYR X 6 26.200 35.860 23.860 12.01 0.00
+ATOM 80 OH TYR X 6 26.400 37.080 23.280 16.00 0.00
+ATOM 81 HH TYR X 6 25.940 37.060 22.420 1.01 0.00
+ATOM 82 CE2 TYR X 6 26.260 35.780 25.260 12.01 0.00
+ATOM 83 HE2 TYR X 6 26.440 36.640 25.880 1.01 0.00
+ATOM 84 CD2 TYR X 6 26.140 34.500 25.880 12.01 0.00
+ATOM 85 HD2 TYR X 6 26.100 34.400 26.960 1.01 0.00
+ATOM 86 C TYR X 6 27.900 31.380 26.120 12.01 0.00
+ATOM 87 O TYR X 6 28.260 31.300 27.280 16.00 0.00
+ATOM 88 N ASP X 7 28.680 31.960 25.180 14.01 0.00
+ATOM 89 H ASP X 7 28.300 32.020 24.240 1.01 0.00
+ATOM 90 CA ASP X 7 30.080 32.480 25.360 12.01 0.00
+ATOM 91 HA ASP X 7 30.400 32.400 26.400 1.01 0.00
+ATOM 92 CB ASP X 7 31.160 31.680 24.580 12.01 0.00
+ATOM 93 HB1 ASP X 7 31.220 30.620 24.880 1.01 0.00
+ATOM 94 HB2 ASP X 7 30.980 31.820 23.500 1.01 0.00
+ATOM 95 CG ASP X 7 32.600 32.180 24.860 12.01 0.00
+ATOM 96 OD1 ASP X 7 33.400 32.320 23.880 16.00 0.00
+ATOM 97 OD2 ASP X 7 32.920 32.600 26.040 16.00 0.00
+ATOM 98 C ASP X 7 30.140 33.980 25.140 12.01 0.00
+ATOM 99 O ASP X 7 30.320 34.360 24.000 16.00 0.00
+ATOM 100 N ASP X 8 30.240 34.740 26.200 14.01 0.00
+ATOM 101 H ASP X 8 30.200 34.460 27.180 1.01 0.00
+ATOM 102 CA ASP X 8 30.080 36.200 25.920 12.01 0.00
+ATOM 103 HA ASP X 8 29.280 36.320 25.200 1.01 0.00
+ATOM 104 CB ASP X 8 29.580 36.880 27.180 12.01 0.00
+ATOM 105 HB1 ASP X 8 28.700 36.380 27.580 1.01 0.00
+ATOM 106 HB2 ASP X 8 30.360 36.840 27.940 1.01 0.00
+ATOM 107 CG ASP X 8 29.180 38.320 26.840 12.01 0.00
+ATOM 108 OD1 ASP X 8 28.240 38.600 26.060 16.00 0.00
+ATOM 109 OD2 ASP X 8 29.720 39.240 27.440 16.00 0.00
+ATOM 110 C ASP X 8 31.360 36.920 25.320 12.01 0.00
+ATOM 111 O ASP X 8 31.160 37.960 24.680 16.00 0.00
+ATOM 112 N ALA X 9 32.520 36.240 25.360 14.01 0.00
+ATOM 113 H ALA X 9 32.560 35.340 25.800 1.01 0.00
+ATOM 114 CA ALA X 9 33.780 36.720 24.660 12.01 0.00
+ATOM 115 HA ALA X 9 34.020 37.740 24.940 1.01 0.00
+ATOM 116 CB ALA X 9 34.980 35.960 25.160 12.01 0.00
+ATOM 117 HB1 ALA X 9 35.940 36.240 24.720 1.01 0.00
+ATOM 118 HB2 ALA X 9 35.140 36.240 26.200 1.01 0.00
+ATOM 119 HB3 ALA X 9 34.740 34.900 25.060 1.01 0.00
+ATOM 120 C ALA X 9 33.680 36.580 23.200 12.01 0.00
+ATOM 121 O ALA X 9 34.000 37.540 22.500 16.00 0.00
+ATOM 122 N THR X 10 33.160 35.420 22.640 14.01 0.00
+ATOM 123 H THR X 10 33.000 34.680 23.320 1.01 0.00
+ATOM 124 CA THR X 10 33.080 35.080 21.220 12.01 0.00
+ATOM 125 HA THR X 10 33.800 35.620 20.600 1.01 0.00
+ATOM 126 CB THR X 10 33.400 33.580 21.020 12.01 0.00
+ATOM 127 HB THR X 10 32.520 33.080 21.400 1.01 0.00
+ATOM 128 CG2 THR X 10 33.520 33.060 19.640 12.01 0.00
+ATOM 129 HG21 THR X 10 32.720 33.300 18.960 1.01 0.00
+ATOM 130 HG22 THR X 10 34.360 33.540 19.160 1.01 0.00
+ATOM 131 HG23 THR X 10 33.640 31.980 19.820 1.01 0.00
+ATOM 132 OG1 THR X 10 34.600 33.280 21.740 16.00 0.00
+ATOM 133 HG1 THR X 10 34.240 32.800 22.480 1.01 0.00
+ATOM 134 C THR X 10 31.700 35.320 20.620 12.01 0.00
+ATOM 135 O THR X 10 31.680 35.500 19.420 16.00 0.00
+ATOM 136 N LYS X 11 30.620 35.380 21.380 14.01 0.00
+ATOM 137 H LYS X 11 30.780 35.260 22.380 1.01 0.00
+ATOM 138 CA LYS X 11 29.160 35.520 20.960 12.01 0.00
+ATOM 139 HA LYS X 11 28.620 35.520 21.900 1.01 0.00
+ATOM 140 CB LYS X 11 28.920 36.860 20.140 12.01 0.00
+ATOM 141 HB1 LYS X 11 29.340 36.700 19.140 1.01 0.00
+ATOM 142 HB2 LYS X 11 27.820 36.940 20.180 1.01 0.00
+ATOM 143 CG LYS X 11 29.500 38.100 20.680 12.01 0.00
+ATOM 144 HG1 LYS X 11 30.580 37.960 20.720 1.01 0.00
+ATOM 145 HG2 LYS X 11 29.240 38.960 20.060 1.01 0.00
+ATOM 146 CD LYS X 11 28.880 38.480 22.000 12.01 0.00
+ATOM 147 HD1 LYS X 11 27.840 38.740 21.820 1.01 0.00
+ATOM 148 HD2 LYS X 11 29.000 37.620 22.660 1.01 0.00
+ATOM 149 CE LYS X 11 29.660 39.640 22.660 12.01 0.00
+ATOM 150 HE1 LYS X 11 30.600 39.140 22.840 1.01 0.00
+ATOM 151 HE2 LYS X 11 29.800 40.460 21.980 1.01 0.00
+ATOM 152 NZ LYS X 11 29.140 40.020 23.960 14.01 0.00
+ATOM 153 HZ1 LYS X 11 28.200 40.380 23.980 1.01 0.00
+ATOM 154 HZ2 LYS X 11 29.180 39.300 24.680 1.01 0.00
+ATOM 155 HZ3 LYS X 11 29.740 40.720 24.400 1.01 0.00
+ATOM 156 C LYS X 11 28.560 34.300 20.280 12.01 0.00
+ATOM 157 O LYS X 11 27.860 34.400 19.260 16.00 0.00
+ATOM 158 N THR X 12 28.780 33.160 20.940 14.01 0.00
+ATOM 159 H THR X 12 29.380 33.160 21.760 1.01 0.00
+ATOM 160 CA THR X 12 28.480 31.820 20.360 12.01 0.00
+ATOM 161 HA THR X 12 27.660 32.000 19.660 1.01 0.00
+ATOM 162 CB THR X 12 29.660 31.240 19.640 12.01 0.00
+ATOM 163 HB THR X 12 29.480 30.240 19.240 1.01 0.00
+ATOM 164 CG2 THR X 12 29.980 32.180 18.440 12.01 0.00
+ATOM 165 HG21 THR X 12 30.820 31.800 17.860 1.01 0.00
+ATOM 166 HG22 THR X 12 29.200 32.340 17.720 1.01 0.00
+ATOM 167 HG23 THR X 12 30.340 33.100 18.900 1.01 0.00
+ATOM 168 OG1 THR X 12 30.820 31.160 20.440 16.00 0.00
+ATOM 169 HG1 THR X 12 31.440 30.500 20.060 1.01 0.00
+ATOM 170 C THR X 12 27.900 30.780 21.320 12.01 0.00
+ATOM 171 O THR X 12 28.200 30.740 22.460 16.00 0.00
+ATOM 172 N PHE X 13 27.120 29.920 20.760 14.01 0.00
+ATOM 173 H PHE X 13 26.940 29.940 19.760 1.01 0.00
+ATOM 174 CA PHE X 13 26.460 28.820 21.400 12.01 0.00
+ATOM 175 HA PHE X 13 26.440 28.900 22.480 1.01 0.00
+ATOM 176 CB PHE X 13 24.980 28.900 21.000 12.01 0.00
+ATOM 177 HB1 PHE X 13 24.900 28.780 19.920 1.01 0.00
+ATOM 178 HB2 PHE X 13 24.380 28.100 21.420 1.01 0.00
+ATOM 179 CG PHE X 13 24.260 30.140 21.420 12.01 0.00
+ATOM 180 CD1 PHE X 13 24.100 31.300 20.580 12.01 0.00
+ATOM 181 HD1 PHE X 13 24.740 31.300 19.720 1.01 0.00
+ATOM 182 CE1 PHE X 13 23.400 32.420 21.020 12.01 0.00
+ATOM 183 HE1 PHE X 13 23.580 33.380 20.560 1.01 0.00
+ATOM 184 CZ PHE X 13 22.780 32.320 22.220 12.01 0.00
+ATOM 185 HZ PHE X 13 22.280 33.200 22.600 1.01 0.00
+ATOM 186 CE2 PHE X 13 22.700 31.140 23.000 12.01 0.00
+ATOM 187 HE2 PHE X 13 22.300 31.140 24.000 1.01 0.00
+ATOM 188 CD2 PHE X 13 23.520 30.060 22.600 12.01 0.00
+ATOM 189 HD2 PHE X 13 23.520 29.100 23.080 1.01 0.00
+ATOM 190 C PHE X 13 27.040 27.400 21.180 12.01 0.00
+ATOM 191 O PHE X 13 27.840 27.200 20.280 16.00 0.00
