add mmtk 2.2

An Open Source program library for molecular simulation applications

PR:		42332
Submitted by:	Glenn Johnson <glennpj@charter.net>

5 files changed, 1046 insertions, 0 deletions

diff --git a/science/mmtk/Makefile b/science/mmtk/Makefile
new file mode 100644
index 000000000000..c10a8268d915
--- /dev/null
+++ b/science/mmtk/Makefile
@@ -0,0 +1,44 @@
+# New ports collection makefile for:	mmtk
+# Date created:		29 August 2002
+# Whom:			Glenn Johnson <gjohnson@srrc.ars.usda.gov>
+#
+# $FreeBSD$
+#
+
+PORTNAME=	mmtk
+PORTVERSION=	2.2
+CATEGORIES=	science python
+MASTER_SITES=	http://starship.python.net/crew/hinsen/MMTK/
+DISTNAME=	MMTK-${PORTVERSION}
+
+MAINTAINER=	gjohnson@srrc.ars.usda.gov
+
+BUILD_DEPENDS=	${PYTHON_SITELIBDIR}/Scientific:${PORTSDIR}/math/py-scientific
+RUN_DEPENDS=	${PYTHON_SITELIBDIR}/Scientific:${PORTSDIR}/math/py-scientific
+
+USE_REINPLACE=	yes
+USE_PYTHON=	yes
+USE_PYDISTUTILS=yes
+
+.include <bsd.port.pre.mk>
+
+MAJOR!=	${UNAME} -r | ${SED} -e 's/\..*//'
+
+PLIST_SUB+=	MAJOR=${MAJOR}
+
+post-patch:
+	@${REINPLACE_CMD} "s#'Include'#'Include','${PREFIX}/include'#" ${WRKSRC}/setup.py
+	@${REINPLACE_CMD} "s#malloc.h#stdlib.h#g" ${WRKSRC}/Include/MMTK/readdcd.h
+
+.if !defined(NOPORTDOCS)
+post-install:
+	@${MKDIR} ${DOCSDIR}
+	@${INSTALL_DATA} ${WRKSRC}/LICENSE ${DOCSDIR}
+	@${MKDIR} ${EXAMPLESDIR}
+	@${TAR} -C ${WRKSRC} -chf - Doc | \
+		${TAR} -xf - -C ${DOCSDIR}
+	@${TAR} -C ${WRKSRC} -chf - Examples | \
+		${TAR} -xf - -C ${EXAMPLESDIR}
+.endif
+
+.include <bsd.port.post.mk>
diff --git a/science/mmtk/distinfo b/science/mmtk/distinfo
new file mode 100644
index 000000000000..c835c1f1b25a
--- /dev/null
+++ b/science/mmtk/distinfo
@@ -0,0 +1 @@
+MD5 (MMTK-2.2.tar.gz) = 369df2f12b712cbaf990640a2aa9fac5
diff --git a/science/mmtk/pkg-comment b/science/mmtk/pkg-comment
new file mode 100644
index 000000000000..7ebc3c98626e
--- /dev/null
+++ b/science/mmtk/pkg-comment
@@ -0,0 +1 @@
+An Open Source program library for molecular simulation applications
diff --git a/science/mmtk/pkg-descr b/science/mmtk/pkg-descr
new file mode 100644
index 000000000000..909b5514dcfa
--- /dev/null
+++ b/science/mmtk/pkg-descr
@@ -0,0 +1,11 @@
+This is a port of MMTK (Molecular Modeling ToolKit).  In addition to
+providing ready-to-use implementations of standard algorithms, MMTK
+serves as a code basis that can be easily extended and modified to deal
+with standard and non-standard problems in molecular simulations.
+
+MMTK consists of nothing more than a collection of Python modules, most
+of which written in Python itself, with only a small time-critical part
+(e.g. energy evaluation) written in C. MMTK applications are Python
+programs that make use of these modules.
