├── README.md ├── RIP-MD ├── dat │ ├── par_all22_prot.prm │ └── top_all22_prot.rtf ├── dependencies │ └── linux │ │ ├── dssp │ │ └── dssp-2.0.4-linux-i386 │ │ └── pdb2pqr-linux-bin64-2.1.1 │ │ ├── BINARY_README.md │ │ ├── _MEI │ │ ├── tcl │ │ │ ├── auto.tcl │ │ │ ├── encoding │ │ │ │ ├── ascii.enc │ │ │ │ ├── big5.enc │ │ │ │ ├── cp1250.enc │ │ │ │ ├── cp1251.enc │ │ │ │ ├── cp1252.enc │ │ │ │ ├── cp1253.enc │ │ │ │ ├── cp1254.enc │ │ │ │ ├── cp1255.enc │ │ │ │ ├── cp1256.enc │ │ │ │ ├── cp1257.enc │ │ │ │ ├── cp1258.enc │ │ │ │ ├── cp437.enc │ │ │ │ ├── cp737.enc │ │ │ │ ├── cp775.enc │ │ │ │ ├── cp850.enc │ │ │ │ ├── cp852.enc │ │ │ │ ├── cp855.enc │ │ │ │ ├── cp857.enc │ │ │ │ ├── cp860.enc │ │ │ │ ├── cp861.enc │ │ │ │ ├── cp862.enc │ │ │ │ ├── cp863.enc │ │ │ │ ├── cp864.enc │ │ │ │ ├── cp865.enc │ │ │ │ ├── cp866.enc │ │ │ │ ├── cp869.enc │ │ │ │ ├── cp874.enc │ │ │ │ ├── cp932.enc │ │ │ │ ├── cp936.enc │ │ │ │ ├── cp949.enc │ │ │ │ ├── cp950.enc │ │ │ │ ├── dingbats.enc │ │ │ │ ├── ebcdic.enc │ │ │ │ ├── euc-cn.enc │ │ │ │ ├── euc-jp.enc │ │ │ │ ├── euc-kr.enc │ │ │ │ ├── gb12345.enc │ │ │ │ ├── gb1988.enc │ │ │ │ ├── gb2312-raw.enc │ │ │ │ ├── gb2312.enc │ │ │ │ ├── iso2022-jp.enc │ │ │ │ ├── iso2022-kr.enc │ │ │ │ ├── iso2022.enc │ │ │ │ ├── iso8859-1.enc │ │ │ │ ├── iso8859-10.enc │ │ │ │ ├── iso8859-13.enc │ │ │ │ ├── iso8859-14.enc │ │ │ │ ├── iso8859-15.enc │ │ │ │ ├── iso8859-16.enc │ │ │ │ ├── iso8859-2.enc │ │ │ │ ├── iso8859-3.enc │ │ │ │ ├── iso8859-4.enc │ │ │ │ ├── iso8859-5.enc │ │ │ │ ├── iso8859-6.enc │ │ │ │ ├── iso8859-7.enc │ │ │ │ ├── iso8859-8.enc │ │ │ │ ├── iso8859-9.enc │ │ │ │ ├── jis0201.enc │ │ │ │ ├── jis0208.enc │ │ │ │ ├── jis0212.enc │ │ │ │ ├── koi8-r.enc │ │ │ │ ├── koi8-u.enc │ │ │ │ ├── ksc5601.enc │ │ │ │ ├── macCentEuro.enc │ │ │ │ ├── macCroatian.enc │ │ │ │ ├── macCyrillic.enc │ │ │ │ ├── macDingbats.enc │ │ │ │ ├── macGreek.enc │ │ │ │ ├── macIceland.enc │ │ │ │ ├── macJapan.enc │ │ │ │ ├── macRoman.enc │ │ │ │ ├── macRomania.enc │ │ │ │ ├── macThai.enc │ │ │ │ ├── macTurkish.enc │ │ │ │ ├── macUkraine.enc │ │ │ │ ├── shiftjis.enc │ │ │ │ ├── symbol.enc │ │ │ │ └── tis-620.enc │ │ │ ├── history.tcl │ │ │ ├── http1.0 │ │ │ │ ├── http.tcl │ │ │ │ └── pkgIndex.tcl │ │ │ ├── http2.5 │ │ │ │ ├── http.tcl │ │ │ │ └── pkgIndex.tcl │ │ │ ├── init.tcl │ │ │ ├── ldAix │ │ │ ├── ldAout.tcl │ │ │ ├── msgcat1.3 │ │ │ │ ├── msgcat.tcl │ │ │ │ └── pkgIndex.tcl │ │ │ ├── opt0.4 │ │ │ │ ├── optparse.tcl │ │ │ │ └── pkgIndex.tcl │ │ │ ├── package.tcl │ │ │ ├── parray.tcl │ │ │ ├── safe.tcl │ │ │ ├── tclAppInit.c │ │ │ ├── tclIndex │ │ │ ├── tcltest2.2 │ │ │ │ ├── constraints.tcl │ │ │ │ ├── files.tcl │ │ │ │ ├── pkgIndex.tcl │ │ │ │ ├── tcltest.tcl │ │ │ │ └── testresults.tcl │ │ │ └── word.tcl │ │ └── tk │ │ │ ├── bgerror.tcl │ │ │ ├── button.tcl │ │ │ ├── choosedir.tcl │ │ │ ├── clrpick.tcl │ │ │ ├── comdlg.tcl │ │ │ ├── console.tcl │ │ │ ├── dialog.tcl │ │ │ ├── entry.tcl │ │ │ ├── focus.tcl │ │ │ ├── images │ │ │ ├── README │ │ │ ├── logo.eps │ │ │ ├── logo100.gif │ │ │ ├── logo64.gif │ │ │ ├── logoLarge.gif │ │ │ ├── logoMed.gif │ │ │ ├── pwrdLogo.eps │ │ │ ├── pwrdLogo100.gif │ │ │ ├── pwrdLogo150.gif │ │ │ ├── pwrdLogo175.gif │ │ │ ├── pwrdLogo200.gif │ │ │ ├── pwrdLogo75.gif │ │ │ └── tai-ku.gif │ │ │ ├── listbox.tcl │ │ │ ├── menu.tcl │ │ │ ├── mkpsenc.tcl │ │ │ ├── msgbox.tcl │ │ │ ├── msgs │ │ │ ├── cs.msg │ │ │ ├── de.msg │ │ │ ├── el.msg │ │ │ ├── en.msg │ │ │ ├── en_gb.msg │ │ │ ├── eo.msg │ │ │ ├── es.msg │ │ │ ├── es_ES.msg │ │ │ ├── fr.msg │ │ │ ├── it.msg │ │ │ ├── nl.msg │ │ │ ├── pl.msg │ │ │ ├── pt.msg │ │ │ └── ru.msg │ │ │ ├── obsolete.tcl │ │ │ ├── optMenu.tcl │ │ │ ├── palette.tcl │ │ │ ├── panedwindow.tcl │ │ │ ├── prolog.ps │ │ │ ├── safetk.tcl │ │ │ ├── scale.tcl │ │ │ ├── scrlbar.tcl │ │ │ ├── spinbox.tcl │ │ │ ├── tclIndex │ │ │ ├── tearoff.tcl │ │ │ ├── text.tcl │ │ │ ├── tk.tcl │ │ │ ├── tkAppInit.c │ │ │ ├── tkfbox.tcl │ │ │ ├── unsupported.tcl │ │ │ └── xmfbox.tcl │ │ ├── _bisect.so │ │ ├── _codecs_cn.so │ │ ├── _codecs_hk.so │ │ ├── _codecs_iso2022.so │ │ ├── _codecs_jp.so │ │ ├── _codecs_kr.so │ │ ├── _codecs_tw.so │ │ ├── _collections.so │ │ ├── _ctypes.so │ │ ├── _curses.so │ │ ├── _elementtree.so │ │ ├── _functools.so │ │ ├── _hashlib.so │ │ ├── _heapq.so │ │ ├── _io.so │ │ ├── _locale.so │ │ ├── _multibytecodec.so │ │ ├── _multiprocessing.so │ │ ├── _random.so │ │ ├── _socket.so │ │ ├── _ssl.so │ │ ├── _struct.so │ │ ├── _tkinter.so │ │ ├── array.so │ │ ├── audioop.so │ │ ├── binascii.so │ │ ├── bz2.so │ │ ├── cPickle.so │ │ ├── cStringIO.so │ │ ├── dat │ │ ├── AA.xml │ │ ├── AMBER.DAT │ │ ├── AMBER.names │ │ ├── CHARMM.DAT │ │ ├── CHARMM.names │ │ ├── HYDROGENS.xml │ │ ├── NA.xml │ │ ├── PARSE.DAT │ │ ├── PARSE.names │ │ ├── PATCHES.xml │ │ ├── PEOEPB.DAT │ │ ├── PEOEPB.names │ │ ├── SWANSON.DAT │ │ ├── SWANSON.names │ │ ├── TOPOLOGY.xml │ │ ├── TYL06.DAT │ │ └── TYL06.names │ │ ├── datetime.so │ │ ├── doc │ │ ├── PDB2PQR Release SOP.md │ │ ├── flowchart.dot │ │ ├── genpydoc.sh │ │ ├── images │ │ │ └── flowchart.png │ │ ├── license.txt │ │ ├── programmerguide.html │ │ ├── pydoc │ │ │ ├── .htaccess │ │ │ ├── copy.html │ │ │ ├── getopt.html │ │ │ ├── index.html │ │ │ ├── math.html │ │ │ ├── os.html │ │ │ ├── pdb2pqr.html │ │ │ ├── re.html │ │ │ ├── src.aa.html │ │ │ ├── src.definitions.html │ │ │ ├── src.forcefield.html │ │ │ ├── src.html │ │ │ ├── src.hydrogens.html │ │ │ ├── src.inputgen.html │ │ │ ├── src.na.html │ │ │ ├── src.pdb.html │ │ │ ├── src.protein.html │ │ │ ├── src.psize.html │ │ │ ├── src.quatfit.html │ │ │ ├── src.routines.html │ │ │ ├── src.server.html │ │ │ ├── src.structures.html │ │ │ ├── src.topology.html │ │ │ ├── src.utilities.html │ │ │ ├── string.html │ │ │ ├── sys.html │ │ │ ├── time.html │ │ │ └── xml.sax.html │ │ ├── template │ │ └── userguide.html │ │ ├── eggs │ │ └── setuptools-8.2.1-py2.7.egg │ │ ├── examples │ │ ├── 1a1p │ │ │ ├── 1a1p.pdb │ │ │ └── README │ │ ├── build_config.py │ │ ├── index.html │ │ ├── ligands │ │ │ ├── LIG_1ABF.mol2 │ │ │ ├── LIG_1HPV.mol2 │ │ │ ├── LIG_1HPX.mol2 │ │ │ ├── LIG_1QBS.mol2 │ │ │ ├── LIG_1XL5.mol2 │ │ │ └── README │ │ ├── pdb2pqr_web_interface_tutorial-01.png │ │ ├── pdb2pqr_web_interface_tutorial-02.png │ │ ├── pdb2pqr_web_interface_tutorial-03.png │ │ ├── pdb2pqr_web_interface_tutorial-04.png │ │ └── pdb2pqr_web_interface_tutorial-05.png │ │ ├── extensions │ │ ├── README │ │ ├── __init__.py │ │ ├── __init__.pyc │ │ ├── chi.py │ │ ├── chi.pyc │ │ ├── contact.py │ │ ├── contact.pyc │ │ ├── hbond.py │ │ ├── hbond.pyc │ │ ├── newresinter.py │ │ ├── newresinter.pyc │ │ ├── rama.py │ │ ├── rama.pyc │ │ ├── resinter.py │ │ ├── resinter.pyc │ │ ├── salt.py │ │ ├── salt.pyc │ │ ├── summary.py │ │ ├── summary.pyc │ │ └── template │ │ ├── fcntl.so │ │ ├── future_builtins.so │ │ ├── grp.so │ │ ├── include │ │ └── python2.7 │ │ │ └── pyconfig.h │ │ ├── itertools.so │ │ ├── lib │ │ └── python2.7 │ │ │ └── config │ │ │ └── Makefile │ │ ├── lib2to3 │ │ ├── Grammar.txt │ │ ├── Grammar2.7.9.final.0.pickle │ │ ├── PatternGrammar.txt │ │ ├── PatternGrammar2.7.9.final.0.pickle │ │ ├── __init__.py │ │ ├── __init__.pyc │ │ ├── __init__.pyo │ │ ├── __main__.py │ │ ├── __main__.pyc │ │ ├── __main__.pyo │ │ ├── btm_matcher.py │ │ ├── btm_matcher.pyc │ │ ├── btm_matcher.pyo │ │ ├── btm_utils.py │ │ ├── btm_utils.pyc │ │ ├── btm_utils.pyo │ │ ├── fixer_base.py │ │ ├── fixer_base.pyc │ │ ├── fixer_base.pyo │ │ ├── fixer_util.py │ │ ├── fixer_util.pyc │ │ ├── fixer_util.pyo │ │ ├── fixes │ │ │ ├── __init__.py │ │ │ ├── __init__.pyc │ │ │ ├── __init__.pyo │ │ │ ├── fix_apply.py │ │ │ ├── fix_apply.pyc │ │ │ ├── fix_apply.pyo │ │ │ ├── fix_asserts.py │ │ │ ├── fix_asserts.pyc │ │ │ ├── fix_asserts.pyo │ │ │ ├── fix_basestring.py │ │ │ ├── fix_basestring.pyc │ │ │ ├── fix_basestring.pyo │ │ │ ├── fix_buffer.py │ │ │ ├── fix_buffer.pyc │ │ │ ├── fix_buffer.pyo │ │ │ ├── fix_callable.py │ │ │ ├── fix_callable.pyc │ │ │ ├── fix_callable.pyo │ │ │ ├── fix_dict.py │ │ │ ├── fix_dict.pyc │ │ │ ├── fix_dict.pyo │ │ │ ├── fix_except.py │ │ │ ├── fix_except.pyc │ │ │ ├── fix_except.pyo │ │ │ ├── fix_exec.py │ │ │ ├── fix_exec.pyc │ │ │ ├── fix_exec.pyo │ │ │ ├── fix_execfile.py │ │ │ ├── fix_execfile.pyc │ │ │ ├── fix_execfile.pyo │ │ │ ├── fix_exitfunc.py │ │ │ ├── fix_exitfunc.pyc │ │ │ ├── fix_exitfunc.pyo │ │ │ ├── fix_filter.py │ │ │ ├── fix_filter.pyc │ │ │ ├── fix_filter.pyo │ │ │ ├── fix_funcattrs.py │ │ │ ├── fix_funcattrs.pyc │ │ │ ├── fix_funcattrs.pyo │ │ │ ├── fix_future.py │ │ │ ├── fix_future.pyc │ │ │ ├── fix_future.pyo │ │ │ ├── fix_getcwdu.py │ │ │ ├── fix_getcwdu.pyc │ │ │ ├── fix_getcwdu.pyo │ │ │ ├── fix_has_key.py │ │ │ ├── fix_has_key.pyc │ │ │ ├── fix_has_key.pyo │ │ │ ├── fix_idioms.py │ │ │ ├── fix_idioms.pyc │ │ │ ├── fix_idioms.pyo │ │ │ ├── fix_import.py │ │ │ ├── fix_import.pyc │ │ │ ├── fix_import.pyo │ │ │ ├── fix_imports.py │ │ │ ├── fix_imports.pyc │ │ │ ├── fix_imports.pyo │ │ │ ├── fix_imports2.py │ │ │ ├── fix_imports2.pyc │ │ │ ├── fix_imports2.pyo │ │ │ ├── fix_input.py │ │ │ ├── fix_input.pyc │ │ │ ├── fix_input.pyo │ │ │ ├── fix_intern.py │ │ │ ├── fix_intern.pyc │ │ │ ├── fix_intern.pyo │ │ │ ├── fix_isinstance.py │ │ │ ├── fix_isinstance.pyc │ │ │ ├── fix_isinstance.pyo │ │ │ ├── fix_itertools.py │ │ │ ├── fix_itertools.pyc │ │ │ ├── fix_itertools.pyo │ │ │ ├── fix_itertools_imports.py │ │ │ ├── fix_itertools_imports.pyc │ │ │ ├── fix_itertools_imports.pyo │ │ │ ├── fix_long.py │ │ │ ├── fix_long.pyc │ │ │ ├── fix_long.pyo │ │ │ ├── fix_map.py │ │ │ ├── fix_map.pyc │ │ │ ├── fix_map.pyo │ │ │ ├── fix_metaclass.py │ │ │ ├── fix_metaclass.pyc │ │ │ ├── fix_metaclass.pyo │ │ │ ├── fix_methodattrs.py │ │ │ ├── fix_methodattrs.pyc │ │ │ ├── fix_methodattrs.pyo │ │ │ ├── fix_ne.py │ │ │ ├── fix_ne.pyc │ │ │ ├── fix_ne.pyo │ │ │ ├── fix_next.py │ │ │ ├── fix_next.pyc │ │ │ ├── fix_next.pyo │ │ │ ├── fix_nonzero.py │ │ │ ├── fix_nonzero.pyc │ │ │ ├── fix_nonzero.pyo │ │ │ ├── fix_numliterals.py │ │ │ ├── fix_numliterals.pyc │ │ │ ├── fix_numliterals.pyo │ │ │ ├── fix_operator.py │ │ │ ├── fix_operator.pyc │ │ │ ├── fix_operator.pyo │ │ │ ├── fix_paren.py │ │ │ ├── fix_paren.pyc │ │ │ ├── fix_paren.pyo │ │ │ ├── fix_print.py │ │ │ ├── fix_print.pyc │ │ │ ├── fix_print.pyo │ │ │ ├── fix_raise.py │ │ │ ├── fix_raise.pyc │ │ │ ├── fix_raise.pyo │ │ │ ├── fix_raw_input.py │ │ │ ├── fix_raw_input.pyc │ │ │ ├── fix_raw_input.pyo │ │ │ ├── fix_reduce.py │ │ │ ├── fix_reduce.pyc │ │ │ ├── fix_reduce.pyo │ │ │ ├── fix_renames.py │ │ │ ├── fix_renames.pyc │ │ │ ├── fix_renames.pyo │ │ │ ├── fix_repr.py │ │ │ ├── fix_repr.pyc │ │ │ ├── fix_repr.pyo │ │ │ ├── fix_set_literal.py │ │ │ ├── fix_set_literal.pyc │ │ │ ├── fix_set_literal.pyo │ │ │ ├── fix_standarderror.py │ │ │ ├── fix_standarderror.pyc │ │ │ ├── fix_standarderror.pyo │ │ │ ├── fix_sys_exc.py │ │ │ ├── fix_sys_exc.pyc │ │ │ ├── fix_sys_exc.pyo │ │ │ ├── fix_throw.py │ │ │ ├── fix_throw.pyc │ │ │ ├── fix_throw.pyo │ │ │ ├── fix_tuple_params.py │ │ │ ├── fix_tuple_params.pyc │ │ │ ├── fix_tuple_params.pyo │ │ │ ├── fix_types.py │ │ │ ├── fix_types.pyc │ │ │ ├── fix_types.pyo │ │ │ ├── fix_unicode.py │ │ │ ├── fix_unicode.pyc │ │ │ ├── fix_unicode.pyo │ │ │ ├── fix_urllib.py │ │ │ ├── fix_urllib.pyc │ │ │ ├── fix_urllib.pyo │ │ │ ├── fix_ws_comma.py │ │ │ ├── fix_ws_comma.pyc │ │ │ ├── fix_ws_comma.pyo │ │ │ ├── fix_xrange.py │ │ │ ├── fix_xrange.pyc │ │ │ ├── fix_xrange.pyo │ │ │ ├── fix_xreadlines.py │ │ │ ├── fix_xreadlines.pyc │ │ │ ├── fix_xreadlines.pyo │ │ │ ├── fix_zip.py │ │ │ ├── fix_zip.pyc │ │ │ └── fix_zip.pyo │ │ ├── main.py │ │ ├── main.pyc │ │ ├── main.pyo │ │ ├── patcomp.py │ │ ├── patcomp.pyc │ │ ├── patcomp.pyo │ │ ├── pgen2 │ │ │ ├── __init__.py │ │ │ ├── __init__.pyc │ │ │ ├── __init__.pyo │ │ │ ├── conv.py │ │ │ ├── conv.pyc │ │ │ ├── conv.pyo │ │ │ ├── driver.py │ │ │ ├── driver.pyc │ │ │ ├── driver.pyo │ │ │ ├── grammar.py │ │ │ ├── grammar.pyc │ │ │ ├── grammar.pyo │ │ │ ├── literals.py │ │ │ ├── literals.pyc │ │ │ ├── literals.pyo │ │ │ ├── parse.py │ │ │ ├── parse.pyc │ │ │ ├── parse.pyo │ │ │ ├── pgen.py │ │ │ ├── pgen.pyc │ │ │ ├── pgen.pyo │ │ │ ├── token.py │ │ │ ├── token.pyc │ │ │ ├── token.pyo │ │ │ ├── tokenize.py │ │ │ ├── tokenize.pyc │ │ │ └── tokenize.pyo │ │ ├── pygram.py │ │ ├── pygram.pyc │ │ ├── pygram.pyo │ │ ├── pytree.py │ │ ├── pytree.pyc │ │ ├── pytree.pyo │ │ ├── refactor.py │ │ ├── refactor.pyc │ │ ├── refactor.pyo │ │ └── tests │ │ │ ├── __init__.py │ │ │ ├── __init__.pyc │ │ │ ├── __init__.pyo │ │ │ ├── data │ │ │ ├── README │ │ │ ├── bom.py │ │ │ ├── crlf.py │ │ │ ├── different_encoding.py │ │ │ ├── false_encoding.py │ │ │ ├── fixers │ │ │ │ ├── bad_order.py │ │ │ │ ├── myfixes │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── fix_explicit.py │ │ │ │ │ ├── fix_first.py │ │ │ │ │ ├── fix_last.py │ │ │ │ │ ├── fix_parrot.py │ │ │ │ │ └── fix_preorder.py │ │ │ │ ├── no_fixer_cls.py │ │ │ │ └── parrot_example.py │ │ │ ├── infinite_recursion.py │ │ │ ├── py2_test_grammar.py │ │ │ └── py3_test_grammar.py │ │ │ ├── pytree_idempotency.py │ │ │ ├── pytree_idempotency.pyc │ │ │ ├── pytree_idempotency.pyo │ │ │ ├── support.py │ │ │ ├── support.pyc │ │ │ ├── support.pyo │ │ │ ├── test_all_fixers.py │ │ │ ├── test_all_fixers.pyc │ │ │ ├── test_all_fixers.pyo │ │ │ ├── test_fixers.py │ │ │ ├── test_fixers.pyc │ │ │ ├── test_fixers.pyo │ │ │ ├── test_main.py │ │ │ ├── test_main.pyc │ │ │ ├── test_main.pyo │ │ │ ├── test_parser.py │ │ │ ├── test_parser.pyc │ │ │ ├── test_parser.pyo │ │ │ ├── test_pytree.py │ │ │ ├── test_pytree.pyc │ │ │ ├── test_pytree.pyo │ │ │ ├── test_refactor.py │ │ │ ├── test_refactor.pyc │ │ │ ├── test_refactor.pyo │ │ │ ├── test_util.py │ │ │ ├── test_util.pyc │ │ │ └── test_util.pyo │ │ ├── libX11.so.6 │ │ ├── libXau.so.6 │ │ ├── libXdmcp.so.6 │ │ ├── libbz2.so.1 │ │ ├── libcom_err.so.2 │ │ ├── libcrypto.so.6 │ │ ├── libgcc_s.so.1 │ │ ├── libgssapi_krb5.so.2 │ │ ├── libk5crypto.so.3 │ │ ├── libkeyutils.so.1 │ │ ├── libkrb5.so.3 │ │ ├── libkrb5support.so.0 │ │ ├── libncursesw.so.5 │ │ ├── libpython2.7.so.1.0 │ │ ├── libreadline.so.5 │ │ ├── libselinux.so.1 │ │ ├── libsepol.so.1 │ │ ├── libssl.so.6 │ │ ├── libstdc++.so.6 │ │ ├── libtcl8.4.so │ │ ├── libtk8.4.so │ │ ├── libz.so.1 │ │ ├── math.so │ │ ├── mmap.so │ │ ├── numpy.core.multiarray.so │ │ ├── numpy.core.scalarmath.so │ │ ├── numpy.core.umath.so │ │ ├── numpy.fft.fftpack_lite.so │ │ ├── numpy.lib._compiled_base.so │ │ ├── numpy.linalg._umath_linalg.so │ │ ├── numpy.linalg.lapack_lite.so │ │ ├── numpy.random.mtrand.so │ │ ├── operator.so │ │ ├── parser.so │ │ ├── pdb2pka._apbslib.so │ │ ├── pdb2pka._pMC_mult.so │ │ ├── pdb2pka.substruct.Algorithms.so │ │ ├── pdb2pka │ │ └── TITRATION.DAT │ │ ├── pdb2pqr │ │ ├── propka30 │ │ └── Source │ │ │ ├── ions.list │ │ │ └── protein_bonds.dat │ │ ├── pyexpat.so │ │ ├── readline.so │ │ ├── select.so │ │ ├── strop.so │ │ ├── syslog.so │ │ ├── termios.so │ │ ├── time.so │ │ ├── unicodedata.so │ │ └── zlib.so ├── libs │ ├── Angle.py │ ├── Calpha.py │ ├── arg_arg.py │ ├── atom_data.py │ ├── cationPi.py │ ├── checkPDB.py │ ├── correlation.py │ ├── coulomb.py │ ├── delConect.py │ ├── delete.py │ ├── delete_hetatm.py │ ├── distance.py │ ├── disulphide.py │ ├── extractFrames.py │ ├── graph.py │ ├── hbond.py │ ├── missingAtoms.py │ ├── nodes.py │ ├── pdb2graph.py │ ├── pi_pi.py │ ├── plotCorr.py │ ├── plotHist.py │ ├── saltBridge.py │ ├── saveGraph.py │ ├── selection.py │ └── vdw.py └── main.py ├── RIP-MD_vmd ├── pkgIndex.tcl └── ripmd.tcl ├── Terms of Use ├── install.sh ├── libraries ├── manual.pdf ├── requirements.sh └── ripmd.tcl /RIP-MD/dependencies/linux/dssp/dssp-2.0.4-linux-i386: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DLab/RIP-MD/08ec2a72ec4f388fbccc24124f19a9b60b152f5b/RIP-MD/dependencies/linux/dssp/dssp-2.0.4-linux-i386 -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/BINARY_README.md: -------------------------------------------------------------------------------- 1 | # Binary builds. 2 | 3 | Binary builds do not require python or numpy be installed to use. Everything needed to run PDB2PQR is included. Just unpack and use. 4 | 5 | In Windows the executable file is called "pdb2pqr.exe". 6 | 7 | In OSX and Linux the executable is called "pdb2pqr" and should already have the executable flag set. 8 | 9 | OSX binaries require OSX 10.6 or newer. The OSX binary is 64-bit. 10 | 11 | Linux binaries require CentOS 6 or newer and have been tested on Ubuntu 12.04 LTS and Linux Mint 13. If you are running 64-bit Linux use the 64-bit libraries. In some cases the needed 32-bit system libraries will not be installed on a 64-bit system. 12 | 13 | Windows binaries are 32 bit and were built and tested on Windows 7 64-bit but should work on Windows XP, Vista, and 8 both 32 and 64-bit systems. 14 | 15 | Instructions on how to create a binary build from source are found in INSTALL.md in the source tarball. -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/ascii.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: ascii, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E0000 13 | 0000000000000000000000000000000000000000000000000000000000000000 14 | 0000000000000000000000000000000000000000000000000000000000000000 15 | 0000000000000000000000000000000000000000000000000000000000000000 16 | 0000000000000000000000000000000000000000000000000000000000000000 17 | 0000000000000000000000000000000000000000000000000000000000000000 18 | 0000000000000000000000000000000000000000000000000000000000000000 19 | 0000000000000000000000000000000000000000000000000000000000000000 20 | 0000000000000000000000000000000000000000000000000000000000000000 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/cp1250.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: cp1250, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 20AC0081201A0083201E2026202020210088203001602039015A0164017D0179 14 | 009020182019201C201D202220132014009821220161203A015B0165017E017A 15 | 00A002C702D8014100A4010400A600A700A800A9015E00AB00AC00AD00AE017B 16 | 00B000B102DB014200B400B500B600B700B80105015F00BB013D02DD013E017C 17 | 015400C100C2010200C40139010600C7010C00C9011800CB011A00CD00CE010E 18 | 01100143014700D300D4015000D600D70158016E00DA017000DC00DD016200DF 19 | 015500E100E2010300E4013A010700E7010D00E9011900EB011B00ED00EE010F 20 | 01110144014800F300F4015100F600F70159016F00FA017100FC00FD016302D9 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/cp1251.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: cp1251, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 04020403201A0453201E20262020202120AC203004092039040A040C040B040F 14 | 045220182019201C201D202220132014009821220459203A045A045C045B045F 15 | 00A0040E045E040800A4049000A600A7040100A9040400AB00AC00AD00AE0407 16 | 00B000B104060456049100B500B600B704512116045400BB0458040504550457 17 | 0410041104120413041404150416041704180419041A041B041C041D041E041F 18 | 0420042104220423042404250426042704280429042A042B042C042D042E042F 19 | 0430043104320433043404350436043704380439043A043B043C043D043E043F 20 | 0440044104420443044404450446044704480449044A044B044C044D044E044F 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/cp1252.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: cp1252, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 20AC0081201A0192201E20262020202102C62030016020390152008D017D008F 14 | 009020182019201C201D20222013201402DC21220161203A0153009D017E0178 15 | 00A000A100A200A300A400A500A600A700A800A900AA00AB00AC00AD00AE00AF 16 | 00B000B100B200B300B400B500B600B700B800B900BA00BB00BC00BD00BE00BF 17 | 00C000C100C200C300C400C500C600C700C800C900CA00CB00CC00CD00CE00CF 18 | 00D000D100D200D300D400D500D600D700D800D900DA00DB00DC00DD00DE00DF 19 | 00E000E100E200E300E400E500E600E700E800E900EA00EB00EC00ED00EE00EF 20 | 00F000F100F200F300F400F500F600F700F800F900FA00FB00FC00FD00FE00FF 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/cp1253.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: cp1253, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 20AC0081201A0192201E20262020202100882030008A2039008C008D008E008F 14 | 009020182019201C201D20222013201400982122009A203A009C009D009E009F 15 | 00A00385038600A300A400A500A600A700A800A9000000AB00AC00AD00AE2015 16 | 00B000B100B200B3038400B500B600B703880389038A00BB038C00BD038E038F 17 | 0390039103920393039403950396039703980399039A039B039C039D039E039F 18 | 03A003A1000003A303A403A503A603A703A803A903AA03AB03AC03AD03AE03AF 19 | 03B003B103B203B303B403B503B603B703B803B903BA03BB03BC03BD03BE03BF 20 | 03C003C103C203C303C403C503C603C703C803C903CA03CB03CC03CD03CE0000 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/cp1254.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: cp1254, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 20AC0081201A0192201E20262020202102C62030016020390152008D008E008F 14 | 009020182019201C201D20222013201402DC21220161203A0153009D009E0178 15 | 00A000A100A200A300A400A500A600A700A800A900AA00AB00AC00AD00AE00AF 16 | 00B000B100B200B300B400B500B600B700B800B900BA00BB00BC00BD00BE00BF 17 | 00C000C100C200C300C400C500C600C700C800C900CA00CB00CC00CD00CE00CF 18 | 011E00D100D200D300D400D500D600D700D800D900DA00DB00DC0130015E00DF 19 | 00E000E100E200E300E400E500E600E700E800E900EA00EB00EC00ED00EE00EF 20 | 011F00F100F200F300F400F500F600F700F800F900FA00FB00FC0131015F00FF 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/cp1255.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: cp1255, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 20AC0081201A0192201E20262020202102C62030008A2039008C008D008E008F 14 | 009020182019201C201D20222013201402DC2122009A203A009C009D009E009F 15 | 00A000A100A200A320AA00A500A600A700A800A900D700AB00AC00AD00AE00AF 16 | 00B000B100B200B300B400B500B600B700B800B900F700BB00BC00BD00BE00BF 17 | 05B005B105B205B305B405B505B605B705B805B9000005BB05BC05BD05BE05BF 18 | 05C005C105C205C305F005F105F205F305F40000000000000000000000000000 19 | 05D005D105D205D305D405D505D605D705D805D905DA05DB05DC05DD05DE05DF 20 | 05E005E105E205E305E405E505E605E705E805E905EA00000000200E200F0000 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/cp1256.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: cp1256, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 20AC067E201A0192201E20262020202102C62030067920390152068606980688 14 | 06AF20182019201C201D20222013201406A921220691203A0153200C200D06BA 15 | 00A0060C00A200A300A400A500A600A700A800A906BE00AB00AC00AD00AE00AF 16 | 00B000B100B200B300B400B500B600B700B800B9061B00BB00BC00BD00BE061F 17 | 06C1062106220623062406250626062706280629062A062B062C062D062E062F 18 | 063006310632063306340635063600D7063706380639063A0640064106420643 19 | 00E0064400E2064506460647064800E700E800E900EA00EB0649064A00EE00EF 20 | 064B064C064D064E00F4064F065000F7065100F9065200FB00FC200E200F06D2 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/cp1257.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: cp1257, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 20AC0081201A0083201E20262020202100882030008A2039008C00A802C700B8 14 | 009020182019201C201D20222013201400982122009A203A009C00AF02DB009F 15 | 00A0000000A200A300A4000000A600A700D800A9015600AB00AC00AD00AE00C6 16 | 00B000B100B200B300B400B500B600B700F800B9015700BB00BC00BD00BE00E6 17 | 0104012E0100010600C400C501180112010C00C90179011601220136012A013B 18 | 01600143014500D3014C00D500D600D701720141015A016A00DC017B017D00DF 19 | 0105012F0101010700E400E501190113010D00E9017A011701230137012B013C 20 | 01610144014600F3014D00F500F600F701730142015B016B00FC017C017E02D9 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/cp1258.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: cp1258, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 20AC0081201A0192201E20262020202102C62030008A20390152008D008E008F 14 | 009020182019201C201D20222013201402DC2122009A203A0153009D009E0178 15 | 00A000A100A200A300A400A500A600A700A800A900AA00AB00AC00AD00AE00AF 16 | 00B000B100B200B300B400B500B600B700B800B900BA00BB00BC00BD00BE00BF 17 | 00C000C100C2010200C400C500C600C700C800C900CA00CB030000CD00CE00CF 18 | 011000D1030900D300D401A000D600D700D800D900DA00DB00DC01AF030300DF 19 | 00E000E100E2010300E400E500E600E700E800E900EA00EB030100ED00EE00EF 20 | 011100F1032300F300F401A100F600F700F800F900FA00FB00FC01B020AB00FF 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/cp437.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: cp437, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 00C700FC00E900E200E400E000E500E700EA00EB00E800EF00EE00EC00C400C5 14 | 00C900E600C600F400F600F200FB00F900FF00D600DC00A200A300A520A70192 15 | 00E100ED00F300FA00F100D100AA00BA00BF231000AC00BD00BC00A100AB00BB 16 | 259125922593250225242561256225562555256325512557255D255C255B2510 17 | 25142534252C251C2500253C255E255F255A25542569256625602550256C2567 18 | 2568256425652559255825522553256B256A2518250C25882584258C25902580 19 | 03B100DF039303C003A303C300B503C403A6039803A903B4221E03C603B52229 20 | 226100B1226522642320232100F7224800B0221900B7221A207F00B225A000A0 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/cp737.