+ATOM 192 N THR X 14 26.600 26.340 21.980 14.01 0.00
+ATOM 193 H THR X 14 25.780 26.360 22.560 1.01 0.00
+ATOM 194 CA THR X 14 27.100 24.900 21.680 12.01 0.00
+ATOM 195 HA THR X 14 28.140 24.900 21.340 1.01 0.00
+ATOM 196 CB THR X 14 27.120 23.960 22.920 12.01 0.00
+ATOM 197 HB THR X 14 27.240 22.900 22.680 1.01 0.00
+ATOM 198 CG2 THR X 14 28.240 24.340 23.960 12.01 0.00
+ATOM 199 HG21 THR X 14 28.300 23.660 24.820 1.01 0.00
+ATOM 200 HG22 THR X 14 29.200 24.180 23.480 1.01 0.00
+ATOM 201 HG23 THR X 14 28.220 25.360 24.340 1.01 0.00
+ATOM 202 OG1 THR X 14 25.880 24.100 23.580 16.00 0.00
+ATOM 203 HG1 THR X 14 26.080 23.480 24.300 1.01 0.00
+ATOM 204 C THR X 14 26.180 24.180 20.680 12.01 0.00
+ATOM 205 O THR X 14 25.140 24.720 20.380 16.00 0.00
+ATOM 206 N VAL X 15 26.560 23.080 20.040 14.01 0.00
+ATOM 207 H VAL X 15 27.480 22.740 20.280 1.01 0.00
+ATOM 208 CA VAL X 15 25.600 22.200 19.300 12.01 0.00
+ATOM 209 HA VAL X 15 25.120 22.800 18.520 1.01 0.00
+ATOM 210 CB VAL X 15 26.480 21.120 18.640 12.01 0.00
+ATOM 211 HB VAL X 15 27.060 20.520 19.340 1.01 0.00
+ATOM 212 CG1 VAL X 15 25.680 20.160 17.800 12.01 0.00
+ATOM 213 HG11 VAL X 15 25.300 19.340 18.400 1.01 0.00
+ATOM 214 HG12 VAL X 15 24.800 20.620 17.320 1.01 0.00
+ATOM 215 HG13 VAL X 15 26.320 19.700 17.060 1.01 0.00
+ATOM 216 CG2 VAL X 15 27.500 21.840 17.720 12.01 0.00
+ATOM 217 HG21 VAL X 15 28.260 22.400 18.260 1.01 0.00
+ATOM 218 HG22 VAL X 15 27.940 21.120 17.040 1.01 0.00
+ATOM 219 HG23 VAL X 15 27.020 22.580 17.060 1.01 0.00
+ATOM 220 C VAL X 15 24.540 21.560 20.240 12.01 0.00
+ATOM 221 O VAL X 15 24.900 20.840 21.120 16.00 0.00
+ATOM 222 N THR X 16 23.280 21.840 19.960 14.01 0.00
+ATOM 223 H THR X 16 23.140 22.480 19.200 1.01 0.00
+ATOM 224 CA THR X 16 22.120 21.280 20.660 12.01 0.00
+ATOM 225 HA THR X 16 22.520 20.560 21.380 1.01 0.00
+ATOM 226 CB THR X 16 21.380 22.280 21.540 12.01 0.00
+ATOM 227 HB THR X 16 20.500 21.800 21.980 1.01 0.00
+ATOM 228 CG2 THR X 16 22.060 22.840 22.780 12.01 0.00
+ATOM 229 HG21 THR X 16 22.980 23.400 22.580 1.01 0.00
+ATOM 230 HG22 THR X 16 21.440 23.640 23.180 1.01 0.00
+ATOM 231 HG23 THR X 16 22.200 22.080 23.560 1.01 0.00
+ATOM 232 OG1 THR X 16 20.960 23.380 20.840 16.00 0.00
+ATOM 233 HG1 THR X 16 20.040 23.520 21.100 1.01 0.00
+ATOM 234 C THR X 16 21.160 20.460 19.740 12.01 0.00
+ATOM 235 O THR X 16 19.920 20.460 19.880 16.00 0.00
+ATOM 236 N GLU X 17 21.740 19.760 18.780 14.01 0.00
+ATOM 237 H GLU X 17 22.740 19.620 18.820 1.01 0.00
+ATOM 238 CA GLU X 17 21.080 18.840 17.820 12.01 0.00
+ATOM 239 HA GLU X 17 20.040 18.660 18.080 1.01 0.00
+ATOM 240 CB GLU X 17 21.060 19.600 16.460 12.01 0.00
+ATOM 241 HB1 GLU X 17 22.120 19.740 16.240 1.01 0.00
+ATOM 242 HB2 GLU X 17 20.720 19.140 15.540 1.01 0.00
+ATOM 243 CG GLU X 17 20.260 20.940 16.520 12.01 0.00
+ATOM 244 HG1 GLU X 17 19.320 20.760 17.060 1.01 0.00
+ATOM 245 HG2 GLU X 17 20.900 21.620 17.080 1.01 0.00
+ATOM 246 CD GLU X 17 20.000 21.520 15.140 12.01 0.00
+ATOM 247 OE1 GLU X 17 20.780 22.260 14.580 16.00 0.00
+ATOM 248 OE2 GLU X 17 19.020 21.140 14.500 16.00 0.00
+ATOM 249 C GLU X 17 21.740 17.440 17.920 12.01 0.00
+ATOM 250 O GLU X 17 22.860 17.280 18.420 16.00 0.00
+ATOM 251 N NME X 18 21.020 16.380 17.480 14.01 0.00
+ATOM 252 H NME X 18 20.140 16.580 17.040 1.01 0.00
+ATOM 253 CH3 NME X 18 21.320 14.940 17.660 12.01 0.00
+ATOM 254 HH31 NME X 18 22.360 14.740 17.380 1.01 0.00
+ATOM 255 HH32 NME X 18 20.620 14.280 17.160 1.01 0.00
+ATOM 256 HH33 NME X 18 21.340 14.700 18.720 1.01 0.00
+END
diff --git a/regtest/python/rt-protein/traj.xyz b/regtest/python/rt-protein/traj.xyz
new file mode 100644
index 0000000000000000000000000000000000000000..0ee8881001d85fbbbf9d854638e64aad97e8e766
--- /dev/null
+++ b/regtest/python/rt-protein/traj.xyz
@@ -0,0 +1,2580 @@
+256
+ 100.0 100.0 100.0
+ HH31 18.200001 28.299999 38.919998
+ CH3 19.200001 28.639999 38.660000
+ HH32 19.799999 28.799999 39.560001
+ HH33 19.260000 29.480000 37.939999
+ C 19.940001 27.420000 38.000000
+ O 19.260000 26.459999 37.779999
+ N 21.180000 27.540001 37.660000
+ H 21.620001 28.379999 38.000000
+ CA 21.860001 26.700001 36.720001
+ HA1 22.219999 25.740000 37.099998
+ HA2 21.139999 26.459999 35.939999
+ C 23.020000 27.379999 36.020000
+ O 23.580000 28.360001 36.459999
+ N 23.260000 26.959999 34.799999
+ H 22.780001 26.180000 34.400002
+ CA 24.379999 27.480000 33.959999
+ HA 24.559999 28.520000 34.200001
+ CB 25.580000 26.559999 34.279999
+ HB1 25.639999 26.340000 35.340000
+ HB2 25.400000 25.620001 33.759998
+ CG 26.860001 27.219999 33.759998
+ HG1 26.740000 27.400000 32.700001
+ HG2 27.040001 28.160000 34.259998
+ CD 28.020000 26.240000 33.959999
+ OE1 28.580000 26.180000 35.060001
+ OE2 28.340000 25.459999 33.099998
+ C 23.920000 27.520000 32.500000
+ O 23.320000 26.540001 32.080002
+ N 24.299999 28.520000 31.639999
+ H 24.900000 29.219999 32.060001
+ CA 24.139999 28.600000 30.160000
+ HA 23.180000 28.120001 29.920000
+ CB 24.059999 30.080000 29.799999
+ HB1 25.040001 30.580000 29.760000
+ HB2 23.600000 30.139999 28.820000
+ CG 23.100000 30.900000 30.600000
+ CD1 23.420000 32.099998 31.160000
+ HD1 24.400000 32.520000 30.980000
+ NE1 22.400000 32.480000 32.000000
+ HE1 22.340000 33.380001 32.459999
+ CE2 21.360001 31.680000 31.719999
+ CZ2 20.059999 31.700001 32.240002
+ HZ2 19.760000 32.500000 32.880001
+ CH2 19.160000 30.740000 31.760000
+ HH2 18.139999 30.799999 32.099998
+ CZ3 19.500000 29.740000 30.799999
+ HZ3 18.820000 29.000000 30.400000
+ CE3 20.820000 29.719999 30.340000
+ HE3 21.160000 29.000000 29.600000
+ CD2 21.799999 30.639999 30.879999
+ C 25.139999 27.719999 29.320000
+ O 26.160000 27.320000 29.799999
+ N 24.940001 27.700001 28.000000
+ H 24.020000 27.860001 27.639999
+ CA 25.959999 27.379999 26.959999
+ HA 26.799999 26.860001 27.420000
+ CB 25.340000 26.340000 26.040001
+ HB 26.020000 26.080000 25.219999
+ CG2 25.080000 25.000000 26.719999
+ HG21 24.820000 24.320000 25.900000
+ HG22 26.040001 24.740000 27.160000