+
+WWW: http://starship.python.net/crew/hinsen/MMTK/index.html
diff --git a/science/mmtk/pkg-plist b/science/mmtk/pkg-plist
new file mode 100644
index 000000000000..d78c51696e72
--- /dev/null
+++ b/science/mmtk/pkg-plist
@@ -0,0 +1,989 @@
+bin/tviewer
+%%PYTHON_SITELIBDIR%%/MMTK/AtomEnvironment.py
+%%PYTHON_SITELIBDIR%%/MMTK/AtomEnvironment.pyc
+%%PYTHON_SITELIBDIR%%/MMTK/AtomEnvironment.pyo
+%%PYTHON_SITELIBDIR%%/MMTK/Biopolymers.py
+%%PYTHON_SITELIBDIR%%/MMTK/Biopolymers.pyc
+%%PYTHON_SITELIBDIR%%/MMTK/Biopolymers.pyo
+%%PYTHON_SITELIBDIR%%/MMTK/Bonds.py
+%%PYTHON_SITELIBDIR%%/MMTK/Bonds.pyc
+%%PYTHON_SITELIBDIR%%/MMTK/Bonds.pyo
+%%PYTHON_SITELIBDIR%%/MMTK/ChargeFit.py
+%%PYTHON_SITELIBDIR%%/MMTK/ChargeFit.pyc
+%%PYTHON_SITELIBDIR%%/MMTK/ChargeFit.pyo
+%%PYTHON_SITELIBDIR%%/MMTK/ChemicalObjects.py
+%%PYTHON_SITELIBDIR%%/MMTK/ChemicalObjects.pyc
+%%PYTHON_SITELIBDIR%%/MMTK/ChemicalObjects.pyo
+%%PYTHON_SITELIBDIR%%/MMTK/Collection.py
+%%PYTHON_SITELIBDIR%%/MMTK/Collection.pyc
+%%PYTHON_SITELIBDIR%%/MMTK/Collection.pyo
+%%PYTHON_SITELIBDIR%%/MMTK/ComplexEnvironment.py
+%%PYTHON_SITELIBDIR%%/MMTK/ComplexEnvironment.pyc
+%%PYTHON_SITELIBDIR%%/MMTK/ComplexEnvironment.pyo
+%%PYTHON_SITELIBDIR%%/MMTK/ConfigIO.py
+%%PYTHON_SITELIBDIR%%/MMTK/ConfigIO.pyc
+%%PYTHON_SITELIBDIR%%/MMTK/ConfigIO.pyo
+%%PYTHON_SITELIBDIR%%/MMTK/CrystalEnvironment.py
+%%PYTHON_SITELIBDIR%%/MMTK/CrystalEnvironment.pyc
+%%PYTHON_SITELIBDIR%%/MMTK/CrystalEnvironment.pyo
+%%PYTHON_SITELIBDIR%%/MMTK/DCD.py
+%%PYTHON_SITELIBDIR%%/MMTK/DCD.pyc
+%%PYTHON_SITELIBDIR%%/MMTK/DCD.pyo
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/al
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/alanine
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/ar
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/arginine
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/asparagine
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/aspartic_acid
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/c
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/ca
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/ch
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/ch2
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/ch3
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/cl
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/cysteine
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/cystine_ss
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/d
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/f
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/fe
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/glutamic_acid
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/glutamine
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/glycine
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/h
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/histidine
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/histidine_deltah
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/histidine_epsilonh
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/histidine_plus
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/isoleucine
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/k
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/leucine
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/lp
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/lysine
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/methionine
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/n
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/nh
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/nh2
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/nh3
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/o
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/oh
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/p
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/phenylalanine
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/proline
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/s
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/serine
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/sh
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/si
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/threonine
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/tryptophan
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/tyrosine
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/valine
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Atoms/zn
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/ace_beginning_nt
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/adenine
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/ala_sidechain
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/ala_sidechain_noh
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/ala_sidechain_uni
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/ala_sidechain_uni2
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/ala_sidechain_uni3
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/alanine
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/alanine_calpha
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/alanine_ct
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/alanine_ct_noh
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/alanine_ct_uni
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/alanine_ct_uni2
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/alanine_ct_uni3
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/alanine_noh
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/alanine_nt
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/alanine_nt_noh
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/alanine_nt_uni
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/alanine_nt_uni2
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/alanine_nt_uni3
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/alanine_uni
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/alanine_uni2
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/alanine_uni3
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/amide
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/amide_uni
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/amide_uni3
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/arg_sidechain
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/arg_sidechain_noh
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/arg_sidechain_uni
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/arg_sidechain_uni2
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/arg_sidechain_uni3
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/arginine
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/arginine_calpha
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/arginine_ct
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/arginine_ct_noh
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/arginine_ct_uni
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/arginine_ct_uni2
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/arginine_ct_uni3
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/arginine_noh
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/arginine_nt
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/arginine_nt_noh
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/arginine_nt_uni
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/arginine_nt_uni2
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/arginine_nt_uni3
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/arginine_uni
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/arginine_uni2
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/arginine_uni3
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/asn_sidechain
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/asn_sidechain_noh
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/asn_sidechain_uni
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/asn_sidechain_uni2
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/asn_sidechain_uni3
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/asp_sidechain
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/asp_sidechain_neutral
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/asp_sidechain_noh
