| Previous changeset 1:b52872a1755a (2013-08-21) |
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Commit message:
Uploaded |
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modified:
convert/ob_convert.xml filter/multi_obgrep.xml filter/ob_filter.xml filter/ob_grep.xml filter/ob_remDuplicates.xml filter/ob_remIons.xml filter/ob_remSmall.xml modify/change_title_to_metadata_value.xml modify/ob_addh.xml modify/ob_genProp.xml modify/remove_protonation_state.xml repository_dependencies.xml search/ob_spectrophore_search.xml subsearch/subsearch.xml tool_dependencies.xml visualisation/ob_depiction_svg.xml |
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| diff -r b52872a1755a -r 125da3a296ca convert/ob_convert.xml --- a/convert/ob_convert.xml Wed Aug 21 03:06:02 2013 -0400 +++ b/convert/ob_convert.xml Wed Jul 15 12:13:08 2015 -0400 |
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| @@ -8,6 +8,7 @@ <requirement type="package" version="2.3.2">openbabel</requirement> </requirements> <command> +<![CDATA[ ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces @@ -16,17 +17,17 @@ #if $format == "fs": ## For the fastsearch index we need to copy the original molecule files to the composite datatype of obfs. ## Because openbabel likes file extensions, we give the molecule file a proper file extension. - mkdir $outfile.extra_files_path; - cp "${infile}" ${os.path.join($outfile.extra_files_path, 'molecule.%s' % $infile.ext )}; + mkdir $outfile.files_path; + cp "${infile}" ${os.path.join($outfile.files_path, 'molecule.%s' % $infile.ext )}; #end if obabel -i "${infile.ext}" #if $format == "fs": ## the fs filetype need his own symlink path, all others can take the original ones - ${os.path.join($outfile.extra_files_path, 'molecule.%s' % $infile.ext )} + ${os.path.join($outfile.files_path, 'molecule.%s' % $infile.ext )} -o "$format" -e - -O ${os.path.join($outfile.extra_files_path,'molecule.fs')} + -O ${os.path.join($outfile.files_path,'molecule.fs')} #if int($oformat.fs_fold) > 0: -xN$oformat.fs_fold #end if @@ -125,7 +126,8 @@ -p $ph #end if - 2>&1 + 2>&1 +]]> </command> <inputs> <param name="infile" type="data" format="sdf,mol2,cml,inchi,smi" label="Select input file with molecules"/> @@ -145,7 +147,7 @@ <option value="cdxml">ChemDraw CDXML format</option> <option value="cht">Chemtool format</option> <option value="cif">Crystallographic Information File</option> - <option value="cml">Chemical Markup Language</option> + <option value="cml">Chemical Markup Language (CML)</option> <option value="cmlr">CML Reaction format</option> <option value="com">Gaussian 98/03 Cartesian Input</option> <option value="copy">Copies raw text</option> @@ -424,13 +426,14 @@ </data> </outputs> <help> +<![CDATA[ .. class:: infomark **What this tool does** -The compound converter joins several `Open Babel`_ command prompt converters in an easy to use tool. It converts various chemistry and moleculare modeling data files. -The output format can be specified as well as several parameters. Some parameters are available for all tools (e.g. protonation state and pH) +The compound converter joins several `Open Babel`_ command prompt converters in an easy to use tool. It converts various chemistry and moleculare modeling data files. +The output format can be specified as well as several parameters. Some parameters are available for all tools (e.g. protonation state and pH) others are specific for a given output format (e.g. exclude isotopes for conversion to canSMI). ----- @@ -456,5 +459,6 @@ .. _`Open Babel`: http://openbabel.org/wiki/Main_Page +]]> </help> </tool> |