+ HG23 24.299999 25.139999 27.480000
+ OG1 24.100000 26.780001 25.600000
+ HG1 23.879999 26.680000 24.660000
+ C 26.540001 28.580000 26.180000
+ O 27.360001 28.340000 25.280001
+ N 26.080000 29.799999 26.379999
+ H 25.280001 29.900000 26.980000
+ CA 26.500000 30.959999 25.620001
+ HA 26.639999 30.580000 24.600000
+ CB 25.459999 32.060001 25.820000
+ HB1 24.540001 31.620001 25.440001
+ HB2 25.299999 32.200001 26.879999
+ CG 25.719999 33.340000 25.139999
+ CD1 25.760000 33.500000 23.740000
+ HD1 25.559999 32.599998 23.180000
+ CE1 25.940001 34.720001 23.100000
+ HE1 25.860001 34.779999 22.020000
+ CZ 26.200001 35.860001 23.860001
+ OH 26.400000 37.080002 23.280001
+ HH 25.940001 37.060001 22.420000
+ CE2 26.260000 35.779999 25.260000
+ HE2 26.440001 36.639999 25.879999
+ CD2 26.139999 34.500000 25.879999
+ HD2 26.100000 34.400002 26.959999
+ C 27.900000 31.379999 26.120001
+ O 28.260000 31.299999 27.280001
+ N 28.680000 31.959999 25.180000
+ H 28.299999 32.020000 24.240000
+ CA 30.080000 32.480000 25.360001
+ HA 30.400000 32.400002 26.400000
+ CB 31.160000 31.680000 24.580000
+ HB1 31.219999 30.620001 24.879999
+ HB2 30.980000 31.820000 23.500000
+ CG 32.599998 32.180000 24.860001
+ OD1 33.400002 32.320000 23.879999
+ OD2 32.919998 32.599998 26.040001
+ C 30.139999 33.980000 25.139999
+ O 30.320000 34.360001 24.000000
+ N 30.240000 34.740002 26.200001
+ H 30.200001 34.459999 27.180000
+ CA 30.080000 36.200001 25.920000
+ HA 29.280001 36.320000 25.200001
+ CB 29.580000 36.880001 27.180000
+ HB1 28.700001 36.380001 27.580000
+ HB2 30.360001 36.840000 27.940001
+ CG 29.180000 38.320000 26.840000
+ OD1 28.240000 38.599998 26.059999
+ OD2 29.719999 39.240002 27.440001
+ C 31.360001 36.919998 25.320000
+ O 31.160000 37.959999 24.680000
+ N 32.520000 36.240002 25.360001
+ H 32.560001 35.340000 25.799999
+ CA 33.779999 36.720001 24.660000
+ HA 34.020000 37.740002 24.940001
+ CB 34.980000 35.959999 25.160000
+ HB1 35.939999 36.240002 24.719999
+ HB2 35.139999 36.240002 26.200001
+ HB3 34.740002 34.900002 25.059999
+ C 33.680000 36.580002 23.200001
+ O 34.000000 37.540001 22.500000
+ N 33.160000 35.419998 22.639999
+ H 33.000000 34.680000 23.320000
+ CA 33.080002 35.080002 21.219999
+ HA 33.799999 35.619999 20.600000
+ CB 33.400002 33.580002 21.020000
+ HB 32.520000 33.080002 21.400000
+ CG2 33.520000 33.060001 19.639999
+ HG21 32.720001 33.299999 18.959999
+ HG22 34.360001 33.540001 19.160000
+ HG23 33.639999 31.980000 19.820000
+ OG1 34.599998 33.279999 21.740000
+ HG1 34.240002 32.799999 22.480000
+ C 31.700001 35.320000 20.620001
+ O 31.680000 35.500000 19.420000
+ N 30.620001 35.380001 21.379999
+ H 30.780001 35.259998 22.379999
+ CA 29.160000 35.520000 20.959999
+ HA 28.620001 35.520000 21.900000
+ CB 28.920000 36.860001 20.139999
+ HB1 29.340000 36.700001 19.139999
+ HB2 27.820000 36.939999 20.180000
+ CG 29.500000 38.099998 20.680000
+ HG1 30.580000 37.959999 20.719999
+ HG2 29.240000 38.959999 20.059999
+ CD 28.879999 38.480000 22.000000
+ HD1 27.840000 38.740002 21.820000
+ HD2 29.000000 37.619999 22.660000
+ CE 29.660000 39.639999 22.660000
+ HE1 30.600000 39.139999 22.840000
+ HE2 29.799999 40.459999 21.980000
+ NZ 29.139999 40.020000 23.959999
+ HZ1 28.200001 40.380001 23.980000
+ HZ2 29.180000 39.299999 24.680000
+ HZ3 29.740000 40.720001 24.400000
+ C 28.559999 34.299999 20.280001
+ O 27.860001 34.400002 19.260000
+ N 28.780001 33.160000 20.940001
+ H 29.379999 33.160000 21.760000
+ CA 28.480000 31.820000 20.360001
+ HA 27.660000 32.000000 19.660000
+ CB 29.660000 31.240000 19.639999
+ HB 29.480000 30.240000 19.240000
+ CG2 29.980000 32.180000 18.440001
+ HG21 30.820000 31.799999 17.860001
+ HG22 29.200001 32.340000 17.719999
+ HG23 30.340000 33.099998 18.900000
+ OG1 30.820000 31.160000 20.440001
+ HG1 31.440001 30.500000 20.059999
+ C 27.900000 30.780001 21.320000
+ O 28.200001 30.740000 22.459999
+ N 27.120001 29.920000 20.760000
+ H 26.940001 29.940001 19.760000
+ CA 26.459999 28.820000 21.400000
+ HA 26.440001 28.900000 22.480000
+ CB 24.980000 28.900000 21.000000
+ HB1 24.900000 28.780001 19.920000
+ HB2 24.379999 28.100000 21.420000
+ CG 24.260000 30.139999 21.420000
+ CD1 24.100000 31.299999 20.580000
+ HD1 24.740000 31.299999 19.719999
+ CE1 23.400000 32.419998 21.020000
+ HE1 23.580000 33.380001 20.559999
+ CZ 22.780001 32.320000 22.219999
+ HZ 22.280001 33.200001 22.600000
+ CE2 22.700001 31.139999 23.000000
+ HE2 22.299999 31.139999 24.000000
+ CD2 23.520000 30.059999 22.600000
+ HD2 23.520000 29.100000 23.080000
+ C 27.040001 27.400000 21.180000
+ O 27.840000 27.200001 20.280001
+ N 26.600000 26.340000 21.980000
+ H 25.780001 26.360001 22.559999
+ CA 27.100000 24.900000 21.680000
+ HA 28.139999 24.900000 21.340000
+ CB 27.120001 23.959999 22.920000
+ HB 27.240000 22.900000 22.680000
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+ HG21 28.299999 23.660000 24.820000
+ HG22 29.200001 24.180000 23.480000
+ HG23 28.219999 25.360001 24.340000
+ OG1 25.879999 24.100000 23.580000
+ HG1 26.080000 23.480000 24.299999
+ C 26.180000 24.180000 20.680000
+ O 25.139999 24.719999 20.379999
+ N 26.559999 23.080000 20.040001
+ H 27.480000 22.740000 20.280001
+ CA 25.600000 22.200001 19.299999
+ HA 25.120001 22.799999 18.520000
+ CB 26.480000 21.120001 18.639999
+ HB 27.059999 20.520000 19.340000
+ CG1 25.680000 20.160000 17.799999
+ HG11 25.299999 19.340000 18.400000
+ HG12 24.799999 20.620001 17.320000
+ HG13 26.320000 19.700001 17.059999
+ CG2 27.500000 21.840000 17.719999
+ HG21 28.260000 22.400000 18.260000
+ HG22 27.940001 21.120001 17.040001
+ HG23 27.020000 22.580000 17.059999
+ C 24.540001 21.559999 20.240000
+ O 24.900000 20.840000 21.120001
+ N 23.280001 21.840000 19.959999
+ H 23.139999 22.480000 19.200001
+ CA 22.120001 21.280001 20.660000
+ HA 22.520000 20.559999 21.379999
+ CB 21.379999 22.280001 21.540001
+ HB 20.500000 21.799999 21.980000
+ CG2 22.059999 22.840000 22.780001
+ HG21 22.980000 23.400000 22.580000
+ HG22 21.440001 23.639999 23.180000
+ HG23 22.200001 22.080000 23.559999