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: cp737, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 039103920393039403950396039703980399039A039B039C039D039E039F03A0 14 | 03A103A303A403A503A603A703A803A903B103B203B303B403B503B603B703B8 15 | 03B903BA03BB03BC03BD03BE03BF03C003C103C303C203C403C503C603C703C8 16 | 259125922593250225242561256225562555256325512557255D255C255B2510 17 | 25142534252C251C2500253C255E255F255A25542569256625602550256C2567 18 | 2568256425652559255825522553256B256A2518250C25882584258C25902580 19 | 03C903AC03AD03AE03CA03AF03CC03CD03CB03CE038603880389038A038C038E 20 | 038F00B12265226403AA03AB00F7224800B0221900B7221A207F00B225A000A0 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/cp775.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: cp775, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 010600FC00E9010100E4012300E501070142011301560157012B017900C400C5 14 | 00C900E600C6014D00F6012200A2015A015B00D600DC00F800A300D800D700A4 15 | 0100012A00F3017B017C017A201D00A600A900AE00AC00BD00BC014100AB00BB 16 | 259125922593250225240104010C01180116256325512557255D012E01602510 17 | 25142534252C251C2500253C0172016A255A25542569256625602550256C017D 18 | 0105010D01190117012F01610173016B017E2518250C25882584258C25902580 19 | 00D300DF014C014300F500D500B5014401360137013B013C0146011201452019 20 | 00AD00B1201C00BE00B600A700F7201E00B0221900B700B900B300B225A000A0 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/cp850.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: cp850, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 00C700FC00E900E200E400E000E500E700EA00EB00E800EF00EE00EC00C400C5 14 | 00C900E600C600F400F600F200FB00F900FF00D600DC00F800A300D800D70192 15 | 00E100ED00F300FA00F100D100AA00BA00BF00AE00AC00BD00BC00A100AB00BB 16 | 2591259225932502252400C100C200C000A9256325512557255D00A200A52510 17 | 25142534252C251C2500253C00E300C3255A25542569256625602550256C00A4 18 | 00F000D000CA00CB00C8013100CD00CE00CF2518250C2588258400A600CC2580 19 | 00D300DF00D400D200F500D500B500FE00DE00DA00DB00D900FD00DD00AF00B4 20 | 00AD00B1201700BE00B600A700F700B800B000A800B700B900B300B225A000A0 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/cp852.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: cp852, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 00C700FC00E900E200E4016F010700E7014200EB0150015100EE017900C40106 14 | 00C90139013A00F400F6013D013E015A015B00D600DC01640165014100D7010D 15 | 00E100ED00F300FA01040105017D017E0118011900AC017A010C015F00AB00BB 16 | 2591259225932502252400C100C2011A015E256325512557255D017B017C2510 17 | 25142534252C251C2500253C01020103255A25542569256625602550256C00A4 18 | 01110110010E00CB010F014700CD00CE011B2518250C258825840162016E2580 19 | 00D300DF00D401430144014801600161015400DA0155017000FD00DD016300B4 20 | 00AD02DD02DB02C702D800A700F700B800B000A802D901710158015925A000A0 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/cp855.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: cp855, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 0452040204530403045104010454040404550405045604060457040704580408 14 | 04590409045A040A045B040B045C040C045E040E045F040F044E042E044A042A 15 | 0430041004310411044604260434041404350415044404240433041300AB00BB 16 | 259125922593250225240445042504380418256325512557255D043904192510 17 | 25142534252C251C2500253C043A041A255A25542569256625602550256C00A4 18 | 043B041B043C041C043D041D043E041E043F2518250C25882584041F044F2580 19 | 042F044004200441042104420422044304230436041604320412044C042C2116 20 | 00AD044B042B0437041704480428044D042D044904290447042700A725A000A0 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/cp857.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: cp857, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 00C700FC00E900E200E400E000E500E700EA00EB00E800EF00EE013100C400C5 14 | 00C900E600C600F400F600F200FB00F9013000D600DC00F800A300D8015E015F 15 | 00E100ED00F300FA00F100D1011E011F00BF00AE00AC00BD00BC00A100AB00BB 16 | 2591259225932502252400C100C200C000A9256325512557255D00A200A52510 17 | 25142534252C251C2500253C00E300C3255A25542569256625602550256C00A4 18 | 00BA00AA00CA00CB00C8000000CD00CE00CF2518250C2588258400A600CC2580 19 | 00D300DF00D400D200F500D500B5000000D700DA00DB00D900EC00FF00AF00B4 20 | 00AD00B1000000BE00B600A700F700B800B000A800B700B900B300B225A000A0 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/cp860.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: cp860, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 00C700FC00E900E200E300E000C100E700EA00CA00E800CD00D400EC00C300C2 14 | 00C900C000C800F400F500F200DA00F900CC00D500DC00A200A300D920A700D3 15 | 00E100ED00F300FA00F100D100AA00BA00BF00D200AC00BD00BC00A100AB00BB 16 | 259125922593250225242561256225562555256325512557255D255C255B2510 17 | 25142534252C251C2500253C255E255F255A25542569256625602550256C2567 18 | 2568256425652559255825522553256B256A2518250C25882584258C25902580 19 | 03B100DF039303C003A303C300B503C403A6039803A903B4221E03C603B52229 20 | 226100B1226522642320232100F7224800B0221900B7221A207F00B225A000A0 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/cp861.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: cp861, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 00C700FC00E900E200E400E000E500E700EA00EB00E800D000F000DE00C400C5 14 | 00C900E600C600F400F600FE00FB00DD00FD00D600DC00F800A300D820A70192 15 | 00E100ED00F300FA00C100CD00D300DA00BF231000AC00BD00BC00A100AB00BB 16 | 259125922593250225242561256225562555256325512557255D255C255B2510 17 | 25142534252C251C2500253C255E255F255A25542569256625602550256C2567 18 | 2568256425652559255825522553256B256A2518250C25882584258C25902580 19 | 03B100DF039303C003A303C300B503C403A6039803A903B4221E03C603B52229 20 | 226100B1226522642320232100F7224800B0221900B7221A207F00B225A000A0 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/cp862.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: cp862, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 05D005D105D205D305D405D505D605D705D805D905DA05DB05DC05DD05DE05DF 14 | 05E005E105E205E305E405E505E605E705E805E905EA00A200A300A520A70192 15 | 00E100ED00F300FA00F100D100AA00BA00BF231000AC00BD00BC00A100AB00BB 16 | 259125922593250225242561256225562555256325512557255D255C255B2510 17 | 25142534252C251C2500253C255E255F255A25542569256625602550256C2567 18 | 2568256425652559255825522553256B256A2518250C25882584258C25902580 19 | 03B100DF039303C003A303C300B503C403A6039803A903B4221E03C603B52229 20 | 226100B1226522642320232100F7224800B0221900B7221A207F00B225A000A0 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/cp863.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: cp863, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 00C700FC00E900E200C200E000B600E700EA00EB00E800EF00EE201700C000A7 14 | 00C900C800CA00F400CB00CF00FB00F900A400D400DC00A200A300D900DB0192 15 | 00A600B400F300FA00A800B800B300AF00CE231000AC00BD00BC00BE00AB00BB 16 | 259125922593250225242561256225562555256325512557255D255C255B2510 17 | 25142534252C251C2500253C255E255F255A25542569256625602550256C2567 18 | 2568256425652559255825522553256B256A2518250C25882584258C25902580 19 | 03B100DF039303C003A303C300B503C403A6039803A903B4221E03C603B52229 20 | 226100B1226522642320232100F7224800B0221900B7221A207F00B225A000A0 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/cp864.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: cp864, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 00200021002200230024066A0026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 00B000B72219221A259225002502253C2524252C251C25342510250C25142518 14 | 03B2221E03C600B100BD00BC224800AB00BBFEF7FEF8009B009CFEFBFEFC009F 15 | 00A000ADFE8200A300A4FE8400000000FE8EFE8FFE95FE99060CFE9DFEA1FEA5 16 | 0660066106620663066406650666066706680669FED1061BFEB1FEB5FEB9061F 17 | 00A2FE80FE81FE83FE85FECAFE8BFE8DFE91FE93FE97FE9BFE9FFEA3FEA7FEA9 18 | FEABFEADFEAFFEB3FEB7FEBBFEBFFEC1FEC5FECBFECF00A600AC00F700D7FEC9 19 | 0640FED3FED7FEDBFEDFFEE3FEE7FEEBFEEDFEEFFEF3FEBDFECCFECEFECDFEE1 20 | FE7D0651FEE5FEE9FEECFEF0FEF2FED0FED5FEF5FEF6FEDDFED9FEF125A00000 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/cp865.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: cp865, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 00C700FC00E900E200E400E000E500E700EA00EB00E800EF00EE00EC00C400C5 14 | 00C900E600C600F400F600F200FB00F900FF00D600DC00F800A300D820A70192 15 | 00E100ED00F300FA00F100D100AA00BA00BF231000AC00BD00BC00A100AB00A4 16 | 259125922593250225242561256225562555256325512557255D255C255B2510 17 | 25142534252C251C2500253C255E255F255A25542569256625602550256C2567 18 | 2568256425652559255825522553256B256A2518250C25882584258C25902580 19 | 03B100DF039303C003A303C300B503C403A6039803A903B4221E03C603B52229 20 | 226100B1226522642320232100F7224800B0221900B7221A207F00B225A000A0 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/cp866.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: cp866, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 0410041104120413041404150416041704180419041A041B041C041D041E041F 14 | 0420042104220423042404250426042704280429042A042B042C042D042E042F 15 | 0430043104320433043404350436043704380439043A043B043C043D043E043F 16 | 259125922593250225242561256225562555256325512557255D255C255B2510 17 | 25142534252C251C2500253C255E255F255A25542569256625602550256C2567 18 | 2568256425652559255825522553256B256A2518250C25882584258C25902580 19 | 0440044104420443044404450446044704480449044A044B044C044D044E044F 20 | 040104510404045404070457040E045E00B0221900B7221A211600A425A000A0 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/cp869.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: cp869, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 0080008100820083008400850386008700B700AC00A620182019038820150389 14 | 038A03AA038C00930094038E03AB00A9038F00B200B303AC00A303AD03AE03AF 15 | 03CA039003CC03CD039103920393039403950396039700BD0398039900AB00BB 16 | 25912592259325022524039A039B039C039D256325512557255D039E039F2510 17 | 25142534252C251C2500253C03A003A1255A25542569256625602550256C03A3 18 | 03A403A503A603A703A803A903B103B203B32518250C2588258403B403B52580 19 | 03B603B703B803B903BA03BB03BC03BD03BE03BF03C003C103C303C203C40384 20 | 00AD00B103C503C603C700A703C8038500B000A803C903CB03B003CE25A000A0 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/cp874.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: cp874, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 20AC008100820083008420260086008700880089008A008B008C008D008E008F 14 | 009020182019201C201D20222013201400980099009A009B009C009D009E009F 15 | 00A00E010E020E030E040E050E060E070E080E090E0A0E0B0E0C0E0D0E0E0E0F 16 | 0E100E110E120E130E140E150E160E170E180E190E1A0E1B0E1C0E1D0E1E0E1F 17 | 0E200E210E220E230E240E250E260E270E280E290E2A0E2B0E2C0E2D0E2E0E2F 18 | 0E300E310E320E330E340E350E360E370E380E390E3A00000000000000000E3F 19 | 0E400E410E420E430E440E450E460E470E480E490E4A0E4B0E4C0E4D0E4E0E4F 20 | 0E500E510E520E530E540E550E560E570E580E590E5A0E5B0000000000000000 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/dingbats.