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| diff -r b52872a1755a -r 125da3a296ca filter/multi_obgrep.xml --- a/filter/multi_obgrep.xml Wed Aug 21 03:06:02 2013 -0400 +++ b/filter/multi_obgrep.xml Wed Jul 15 12:13:08 2015 -0400 |
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| @@ -4,6 +4,7 @@ <requirement type="package" version="2.3.2">openbabel</requirement> </requirements> <command interpreter="python"> +<![CDATA[ multi_obgrep.py -i $infile @@ -15,8 +16,9 @@ $only_name $full_match $number_of_matches - --processors 10 + --processors "\${GALAXY_SLOTS:-12}" +]]> </command> <inputs> <param name="infile" type="data" format="sdf,mol,mol2,cml,inchi,smi" label="Compound File" help="Specify a compound file in SDF Format"/> @@ -35,6 +37,7 @@ </test> </tests> <help> +<![CDATA[ .. class:: infomark @@ -80,5 +83,6 @@ .. _`Open Babel`: http://openbabel.org/wiki/Main_Page +]]> </help> </tool> |
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| diff -r b52872a1755a -r 125da3a296ca filter/ob_filter.xml --- a/filter/ob_filter.xml Wed Aug 21 03:06:02 2013 -0400 +++ b/filter/ob_filter.xml Wed Jul 15 12:13:08 2015 -0400 |
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| @@ -6,6 +6,7 @@ <requirement type="package" version="0.1">cheminfolib</requirement> </requirements> <command interpreter="python"> +<![CDATA[ ob_filter.py -i "${infile}" -o "${outfile}" @@ -40,6 +41,7 @@ #end for #end if }' +]]> </command> <inputs> <param name="infile" type="data" format="sdf,smi,mol,mol2,cml,inchi" label="Select input file previously created with the 'Compute physico-chemical properties' tool"/> @@ -136,13 +138,14 @@ --> </tests> <help> +<![CDATA[ .. class:: infomark **What this tool does** -Filters a library of compounds based on user-defined physico-chemical parameters or predefined options (e.g. Ro5, lead-like properties, etc.). Multiple parameters can be selected for more specific queries. +Filters a library of compounds based on user-defined physico-chemical parameters or predefined options (e.g. Ro5, lead-like properties, etc.). Multiple parameters can be selected for more specific queries. ----- @@ -151,9 +154,9 @@ **Hint** | If your input file is in SDF format you can use the *Compute physico-chemical properties* tool to precalulate the properties and use the filter on that precomputed dataset. It should be faster and can be reused but it's bigger than a SMILES file. -| +| | For exact matches please use the target value for both minimum and maximum parameters (e.g. a selection of exactly 4 rotatable bonds can be performed by selecting 4 as minimum and maximum value). -| +| | Selecting the same property multiple times with different parameters will result in querying the largest overlapping subset of values for the parameter (e.g. a selection of between 0 and 3 rotatable bonds plus a selection between 2 and 4 will result in a query for compounds between 2 and 3 rotatable bonds). ----- @@ -163,38 +166,38 @@ **Definition of the pre-defined filtering rules** **# Lipinski's Rule of Five:** - =< 5 Hydrogen-bond donor groups + =< 5 Hydrogen-bond donor groups - =< 10 Hydrogen-bond acceptor groups + =< 10 Hydrogen-bond acceptor groups - =< 500 Molecular weight + =< 500 Molecular weight - =< 5 octanol/water partition coefficient (log P) + =< 5 octanol/water partition coefficient (log P) **# Lead Like properties** (Teague, Davis, Leeson, Oprea, Angew Chem Int Ed Engl. 1999 Dec 16;38(24):3743-3748): - =< 7 rotatable bonds + =< 7 rotatable bonds - =< 350 Molecular weight + =< 350 Molecular weight - =< 3.5 octanol/water partition coefficient (log P) + =< 3.5 octanol/water partition coefficient (log P) **# Drug Like properties** (Lipinski, J Pharmacol Toxicol Methods. 