Mercurial > repos > bgruening > silicos_it
changeset 9:6e6b05e75a3f
several updates to the silics-it repository
| author | Björn Grüning <bjoern.gruening@gmail.com> |
|---|---|
| date | Sun, 26 May 2013 16:50:00 +0200 |
| parents | 147814e45209 |
| children | c5a538ec7b43 |
| files | .hgignore align-it/align-it.xml align-it/align-it_create_db.xml qed/qed.py qed/silicos_qed.xml repository_dependencies.xml shape-it/shape-it.xml tool_dependencies.xml |
| diffstat | 8 files changed, 294 insertions(+), 56 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.hgignore Sun May 26 16:50:00 2013 +0200 @@ -0,0 +1,1 @@ +.tar* \ No newline at end of file
--- a/align-it/align-it.xml Sat May 25 12:56:15 2013 -0400 +++ b/align-it/align-it.xml Sun May 26 16:50:00 2013 +0200 @@ -5,41 +5,131 @@ <requirement type="package" version="2.3.2">openbabel</requirement> </requirements> <command> - align-it --format ${database.ext} --dbase $database --pharmacophore $alignedPharmacophores --dbType 'MOL' --scores $result --epsilon $0epsilon $merge $noHybrid $withExclusion 2>&1 + align-it + #if str($database.ext).strip() == 'phar': + --dbType PHAR + #else: + --dbType MOL + #end if + --dbase $database + + --reference $reference + #if str($reference.ext).strip() == 'phar': + --refType PHAR + #else: + --refType MOL + #end if + ####################################### + #### output options + ####################################### + --pharmacophore $aligned_pharmacophores + + + ##--out $aligned_structures + ##--outType $oformat + + #if float( str($cutoff) ) > 0: + --cutOff $cutoff + #end if + #if int( str($best) ) > 0: + --best $best + #end if + --rankBy $rankBy + --scores $score_result_file + + ####################################### + #### Options + ####################################### + + #set $fgroups_combined = str( $fgroups ).strip() + --funcGroup $fgroups_combined + + --epsilon $epsilon + $merge + $noNormal + $noHybrid + $scoreOnly + $withExclusion + + 2>&1 </command> <inputs> - <param name="database" type="data" format='mol,mol2,sdf,smi' label="database"/> - <param name="epsilon" type="float" label='change the tolerance for points to be matched' value="0.5" /> - <param name='merge' type='boolean' truevalue='--merge' falsvalue='' label='merge pharmacophore points' /> - <param name='noHybrid' type='boolean' truevalue='--noHybrid' falsvalue='' label='disable the use of hybrid pharmacophore points' /> - <param name='withExclusion' type='boolean' truevalue='--withExclusion' falsvalue='' label='add exclusion spheres into the optimization process instead of processing them afterwards' /> + <param name="database" type="data" format='mol,mol2,sdf,smi,phar' label="Defines the database of molecules that will be used to screen"/> + <param name="reference" type="data" format='mol,mol2,sdf,smi,phar' label="Reference Molecule"/> + + <param name="fgroups" type="select" multiple="True" display="checkboxes" label="Specify a subset of the available functional groups that are used in the alignment"> + <option value='AROM' selected="true">aromatic rings</option> + <option value='HDON' selected="true">hydrogen bond donors</option> + <option value='HACC' selected="true">hydrogen bond acceptors</option> + <option value='LIPO' selected="true">lipophilic spots</option> + <option value='CHARGE' selected="true">charge centers</option> + </param> + + + <param name="epsilon" type="float" value="0.5" label='Change the tolerance for points to be matched in the alignment phase' help="The lower this value, the more strict the matching between two pharmacophores will have to be before they can be aligned."> + <validator type="in_range" min="0" max="1" /> + </param> + <param name='merge' type='boolean' truevalue='--merge' falsevalue='' label='Merge pharmacophore points' /> + <param name='noNormal' type='boolean' truevalue='--noNormal' falsevalue='' label='No normal information is included during the alignment' help="Using this flag makes the pharmacophore models less specific but also less conformation-dependent."/> + <param name='noHybrid' type='boolean' truevalue='--noHybrid' falsevalue='' label='Disable the use of hybrid pharmacophore points' help="Using this flag will increase the number of pharmacophore points."/> + <param name='withExclusion' type='boolean' truevalue='--withExclusion' falsevalue='' label='Add exclusion spheres into the optimization process instead of processing them afterwards' help="When this flag is set, the exclusion spheres have also an impact on the optimization procedure." /> + <param name='scoreOnly' type='boolean' truevalue='--scoreOnly' falsevalue='' label='No translational or rotational optimization will be performed' help=""/> + + <!-- + <param name='oformat' type='select' format='text' label="The aligned database structures are written to an output file of the following format"> + <option value='smi'>SMILES</option> + <option value='inchi'>InChI</option> + <option value='sdf'>SD file</option> + </param> + --> + + <param name="cutoff" type="float" value="0" label="Only structures with a score larger than this cutoff will be written to the files" help="This value should be between 0 and 1."