+ OG1 20.959999 23.379999 20.840000
+ HG1 20.040001 23.520000 21.100000
+ C 21.160000 20.459999 19.740000
+ O 19.920000 20.459999 19.879999
+ N 21.740000 19.760000 18.780001
+ H 22.740000 19.620001 18.820000
+ CA 21.080000 18.840000 17.820000
+ HA 20.040001 18.660000 18.080000
+ CB 21.059999 19.600000 16.459999
+ HB1 22.120001 19.740000 16.240000
+ HB2 20.719999 19.139999 15.540000
+ CG 20.260000 20.940001 16.520000
+ HG1 19.320000 20.760000 17.059999
+ HG2 20.900000 21.620001 17.080000
+ CD 20.000000 21.520000 15.140000
+ OE1 20.780001 22.260000 14.580000
+ OE2 19.020000 21.139999 14.500000
+ C 21.740000 17.440001 17.920000
+ O 22.860001 17.280001 18.420000
+ N 21.020000 16.379999 17.480000
+ H 20.139999 16.580000 17.040001
+ CH3 21.320000 14.940000 17.660000
+ HH31 22.360001 14.740000 17.379999
+ HH32 20.620001 14.280000 17.160000
+ HH33 21.340000 14.700000 18.719999
+256
+ 100.0 100.0 100.0
+ HH31 18.200001 28.299999 38.919998
+ CH3 19.200001 28.639999 38.660000
+ HH32 19.799999 28.799999 39.560001
+ HH33 19.260000 29.480000 37.939999
+ C 19.940001 27.420000 38.000000
+ O 19.260000 26.459999 37.779999
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+ HA 29.334999 37.175999 22.506001
+ CB 29.319000 38.431000 20.767000
+ HB1 29.378000 38.412998 19.679001
+ HB2 28.319000 38.794998 20.995001
+ CG 30.370001 39.355000 21.289000
+ HG1 31.382999 38.987000 21.120001
+ HG2 30.200001 40.240002 20.676001
+ CD 30.058001 39.771999 22.750999
+ HD1 28.996000 40.070000 22.837999
+ HD2 30.190001 38.874001 23.344000
+ CE 30.902000 40.890999 23.153000
+ HE1 31.943001 40.518002 23.174999
+ HE2 30.707001 41.706001 22.472000
+ NZ 30.426001 41.414001 24.451000
+ HZ1 31.091000 42.073002 24.837000
+ HZ2 29.593000 41.973000 24.551001
+ HZ3 30.309999 40.638000 25.093000
+ C 28.358000 36.015999 20.975000
+ O 27.566000 36.214001 20.011999
+ N 28.434999 34.848000 21.570999
+ H 29.049999 34.742001 22.367001
+ CA 27.562000 33.685001 21.214001
+ HA 26.742001 34.077000 20.638000
+ CB 28.368999 32.744999 20.309999
+ HB 27.702999 31.899000 20.131001
+ CG2 28.638000 33.437000 18.931999
+ HG21 27.679001 33.668999 18.466000
+ HG22 29.268999 34.280998 19.139000
+ HG23 29.094999 32.673000 18.313999
+ OG1 29.539000 32.284000 20.812000
+ HG1 30.266001 32.854000 20.577000
+ C 26.972000 32.923000 22.384001
+ O 27.521000 32.944000 23.441000
+ N 25.962999 32.084000 22.007999
+ H 25.865000 32.021999 21.007000
+ CA 25.403999 30.930000 22.757999
+ HA 25.906000 30.969000 23.731001
+ CB 23.889000 31.089001 22.895000
+ HB1 23.617001 30.223000 23.490999
+ HB2 23.729000 31.948000 23.549999
+ CG 23.031000 31.062000 21.667000
+ CD1 22.431000 32.248001 21.125000
+ HD1 22.554001 33.136002 21.705000
+ CE1 21.669001 32.299999 19.982000
+ HE1 21.177000 33.179001 19.583000
+ CZ 21.533001 31.052000 19.287001
+ HZ 20.934999 31.059000 18.386999
+ CE2 21.938999 29.825001 19.841999
+ HE2 21.673000 28.896999 19.379000
+ CD2 22.771999 29.850000 20.980000
+ HD2 23.201000 28.940001 21.399000
+ C 25.896999 29.643000 22.183001
+ O 26.080999 29.476999 20.976999
+ N 25.959999 28.620001 23.091999
+ H 25.971001 28.808001 24.070999
+ CA 26.261999 27.208000 22.680000
+ HA 26.077999 27.054001 21.604000
+ CB 27.768000 26.922001 22.948000
+ HB 27.993999 27.046000 23.986000
+ CG2 28.186001 25.521999 22.409000
+ HG21 27.702000 24.667999 22.915001
+ HG22 27.896000 25.436001 21.367001
+ HG23 29.280001 25.400999 22.483000
+ OG1 28.568001 27.728001 22.315001
+ HG1 28.482000 28.584999 22.747999
+ C 25.395000 26.250000 23.441000
+ O 25.070999 26.565001 24.632000
+ N 24.757999 25.218000 22.849001
+ H 25.002001 25.084999 21.892000
+ CA 23.830999 24.202999 23.441999
+ HA 23.827999 24.283001 24.521000
+ CB 22.398001 24.461000 23.034000
+ HB 21.877001 23.511999 23.152000
+ CG1 21.677999 25.534000 23.802999
+ HG11 21.445999 25.143999 24.788000
+ HG12 22.287001 26.436001 23.731001
+ HG13 20.702000 25.657000 23.362000
+ CG2 22.216000 24.761999 21.566999
+ HG21 21.171000 24.646999 21.256001
+ HG22 22.603001 25.714001 21.239000
+ HG23 22.774000 24.042000 20.950001
+ C 24.283001 22.764999 23.084999
+ O 24.275999 22.414000 21.964001
+ N 24.479000 21.902000 24.077000
+ H 24.421000 22.325001 25.011000
+ CA 24.857000 20.399000 23.965000
+ HA 25.766001 20.344999 23.358000
+ CB 24.993000 19.683001 25.313000
+ HB 24.937000 18.591999 25.308001
+ CG2 26.284000 20.070999 26.160999
+ HG21 26.103001 21.076000 26.535000
+ HG22 26.541000 19.339001 26.929001
+ HG23 27.165001 20.066999 25.496000
+ OG1 23.888000 20.103001 26.046000
+ HG1 23.966000 19.698000 26.914000
+ C 23.861000 19.577000 23.149000
+ O 24.201000 18.513000 22.552000
+ N 22.613001 20.083000 22.927000
+ H 22.277000 20.795000 23.591000
+ CA 21.573999 19.452999 22.023001
+ HA 21.900000 18.473000 21.660000
+ CB 20.421000 19.098000 22.924000
+ HB1 20.073999 19.976999 23.478001
+ HB2 19.594000 18.708000 22.323000
+ CG 20.723000 17.882000 23.851000
+ HG1 21.205000 17.117001 23.247999
+ HG2 21.367001 18.174999 24.684999
+ CD 19.469999 17.253000 24.382000
+ OE1 19.549000 16.103001 24.924000
+ OE2 18.408001 17.878000 24.290001
+ C 21.118999 20.205999 20.753000
+ O 20.164000 19.771999 20.061001
+ N 21.747999 21.363001 20.391001
+ H 22.556000 21.718000 20.891001
+ CH3 21.469000 22.047001 19.132999
+ HH31 22.375000 22.320999 18.615999
+ HH32 20.775999 22.879999 19.308001
+ HH33 21.098000 21.313999 18.417999
+256
+ 100.0 100.0 100.0
+ HH31 24.733000 17.898001 29.659000
+ CH3 24.452000 18.396000 28.732000
+ HH32 24.849001 17.715000 27.974001
+ HH33 24.965000 19.354000 28.670000
+ C 22.969000 18.635000 28.725000
+ O 22.274000 18.607000 29.781000
+ N 22.459999 18.916000 27.489000
+ H 23.103001 18.801001 26.731001
+ CA 21.139000 19.462999 27.219999
+ HA1 20.993000 19.355000 26.146999
+ HA2 20.459999 18.827999 27.792999
+ C 20.986000 20.922001 27.518999
+ O 20.018000 21.545000 27.117001
+ N 21.937000 21.503000 28.302999
+ H 22.652000 20.903999 28.712000
+ CA 21.875999 22.875000 28.879999
+ HA 20.823999 23.103001 28.978001