2000 Jul-Aug;44(1):235-49): - =< 10 Hydrogen-bond acceptor groups + =< 10 Hydrogen-bond acceptor groups - =< 8 rotatable bonds + =< 8 rotatable bonds - 150 =< Molecular weight =< 500 + 150 =< Molecular weight =< 500 - =< 150 Polar Surface Area + =< 150 Polar Surface Area - =< 5 octanol/water partition coefficient (log P) + =< 5 octanol/water partition coefficient (log P) **# Fragment Like properties** (Carr RA, Congreve M, Murray CW, Rees DC, Drug Discov Today. 2005 Jul 15;10(14):987): - =< 5 rotatable bonds + =< 5 rotatable bonds - =< 250 Molecular weight + =< 250 Molecular weight - =< 2.5 octanol/water partition coefficient (log P) + =< 2.5 octanol/water partition coefficient (log P) ----- @@ -212,10 +215,10 @@ .. class:: infomark -**Output** +**Output** | SDF formatted coordinates of the molecules, with selected properties stored as meta-data for each compound. -| +| | SMILES, InChI or mol2 formatted files containing the 1D strings or 3D coordinates of each compound. ----- @@ -236,5 +239,6 @@ .. _`Open Babel`: http://openbabel.org/wiki/Main_Page +]]> </help> </tool> |
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| diff -r b52872a1755a -r 125da3a296ca filter/ob_grep.xml --- a/filter/ob_grep.xml Wed Aug 21 03:06:02 2013 -0400 +++ b/filter/ob_grep.xml Wed Jul 15 12:13:08 2015 -0400 |
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| @@ -5,6 +5,7 @@ <requirement type="package" version="2.3.2">openbabel</requirement> </requirements> <command> +<![CDATA[ ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces obgrep @@ -20,7 +21,8 @@ -i ${infile.ext} "${smarts_pattern}" "${infile}" - > "${outfile}" 2>&1 + > "${outfile}" 2>&1 +]]> </command> <inputs> <param name="infile" type="data" format="sdf,mol,mol2,cml,inchi,smi" label="Compound File" help="Specify a compound file in SDF Format."/> @@ -48,6 +50,7 @@ </test> </tests> <help> +<![CDATA[ .. class:: infomark @@ -94,5 +97,6 @@ .. _`Open Babel`: http://openbabel.org/wiki/Main_Page +]]> </help> </tool> |
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| diff -r b52872a1755a -r 125da3a296ca filter/ob_remDuplicates.xml --- a/filter/ob_remDuplicates.xml Wed Aug 21 03:06:02 2013 -0400 +++ b/filter/ob_remDuplicates.xml Wed Jul 15 12:13:08 2015 -0400 |
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| @@ -5,6 +5,7 @@ <requirement type="package" version="2.3.2">openbabel</requirement> </requirements> <command> +<![CDATA[ obabel -i"${infile.ext}" "${infile}" @@ -12,7 +13,8 @@ --unique "${descriptor}" -O "${outfile}" -e - 2>&1 + 2>&1 +]]> </command> <inputs> <param name="infile" type="data" format="sdf,mol,mol2,cml,inchi,smi" label="Molecular input file"/> @@ -33,6 +35,7 @@ </test> </tests> <help> +<![CDATA[ .. class:: infomark @@ -64,7 +67,7 @@ .. class:: infomark -**Output** +**Output** Same as input format. @@ -82,5 +85,6 @@ .. _`Open Babel`: http://openbabel.org/wiki/Main_Page +]]> </help> </tool> |