> + <validator type="in_range" min="0" max="1" /> + </param> + <param name="best" type="integer" value="0" label="With this option only a limited number of best scoring structures are written to the files" help="0 means this option is deactivated"> + <validator type="in_range" min="0"/> + </param> + + <param name='rankBy' type='select' format='text' label="This option defines the used scoring scheme"> + <option value='TANIMOTO'>Tanimoto</option> + <option value='TVERSKY_REF'>TVERSKY_REF</option> + <option value='TVERSKY_DB'>TVERSKY_DB</option> + </param> + </inputs> <outputs> - <data name="alignedPharmacophores" format="phar" /> - <data name="result" format="tabular" /> + <data name="aligned_pharmacophores" format="phar" label="${tool.name} on ${on_string} (aligned pharmacophores)"/> + <!--<data name="aligned_structures" format="smi" label="${tool.name} on ${on_string} (aligned structures)"> + <change_format> + <when input="oformat" value="inchi" format="inchi"/> + <when input="oformat" value="sdf" format="sdf"/> + </change_format> + </data>--> + <data name="score_result_file" format="tabular" label="${tool.name} on ${on_string} (scores)"/> </outputs> <tests> <test> - <param name="database" ftype='sdf' value='CID_2244.sdf'/> - <param name="epsilon" value="0.5" /> - <param name='merge' value='' /> - <param name='noHybrid' value='' /> - <param name='withExclusion' value='' /> - <output name="alignedPharmacophores" ftype="phar" file="alignit_on_CID2244.phar" /> - <output name="result" file="aliginit_scores.tabular" /> </test> </tests> <help> **What it does** -Align-it is a tool to align molecules according their pharmacophores. A -pharmacophore is an abstract concept based on the specific interactions -that have been observed in drug-receptor interactions: hydrogen bonding, -charge transfer, electrostatic and hydrophobic interactions. Molecular -modeling and/or screening using pharmacophores have proven to be an -important and useful method in drug discovery. +Align-it_ is a tool to align molecules according their pharmacophores. +A pharmacophore is an abstract concept based on the specific interactions +that have been observed in drug-receptor interactions: hydrogen bonding, +charge transfer, electrostatic and hydrophobic interactions. +Molecular modeling and/or screening based on pharmacophore similarities +have proven to be an important and useful method in drug discovery. +The functionality of Align-it_ consists mainly of two parts. +The first functionality consists of the **generation of pharmacophores from molecules** +(use the tool *Pharmacophore generation* if you want to store these for later use). +Second, pairs of pharmacophores can be aligned and the resulting +score is calculated from the volume overlap resulting from the alignments. + + +.. _Align-it: http://www.silicos-it.com/software/align-it/1.0.3/align-it.html ----- @@ -96,6 +186,25 @@ $$$$ +The format of this scores output file is as follows: + +====== ===================================================================== +Column Content +====== ===================================================================== + 1 Id of the reference structure + 2 Maximum volume of the reference structure + 3 Id of the database structure + 4 Maximum volume of the database structure + 5 Maximum volume overlap of the two structures + 6 Overlap between pharmacophore and exclusion spheres in the reference + 7 Corrected volume overlap between database pharmacophore and reference + 8 Number of pharmacophore points in the processed pharmacophore + 9 TANIMOTO score + 10 TVERSKY_REF score + 11 TVERSKY_DB score +====== ===================================================================== + + </help> </tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/align-it/align-it_create_db.xml Sun May 26 16:50:00 2013 +0200 @@ -0,0 +1,111 @@ +<tool id="ctb_alignit_create_db" name="Pharmacophore"> + <description>generation (Align-it)</description> + <requirements> + <requirement type="package" version="1.0.0">silicos_it</requirement> + <requirement type="package" version="2.3.2">openbabel</requirement> + </requirements> + <command> + align-it + #if str($database.ext).strip() == 'phar': + --dbType PHAR + #else: + --dbType MOL + #end if + --dbase $database + --pharmacophore $pharmacophores + $merge + $noHybrid + + 2>&1 + </command> + <inputs> + <param name="database" type="data" format='mol,mol2,sdf,smi,phar' label="Defines the database of molecules that will be converted to pharmacophores" /> + <param name='merge' type='boolean' truevalue='--merge' falsevalue='' label='Merge pharmacophore points' /> + <param name='noHybrid' type='boolean' truevalue='--noHybrid' falsevalue='' label='Disable the use of hybrid pharmacophore points' help="Using this flag will increase the number of pharmacophore points."