+ CB 22.490999 22.930000 30.322001
+ HB1 22.283001 23.941999 30.622999
+ HB2 21.829000 22.294001 30.936001
+ CG 23.952999 22.636000 30.528999
+ HG1 24.087000 21.563999 30.480000
+ HG2 24.382999 23.082001 29.620001
+ CD 24.664000 23.216999 31.731001
+ OE1 25.924999 23.066000 31.792000
+ OE2 24.062000 23.813000 32.638000
+ C 22.455000 23.982000 27.962999
+ O 23.288000 23.715000 27.105000
+ N 22.066999 25.257999 28.238001
+ H 21.582001 25.348000 29.114000
+ CA 22.514999 26.488001 27.599001
+ HA 22.579000 26.171000 26.551001
+ CB 21.296000 27.472000 27.627001
+ HB1 20.349001 26.957001 27.518999
+ HB2 21.292000 27.892000 28.624001
+ CG 21.295000 28.688000 26.698000
+ CD1 20.809999 28.739000 25.419001
+ HD1 20.245001 27.996000 24.898001
+ NE1 21.153000 29.927000 24.822001
+ HE1 20.910999 30.128000 23.862000
+ CE2 21.830000 30.771000 25.705000
+ CZ2 22.299999 32.084000 25.590000
+ HZ2 22.004999 32.647999 24.718000
+ CH2 22.936001 32.709999 26.669001
+ HH2 23.256001 33.729000 26.532000
+ CZ3 23.180000 31.929001 27.827000
+ HZ3 23.761999 32.296001 28.660000
+ CE3 22.704000 30.584000 27.972000
+ HE3 22.966000 30.039000 28.858000
+ CD2 21.937000 30.024000 26.900000
+ C 23.790001 27.049000 28.077000
+ O 23.979000 27.245001 29.250000
+ N 24.664000 27.459000 27.167999
+ H 24.493999 27.230000 26.198000
+ CA 25.944000 28.215000 27.511999
+ HA 25.858000 28.559000 28.531000
+ CB 27.127001 27.233999 27.625000
+ HB 28.094000 27.754999 27.599001
+ CG2 27.125999 26.485001 28.971001
+ HG21 28.070999 25.936001 28.988001
+ HG22 27.077999 27.235001 29.771000
+ HG23 26.226000 25.895000 29.132999
+ OG1 27.122000 26.291000 26.610001
+ HG1 26.299000 26.406000 26.128000
+ C 26.318001 29.334999 26.612000
+ O 25.931000 29.290001 25.406000
+ N 26.937000 30.419001 27.214001
+ H 27.208000 30.348000 28.184000
+ CA 27.393000 31.665001 26.514999
+ HA 26.924000 31.650999 25.537001
+ CB 26.936001 32.923000 27.348000
+ HB1 25.841000 32.842999 27.466000
+ HB2 27.365999 32.735001 28.327999
+ CG 27.353001 34.301998 26.784000
+ CD1 28.195000 35.095001 27.549999
+ HD1 28.518000 34.873001 28.552999
+ CE1 28.516001 36.407001 27.080999
+ HE1 29.082001 37.053001 27.733999
+ CZ 27.983999 36.919998 25.889000
+ OH 28.358999 38.113998 25.357000
+ HH 29.028999 38.589001 25.847000
+ CE2 27.202000 36.049999 25.077999
+ HE2 26.775999 36.417000 24.158001
+ CD2 26.856001 34.779999 25.548000
+ HD2 26.242001 34.161999 24.915001
+ C 28.908001 31.686001 26.368999
+ O 29.594999 30.900999 27.076000
+ N 29.541000 32.520000 25.540001
+ H 28.945999 33.144001 25.034000
+ CA 30.965000 32.807999 25.399000
+ HA 31.499001 32.728001 26.368000
+ CB 31.775000 31.896000 24.535999
+ HB1 32.002998 30.976000 25.030001
+ HB2 31.254999 31.729000 23.584000
+ CG 33.110001 32.515999 24.207001
+ OD1 33.905998 32.730999 25.113001
+ OD2 33.334000 32.654999 22.987000
+ C 31.105000 34.262001 24.892000
+ O 30.858000 34.618000 23.715000
+ N 31.629999 35.123001 25.740000
+ H 31.801001 34.918999 26.709999
+ CA 31.686001 36.534000 25.382000
+ HA 30.695000 36.832001 25.011000
+ CB 31.891001 37.368000 26.670000
+ HB1 31.207001 36.912998 27.393999
+ HB2 32.882000 37.275002 27.114000
+ CG 31.686001 38.876999 26.488001
+ OD1 30.497999 39.277000 26.441999
+ OD2 32.632999 39.618999 26.233999
+ C 32.693001 36.846001 24.339001
+ O 32.523998 37.744999 23.490999
+ N 33.800999 36.090000 24.323999
+ H 33.880001 35.432999 25.098000
+ CA 34.862999 36.185001 23.351000
+ HA 35.362000 37.127998 23.506001
+ CB 35.958000 35.210999 23.770000
+ HB1 35.625999 34.160000 23.805000
+ HB2 36.679001 35.311001 22.966000
+ HB3 36.372002 35.522999 24.739000
+ C 34.466999 35.936001 21.872999
+ O 35.224998 36.155998 20.940001
+ N 33.238998 35.365002 21.695999
+ H 32.812000 34.952000 22.509001
+ CA 32.587002 35.181000 20.334999
+ HA 33.251999 35.653000 19.600000
+ CB 32.472000 33.657001 19.893000
+ HB 31.891001 33.698002 18.981001
+ CG2 33.896999 33.044998 19.625000
+ HG21 34.542999 33.022999 20.490999
+ HG22 33.709000 32.033001 19.254000
+ HG23 34.313999 33.556000 18.770000
+ OG1 31.795000 32.990002 20.917999
+ HG1 32.449001 32.827999 21.584000
+ C 31.194000 35.888000 20.263000
+ O 30.659000 36.123001 19.143000
+ N 30.684000 36.381001 21.351999
+ H 31.156000 36.174000 22.226999
+ CA 29.305000 36.761002 21.459999
+ HA 29.184999 36.771000 22.552999
+ CB 28.923000 38.148998 20.962000
+ HB1 28.908001 38.033001 19.863001
+ HB2 27.922001 38.449001 21.261000
+ CG 29.847000 39.402000 21.191999
+ HG1 30.841999 39.118000 20.856001
+ HG2 29.415001 40.252998 20.653000
+ CD 29.893000 39.845001 22.681000
+ HD1 28.910000 40.095001 23.089001
+ HD2 30.285000 39.061001 23.325001
+ CE 30.825001 41.063999 22.917000
+ HE1 31.714001 40.983002 22.291000
+ HE2 30.344000 42.000999 22.671000
+ NZ 31.319000 41.192001 24.323000
+ HZ1 31.575001 40.334999 24.798000
+ HZ2 32.103001 41.823002 24.355000
+ HZ3 30.577000 41.567001 24.905001
+ C 28.257000 35.695999 21.091999
+ O 27.073999 36.021999 20.809000
+ N 28.570000 34.408001 21.002001
+ H 29.448000 34.092999 21.361000
+ CA 27.709999 33.388000 20.556999
+ HA 26.907000 33.828999 19.976999
+ CB 28.520000 32.305000 19.747999
+ HB 27.795000 31.548000 19.447001
+ CG2 28.986000 33.018002 18.510000
+ HG21 28.219999 33.407001 17.856001
+ HG22 29.559999 33.907001 18.740000
+ HG23 29.541000 32.311001 17.871000
+ OG1 29.524000 31.665001 20.492001
+ HG1 30.228001 32.300999 20.673000
+ C 26.987000 32.577000 21.724001
+ O 27.351999 32.762001 22.864000
+ N 25.985001 31.763000 21.419001
+ H 25.613001 31.841000 20.490999
+ CA 25.412001 30.754000 22.336000
+ HA 26.086000 30.739000 23.201000
+ CB 24.010000 31.070999 22.820000
+ HB1 23.674999 30.299999 23.518999
+ HB2 24.129999 32.029999 23.333000
+ CG 22.889000 31.415001 21.846001
+ CD1 22.771999 32.722000 21.333000
+ HD1 23.465000 33.449001 21.714001
+ CE1 21.705000 33.063999 20.549999
+ HE1 21.652000 34.113998 20.354000
+ CZ 20.819000 32.152000 20.070000
+ HZ 20.033001 32.436001 19.392000
+ CE2 20.902000 30.856001 20.548000
+ HE2 20.169001 30.180000 20.174999