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| diff -r b52872a1755a -r 125da3a296ca filter/ob_remIons.xml --- a/filter/ob_remIons.xml Wed Aug 21 03:06:02 2013 -0400 +++ b/filter/ob_remIons.xml Wed Jul 15 12:13:08 2015 -0400 |
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| @@ -5,10 +5,12 @@ <requirement type="package" version="2.3.2">openbabel</requirement> </requirements> <command interpreter="python"> +<![CDATA[ ob_remIons.py -i "${infile}" -iformat "${infile.ext}" -o "${outfile}" +]]> </command> <inputs> <param name="infile" type="data" format="sdf,mol,mol2,cml,inchi,smi" label="Select input file with multiple molecules"/> @@ -23,6 +25,7 @@ </test> </tests> <help> +<![CDATA[ .. class:: infomark @@ -37,7 +40,7 @@ **Hint** | Only the **largest fragment** on every molecule is extracted. -| +| | Only molecules with more than 5 heavy atoms are parsed. ----- @@ -58,5 +61,6 @@ .. _`Open Babel`: http://openbabel.org/wiki/Main_Page +]]> </help> </tool> |
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| diff -r b52872a1755a -r 125da3a296ca filter/ob_remSmall.xml --- a/filter/ob_remSmall.xml Wed Aug 21 03:06:02 2013 -0400 +++ b/filter/ob_remSmall.xml Wed Jul 15 12:13:08 2015 -0400 |
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| @@ -5,6 +5,7 @@ <requirement type="package" version="2.3.2">openbabel</requirement> </requirements> <command> +<![CDATA[ obabel -i"${infile.ext}" "${infile}" @@ -12,7 +13,8 @@ -O "${outfile}" --filter "atoms > $cutoff" -e - 2>&1 + 2>&1 +]]> </command> <inputs> <param name="infile" format="sdf,mol,mol2,cml,inchi,smi" type="data" label="Molecular input file" /> @@ -29,6 +31,7 @@ </test> </tests> <help> +<![CDATA[ .. class:: infomark @@ -66,5 +69,6 @@ .. _`Open Babel`: http://openbabel.org/wiki/Main_Page +]]> </help> </tool> |
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| diff -r b52872a1755a -r 125da3a296ca modify/change_title_to_metadata_value.xml --- a/modify/change_title_to_metadata_value.xml Wed Aug 21 03:06:02 2013 -0400 +++ b/modify/change_title_to_metadata_value.xml Wed Jul 15 12:13:08 2015 -0400 |
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| @@ -5,12 +5,14 @@ <requirement type="package" version="2.3.2">openbabel</requirement> </requirements> <command interpreter="python"> +<![CDATA[ ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces change_title_to_metadata_value.py --infile "${infile}" --key "${key}" --outfile "${outfile}" +]]> </command> <inputs> <param name="infile" type="data" format="sdf,mol2" label="Compound File" help="Specify a compound file in SD- or MOL2-format."/> @@ -25,6 +27,7 @@ <data name="output" type="sdf" file="change_title_on_CID_3033.sdf"/> </tests> <help> +<![CDATA[ .. class:: infomark @@ -60,5 +63,6 @@ .. _Open Babel: http://openbabel.org/wiki/Main_Page +]]> </help> </tool> |
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| diff -r b52872a1755a -r 125da3a296ca modify/ob_addh.xml --- a/modify/ob_addh.xml Wed Aug 21 03:06:02 2013 -0400 +++ b/modify/ob_addh.xml Wed Jul 15 12:13:08 2015 -0400 |