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: dingbats, single-byte 2 | S 3 | 003F 1 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 00202701270227032704260E2706270727082709261B261E270C270D270E270F 8 | 2710271127122713271427152716271727182719271A271B271C271D271E271F 9 | 2720272127222723272427252726272726052729272A272B272C272D272E272F 10 | 2730273127322733273427352736273727382739273A273B273C273D273E273F 11 | 2740274127422743274427452746274727482749274A274B25CF274D25A0274F 12 | 27502751275225B225BC25C6275625D727582759275A275B275C275D275E007F 13 | 0080008100820083008400850086008700880089008A008B008C008D008E008F 14 | 0090009100920093009400950096009700980099009A009B009C009D009E009F 15 | 0000276127622763276427652766276726632666266526602460246124622463 16 | 2464246524662467246824692776277727782779277A277B277C277D277E277F 17 | 2780278127822783278427852786278727882789278A278B278C278D278E278F 18 | 2790279127922793279421922194219527982799279A279B279C279D279E279F 19 | 27A027A127A227A327A427A527A627A727A827A927AA27AB27AC27AD27AE27AF 20 | 000027B127B227B327B427B527B627B727B827B927BA27BB27BC27BD27BE0000 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/ebcdic.enc: -------------------------------------------------------------------------------- 1 | S 2 | 006F 0 1 3 | 00 4 | 0000000100020003008500090086007F0087008D008E000B000C000D000E000F 5 | 0010001100120013008F000A0008009700180019009C009D001C001D001E001F 6 | 0080008100820083008400920017001B00880089008A008B008C000500060007 7 | 0090009100160093009400950096000400980099009A009B00140015009E001A 8 | 002000A000E200E400E000E100E300E500E700F10060002E003C0028002B007C 9 | 002600E900EA00EB00E800ED00EE00EF00EC00DF00210024002A0029003B009F 10 | 002D002F00C200C400C000C100C300C500C700D1005E002C0025005F003E003F 11 | 00F800C900CA00CB00C800CD00CE00CF00CC00A8003A002300400027003D0022 12 | 00D800610062006300640065006600670068006900AB00BB00F000FD00FE00B1 13 | 00B0006A006B006C006D006E006F00700071007200AA00BA00E600B800C600A4 14 | 00B500AF0073007400750076007700780079007A00A100BF00D000DD00DE00AE 15 | 00A200A300A500B700A900A700B600BC00BD00BE00AC005B005C005D00B400D7 16 | 00F900410042004300440045004600470048004900AD00F400F600F200F300F5 17 | 00A6004A004B004C004D004E004F00500051005200B900FB00FC00DB00FA00FF 18 | 00D900F70053005400550056005700580059005A00B200D400D600D200D300D5 19 | 003000310032003300340035003600370038003900B3007B00DC007D00DA007E 20 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/gb1988.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: gb1988, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 002000210022002300A500250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D203E007F 13 | 0080008100820083008400850086008700880089008A008B008C008D008E008F 14 | 0090009100920093009400950096009700980099009A009B009C009D009E009F 15 | 0000FF61FF62FF63FF64FF65FF66FF67FF68FF69FF6AFF6BFF6CFF6DFF6EFF6F 16 | FF70FF71FF72FF73FF74FF75FF76FF77FF78FF79FF7AFF7BFF7CFF7DFF7EFF7F 17 | FF80FF81FF82FF83FF84FF85FF86FF87FF88FF89FF8AFF8BFF8CFF8DFF8EFF8F 18 | FF90FF91FF92FF93FF94FF95FF96FF97FF98FF99FF9AFF9BFF9CFF9DFF9EFF9F 19 | 0000000000000000000000000000000000000000000000000000000000000000 20 | 0000000000000000000000000000000000000000000000000000000000000000 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/iso2022-jp.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: iso2022-jp, escape-driven 2 | E 3 | name iso2022-jp 4 | init {} 5 | final {} 6 | ascii \x1b(B 7 | jis0201 \x1b(J 8 | jis0208 \x1b$B 9 | jis0208 \x1b$@ 10 | jis0212 \x1b$(D 11 | gb2312 \x1b$A 12 | ksc5601 \x1b$(C 13 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/iso2022-kr.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: iso2022-kr, escape-driven 2 | E 3 | name iso2022-kr 4 | init \x1b$)C 5 | final {} 6 | iso8859-1 \x0f 7 | ksc5601 \x0e 8 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/iso2022.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: iso2022, escape-driven 2 | E 3 | name iso2022 4 | init {} 5 | final {} 6 | iso8859-1 \x1b(B 7 | jis0201 \x1b(J 8 | gb1988 \x1b(T 9 | jis0208 \x1b$B 10 | jis0208 \x1b$@ 11 | jis0212 \x1b$(D 12 | gb2312 \x1b$A 13 | ksc5601 \x1b$(C 14 | jis0208 \x1b&@\x1b$B 15 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/iso8859-1.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: iso8859-1, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 0080008100820083008400850086008700880089008A008B008C008D008E008F 14 | 0090009100920093009400950096009700980099009A009B009C009D009E009F 15 | 00A000A100A200A300A400A500A600A700A800A900AA00AB00AC00AD00AE00AF 16 | 00B000B100B200B300B400B500B600B700B800B900BA00BB00BC00BD00BE00BF 17 | 00C000C100C200C300C400C500C600C700C800C900CA00CB00CC00CD00CE00CF 18 | 00D000D100D200D300D400D500D600D700D800D900DA00DB00DC00DD00DE00DF 19 | 00E000E100E200E300E400E500E600E700E800E900EA00EB00EC00ED00EE00EF 20 | 00F000F100F200F300F400F500F600F700F800F900FA00FB00FC00FD00FE00FF 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/iso8859-10.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: iso8859-10, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 0080008100820083008400850086008700880089008A008B008C008D008E008F 14 | 0090009100920093009400950096009700980099009A009B009C009D009E009F 15 | 00A0010401120122012A0128013600A7013B011001600166017D00AD016A014A 16 | 00B0010501130123012B0129013700B7013C011101610167017E2015016B014B 17 | 010000C100C200C300C400C500C6012E010C00C9011800CB011600CD00CE00CF 18 | 00D00145014C00D300D400D500D6016800D8017200DA00DB00DC00DD00DE00DF 19 | 010100E100E200E300E400E500E6012F010D00E9011900EB011700ED00EE00EF 20 | 00F00146014D00F300F400F500F6016900F8017300FA00FB00FC00FD00FE0138 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/iso8859-13.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: iso8859-13, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 0080008100820083008400850086008700880089008A008B008C008D008E008F 14 | 0090009100920093009400950096009700980099009A009B009C009D009E009F 15 | 00A0201D00A200A300A4201E00A600A700D800A9015600AB00AC00AD00AE00C6 16 | 00B000B100B200B3201C00B500B600B700F800B9015700BB00BC00BD00BE00E6 17 | 0104012E0100010600C400C501180112010C00C90179011601220136012A013B 18 | 01600143014500D3014C00D500D600D701720141015A016A00DC017B017D00DF 19 | 0105012F0101010700E400E501190113010D00E9017A011701230137012B013C 20 | 01610144014600F3014D00F500F600F701730142015B016B00FC017C017E2019 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/iso8859-14.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: iso8859-14, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 0080008100820083008400850086008700880089008A008B008C008D008E008F 14 | 0090009100920093009400950096009700980099009A009B009C009D009E009F 15 | 00A01E021E0300A3010A010B1E0A00A71E8000A91E821E0B1EF200AD00AE0178 16 | 1E1E1E1F012001211E401E4100B61E561E811E571E831E601EF31E841E851E61 17 | 00C000C100C200C300C400C500C600C700C800C900CA00CB00CC00CD00CE00CF 18 | 017400D100D200D300D400D500D61E6A00D800D900DA00DB00DC00DD017600DF 19 | 00E000E100E200E300E400E500E600E700E800E900EA00EB00EC00ED00EE00EF 20 | 017500F100F200F300F400F500F61E6B00F800F900FA00FB00FC00FD017700FF 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/iso8859-15.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: iso8859-15, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 0080008100820083008400850086008700880089008A008B008C008D008E008F 14 | 0090009100920093009400950096009700980099009A009B009C009D009E009F 15 | 00A000A100A200A320AC00A5016000A7016100A900AA00AB00AC00AD00AE00AF 16 | 00B000B100B200B3017D00B500B600B7017E00B900BA00BB01520153017800BF 17 | 00C000C100C200C300C400C500C600C700C800C900CA00CB00CC00CD00CE00CF 18 | 00D000D100D200D300D400D500D600D700D800D900DA00DB00DC00DD00DE00DF 19 | 00E000E100E200E300E400E500E600E700E800E900EA00EB00EC00ED00EE00EF 20 | 00F000F100F200F300F400F500F600F700F800F900FA00FB00FC00FD00FE00FF 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/iso8859-16.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: iso8859-16, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 0080008100820083008400850086008700880089008A008B008C008D008E008F 14 | 0090009100920093009400950096009700980099009A009B009C009D009E009F 15 | 00A001040105014120AC201E016000A7016100A9021800AB017900AD017A017B 16 | 00B000B1010C0142017D201D00B600B7017E010D021900BB015201530178017C 17 | 00C000C100C2010200C4010600C600C700C800C900CA00CB00CC00CD00CE00CF 18 | 0110014300D200D300D4015000D6015A017000D900DA00DB00DC0118021A00DF 19 | 00E000E100E2010300E4010700E600E700E800E900EA00EB00EC00ED00EE00EF 20 | 0111014400F200F300F4015100F6015B017100F900FA00FB00FC0119021B00FF 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/iso8859-2.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: iso8859-2, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 0080008100820083008400850086008700880089008A008B008C008D008E008F 14 | 0090009100920093009400950096009700980099009A009B009C009D009E009F 15 | 00A0010402D8014100A4013D015A00A700A80160015E0164017900AD017D017B 16 | 00B0010502DB014200B4013E015B02C700B80161015F0165017A02DD017E017C 17 | 015400C100C2010200C40139010600C7010C00C9011800CB011A00CD00CE010E 18 | 01100143014700D300D4015000D600D70158016E00DA017000DC00DD016200DF 19 | 015500E100E2010300E4013A010700E7010D00E9011900EB011B00ED00EE010F 20 | 01110144014800F300F4015100F600F70159016F00FA017100FC00FD016302D9 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/iso8859-3.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: iso8859-3, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 0080008100820083008400850086008700880089008A008B008C008D008E008F 14 | 0090009100920093009400950096009700980099009A009B009C009D009E009F 15 | 00A0012602D800A300A40000012400A700A80130015E011E013400AD0000017B 16 | 00B0012700B200B300B400B5012500B700B80131015F011F013500BD0000017C 17 | 00C000C100C2000000C4010A010800C700C800C900CA00CB00CC00CD00CE00CF 18 | 000000D100D200D300D4012000D600D7011C00D900DA00DB00DC016C015C00DF 19 | 00E000E100E2000000E4010B010900E700E800E900EA00EB00EC00ED00EE00EF 20 | 000000F100F200F300F4012100F600F7011D00F900FA00FB00FC016D015D02D9 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/iso8859-4.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: iso8859-4, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 0080008100820083008400850086008700880089008A008B008C008D008E008F 14 | 0090009100920093009400950096009700980099009A009B009C009D009E009F 15 | 00A001040138015600A40128013B00A700A8016001120122016600AD017D00AF 16 | 00B0010502DB015700B40129013C02C700B80161011301230167014A017E014B 17 | 010000C100C200C300C400C500C6012E010C00C9011800CB011600CD00CE012A 18 | 01100145014C013600D400D500D600D700D8017200DA00DB00DC0168016A00DF 19 | 010100E100E200E300E400E500E6012F010D00E9011900EB011700ED00EE012B 20 | 01110146014D013700F400F500F600F700F8017300FA00FB00FC0169016B02D9 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/iso8859-5.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: iso8859-5, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 0080008100820083008400850086008700880089008A008B008C008D008E008F 14 | 0090009100920093009400950096009700980099009A009B009C009D009E009F 15 | 00A0040104020403040404050406040704080409040A040B040C00AD040E040F 16 | 0410041104120413041404150416041704180419041A041B041C041D041E041F 17 | 0420042104220423042404250426042704280429042A042B042C042D042E042F 18 | 0430043104320433043404350436043704380439043A043B043C043D043E043F 19 | 0440044104420443044404450446044704480449044A044B044C044D044E044F 20 | 2116045104520453045404550456045704580459045A045B045C00A7045E045F 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/iso8859-6.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: iso8859-6, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 0080008100820083008400850086008700880089008A008B008C008D008E008F 14 | 0090009100920093009400950096009700980099009A009B009C009D009E009F 15 | 00A000000000000000A40000000000000000000000000000060C00AD00000000 16 | 00000000000000000000000000000000000000000000061B000000000000061F 17 | 0000062106220623062406250626062706280629062A062B062C062D062E062F 18 | 0630063106320633063406350636063706380639063A00000000000000000000 19 | 0640064106420643064406450646064706480649064A064B064C064D064E064F 20 | 0650065106520000000000000000000000000000000000000000000000000000 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/iso8859-7.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: iso8859-7, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 0080008100820083008400850086008700880089008A008B008C008D008E008F 14 | 0090009100920093009400950096009700980099009A009B009C009D009E009F 15 | 00A02018201900A30000000000A600A700A800A9000000AB00AC00AD00002015 16 | 00B000B100B200B303840385038600B703880389038A00BB038C00BD038E038F 17 | 0390039103920393039403950396039703980399039A039B039C039D039E039F 18 | 03A003A1000003A303A403A503A603A703A803A903AA03AB03AC03AD03AE03AF 19 | 03B003B103B203B303B403B503B603B703B803B903BA03BB03BC03BD03BE03BF 20 | 03C003C103C203C303C403C503C603C703C803C903CA03CB03CC03CD03CE0000 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/iso8859-8.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: iso8859-8, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 0080008100820083008400850086008700880089008A008B008C008D008E008F 14 | 0090009100920093009400950096009700980099009A009B009C009D009E009F 15 | 00A0000000A200A300A400A500A600A700A800A900D700AB00AC00AD00AE00AF 16 | 00B000B100B200B300B400B500B600B700B800B900F700BB00BC00BD00BE0000 17 | 0000000000000000000000000000000000000000000000000000000000000000 18 | 0000000000000000000000000000000000000000000000000000000000002017 19 | 05D005D105D205D305D405D505D605D705D805D905DA05DB05DC05DD05DE05DF 20 | 05E005E105E205E305E405E505E605E705E805E905EA00000000200E200F0000 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/iso8859-9.