+ CD2 21.929001 30.468000 21.473000
+ HD2 22.025999 29.465000 21.884001
+ C 25.471001 29.308001 21.680000
+ O 25.422001 29.070999 20.487000
+ N 25.547001 28.389999 22.624001
+ H 25.438999 28.750999 23.565001
+ CA 25.743999 26.962000 22.444000
+ HA 25.503000 26.646999 21.423000
+ CB 27.216999 26.635000 22.723000
+ HB 27.507000 27.037001 23.686001
+ CG2 27.459000 25.172001 22.698000
+ HG21 27.174000 24.802000 21.704000
+ HG22 28.525000 24.992001 22.799000
+ HG23 26.974001 24.705000 23.562000
+ OG1 28.183001 27.145000 21.778999
+ HG1 28.490999 27.962000 22.174000
+ C 24.840000 26.252001 23.396000
+ O 24.993999 26.368000 24.650000
+ N 23.921000 25.407000 22.864000
+ H 23.792000 25.363001 21.862000
+ CA 23.184999 24.448999 23.674000
+ HA 23.176001 24.722000 24.738001
+ CB 21.681000 24.237000 23.173000
+ HB 21.579000 23.358999 22.538000
+ CG1 20.811001 24.122999 24.396000
+ HG11 21.056000 23.201000 24.931999
+ HG12 20.853001 25.014000 25.046000
+ HG13 19.746000 24.146999 24.155001
+ CG2 21.216000 25.393000 22.268000
+ HG21 21.138000 26.372000 22.688999
+ HG22 21.896999 25.462999 21.410999
+ HG23 20.205999 25.216999 21.903999
+ C 23.813000 23.059999 23.599001
+ O 23.926001 22.535000 22.535999
+ N 24.299000 22.615999 24.763000
+ H 24.115999 23.039000 25.677999
+ CA 25.055000 21.367001 24.976000
+ HA 25.730000 21.396999 24.101999
+ CB 25.955999 21.405001 26.252001
+ HB 26.698999 20.606001 26.297001
+ CG2 26.799000 22.662001 26.341999
+ HG21 26.400000 23.490000 26.900000
+ HG22 27.726999 22.270000 26.746000
+ HG23 26.997000 23.023001 25.341000
+ OG1 25.091999 21.486000 27.341999
+ HG1 24.570999 22.270000 27.320999
+ C 24.242001 20.051001 24.921000
+ O 24.604000 18.999001 25.445000
+ N 23.042999 20.115000 24.253000
+ H 22.997999 20.992001 23.731001
+ CA 22.235001 18.993999 23.775000
+ HA 22.077999 18.368000 24.646999
+ CB 20.777000 19.410000 23.356001
+ HB1 20.219000 18.511000 23.118999
+ HB2 20.305000 19.875000 24.226999
+ CG 20.764000 20.438000 22.186001
+ HG1 20.070999 21.218000 22.458000
+ HG2 21.771999 20.841999 22.122000
+ CD 20.354000 19.847000 20.841999
+ OE1 21.136000 19.959000 19.878000
+ OE2 19.327000 19.124001 20.763000
+ C 22.938000 18.226999 22.639000
+ O 23.724001 18.790001 21.837999
+ N 22.670000 16.910000 22.429001
+ H 21.915001 16.459000 22.921000
+ CH3 23.198000 16.097000 21.344999
+ HH31 23.355000 15.066000 21.643999
+ HH32 24.146999 16.496000 20.975000
+ HH33 22.497999 16.171000 20.511999
diff --git a/regtest/scripts/run b/regtest/scripts/run
index a3d6c955a307a66fe3f5c2adce06b98a323b7cbe..c45c26ad1fca807d66c03f17eebb537f66cdc327 100755
--- a/regtest/scripts/run
+++ b/regtest/scripts/run
@@ -138,6 +138,9 @@ case "$type" in
(plumed)
$mpi $valgrind $plumed $arg > out 2> err
;;
+(python)
+ python $arg > out 2> err
+ ;;
(*) echo "unknown test type" ; exit 1 ;;
esac
diff --git a/sourceme.sh.in b/sourceme.sh.in
index a98ab0889a5e0cab0dc7fe82df5f22cbac539ace..53518dd2e3cd13557d9d324442c8831d7e45df9f 100644
--- a/sourceme.sh.in
+++ b/sourceme.sh.in
@@ -4,3 +4,4 @@ export LD_LIBRARY_PATH="@build_dir@/src/lib/:$LD_LIBRARY_PATH"
export DYLD_LIBRARY_PATH="@build_dir@/src/lib/:$DYLD_LIBRARY_PATH"
export PLUMED_KERNEL="@build_dir@/src/lib/libplumedKernel.@SOEXT@"
export PLUMED_VIMPATH="@build_dir@/vim"
+export PYTHONPATH="@build_dir@/python:$PYTHONPATH"
diff --git a/src/.gitignore b/src/.gitignore
index ae37745087fb10928c38d1dfb9b419ec83f5f32c..17fcc4e5c87444c37e8a8815f062afb60762c2a1 100644
--- a/src/.gitignore
+++ b/src/.gitignore
@@ -27,6 +27,7 @@
!/manyrestraints
!/molfile
!/multicolvar
+!/python
!/pamm
!/reference
!/secondarystructure
diff --git a/src/cltools/Info.cpp b/src/cltools/Info.cpp
index 3a8600abdb61144b22bb0b04f5d827eb7f0d7413..d23a0f1fb5dca3e5c182503a5aa70bfc08602b73 100644
--- a/src/cltools/Info.cpp
+++ b/src/cltools/Info.cpp
@@ -72,6 +72,7 @@ void Info::registerKeywords( Keywords& keys ) {
keys.addFlag("--version",false,"print the version number");
keys.addFlag("--long-version",false,"print the version number (long version)");
keys.addFlag("--git-version",false,"print the version number (git version, if available)");
+ keys.addFlag("--include-dir",false,"print the location of the include dir");
}
Info::Info(const CLToolOptions& co ):
@@ -89,8 +90,10 @@ int Info::main(FILE* in, FILE*out,Communicator& pc) {
bool printversion; parseFlag("--version",printversion);
bool printlongversion; parseFlag("--long-version",printlongversion);
bool printgitversion; parseFlag("--git-version",printgitversion);
+ bool printincludedir; parseFlag("--include-dir",printincludedir);
if(printroot) fprintf(out,"%s\n",config::getPlumedRoot().c_str());
if(printconfiguration) fprintf(out,"%s",config::getMakefile().c_str());
+ if(printincludedir) fprintf(out,"%s\n",config::getPlumedIncludedir().c_str());
if(printuserdoc) {
std::string userdoc=config::getPlumedHtmldir()+"/user-doc/html/index.html";
FILE *ff=std::fopen(userdoc.c_str(),"r");
diff --git a/src/core/DataFetchingObject.cpp b/src/core/DataFetchingObject.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..8cb51f3498caeaf7926e15ef130206f17aebb09f
--- /dev/null
+++ b/src/core/DataFetchingObject.cpp
@@ -0,0 +1,158 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2011-2015 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#include "DataFetchingObject.h"
+#include "PlumedMain.h"
+#include "ActionSet.h"
+#include "Action.h"
+#include "ActionWithValue.h"
+#include "Value.h"
+
+namespace PLMD {
+
+template <class T>
+class DataFetchingObjectTyped : public DataFetchingObject {
+private:
+/// A map containing the data we are grabbing
+ std::map<std::string,T*> data;
+public:
+ explicit DataFetchingObjectTyped(PlumedMain&plumed);
+ ~DataFetchingObjectTyped() {}
+ void setData( const std::string& key, const std::string& type, void* outval );
+ void finishDataGrab();
+};
+
+DataFetchingObject* DataFetchingObject::create(unsigned n, PlumedMain& p) {
+ if(n==sizeof(double)) {
+ return new DataFetchingObjectTyped<double>(p);