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| @@ -5,12 +5,14 @@ <requirement type="package" version="2.3.2">openbabel</requirement> </requirements> <command interpreter="python"> +<![CDATA[ ob_addh.py -i "${infile}" --iformat "${infile.ext}" -o "${outfile}" $polar --pH "${pH_value}" +]]> </command> <inputs> <param name="infile" type="data" format="sdf,smi,mol,mol2,cml,inchi" label="Select input file"/> @@ -29,6 +31,7 @@ </test> </tests> <help> +<![CDATA[ .. class:: infomark @@ -55,7 +58,7 @@ .. class:: warningmark -**Hint** +**Hint** To avoid possible crashes, only molecules with more than five heavy atoms are parsed. @@ -63,7 +66,7 @@ .. class:: infomark -**Output** +**Output** Same output format as the input format. @@ -81,5 +84,6 @@ .. _`Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`: http://www.biomedcentral.com/content/pdf/1752-153X-2-5.pdf +]]> </help> </tool> |
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| diff -r b52872a1755a -r 125da3a296ca modify/ob_genProp.xml --- a/modify/ob_genProp.xml Wed Aug 21 03:06:02 2013 -0400 +++ b/modify/ob_genProp.xml Wed Jul 15 12:13:08 2015 -0400 |
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| @@ -6,6 +6,7 @@ <requirement type="package" version="0.1">cheminfolib</requirement> </requirements> <command interpreter="python"> +<![CDATA[ ob_genProp.py -i "${infile}" --iformat "${infile.ext}" @@ -14,6 +15,7 @@ --header $output_opts.header #end if -o "${outfile}" +]]> </command> <inputs> <param name="infile" type="data" format="sdf,mol,mol2,cml,inchi,smi" label="Select input file with multiple molecules."/> @@ -51,6 +53,7 @@ </test> </tests> <help> +<![CDATA[ .. class:: infomark @@ -131,5 +134,6 @@ .. _Silicos: http://openbabel.org/docs/dev/Fingerprints/spectrophore.html +]]> </help> </tool> |
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| diff -r b52872a1755a -r 125da3a296ca modify/remove_protonation_state.xml --- a/modify/remove_protonation_state.xml Wed Aug 21 03:06:02 2013 -0400 +++ b/modify/remove_protonation_state.xml Wed Jul 15 12:13:08 2015 -0400 |
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| @@ -5,11 +5,13 @@ <requirement type="package" version="2.3.2">openbabel</requirement> </requirements> <command interpreter='python'> +<![CDATA[ remove_protonation_state.py -i $infile -o $outfile --iformat "${infile.ext}" - 2>&1 + 2>&1 +]]> </command> <inputs> <param name="infile" type="data" format="sdf,smi,mol,inchi" label="Molecule file" help="Dataset missing? See TIP below"/> @@ -22,6 +24,7 @@ </test> </tests> <help> +<![CDATA[ .. class:: infomark @@ -39,5 +42,6 @@ .. _Open Babel: http://openbabel.org/wiki/Main_Page +]]> </help> </tool> |
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| diff -r b52872a1755a -r 125da3a296ca repository_dependencies.xml --- a/repository_dependencies.xml Wed Aug 21 03:06:02 2013 -0400 +++ b/repository_dependencies.xml Wed Jul 15 12:13:08 2015 -0400 |
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| @@ -1,4 +1,4 @@ <?xml version="1.0"?> <repositories description="This requires the Molecule datatype definitions (e.g. SMILES, InChI, SD-format)."> - <repository changeset_revision="85eca06eefc6" name="molecule_datatypes" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="85eca06eefc6" name="molecule_datatypes" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </repositories> |
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| diff -r b52872a1755a -r 125da3a296ca search/ob_spectrophore_search.xml --- a/search/ob_spectrophore_search.xml Wed Aug 21 03:06:02 2013 -0400 +++ b/search/ob_spectrophore_search.xml Wed Jul 15 12:13:08 2015 -0400 |