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: iso8859-9, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 0080008100820083008400850086008700880089008A008B008C008D008E008F 14 | 0090009100920093009400950096009700980099009A009B009C009D009E009F 15 | 00A000A100A200A300A400A500A600A700A800A900AA00AB00AC00AD00AE00AF 16 | 00B000B100B200B300B400B500B600B700B800B900BA00BB00BC00BD00BE00BF 17 | 00C000C100C200C300C400C500C600C700C800C900CA00CB00CC00CD00CE00CF 18 | 011E00D100D200D300D400D500D600D700D800D900DA00DB00DC0130015E00DF 19 | 00E000E100E200E300E400E500E600E700E800E900EA00EB00EC00ED00EE00EF 20 | 011F00F100F200F300F400F500F600F700F800F900FA00FB00FC0131015F00FF 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/jis0201.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: jis0201, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D203E007F 13 | 0080008100820083008400850086008700880089008A008B008C008D008E008F 14 | 0090009100920093009400950096009700980099009A009B009C009D009E009F 15 | 0000FF61FF62FF63FF64FF65FF66FF67FF68FF69FF6AFF6BFF6CFF6DFF6EFF6F 16 | FF70FF71FF72FF73FF74FF75FF76FF77FF78FF79FF7AFF7BFF7CFF7DFF7EFF7F 17 | FF80FF81FF82FF83FF84FF85FF86FF87FF88FF89FF8AFF8BFF8CFF8DFF8EFF8F 18 | FF90FF91FF92FF93FF94FF95FF96FF97FF98FF99FF9AFF9BFF9CFF9DFF9EFF9F 19 | 0000000000000000000000000000000000000000000000000000000000000000 20 | 0000000000000000000000000000000000000000000000000000000000000000 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/koi8-r.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: koi8-r, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 25002502250C251025142518251C2524252C2534253C258025842588258C2590 14 | 259125922593232025A02219221A22482264226500A0232100B000B200B700F7 15 | 25502551255204512553255425552556255725582559255A255B255C255D255E 16 | 255F25602561040125622563256425652566256725682569256A256B256C00A9 17 | 044E0430043104460434043504440433044504380439043A043B043C043D043E 18 | 043F044F044004410442044304360432044C044B04370448044D04490447044A 19 | 042E0410041104260414041504240413042504180419041A041B041C041D041E 20 | 041F042F042004210422042304160412042C042B04170428042D04290427042A 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/koi8-u.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: koi8-u, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 25002502250C251025142518251C2524252C2534253C258025842588258C2590 14 | 259125922593232025A02219221A22482264226500A0232100B000B200B700F7 15 | 25502551255204510454255404560457255725582559255A255B0491255D255E 16 | 255F25602561040104032563040604072566256725682569256A0490256C00A9 17 | 044E0430043104460434043504440433044504380439043A043B043C043D043E 18 | 043F044F044004410442044304360432044C044B04370448044D04490447044A 19 | 042E0410041104260414041504240413042504180419041A041B041C041D041E 20 | 041F042F042004210422042304160412042C042B04170428042D04290427042A 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/macCentEuro.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: macCentEuro, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 00C40100010100C9010400D600DC00E10105010C00E4010D0106010700E90179 14 | 017A010E00ED010F01120113011600F3011700F400F600F500FA011A011B00FC 15 | 202000B0011800A300A7202200B600DF00AE00A92122011900A822600123012E 16 | 012F012A22642265012B0136220222110142013B013C013D013E0139013A0145 17 | 0146014300AC221A01440147220600AB00BB202600A00148015000D50151014C 18 | 20132014201C201D2018201900F725CA014D0154015501582039203A01590156 19 | 01570160201A201E0161015A015B00C10164016500CD017D017E016A00D300D4 20 | 016B016E00DA016F017001710172017300DD00FD0137017B0141017C012202C7 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/macCroatian.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: macCroatian, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 00C400C500C700C900D100D600DC00E100E000E200E400E300E500E700E900E8 14 | 00EA00EB00ED00EC00EE00EF00F100F300F200F400F600F500FA00F900FB00FC 15 | 202000B000A200A300A7202200B600DF00AE0160212200B400A82260017D00D8 16 | 221E00B122642265220600B522022211220F0161222B00AA00BA03A9017E00F8 17 | 00BF00A100AC221A01922248010600AB010C202600A000C000C300D501520153 18 | 01102014201C201D2018201900F725CAF8FF00A9204420AC2039203A00C600BB 19 | 201300B7201A201E203000C2010700C1010D00C800CD00CE00CF00CC00D300D4 20 | 011100D200DA00DB00D9013102C602DC00AF03C000CB02DA00B800CA00E602C7 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/macCyrillic.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: macCyrillic, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 0410041104120413041404150416041704180419041A041B041C041D041E041F 14 | 0420042104220423042404250426042704280429042A042B042C042D042E042F 15 | 202000B0049000A300A7202200B6040600AE00A9212204020452226004030453 16 | 221E00B122642265045600B504910408040404540407045704090459040A045A 17 | 0458040500AC221A01922248220600AB00BB202600A0040B045B040C045C0455 18 | 20132014201C201D2018201900F7201E040E045E040F045F211604010451044F 19 | 0430043104320433043404350436043704380439043A043B043C043D043E043F 20 | 0440044104420443044404450446044704480449044A044B044C044D044E20AC 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/macDingbats.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: macDingbats, single-byte 2 | S 3 | 003F 1 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 00202701270227032704260E2706270727082709261B261E270C270D270E270F 8 | 2710271127122713271427152716271727182719271A271B271C271D271E271F 9 | 2720272127222723272427252726272726052729272A272B272C272D272E272F 10 | 2730273127322733273427352736273727382739273A273B273C273D273E273F 11 | 2740274127422743274427452746274727482749274A274B25CF274D25A0274F 12 | 27502751275225B225BC25C6275625D727582759275A275B275C275D275E007F 13 | F8D7F8D8F8D9F8DAF8DBF8DCF8DDF8DEF8DFF8E0F8E1F8E2F8E3F8E4008E008F 14 | 0090009100920093009400950096009700980099009A009B009C009D009E009F 15 | 0000276127622763276427652766276726632666266526602460246124622463 16 | 2464246524662467246824692776277727782779277A277B277C277D277E277F 17 | 2780278127822783278427852786278727882789278A278B278C278D278E278F 18 | 2790279127922793279421922194219527982799279A279B279C279D279E279F 19 | 27A027A127A227A327A427A527A627A727A827A927AA27AB27AC27AD27AE27AF 20 | 000027B127B227B327B427B527B627B727B827B927BA27BB27BC27BD27BE0000 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/macGreek.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: macGreek, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 00C400B900B200C900B300D600DC038500E000E200E4038400A800E700E900E8 14 | 00EA00EB00A3212200EE00EF202200BD203000F400F600A600AD00F900FB00FC 15 | 2020039303940398039B039E03A000DF00AE00A903A303AA00A7226000B000B7 16 | 039100B12264226500A503920395039603970399039A039C03A603AB03A803A9 17 | 03AC039D00AC039F03A1224803A400AB00BB202600A003A503A7038603880153 18 | 20132015201C201D2018201900F70389038A038C038E03AD03AE03AF03CC038F 19 | 03CD03B103B203C803B403B503C603B303B703B903BE03BA03BB03BC03BD03BF 20 | 03C003CE03C103C303C403B803C903C203C703C503B603CA03CB039003B0F8A0 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/macIceland.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: macIceland, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 00C400C500C700C900D100D600DC00E100E000E200E400E300E500E700E900E8 14 | 00EA00EB00ED00EC00EE00EF00F100F300F200F400F600F500FA00F900FB00FC 15 | 00DD00B000A200A300A7202200B600DF00AE00A9212200B400A8226000C600D8 16 | 221E00B12264226500A500B522022211220F03C0222B00AA00BA03A900E600F8 17 | 00BF00A100AC221A01922248220600AB00BB202600A000C000C300D501520153 18 | 20132014201C201D2018201900F725CA00FF0178204420AC00D000F000DE00FE 19 | 00FD00B7201A201E203000C200CA00C100CB00C800CD00CE00CF00CC00D300D4 20 | F8FF00D200DA00DB00D9013102C602DC00AF02D802D902DA00B802DD02DB02C7 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/macRoman.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: macRoman, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 00C400C500C700C900D100D600DC00E100E000E200E400E300E500E700E900E8 14 | 00EA00EB00ED00EC00EE00EF00F100F300F200F400F600F500FA00F900FB00FC 15 | 202000B000A200A300A7202200B600DF00AE00A9212200B400A8226000C600D8 16 | 221E00B12264226500A500B522022211220F03C0222B00AA00BA03A900E600F8 17 | 00BF00A100AC221A01922248220600AB00BB202600A000C000C300D501520153 18 | 20132014201C201D2018201900F725CA00FF0178204420AC2039203AFB01FB02 19 | 202100B7201A201E203000C200CA00C100CB00C800CD00CE00CF00CC00D300D4 20 | F8FF00D200DA00DB00D9013102C602DC00AF02D802D902DA00B802DD02DB02C7 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/macRomania.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: macRomania, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 00C400C500C700C900D100D600DC00E100E000E200E400E300E500E700E900E8 14 | 00EA00EB00ED00EC00EE00EF00F100F300F200F400F600F500FA00F900FB00FC 15 | 202000B000A200A300A7202200B600DF00AE00A9212200B400A822600102015E 16 | 221E00B12264226500A500B522022211220F03C0222B00AA00BA21260103015F 17 | 00BF00A100AC221A01922248220600AB00BB202600A000C000C300D501520153 18 | 20132014201C201D2018201900F725CA00FF0178204400A42039203A01620163 19 | 202100B7201A201E203000C200CA00C100CB00C800CD00CE00CF00CC00D300D4 20 | F8FF00D200DA00DB00D9013102C602DC00AF02D802D902DA00B802DD02DB02C7 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/macThai.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: macThai, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 00AB00BB2026F88CF88FF892F895F898F88BF88EF891F894F897201C201DF899 14 | FFFD2022F884F889F885F886F887F888F88AF88DF890F893F89620182019FFFD 15 | 00A00E010E020E030E040E050E060E070E080E090E0A0E0B0E0C0E0D0E0E0E0F 16 | 0E100E110E120E130E140E150E160E170E180E190E1A0E1B0E1C0E1D0E1E0E1F 17 | 0E200E210E220E230E240E250E260E270E280E290E2A0E2B0E2C0E2D0E2E0E2F 18 | 0E300E310E320E330E340E350E360E370E380E390E3AFEFF200B201320140E3F 19 | 0E400E410E420E430E440E450E460E470E480E490E4A0E4B0E4C0E4D21220E4F 20 | 0E500E510E520E530E540E550E560E570E580E5900AE00A9FFFDFFFDFFFDFFFD 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/macTurkish.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: macTurkish, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E007F 13 | 00C400C500C700C900D100D600DC00E100E000E200E400E300E500E700E900E8 14 | 00EA00EB00ED00EC00EE00EF00F100F300F200F400F600F500FA00F900FB00FC 15 | 202000B000A200A300A7202200B600DF00AE00A9212200B400A8226000C600D8 16 | 221E00B12264226500A500B522022211220F03C0222B00AA00BA03A900E600F8 17 | 00BF00A100AC221A01922248220600AB00BB202600A000C000C300D501520153 18 | 20132014201C201D2018201900F725CA00FF0178011E011F01300131015E015F 19 | 202100B7201A201E203000C200CA00C100CB00C800CD00CE00CF00CC00D300D4 20 | F8FF00D200DA00DB00D9F8A002C602DC00AF02D802D902DA00B802DD02DB02C7 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/symbol.