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/asp_sidechain_uni
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/asp_sidechain_uni2
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/asp_sidechain_uni3
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/asparagine
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/asparagine_calpha
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/asparagine_ct
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/asparagine_ct_noh
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/asparagine_ct_uni
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/asparagine_ct_uni2
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/asparagine_ct_uni3
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/asparagine_noh
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/asparagine_nt
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/asparagine_nt_noh
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/asparagine_nt_uni
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/asparagine_nt_uni2
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/asparagine_nt_uni3
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/asparagine_uni
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/asparagine_uni2
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/asparagine_uni3
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/aspartic_acid
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/aspartic_acid_calpha
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/aspartic_acid_ct
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/aspartic_acid_ct_noh
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/aspartic_acid_ct_uni
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/aspartic_acid_ct_uni2
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/aspartic_acid_ct_uni3
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/aspartic_acid_neutral
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/aspartic_acid_noh
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/aspartic_acid_nt
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/aspartic_acid_nt_noh
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/aspartic_acid_nt_uni
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/aspartic_acid_nt_uni2
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/aspartic_acid_nt_uni3
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/aspartic_acid_uni
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/aspartic_acid_uni2
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/aspartic_acid_uni3
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/bound_heme
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/cym_sidechain
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/cys_sidechain
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/cys_sidechain_noh
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/cys_sidechain_uni
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/cys_sidechain_uni2
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/cys_sidechain_uni3
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/cysteine
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/cysteine_calpha
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/cysteine_ct
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/cysteine_ct_noh
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/cysteine_ct_uni
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/cysteine_ct_uni2
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/cysteine_ct_uni3
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/cysteine_noh
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/cysteine_nt
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/cysteine_nt_noh
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/cysteine_nt_uni
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/cysteine_nt_uni2
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/cysteine_nt_uni3
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/cysteine_uni
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/cysteine_uni2
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/cysteine_uni3
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/cysteine_with_negative_charge
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/cystine_ss
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/cystine_ss_calpha
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/cystine_ss_ct
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/cystine_ss_ct_noh
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/cystine_ss_ct_uni
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/cystine_ss_ct_uni2
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/cystine_ss_ct_uni3
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/cystine_ss_noh
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/cystine_ss_nt
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/cystine_ss_nt_noh
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/cystine_ss_nt_uni
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/cystine_ss_nt_uni2
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/cystine_ss_nt_uni3
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/cystine_ss_uni
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/cystine_ss_uni2
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/cystine_ss_uni3
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/cytosine
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/cyx_sidechain
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/cyx_sidechain_noh
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/cyx_sidechain_uni
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/cyx_sidechain_uni2
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/cyx_sidechain_uni3
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/d-adenosine
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/d-adenosine_3ter
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/d-adenosine_5ter
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/d-adenosine_5ter_3ter
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/d-cytosine
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/d-cytosine_3ter
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/d-cytosine_5ter
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/d-cytosine_5ter_3ter
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/d-guanosine
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/d-guanosine_3ter
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/d-guanosine_5ter
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/d-guanosine_5ter_3ter
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/d-thymine
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/d-thymine_3ter
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/d-thymine_5ter
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/d-thymine_5ter_3ter
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/desoxyribose
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/desoxyribose_3ter
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/desoxyribose_5ter
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/desoxyribose_5ter_3ter
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/gln_sidechain
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/gln_sidechain_noh
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/gln_sidechain_uni
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/gln_sidechain_uni2
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/gln_sidechain_uni3
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/glu_sidechain
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/glu_sidechain_neutral
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/glu_sidechain_noh
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/glu_sidechain_uni
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/glu_sidechain_uni2
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/glu_sidechain_uni3
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+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/glutamic_acid_calpha
+%%PYTHON_SITELIBDIR%%/MMTK/Database/Groups/glutamic_acid_ct
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