+ } else if(n==sizeof(float)) {
+ return new DataFetchingObjectTyped<float>(p);
+ }
+ std::string pp; Tools::convert(n,pp);
+ plumed_merror("cannot create an MD interface with sizeof(real)=="+ pp);
+ return NULL;
+}
+
+DataFetchingObject::DataFetchingObject(PlumedMain&p):
+ plumed(p)
+{
+}
+
+bool DataFetchingObject::activate() const {
+ for(unsigned j=0; j<myactions.size(); ++j) myactions[j]->activate();
+ if( myactions.size()>0 ) return true;
+ return false;
+}
+
+ActionWithValue* DataFetchingObject::findAction( const ActionSet& a, const std::string& key ) {
+ std::string aname = key; std::size_t dot = key.find(".");
+ if( dot!=std::string::npos ) aname = key.substr(0,dot);
+ return a.selectWithLabel<ActionWithValue*>( aname );
+}
+
+void DataFetchingObject::get_rank( const ActionSet& a, const std::string& key, const std::string& type, long* dims ) {
+ plumed_assert( Tools::getWords(key,"\t\n ,").size()==1 );
+ plumed_massert( key.find("*")==std::string::npos, "cannot use wildcards in python interface");
+
+ // Find the appropriate action and store value containing quantity of interest
+ ActionWithValue* myv = findAction( a, key );
+ Value* val = myv->copyOutput( key );
+
+ // Now work out what we are returning for this action
+ if( type=="" ) {
+ // Return a single value in this case
+ dims[0]=1;
+ } else if( type=="derivatives" ) {
+ plumed_merror("not yet implemented");
+ } else if( type=="forces" ) {
+ plumed_merror("not yet implemented");
+ } else {
+ plumed_merror("invalid type specifier");
+ }
+}
+
+void DataFetchingObject::get_shape( const ActionSet& a, const std::string& key, const std::string& type, long* dims ) {
+ plumed_assert( Tools::getWords(key,"\t\n ,").size()==1 );
+ plumed_massert( key.find("*")==std::string::npos, "cannot use wildcards in python interface");
+
+ // Find the appropriate action and store value containing quantity of interest
+ ActionWithValue* myv = findAction( a, key );
+ Value* val = myv->copyOutput( key );
+
+ // Now work out what we are returning for this action
+ if( type=="" ) {
+ // Return a single value in this case
+ dims[0]=1;
+ } else if( type=="derivatives" ) {
+ plumed_merror("not yet implemented");
+ } else if( type=="forces" ) {
+ plumed_merror("not yet implemented");
+ } else {
+ plumed_merror("invalid type specifier");
+ }
+}
+
+template <class T>
+DataFetchingObjectTyped<T>::DataFetchingObjectTyped(PlumedMain&p):
+ DataFetchingObject(p)
+{
+}
+
+template <class T>
+void DataFetchingObjectTyped<T>::setData( const std::string& key, const std::string& type, void* outval ) {
+ plumed_assert( Tools::getWords(key,"\t\n ,").size()==1 );
+ plumed_massert( key.find("*")==std::string::npos, "cannot use wildcards in python interface");
+ plumed_massert( !data.count(key + " " + type), "already collecting this data elsewhere");
+ // Add the space to store the data to the data map
+ T* f=static_cast<T*>(outval);
+ data.insert(std::pair<std::string,T*>(key + " " + type,f));
+
+ // Find the appropriate action and store value containing quantity of interest
+ ActionWithValue* myv = DataFetchingObject::findAction( plumed.getActionSet(), key );
+ // Store the action if not already stored
+ bool found=false;
+ for(const auto & p : myactions) {
+ if( p->getLabel()==myv->getLabel() ) { found=true; break; }
+ }
+ if( !found ) myactions.push_back( myv );
+ // Store the value
+ myvalues.push_back( myv->copyOutput( key ) );
+}
+
+template <class T>
+void DataFetchingObjectTyped<T>::finishDataGrab() {
+ // Run over all values and collect data
+ for(const auto & p : myvalues ) {
+ T* val = static_cast<T*>( data.find(p->getName() + " ")->second );
+ if( data.find(p->getName() + " ")!=data.end() ) {
+ val[0] = static_cast<T>( p->get() );
+ }
+ if( data.find(p->getName() + " derivatives")!=data.end() ) {
+ plumed_merror("not implemented yet");
+ }
+ if( data.find(p->getName() + " forces")!=data.end() ) {
+ plumed_merror("not implemented yet");
+ }
+ }
+}
+
+}
+
diff --git a/src/core/DataFetchingObject.h b/src/core/DataFetchingObject.h
new file mode 100644
index 0000000000000000000000000000000000000000..ab38eab9391c0536a13814bdd13c79067303ce54
--- /dev/null
+++ b/src/core/DataFetchingObject.h
@@ -0,0 +1,65 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2011-2015 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_core_DataFetchingObject_h
+#define __PLUMED_core_DataFetchingObject_h
+
+#include <string>
+#include <vector>
+#include <set>
+#include <map>
+
+namespace PLMD {
+
+class ActionSet;
+class PlumedMain;
+class ActionWithValue;
+class Value;
+
+class DataFetchingObject {
+protected:
+/// Pointers to the various actions required by the grabber
+ std::vector<ActionWithValue*> myactions;
+/// The values required by the user
+ std::vector<Value*> myvalues;
+/// A copy of the plumed main object
+ PlumedMain & plumed;
+public:
+ static DataFetchingObject* create(unsigned n, PlumedMain& p);
+/// A constructor so that we can create the plumed main object
+ explicit DataFetchingObject(PlumedMain&p);
+ virtual ~DataFetchingObject() {}
+///
+ bool activate() const ;
+/// Return the rank required for a particular key
+ static void get_rank( const ActionSet& a, const std::string& key, const std::string& type, long* rank );
+/// Return the shape required for a particular key
+ static void get_shape( const ActionSet& a, const std::string& key, const std::string& type, long* dims );
+/// Find the action that calculates a particular value
+ static ActionWithValue* findAction( const ActionSet& a, const std::string& key );
+/// Set the pointer to the data
+ virtual void setData( const std::string& key, const std::string& type, void* outval )=0;
+/// After calc has been performed grab all the data and put it in the relevant arrays
+ virtual void finishDataGrab()=0;
+};
+
+}
+#endif
diff --git a/src/core/PlumedMain.cpp b/src/core/PlumedMain.cpp
index 9a28cc0a065df28d2a7c070e466f14cd6f26d00d..f23f87d11ac92a2759734dba349afe3e8af63462 100644