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| @@ -5,11 +5,13 @@ <requirement type="package" version="1.7.1">numpy</requirement> </requirements> <command interpreter="python"> +<![CDATA[ ob_spectrophore_search.py --target $target --library $library --output $outfile --column $column +]]> </command> <inputs> <param name="target" type="data" format="sdf" label="Target molecule in SDF format (it must contain its Spectrophores(TM) stored as meta-data)"/> @@ -28,6 +30,7 @@ </test> </tests> <help> +<![CDATA[ .. class:: infomark @@ -59,7 +62,7 @@ .. class:: infomark -**Input** +**Input** The target molecule must be a SD formatted file with the |Spectrophores (TM)| descriptors stored as metadata. Such files can be generated using the *Compute physico-chemical properties* tool. @@ -84,5 +87,6 @@ .. _`Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`: http://www.biomedcentral.com/content/pdf/1752-153X-2-5.pdf .. _Silicos: http://openbabel.org/docs/dev/Fingerprints/spectrophore.html +]]> </help> </tool> |
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| diff -r b52872a1755a -r 125da3a296ca subsearch/subsearch.xml --- a/subsearch/subsearch.xml Wed Aug 21 03:06:02 2013 -0400 +++ b/subsearch/subsearch.xml Wed Jul 15 12:13:08 2015 -0400 |
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| @@ -4,16 +4,18 @@ <requirement type="package" version="2.3.2">openbabel</requirement> </requirements> <command interpreter="python"> +<![CDATA[ subsearch.py -i $query --iformat "${query.ext}" - --fastsearch-index "${os.path.join($fastsearch.extra_files_path,'molecule.fs')}" + --fastsearch-index "${os.path.join($fastsearch.files_path,'molecule.fs')}" -o "${outfile}" --oformat $oformat --max-candidates $max_candidates - --processors 10 + --processors "\${GALAXY_SLOTS:-12}" +]]> </command> <inputs> <param name="query" type='data' format="tabular,smi,sdf,inchi,text" label="query"/> @@ -42,6 +44,7 @@ </test> </tests> <help> +<![CDATA[ .. class:: infomark @@ -69,5 +72,6 @@ .. _Open Babel: http://openbabel.org/wiki/Main_Page +]]> </help> </tool> |
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| diff -r b52872a1755a -r 125da3a296ca tool_dependencies.xml --- a/tool_dependencies.xml Wed Aug 21 03:06:02 2013 -0400 +++ b/tool_dependencies.xml Wed Jul 15 12:13:08 2015 -0400 |
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| @@ -1,10 +1,10 @@ <?xml version="1.0"?> <tool_dependency> <package name="openbabel" version="2.3.2"> - <repository changeset_revision="99a10425de93" name="package_openbabel_2_3" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="e5ef70185d24" name="package_openbabel_2_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="numpy" version="1.7.1"> - <repository changeset_revision="74c21f9bdc39" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="8b3a5c7061d8" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="cheminfolib" version="0.1"> <install version="1.0"> |
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| diff -r b52872a1755a -r 125da3a296ca visualisation/ob_depiction_svg.xml --- a/visualisation/ob_depiction_svg.xml Wed Aug 21 03:06:02 2013 -0400 +++ b/visualisation/ob_depiction_svg.xml Wed Jul 15 12:13:08 2015 -0400 |