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: symbol, single-byte 2 | S 3 | 003F 1 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002122000023220300250026220D002800292217002B002C2212002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 22450391039203A70394039503A603930397039903D1039A039B039C039D039F 10 | 03A0039803A103A303A403A503C203A9039E03A80396005B2234005D22A5005F 11 | F8E503B103B203C703B403B503C603B303B703B903D503BA03BB03BC03BD03BF 12 | 03C003B803C103C303C403C503D603C903BE03C803B6007B007C007D223C007F 13 | 0080008100820083008400850086008700880089008A008B008C008D008E008F 14 | 0090009100920093009400950096009700980099009A009B009C009D009E009F 15 | 000003D2203222642044221E0192266326662665266021942190219121922193 16 | 00B000B12033226500D7221D2202202200F72260226122482026F8E6F8E721B5 17 | 21352111211C21182297229522052229222A2283228722842282228622082209 18 | 2220220700AE00A92122220F221A22C500AC2227222821D421D021D121D221D3 19 | 22C42329F8E8F8E9F8EA2211F8EBF8ECF8EDF8EEF8EFF8F0F8F1F8F2F8F3F8F4 20 | F8FF232A222B2320F8F52321F8F6F8F7F8F8F8F9F8FAF8FBF8FCF8FDF8FE0000 21 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/encoding/tis-620.enc: -------------------------------------------------------------------------------- 1 | # Encoding file: tis-620, single-byte 2 | S 3 | 003F 0 1 4 | 00 5 | 0000000100020003000400050006000700080009000A000B000C000D000E000F 6 | 0010001100120013001400150016001700180019001A001B001C001D001E001F 7 | 0020002100220023002400250026002700280029002A002B002C002D002E002F 8 | 0030003100320033003400350036003700380039003A003B003C003D003E003F 9 | 0040004100420043004400450046004700480049004A004B004C004D004E004F 10 | 0050005100520053005400550056005700580059005A005B005C005D005E005F 11 | 0060006100620063006400650066006700680069006A006B006C006D006E006F 12 | 0070007100720073007400750076007700780079007A007B007C007D007E0000 13 | 0000000000000000000000000000000000000000000000000000000000000000 14 | 0000000000000000000000000000000000000000000000000000000000000000 15 | 00000E010E020E030E040E050E060E070E080E090E0A0E0B0E0C0E0D0E0E0E0F 16 | 0E100E110E120E130E140E150E160E170E180E190E1A0E1B0E1C0E1D0E1E0E1F 17 | 0E200E210E220E230E240E250E260E270E280E290E2A0E2B0E2C0E2D0E2E0E2F 18 | 0E300E310E320E330E340E350E360E370E380E390E3A00000000000000000E3F 19 | 0E400E410E420E430E440E450E460E470E480E490E4A0E4B0E4C0E4D0E4E0E4F 20 | 0E500E510E520E530E540E550E560E570E580E590E5A0E5B0000000000000000 -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/http1.0/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.0 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded http 1.0 [list tclPkgSetup $dir http 1.0 {{http.tcl source {httpCopyDone httpCopyStart httpEof httpEvent httpFinish httpMapReply httpProxyRequired http_code http_config http_data http_formatQuery http_get http_reset http_size http_status http_wait}}}] 12 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/http2.5/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | if {![package vsatisfies [package provide Tcl] 8.4]} {return} 12 | package ifneeded http 2.5.2 [list tclPkgSetup $dir http 2.5.2 {{http.tcl source {::http::config ::http::formatQuery ::http::geturl ::http::reset ::http::wait ::http::register ::http::unregister}}}] 13 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/msgcat1.3/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | if {![package vsatisfies [package provide Tcl] 8.2]} {return} 2 | package ifneeded msgcat 1.3.3 [list source [file join $dir msgcat.tcl]] 3 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/opt0.4/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex -direct" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | if {![package vsatisfies [package provide Tcl] 8.2]} {return} 12 | package ifneeded opt 0.4.4.1 [list source [file join $dir optparse.tcl]] 13 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/parray.tcl: -------------------------------------------------------------------------------- 1 | # parray: 2 | # Print the contents of a global array on stdout. 3 | # 4 | # RCS: @(#) $Id: parray.tcl,v 1.3 1998/09/14 18:40:03 stanton Exp $ 5 | # 6 | # Copyright (c) 1991-1993 The Regents of the University of California. 7 | # Copyright (c) 1994 Sun Microsystems, Inc. 8 | # 9 | # See the file "license.terms" for information on usage and redistribution 10 | # of this file, and for a DISCLAIMER OF ALL WARRANTIES. 11 | # 12 | 13 | proc parray {a {pattern *}} { 14 | upvar 1 $a array 15 | if {![array exists array]} { 16 | error "\"$a\" isn't an array" 17 | } 18 | set maxl 0 19 | foreach name [lsort [array names array $pattern]] { 20 | if {[string length $name] > $maxl} { 21 | set maxl [string length $name] 22 | } 23 | } 24 | set maxl [expr {$maxl + [string length $a] + 2}] 25 | foreach name [lsort [array names array $pattern]] { 26 | set nameString [format %s(%s) $a $name] 27 | puts stdout [format "%-*s = %s" $maxl $nameString $array($name)] 28 | } 29 | } 30 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tcl/tcltest2.2/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex -direct" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | if {![package vsatisfies [package provide Tcl] 8.3]} {return} 12 | package ifneeded tcltest 2.2.8 [list source [file join $dir tcltest.tcl]] 13 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tk/images/README: -------------------------------------------------------------------------------- 1 | README - images directory 2 | 3 | RCS: @(#) $Id: README,v 1.2 1998/09/14 18:23:32 stanton Exp $ 4 | 5 | 6 | This directory includes images for the Tcl Logo and the Tcl Powered 7 | Logo. Please feel free to use the Tcl Powered Logo on any of your 8 | products that employ the use of Tcl or Tk. The Tcl logo may also be 9 | used to promote Tcl in your product documentation, web site or other 10 | places you so desire. 11 | 12 | 13 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tk/images/logo100.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DLab/RIP-MD/08ec2a72ec4f388fbccc24124f19a9b60b152f5b/RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tk/images/logo100.gif -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tk/images/logo64.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DLab/RIP-MD/08ec2a72ec4f388fbccc24124f19a9b60b152f5b/RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tk/images/logo64.gif 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/RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tk/msgs/es_ES.msg: -------------------------------------------------------------------------------- 1 | namespace eval ::tk { 2 | ::msgcat::mcset es_ES "&Save" "&Guardar" 3 | ::msgcat::mcset es_ES "Save As" "Guardar como" 4 | ::msgcat::mcset es_ES "Save To Log" "Guardar al archivo de traza" 5 | } 6 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/_MEI/tk/obsolete.tcl: -------------------------------------------------------------------------------- 1 | # obsolete.tcl -- 2 | # 3 | # This file contains obsolete procedures that people really shouldn't 4 | # be using anymore, but which are kept around for backward compatibility. 5 | # 6 | # RCS: @(#) $Id: obsolete.tcl,v 1.2 1998/09/14 18:23:24 stanton Exp $ 7 | # 8 | # Copyright (c) 1994 The Regents of the University of California. 9 | # Copyright (c) 1994 Sun Microsystems, Inc. 10 | # 11 | # See 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The procedures are no longer needed, so 17 | # they are no-ops. 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{output-path}.summary.' 18 | 19 | def create_summary_output(routines, outfile): 20 | """ 21 | Output the interaction energy between each possible residue pair. 22 | """ 23 | routines.write("Printing protein summary...\n") 24 | 25 | output = extensions.extOutputHelper(routines, outfile) 26 | 27 | output.write(routines.protein.getSummary() + '\n') 28 | 29 | for residue in routines.protein.getResidues(): 30 | output.write(str(residue)+'\n') 31 | 32 | def run_extension(routines, outroot, options): 33 | outname = outroot + ".summary" 34 | with open(outname, "w") as outfile: 35 | create_summary_output(routines, outfile) -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/extensions/summary.pyc: -------------------------------------------------------------------------------- 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All Rights Reserved. 2 | # Licensed to PSF under a Contributor Agreement. 3 | 4 | # A grammar to describe tree matching patterns. 5 | # Not shown here: 6 | # - 'TOKEN' stands for any token (leaf node) 7 | # - 'any' stands for any node (leaf or interior) 8 | # With 'any' we can still specify the sub-structure. 9 | 10 | # The start symbol is 'Matcher'. 11 | 12 | Matcher: Alternatives ENDMARKER 13 | 14 | Alternatives: Alternative ('|' Alternative)* 15 | 16 | Alternative: (Unit | NegatedUnit)+ 17 | 18 | Unit: [NAME '='] ( STRING [Repeater] 19 | | NAME [Details] [Repeater] 20 | | '(' Alternatives ')' [Repeater] 21 | | '[' Alternatives ']' 22 | ) 23 | 24 | NegatedUnit: 'not' (STRING | NAME [Details] | '(' Alternatives ')') 25 | 26 | Repeater: '*' | '+' | '{' NUMBER [',' NUMBER] '}' 27 | 28 | Details: '<' Alternatives '>' 29 | -------------------------------------------------------------------------------- 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failUnlessAlmostEqual="assertAlmostEqual", 19 | failIfAlmostEqual="assertNotAlmostEqual", 20 | failUnless="assertTrue", 21 | failUnlessRaises="assertRaises", 22 | failIf="assertFalse", 23 | ) 24 | 25 | 26 | class FixAsserts(BaseFix): 27 | 28 | PATTERN = """ 29 | power< any+ trailer< '.' meth=(%s)> any* > 30 | """ % '|'.join(map(repr, NAMES)) 31 | 32 | def transform(self, node, results): 33 | name = results["meth"][0] 34 | name.replace(Name(NAMES[str(name)], prefix=name.prefix)) 35 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_asserts.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DLab/RIP-MD/08ec2a72ec4f388fbccc24124f19a9b60b152f5b/RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_asserts.pyc -------------------------------------------------------------------------------- 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All Rights Reserved. 2 | # Licensed to PSF under a Contributor Agreement. 3 | 4 | """Fixer that changes buffer(...) into memoryview(...).""" 5 | 6 | # Local imports 7 | from .. import fixer_base 8 | from ..fixer_util import Name 9 | 10 | 11 | class FixBuffer(fixer_base.BaseFix): 12 | BM_compatible = True 13 | 14 | explicit = True # The user must ask for this fixer 15 | 16 | PATTERN = """ 17 | power< name='buffer' trailer< '(' [any] ')' > any* > 18 | """ 19 | 20 | def transform(self, node, results): 21 | name = results["name"] 22 | name.replace(Name(u"memoryview", prefix=name.prefix)) 23 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_buffer.pyc: -------------------------------------------------------------------------------- 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Name 7 | 8 | 9 | class FixFuncattrs(fixer_base.BaseFix): 10 | BM_compatible = True 11 | 12 | PATTERN = """ 13 | power< any+ trailer< '.' attr=('func_closure' | 'func_doc' | 'func_globals' 14 | | 'func_name' | 'func_defaults' | 'func_code' 15 | | 'func_dict') > any* > 16 | """ 17 | 18 | def transform(self, node, results): 19 | attr = results["attr"][0] 20 | attr.replace(Name((u"__%s__" % attr.value[5:]), 21 | prefix=attr.prefix)) 22 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_funcattrs.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DLab/RIP-MD/08ec2a72ec4f388fbccc24124f19a9b60b152f5b/RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_funcattrs.pyc -------------------------------------------------------------------------------- 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run last -- some things check for the import 17 | run_order = 10 18 | 19 | def transform(self, node, results): 20 | new = BlankLine() 21 | new.prefix = node.prefix 22 | return new 23 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_future.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DLab/RIP-MD/08ec2a72ec4f388fbccc24124f19a9b60b152f5b/RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_future.pyc -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_future.pyo: -------------------------------------------------------------------------------- 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import Call, Name 7 | from .. import patcomp 8 | 9 | 10 | context = patcomp.compile_pattern("power< 'eval' trailer< '(' any ')' > >") 11 | 12 | 13 | class FixInput(fixer_base.BaseFix): 14 | BM_compatible = True 15 | PATTERN = """ 16 | power< 'input' args=trailer< '(' [any] ')' > > 17 | """ 18 | 19 | def transform(self, node, results): 20 | # If we're already wrapped in a eval() call, we're done. 21 | if context.match(node.parent.parent): 22 | return 23 | 24 | new = node.clone() 25 | new.prefix = u"" 26 | return Call(Name(u"eval"), [new], prefix=node.prefix) 27 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_input.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DLab/RIP-MD/08ec2a72ec4f388fbccc24124f19a9b60b152f5b/RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_input.pyc 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All Rights Reserved. 2 | # Licensed to PSF under a Contributor Agreement. 3 | 4 | """Fixer that turns 'long' into 'int' everywhere. 5 | """ 6 | 7 | # Local imports 8 | from lib2to3 import fixer_base 9 | from lib2to3.fixer_util import is_probably_builtin 10 | 11 | 12 | class FixLong(fixer_base.BaseFix): 13 | BM_compatible = True 14 | PATTERN = "'long'" 15 | 16 | def transform(self, node, results): 17 | if is_probably_builtin(node): 18 | node.value = u"int" 19 | node.changed() 20 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_long.