--- a/src/core/PlumedMain.cpp
+++ b/src/core/PlumedMain.cpp
@@ -40,6 +40,7 @@
#include "tools/OpenMP.h"
#include "tools/Tools.h"
#include "tools/Stopwatch.h"
+#include "DataFetchingObject.h"
#include <cstdlib>
#include <cstring>
#include <set>
@@ -87,6 +88,7 @@ PlumedMain::PlumedMain():
{
log.link(comm);
log.setLinePrefix("PLUMED: ");
+ mydatafetcher.reset(DataFetchingObject::create(sizeof(double),*this));
stopwatch.start();
stopwatch.pause();
}
@@ -247,6 +249,21 @@ void PlumedMain::cmd(const std::string & word,void*val) {
CHECK_INIT(initialized,word);
atoms.clearFullList();
break;
+ case cmd_getDataRank:
+ CHECK_INIT(initialized,words[0]); plumed_assert(nw==2 || nw==3);
+ if( nw==2 ) DataFetchingObject::get_rank( actionSet, words[1], "", static_cast<long*>(val) );
+ else DataFetchingObject::get_rank( actionSet, words[1], words[2], static_cast<long*>(val) );
+ break;
+ case cmd_getDataShape:
+ CHECK_INIT(initialized,words[0]); plumed_assert(nw==2 || nw==3);
+ if( nw==2 ) DataFetchingObject::get_shape( actionSet, words[1], "", static_cast<long*>(val) );
+ else DataFetchingObject::get_shape( actionSet, words[1], words[2], static_cast<long*>(val) );
+ break;
+ case cmd_setMemoryForData:
+ CHECK_INIT(initialized,words[0]); plumed_assert(nw==2 || nw==3);
+ if( nw==2 ) mydatafetcher->setData( words[1], "", val );
+ else mydatafetcher->setData( words[1], words[2], val );
+ break;
case cmd_read:
CHECK_INIT(initialized,word);
if(val)readInputFile(static_cast<char*>(val));
@@ -274,6 +291,7 @@ void PlumedMain::cmd(const std::string & word,void*val) {
CHECK_NOTINIT(initialized,word);
CHECK_NOTNULL(val,word);
atoms.setRealPrecision(*static_cast<int*>(val));
+ mydatafetcher.reset(DataFetchingObject::create(*static_cast<int*>(val),*this));
break;
case cmd_setMDLengthUnits:
CHECK_NOTINIT(initialized,word);
@@ -586,7 +604,7 @@ void PlumedMain::prepareDependencies() {
}
// for optimization, an "active" flag remains false if no action at all is active
- active=false;
+ active=mydatafetcher->activate();
for(unsigned i=0; i<pilots.size(); ++i) {
if(pilots[i]->onStep()) {
pilots[i]->activate();
@@ -623,6 +641,7 @@ void PlumedMain::performCalc() {
justCalculate();
backwardPropagate();
update();
+ mydatafetcher->finishDataGrab();
}
void PlumedMain::waitData() {
@@ -826,6 +845,10 @@ void PlumedMain::runJobsAtEndOfCalculation() {
}
}
+#ifdef __PLUMED_HAS_PYTHON
+// This is here to stop cppcheck throwing an error
+#endif
+
}
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////
diff --git a/src/core/PlumedMain.h b/src/core/PlumedMain.h
index 35f4e130a293f6dfd95b5152e6deb80a3252a6c3..e19df3b2461270587050835e1b8974420be0a34a 100644
--- a/src/core/PlumedMain.h
+++ b/src/core/PlumedMain.h
@@ -63,6 +63,7 @@ class Stopwatch;
class Citations;
class ExchangePatterns;
class FileBase;
+class DataFetchingObject;
/**
Main plumed object.
@@ -130,6 +131,9 @@ private:
/// Name of the input file
std::string plumedDat;
+/// Object containing data we would like to grab and pass back
+ std::unique_ptr<DataFetchingObject> mydatafetcher;
+
/// End of input file.
/// Set to true to terminate reading
bool endPlumed;
diff --git a/src/lib/Makefile b/src/lib/Makefile
index a86e5ecdeee676f70696b9baa900bf8c136f88fb..b27f65adc0c8f734588205280fc93a7ee74a9a73 100644
--- a/src/lib/Makefile
+++ b/src/lib/Makefile
@@ -200,6 +200,12 @@ endif
if test -d ../../vim/syntax ; then mkdir -p "$(DESTDIR)$(libdir)/$(program_name)" && cd ../../ && tar cf - vim/syntax | tar xf - -C "$(DESTDIR)$(libdir)/$(program_name)/" ; fi
if test -d ../../vim/help ; then mkdir -p "$(DESTDIR)$(libdir)/$(program_name)" && cd ../../ && tar cf - vim/help | tar xf - -C "$(DESTDIR)$(libdir)/$(program_name)/" ; fi
if test -f ../../vim/scripts.vim ; then cp ../../vim/scripts.vim "$(DESTDIR)$(libdir)/$(program_name)/vim/" ; fi
+# python installation (rebuild prior to installation so as to discover plumed in path)
+ifneq (,$(findstring __PLUMED_HAS_PYTHON,$(CPPFLAGS)))
+ cp -pr ../../python install
+ cd install/python && rm -fr *.so plumed.cpp build && python buildPythonInterface.py build_ext -i
+ cp -pr install/python "$(DESTDIR)$(libdir)/$(program_name)/"
+endif
# making everything visible:
chmod -R go+rX,go-w "$(DESTDIR)$(libdir)/$(program_name)"
chmod -R go+rX,go-w "$(DESTDIR)$(includedir)/$(program_name)"
@@ -243,6 +249,11 @@ endif
@if test -d ../../vim/help ; then echo "- Set this environment variable : PLUMED_VIMPATH=$(libdir)/$(program_name)/vim" ; fi
@if test -d ../../vim/help ; then echo "- Add the command 'let &runtimepath.=','.\$$PLUMED_VIMPATH' to your .vimrc file" ; fi
@if test -d ../../vim/help ; then echo "From vim, you can use :set syntax=$(program_name) to enable it" ; fi
+ @if test -d ../../python/build ; then echo "A python plugin can be found here: $(libdir)/$(program_name)/python/" ; fi
+ @if test -d ../../python/build ; then echo "To use PLUMED through python either : " ; fi
+ @if test -d ../../python/build ; then echo "- Add $(libdir)/$(program_name)/python/ to your PYTHONPATH" ; fi
+ @if test -d ../../python/build ; then echo "- Execute the command python buildPythonInterface.py install in the plumed2/python directory"; fi
+ @if test -d ../../python/build ; then echo "Plumed can be loaded in a python script using the command import plumed" ; fi
ifeq ($(program_can_run),no)
@echo "WARNING: $(program_name) executable will not run on this machine"
@echo "WARNING: to patch an MD code use 'plumed-patch'"
diff --git a/src/lib/modulefile.in b/src/lib/modulefile.in
index 3f92600ada01fcf39b6bff95a77ccadb599247a3..3d84958d43a57214871e37b5ab52cb3279e38319 100644
--- a/src/lib/modulefile.in
+++ b/src/lib/modulefile.in
@@ -43,6 +43,7 @@ if { [module-info mode load] && [ info exists ::env(PLUMED_KERNEL) ] } {
prepend-path LIBRARY_PATH $libdir
prepend-path LD_LIBRARY_PATH $libdir
prepend-path DYLD_LIBRARY_PATH $libdir
+prepend-path PYTHONPATH $libdir/$progname/python
setenv PLUMED_KERNEL $libdir/lib${progname}Kernel.$soext
setenv PLUMED_VIMPATH $libdir/$progname/vim
}