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| b'@@ -1,127 +1,131 @@\n-<tool id="ctb_ob_svg_depiction" name="Visualisation">\r\n- <description>of compounds</description>\r\n- <requirements>\r\n- <requirement type="package" version="2.3.2">openbabel</requirement>\r\n- </requirements>\r\n- <command>\r\n- obabel -i${infile.ext} $infile\r\n- $embed_molecule_as_cml\r\n- $draw_all_carbon_atoms\r\n- -xC \r\n- -O \r\n- $outfile -o$oformat\r\n- #if str($sort) != "none":\r\n- --sort $sort\r\n- #end if\r\n- #if str($display_name) != "None" and len(str($display_name)) > 0 and str($display_name) != \'title\':\r\n- --append "$display_name"\r\n- --title ""\r\n- #end if\r\n- $thick_lines\r\n- 2>&1\r\n- </command>\r\n- <inputs>\r\n- <param name="infile" type="data" format="mol,sdf,smi,inchi" label="Input format"/>\r\n- <param name="embed_molecule_as_cml" type="boolean" truevalue="-e" falsevalue="" label="Embed molecule as CML"/>\r\n- <param name="draw_all_carbon_atoms" type="boolean" truevalue="-a" falsevalue="" label="draw all carbon atoms"/>\r\n- <param name="thick_lines" type="boolean" truevalue="-xt" falsevalue="" label="use thicker lines"/>\r\n-\r\n- <param name=\'display_name\' type=\'select\' format=\'text\' label="The property which is displayed under the molecule">\r\n- <option value=\'title\'>Molecule\'s title</option>\r\n- <option value=\'MW\'>Molecular Weight</option>\r\n- <option value=\'abonds\'>Number of aromatic bonds</option>\r\n- <option value=\'atoms\'>Number of atoms</option>\r\n- <option value=\'bonds\'>Number of bonds</option>\r\n- <option value=\'cansmi\'>Canonical SMILES</option>\r\n- <option value=\'cansmiNS\'>Canonical SMILES without isotopes or stereo</option>\r\n- <option value=\'dbonds\'>Number of double bonds</option>\r\n- <option value=\'formula\'>Chemical formula</option>\r\n- <option value=\'HBA1\'>Number of Hydrogen Bond Acceptors 1 (JoelLib)</option>\r\n- <option value=\'HBA2\'>Number of Hydrogen Bond Acceptors 2 (JoelLib)</option>\r\n- <option value=\'HBD\'>Number of Hydrogen Bond Donors (JoelLib)</option>\r\n- <option value=\'InChI\'>IUPAC InChI identifier</option>\r\n- <option value=\'L5\'>Lipinski Rule of Five</option>\r\n- <option value=\'logP\'>octanol/water partition coefficient</option>\r\n- <option value=\'MR\'>molar refractivity</option>\r\n- <option value=\'nF\'>Number of Fluorine Atoms</option>\r\n- <option value=\'s\'>SMARTS filter</option>\r\n- <option value=\'sbonds\'>Number of single bonds</option>\r\n- <option value=\'smarts\'>SMARTS filter</option>\r\n- <option value=\'tbonds\'>Number of triple bonds</option>\r\n- <option value=\'TPSA\'>topological polar surface area</option>\r\n- </param>\r\n-\r\n- <param name=\'sort\' type=\'select\' format=\'text\' label="Sorting the displayed molecules by">\r\n- <option value=\'none\'>No sorting</option>\r\n- <option value=\'MW\'>Molecular Weight</option>\r\n- <option value=\'abonds\'>Number of aromatic bonds</option>\r\n- <option value=\'atoms\'>Number of atoms</option>\r\n- <option value=\'bonds\'>Number of bonds</option>\r\n- <option value=\'dbonds\'>Number of double bonds</option>\r\n- <option value=\'HBA1\'>Number of Hydrogen Bond Acceptors 1 (JoelLib)</option>\r\n- <option value=\'HBA2\'>Number of Hydrogen Bond Acceptors 2 (JoelLib)</option>\r\n- <option value=\'HBD\'>Number of Hydrogen Bond Donors (JoelLib)</option>\r\n- <option value=\'L5\'>Lipinski Rule of Five</option>\r\n- <option value=\'logP\'>octanol/water partition coefficient</option>\r\n- <option value=\'MR\'>molar refractivity</option>\r\n- <option value=\'nF\'>Number of Fluorine Atoms</option>\r\n- <option value=\'sbonds\'>Number of single bonds</option>\r\n- <option va'..b'nonical SMILES</option>\n+ <option value=\'cansmiNS\'>Canonical SMILES without isotopes or stereo</option>\n+ <option value=\'dbonds\'>Number of double bonds</option>\n+ <option