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DLab/RIP-MD/08ec2a72ec4f388fbccc24124f19a9b60b152f5b/RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_long.pyc -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_long.pyo: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DLab/RIP-MD/08ec2a72ec4f388fbccc24124f19a9b60b152f5b/RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_long.pyo -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_map.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DLab/RIP-MD/08ec2a72ec4f388fbccc24124f19a9b60b152f5b/RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_map.pyc -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_map.pyo: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DLab/RIP-MD/08ec2a72ec4f388fbccc24124f19a9b60b152f5b/RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_map.pyo -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_metaclass.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DLab/RIP-MD/08ec2a72ec4f388fbccc24124f19a9b60b152f5b/RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_metaclass.pyc -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_metaclass.pyo: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DLab/RIP-MD/08ec2a72ec4f388fbccc24124f19a9b60b152f5b/RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_metaclass.pyo -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_methodattrs.py: -------------------------------------------------------------------------------- 1 | """Fix bound method attributes (method.im_? -> method.__?__). 2 | """ 3 | # Author: Christian Heimes 4 | 5 | # Local imports 6 | from .. import fixer_base 7 | from ..fixer_util import Name 8 | 9 | MAP = { 10 | "im_func" : "__func__", 11 | "im_self" : "__self__", 12 | "im_class" : "__self__.__class__" 13 | } 14 | 15 | class FixMethodattrs(fixer_base.BaseFix): 16 | BM_compatible = True 17 | PATTERN = """ 18 | power< any+ trailer< '.' attr=('im_func' | 'im_self' | 'im_class') > any* > 19 | """ 20 | 21 | def transform(self, node, results): 22 | attr = results["attr"][0] 23 | new = unicode(MAP[attr.value]) 24 | attr.replace(Name(new, prefix=attr.prefix)) 25 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_methodattrs.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DLab/RIP-MD/08ec2a72ec4f388fbccc24124f19a9b60b152f5b/RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_methodattrs.pyc -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_methodattrs.pyo: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DLab/RIP-MD/08ec2a72ec4f388fbccc24124f19a9b60b152f5b/RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_methodattrs.pyo -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_ne.py: -------------------------------------------------------------------------------- 1 | # Copyright 2006 Google, Inc. All Rights Reserved. 2 | # Licensed to PSF under a Contributor Agreement. 3 | 4 | """Fixer that turns <> into !=.""" 5 | 6 | # Local imports 7 | from .. import pytree 8 | from ..pgen2 import token 9 | from .. import fixer_base 10 | 11 | 12 | class FixNe(fixer_base.BaseFix): 13 | # This is so simple that we don't need the pattern compiler. 14 | 15 | _accept_type = token.NOTEQUAL 16 | 17 | def match(self, node): 18 | # Override 19 | return node.value == u"<>" 20 | 21 | def transform(self, node, results): 22 | new = pytree.Leaf(token.NOTEQUAL, u"!=", prefix=node.prefix) 23 | return new 24 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_ne.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DLab/RIP-MD/08ec2a72ec4f388fbccc24124f19a9b60b152f5b/RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_ne.pyc 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Name(u"__bool__", prefix=name.prefix) 21 | name.replace(new) 22 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_nonzero.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DLab/RIP-MD/08ec2a72ec4f388fbccc24124f19a9b60b152f5b/RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_nonzero.pyc -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_nonzero.pyo: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DLab/RIP-MD/08ec2a72ec4f388fbccc24124f19a9b60b152f5b/RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_nonzero.pyo -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- 1 | # Copyright 2008 Armin Ronacher. 2 | # Licensed to PSF under a Contributor Agreement. 3 | 4 | """Fixer for reduce(). 5 | 6 | Makes sure reduce() is imported from the functools module if reduce is 7 | used in that module. 8 | """ 9 | 10 | from lib2to3 import fixer_base 11 | from lib2to3.fixer_util import touch_import 12 | 13 | 14 | 15 | class FixReduce(fixer_base.BaseFix): 16 | 17 | BM_compatible = True 18 | order = "pre" 19 | 20 | PATTERN = """ 21 | power< 'reduce' 22 | trailer< '(' 23 | arglist< ( 24 | (not(argument) any ',' 27 | not(argument 31 | > 32 | """ 33 | 34 | def transform(self, node, results): 35 | touch_import(u'functools', u'reduce', node) 36 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_reduce.pyc: -------------------------------------------------------------------------------- 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All Rights Reserved. 2 | # Licensed to PSF under a Contributor Agreement. 3 | 4 | """Fixer that transforms `xyzzy` into repr(xyzzy).""" 5 | 6 | # Local imports 7 | from .. import fixer_base 8 | from ..fixer_util import Call, Name, parenthesize 9 | 10 | 11 | class FixRepr(fixer_base.BaseFix): 12 | 13 | BM_compatible = True 14 | PATTERN = """ 15 | atom < '`' expr=any '`' > 16 | """ 17 | 18 | def transform(self, node, results): 19 | expr = results["expr"].clone() 20 | 21 | if expr.type == self.syms.testlist1: 22 | expr = parenthesize(expr) 23 | return Call(Name(u"repr"), [expr], prefix=node.prefix) 24 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_repr.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DLab/RIP-MD/08ec2a72ec4f388fbccc24124f19a9b60b152f5b/RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_repr.pyc -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_repr.pyo: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DLab/RIP-MD/08ec2a72ec4f388fbccc24124f19a9b60b152f5b/RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_repr.pyo -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_set_literal.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DLab/RIP-MD/08ec2a72ec4f388fbccc24124f19a9b60b152f5b/RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_set_literal.pyc -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_set_literal.pyo: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DLab/RIP-MD/08ec2a72ec4f388fbccc24124f19a9b60b152f5b/RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_set_literal.pyo -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_standarderror.py: -------------------------------------------------------------------------------- 1 | # Copyright 2007 Google, Inc. All Rights Reserved. 2 | # Licensed to PSF under a Contributor Agreement. 3 | 4 | """Fixer for StandardError -> Exception.""" 5 | 6 | # Local imports 7 | from .. import fixer_base 8 | from ..fixer_util import Name 9 | 10 | 11 | class FixStandarderror(fixer_base.BaseFix): 12 | BM_compatible = True 13 | PATTERN = """ 14 | 'StandardError' 15 | """ 16 | 17 | def transform(self, node, results): 18 | return Name(u"Exception", prefix=node.prefix) 19 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_standarderror.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DLab/RIP-MD/08ec2a72ec4f388fbccc24124f19a9b60b152f5b/RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_standarderror.pyc -------------------------------------------------------------------------------- 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15 | # This order matches the ordering of sys.exc_info(). 16 | exc_info = [u"exc_type", u"exc_value", u"exc_traceback"] 17 | BM_compatible = True 18 | PATTERN = """ 19 | power< 'sys' trailer< dot='.' attribute=(%s) > > 20 | """ % '|'.join("'%s'" % e for e in exc_info) 21 | 22 | def transform(self, node, results): 23 | sys_attr = results["attribute"][0] 24 | index = Number(self.exc_info.index(sys_attr.value)) 25 | 26 | call = Call(Name(u"exc_info"), prefix=sys_attr.prefix) 27 | attr = Attr(Name(u"sys"), call) 28 | attr[1].children[0].prefix = results["dot"].prefix 29 | attr.append(Subscript(index)) 30 | return Node(syms.power, attr, prefix=node.prefix) 31 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_sys_exc.pyc: -------------------------------------------------------------------------------- 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Local imports 7 | from .. import fixer_base 8 | from ..fixer_util import Name 9 | 10 | 11 | class FixXreadlines(fixer_base.BaseFix): 12 | BM_compatible = True 13 | PATTERN = """ 14 | power< call=any+ trailer< '.' 'xreadlines' > trailer< '(' ')' > > 15 | | 16 | power< any+ trailer< '.' no_call='xreadlines' > > 17 | """ 18 | 19 | def transform(self, node, results): 20 | no_call = results.get("no_call") 21 | 22 | if no_call: 23 | no_call.replace(Name(u"__iter__", prefix=no_call.prefix)) 24 | else: 25 | node.replace([x.clone() for x in results["call"]]) 26 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_xreadlines.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DLab/RIP-MD/08ec2a72ec4f388fbccc24124f19a9b60b152f5b/RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_xreadlines.pyc -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_xreadlines.pyo: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DLab/RIP-MD/08ec2a72ec4f388fbccc24124f19a9b60b152f5b/RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_xreadlines.pyo -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_zip.py: -------------------------------------------------------------------------------- 1 | """ 2 | Fixer that changes zip(seq0, seq1, ...) into list(zip(seq0, seq1, ...) 3 | unless there exists a 'from future_builtins import zip' statement in the 4 | top-level namespace. 5 | 6 | We avoid the transformation if the zip() call is directly contained in 7 | iter(<>), list(<>), tuple(<>), sorted(<>), ...join(<>), or for V in <>:. 8 | """ 9 | 10 | # Local imports 11 | from .. import fixer_base 12 | from ..fixer_util import Name, Call, in_special_context 13 | 14 | class FixZip(fixer_base.ConditionalFix): 15 | 16 | BM_compatible = True 17 | PATTERN = """ 18 | power< 'zip' args=trailer< '(' [any] ')' > 19 | > 20 | """ 21 | 22 | skip_on = "future_builtins.zip" 23 | 24 | def transform(self, node, results): 25 | if self.should_skip(node): 26 | return 27 | 28 | if in_special_context(node): 29 | return None 30 | 31 | new = node.clone() 32 | new.prefix = u"" 33 | new = Call(Name(u"list"), [new]) 34 | new.prefix = node.prefix 35 | return new 36 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_zip.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DLab/RIP-MD/08ec2a72ec4f388fbccc24124f19a9b60b152f5b/RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_zip.pyc -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_zip.pyo: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DLab/RIP-MD/08ec2a72ec4f388fbccc24124f19a9b60b152f5b/RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/fixes/fix_zip.pyo -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/main.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DLab/RIP-MD/08ec2a72ec4f388fbccc24124f19a9b60b152f5b/RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/main.pyc -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/main.pyo: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DLab/RIP-MD/08ec2a72ec4f388fbccc24124f19a9b60b152f5b/RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/main.pyo -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/patcomp.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DLab/RIP-MD/08ec2a72ec4f388fbccc24124f19a9b60b152f5b/RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/patcomp.pyc -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/patcomp.pyo: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DLab/RIP-MD/08ec2a72ec4f388fbccc24124f19a9b60b152f5b/RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/patcomp.pyo -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/pgen2/__init__.py: -------------------------------------------------------------------------------- 1 | # Copyright 2004-2005 Elemental Security, Inc. 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This allows us to "import tests" and 2 | have tests.all_tests be a TestSuite representing all test cases 3 | from all test_*.py files in tests/.""" 4 | # Author: Collin Winter 5 | 6 | import os 7 | import os.path 8 | import unittest 9 | import types 10 | 11 | from . import support 12 | 13 | all_tests = unittest.TestSuite() 14 | 15 | tests_dir = os.path.join(os.path.dirname(__file__), '..', 'tests') 16 | tests = [t[0:-3] for t in os.listdir(tests_dir) 17 | if t.startswith('test_') and t.endswith('.py')] 18 | 19 | loader = unittest.TestLoader() 20 | 21 | for t in tests: 22 | __import__("",globals(),locals(),[t],level=1) 23 | mod = globals()[t] 24 | all_tests.addTests(loader.loadTestsFromModule(mod)) 25 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/tests/__init__.pyc: -------------------------------------------------------------------------------- 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3.x's grammar. 4 | - infinite_recursion.py -- test file that causes lib2to3's faster recursive pattern matching 5 | scheme to fail, but passes when lib2to3 falls back to iterative pattern matching. 6 | - fixes/ -- for use by test_refactor.py 7 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/tests/data/bom.py: -------------------------------------------------------------------------------- 1 | # coding: utf-8 2 | print "BOM BOOM!" 3 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/tests/data/crlf.py: -------------------------------------------------------------------------------- 1 | print "hi" 2 | 3 | print "Like bad Windows newlines?" 4 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/tests/data/different_encoding.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | # -*- coding: utf-8 -*- 3 | print u'ßàáâãäåæçèéêëìíîïðñòóôõöøùúûüýþÿÀÁÂÃÄÅÆÇÈÉÊËÌÍÎÏÐÑÒÓÔÕÖØÙÚÛÜÝÞ' 4 | 5 | def f(x): 6 | print '%s\t-> α(%2i):%s β(%s)' 7 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/tests/data/false_encoding.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | print '#coding=0' 3 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/tests/data/fixers/bad_order.py: -------------------------------------------------------------------------------- 1 | from lib2to3.fixer_base import BaseFix 2 | 3 | class FixBadOrder(BaseFix): 4 | 5 | order = "crazy" 6 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/tests/data/fixers/myfixes/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DLab/RIP-MD/08ec2a72ec4f388fbccc24124f19a9b60b152f5b/RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/tests/data/fixers/myfixes/__init__.py -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/tests/data/fixers/myfixes/fix_explicit.py: -------------------------------------------------------------------------------- 1 | from lib2to3.fixer_base import BaseFix 2 | 3 | class FixExplicit(BaseFix): 4 | explicit = True 5 | 6 | def match(self): return False 7 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/tests/data/fixers/myfixes/fix_first.py: -------------------------------------------------------------------------------- 1 | from lib2to3.fixer_base import BaseFix 2 | 3 | class FixFirst(BaseFix): 4 | run_order = 1 5 | 6 | def match(self, node): return False 7 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/tests/data/fixers/myfixes/fix_last.py: -------------------------------------------------------------------------------- 1 | from lib2to3.fixer_base import BaseFix 2 | 3 | class FixLast(BaseFix): 4 | 5 | run_order = 10 6 | 7 | def match(self, node): return False 8 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/tests/data/fixers/myfixes/fix_parrot.py: -------------------------------------------------------------------------------- 1 | from lib2to3.fixer_base import BaseFix 2 | from lib2to3.fixer_util import Name 3 | 4 | class FixParrot(BaseFix): 5 | """ 6 | Change functions named 'parrot' to 'cheese'. 7 | """ 8 | 9 | PATTERN = """funcdef < 'def' name='parrot' any* >""" 10 | 11 | def transform(self, node, results): 12 | name = results["name"] 13 | name.replace(Name("cheese", name.prefix)) 14 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/tests/data/fixers/myfixes/fix_preorder.py: -------------------------------------------------------------------------------- 1 | from lib2to3.fixer_base import BaseFix 2 | 3 | class FixPreorder(BaseFix): 4 | order = "pre" 5 | 6 | def match(self, node): return False 7 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/lib2to3/tests/data/fixers/no_fixer_cls.py: 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#Manganese (ii) Ion 9 | K 1 #Potassium Ion 10 | CD 2 #Cadmium Ion 11 | FE 3 #Fe (iii) Ion 12 | SR 2 #Strontium Ion 13 | CU 2 #Copper (ii) Ion 14 | IOD -1 #Iodide Ion 15 | HG 2 #Mercury (ii) Ion 16 | BR -1 #Bromide Ion 17 | CO 2 #Cobalt (ii) Ion 18 | NI 2 #Nickel (ii) Ion 19 | FE2 2 #Fe (ii) Ion 20 | -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/pyexpat.so: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DLab/RIP-MD/08ec2a72ec4f388fbccc24124f19a9b60b152f5b/RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/pyexpat.so -------------------------------------------------------------------------------- /RIP-MD/dependencies/linux/pdb2pqr-linux-bin64-2.1.1/readline.so: -------------------------------------------------------------------------------- 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/RIP-MD/libs/checkPDB.py: -------------------------------------------------------------------------------- 1 | import MDAnalysis 2 | 3 | 4 | def check(Output, pdbList, nproc): 5 | pdbNames=pdbList 6 | output=Output 7 | idList=[] 8 | repeated=[] 9 | flag=0 10 | #we will loop the structure, to discover if exist any problem with the structure 11 | u = None 12 | try: 13 | u = MDAnalysis.Universe(pdbNames["frame_0"]) 14 | except: 15 | print "Problem while trying to check your structure using MDAnalysis. Maybe you should try to:\n- Use \"protein\" selection\n- Not use --missing_atoms flag\nexiting." 16 | return 1 17 | 18 | for resid in u.atoms.residues: 19 | if (str(resid.resname)+":"+str(resid.segment.segid)+":"+str(resid.resid)) not in idList: 20 | idList.append(str(resid.resname)+":"+str(resid.segment.segid)+":"+str(resid.resid)) 21 | else: 22 | flag=1 23 | if "Chain "+str(resid.segment.segid)+" Res. Number"+str(resid.resid) not in repeated: 24 | repeated.append("Chain "+str(resid.segment.segid)+" Res. Number"+str(resid.resid)) 25 | if flag==1: 26 | print "Some residues are sharing the same number in the same chain ("+str(repeated)[1:-1]+"), exiting" 27 | return 1 28 | else: 29 | return 0 30 | -------------------------------------------------------------------------------- /RIP-MD/libs/delConect.py: -------------------------------------------------------------------------------- 1 | import multiprocessing as mp 2 | import os 3 | 4 | def parallelDel(pdb): 5 | os.system("sed -i '/CONECT/d' "+pdb[1].replace(" ","\ ")) 6 | 7 | 8 | 9 | def Delete(pdbDict, nproc): 10 | pool=mp.Pool(processes=int(nproc)) 11 | pool.map(parallelDel,(pdbDict.items())) 12 | 13 | -------------------------------------------------------------------------------- /RIP-MD/libs/delete.py: -------------------------------------------------------------------------------- 1 | import os 2 | import glob 3 | ######################################################################## 4 | ## 5 | ## library to delete a set of file with some formats 6 | ## 7 | ######################################################################## 8 | 9 | def delete(folder, Format): 10 | toDelete=glob.glob(folder+"/*."+Format) 11 | for File in toDelete: 12 | os.remove(File) 13 | 14 | -------------------------------------------------------------------------------- /RIP-MD/libs/distance.py: -------------------------------------------------------------------------------- 1 | import math 2 | ######################################################################## 3 | ## 4 | ## function that take 2 arrays and calculate euclidian distance 5 | ## 6 | ######################################################################## 7 | def euclidean(array1, array2): 8 | x1=float(array1[0]) 9 | y1=float(array1[1]) 10 | z1=float(array1[2]) 11 | 12 | x2=float(array2[0]) 13 | y2=float(array2[1]) 14 | z2=float(array2[2]) 15 | 16 | distance=math.sqrt((x1-x2)**2+(y1-y2)**2+(z1-z2)**2) 17 | return distance 18 | -------------------------------------------------------------------------------- /RIP-MD/libs/saveGraph.py: -------------------------------------------------------------------------------- 1 | import networkx as nx 2 | 3 | 4 | ######################################################################## 5 | ## 6 | ## this library take one graph and the output folder and save the graph 7 | ## in a specific format. available. Edge_List, GEXF, GML, GraphML, JSON 8 | ## YAML. 9 | ## 10 | ######################################################################## 11 | 12 | def gml(graph,outputfolder): 13 | nx.write_gml(graph,outputfolder) 14 | 15 | def edgelist(graph, outputfolder): 16 | nx.write_edgelist(graph,outputfolder) 17 | 18 | def gexf(graph, outputfolder): 19 | nx.write_gexf(graph,outputfolder) 20 | 21 | def graphml(graph, outputfolder): 22 | nx.write_graphml(graph,outputfolder) 23 | 24 | def pajek(graph, outputfolder): 25 | nx.write_pajek(graph,outputfolder) 26 | 27 | def saveList(graph, outputfolder): 28 | nx.write_edgelist(graph,outputfolder) 29 | 30 | 31 | 32 | -------------------------------------------------------------------------------- /RIP-MD/libs/selection.py: -------------------------------------------------------------------------------- 1 | import MDAnalysis as mda 2 | def save_selection(selection, pdbName, outName): 3 | try: 4 | universe = mda.Universe(pdbName) 5 | #selecting atoms to work 6 | sel = None 7 | try: 8 | sel = universe.selectAtoms(selection) #in v<0.11 or v>0.16 we need to use select_atoms 9 | except: 10 | sel = universe.select_atoms(selection) 11 | #saving a local copy of selected residues 12 | writerPDB=mda.Writer(outName) 13 | writerPDB.write(sel) 14 | return outName 15 | except: 16 | pass 17 | return False 18 | -------------------------------------------------------------------------------- /RIP-MD_vmd/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.0 2 | # This file is generated by the "pkg_mkIndex" 3 | 4 | # This code makes grin into a package. 5 | # VMD startup code executes 'package require', 6 | # looks for this file and uses the one-liner to create an index of Bendix (specifying what version to use, where appropriate) 7 | # where available packages are listed, so that Tcl can use this index to load Bendix by the path provided below. 8 | # 'Package provide' in the main bendix code, checks that the package exists. 9 | 10 | 11 | package ifneeded ripmd 1.0 [list source [file join $dir ripmd.tcl]] 12 | -------------------------------------------------------------------------------- /libraries: -------------------------------------------------------------------------------- 1 | biopython==1.70 2 | matplotlib==2.1.0 3 | MDAnalysis==0.16.2 4 | networkx==2.0 5 | numpy==1.13.3 6 | scipy==1.0.0 7 | -------------------------------------------------------------------------------- /manual.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DLab/RIP-MD/08ec2a72ec4f388fbccc24124f19a9b60b152f5b/manual.pdf -------------------------------------------------------------------------------- /requirements.sh: -------------------------------------------------------------------------------- 1 | #! /bin/bash 2 | 3 | wget -q --tries=10 --timeout=20 --spider http://google.com 4 | if [[ $? -eq 0 ]]; then 5 | echo "Looking for dependencies..." 6 | toInstallPip="0" 7 | hash pip || toInstallPip="1" 8 | if [[ $toInstallPip == "1" ]]; then 9 | echo " Installing pip..."; 10 | errorAPT="0" 11 | apt-get install python-pip python-dev build-essential || errorAPT="1" 12 | if [[ $errorAPT == "1" ]]; then 13 | echo " Error while trying to install pip, are you in sudo mode?. Exiting" 14 | exit 1 15 | fi 16 | fi 17 | 18 | echo "Installing python-tk" 19 | apt-get install python-tk 20 | 21 | errorPIP="0" 22 | pip install --upgrade pip || errorPIP="1" 23 | if [[ $errorPIP == "1" ]]; then 24 | echo " Error upgrading pip, are you in sudo mode?. Exiting" 25 | exit 1 26 | fi 27 | pip install -r libraries || errorPIP="1" 28 | if [[ $errorPIP == "1" ]]; then 29 | echo " Error installing pip libraries, are you in sudo mode?. Exiting" 30 | exit 1 31 | fi 32 | else 33 | echo "Can not connect to internet. Exiting." 34 | exit 1 35 | fi 36 | --------------------------------------------------------------------------------