value=\'formula\'>Chemical formula</option>\n+ <option value=\'HBA1\'>Number of Hydrogen Bond Acceptors 1 (JoelLib)</option>\n+ <option value=\'HBA2\'>Number of Hydrogen Bond Acceptors 2 (JoelLib)</option>\n+ <option value=\'HBD\'>Number of Hydrogen Bond Donors (JoelLib)</option>\n+ <option value=\'InChI\'>IUPAC InChI identifier</option>\n+ <option value=\'L5\'>Lipinski Rule of Five</option>\n+ <option value=\'logP\'>octanol/water partition coefficient</option>\n+ <option value=\'MR\'>molar refractivity</option>\n+ <option value=\'nF\'>Number of Fluorine Atoms</option>\n+ <option value=\'s\'>SMARTS filter</option>\n+ <option value=\'sbonds\'>Number of single bonds</option>\n+ <option value=\'smarts\'>SMARTS filter</option>\n+ <option value=\'tbonds\'>Number of triple bonds</option>\n+ <option value=\'TPSA\'>topological polar surface area</option>\n+ </param>\n+\n+ <param name=\'sort\' type=\'select\' format=\'text\' label="Sorting the displayed molecules by">\n+ <option value=\'none\'>No sorting</option>\n+ <option value=\'MW\'>Molecular Weight</option>\n+ <option value=\'abonds\'>Number of aromatic bonds</option>\n+ <option value=\'atoms\'>Number of atoms</option>\n+ <option value=\'bonds\'>Number of bonds</option>\n+ <option value=\'dbonds\'>Number of double bonds</option>\n+ <option value=\'HBA1\'>Number of Hydrogen Bond Acceptors 1 (JoelLib)</option>\n+ <option value=\'HBA2\'>Number of Hydrogen Bond Acceptors 2 (JoelLib)</option>\n+ <option value=\'HBD\'>Number of Hydrogen Bond Donors (JoelLib)</option>\n+ <option value=\'L5\'>Lipinski Rule of Five</option>\n+ <option value=\'logP\'>octanol/water partition coefficient</option>\n+ <option value=\'MR\'>molar refractivity</option>\n+ <option value=\'nF\'>Number of Fluorine Atoms</option>\n+ <option value=\'sbonds\'>Number of single bonds</option>\n+ <option value=\'tbonds\'>Number of triple bonds</option>\n+ <option value=\'TPSA\'>topological polar surface area</option>\n+ </param>\n+\n+ <param name=\'oformat\' type=\'select\' format=\'text\' label="Format of the resulting picture">\n+ <option value=\'svg\'>SVG</option>\n+ <option value=\'png\'>PNG</option>\n+ </param>\n+\n+ </inputs>\n+ <outputs>\n+ <data name="outfile" type="data" format="png" label="${tool.name} on ${on_string}">\n+ <change_format>\n+ <when input="oformat" value="svg" format="svg"/>\n+ </change_format>\n+ </data>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="infile" ftype="smi" value="8_mol.smi" />\n+ <param name="embed_molecule_as_cml" value="" />\n+ <param name="draw_all_carbon_atoms" value="-a" />\n+ <param name="thick_lines" value="-xt" />\n+ <param name=\'display_name\' value="title" />\n+ <param name=\'sort\' value=\'none\' />\n+ <output name="outfile" ftype="svg" file="ob_depiction_svg_on_8_mol.svg" />\n+ </test>\n+ </tests>\n+ <help>\n+<![CDATA[\n+\n+.. class:: infomark\n+\n+**What this tool does**\n+\n+Creates an .svg or .png image of a small set of molecules (few hundreds). Based on Open Babel PNG_/SVG_ 2D depiction.\n+\n+.. _PNG: http://openbabel.org/docs/dev/FileFormats/PNG_2D_depiction.html\n+.. _SVG: http://openbabel.org/docs/dev/FileFormats/SVG_2D_depiction.html\n+\n+-----\n+\n+.. class:: warningmark\n+\n+**Hint**\n+\n+Use only libraries with at most a few hundred molecules.\n+\n+-----\n+\n+.. class:: infomark\n+\n+**Cite**\n+\n+`Open Babel`_\n+\n+.. _Open Babel: http://openbabel.org/wiki/Main_Page\n+\n+]]>\n+ </help>\n+</tool>\n' |