/> + </inputs> + <outputs> + <data name="pharmacophores" format="phar" label="${tool.name} on ${on_string} (scores)"/> + </outputs> + <tests> + <test> + </test> + </tests> + <help> + +**What it does** + +Align-it_ is a tool to align molecules according their pharmacophores. +A pharmacophore is an abstract concept based on the specific interactions +that have been observed in drug-receptor interactions: hydrogen bonding, +charge transfer, electrostatic and hydrophobic interactions. +Molecular modeling and/or screening based on pharmacophore similarities +have proven to be an important and useful method in drug discovery. + +The functionality of Align-it_ consists mainly of two parts. +The first functionality consists of the **generation of pharmacophores from molecules** +(thats the function of this tool). Second, pairs of pharmacophores +can be aligned (use the tool *Pharmacophore Alignment*) and the resulting +score is calculated from the volume overlap resulting from the alignments. + + +.. _Align-it: http://www.silicos-it.com/software/align-it/1.0.3/align-it.html + + +----- + +**Example** + +* input:: + + - database + + 30 31 0 0 0 0 0 0 0999 V2000 + 1.9541 1.1500 -2.5078 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + 1.1377 -1.6392 2.1136 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + -3.2620 -2.9284 -1.0647 O 0 0 0 0 0 0 0 0 0 0 0 0 + -2.7906 -1.9108 0.9092 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.2679 -0.2051 -0.3990 N 0 0 0 0 0 0 0 0 0 0 0 0 + -2.0640 0.5139 -0.3769 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.7313 0.7178 -0.0192 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.4761 -0.6830 -1.1703 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.6571 -0.2482 -0.1795 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.0382 1.4350 0.0081 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.3728 1.8429 0.7234 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.6797 2.5600 0.7506 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.3470 2.7640 1.1083 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.5353 0.3477 -1.0918 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.1740 -0.8865 0.9534 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.8480 -1.8749 -0.3123 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.9124 0.3058 -0.8739 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.5511 -0.9285 1.1713 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.4203 -0.3324 0.2576 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.7086 -0.9792 -1.8930 H 0 0 0 0 0 0 0 0 0 0 0 0 + -3.3614 -0.4266 -1.7676 H 0 0 0 0 0 0 0 0 0 0 0 0 + -0.0861 -1.1146 -0.6780 H 0 0 0 0 0 0 0 0 0 0 0 0 + -4.0812 1.2885 -0.2604 H 0 0 0 0 0 0 0 0 0 0 0 0 + 0.6569 2.0278 1.0167 H 0 0 0 0 0 0 0 0 0 0 0 0 + -3.4382 3.2769 1.0511 H 0 0 0 0 0 0 0 0 0 0 0 0 + -1.0683 3.6399 1.6868 H 0 0 0 0 0 0 0 0 0 0 0 0 + 4.6037 0.7654 -1.5758 H 0 0 0 0 0 0 0 0 0 0 0 0 + 3.9635 -1.4215 2.0480 H 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4925 -0.3651 0.4274 H 0 0 0 0 0 0 0 0 0 0 0 0 + -3.5025 -3.7011 -0.5102 H 0 0 0 0 0 0 0 0 0 0 0 0 + + - cutoff : 0.0 + +* output:: + + - aligned Pharmacophores + + 3033 + HYBL -1.98494 1.9958 0.532089 0.7 0 0 0 0 + HYBL 3.52122 -0.309347 0.122783 0.7 0 0 0 0 + HYBH -3.262 -2.9284 -1.0647 1 1 -3.5666 -3.7035 -1.61827 + HDON 0.2679 -0.2051 -0.399 1 1 -0.076102 -0.981133 -0.927616 + HACC -2.7906 -1.9108 0.9092 1 1 -2.74368 -1.94015 1.90767 + $$$$ + + + + </help> +</tool>
--- a/qed/qed.py Sat May 25 12:56:15 2013 -0400 +++ b/qed/qed.py Sun May 26 16:50:00 2013 +0200 @@ -16,17 +16,22 @@ def check_filetype(filepath): mol = False - for line in open(filepath): + possible_inchi = True + for line_counter, line in enumerate(open(filepath)): + if line_counter > 10000: + break if line.find('$$$$') != -1: return 'sdf' elif line.find('@<TRIPOS>MOLECULE') != -1: return 'mol2' elif line.find('ligand id') != -1: return 'drf' - elif re.findall('^InChI=', line): + elif possible_inchi and re.findall('^InChI=', line): return 'inchi' elif re.findall('^M\s+END', line): mol = True + # first line is not an InChI, so it can't be an InChI file + possible_inchi = False if mol: # END can occures before $$$$, so and SDF file will @@ -288,17 +293,22 @@ if __name__ == "__main__": parser = argparse.ArgumentParser() - parser.add_argument('-i', '--input', required=True, help='path to the input file name') - parser.add_argument("-m", "--method", dest="method", choices=['max', 'mean', 'unweighted'], - default="mean", - help="Specify the method you want to use.") - + parser.add_argument('-i', '--input', + required=True, + help='path to the input file name') + parser.add_argument("-m", "--method", + dest="method", + choices=['max', 'mean', 'unweighted'], + default="mean", + help="Specify the method you want to use.") + parser.add_argument("--iformat", + help="Input format. It must be supported by openbabel.") parser.add_argument('-o', '--outfile', type=argparse.FileType('w+'), - default=sys.stdout, help="path to the result file, default it sdtout") - + default=sys.stdout, + help="path to the result file, default it sdtout") parser.add_argument("--header", dest="header", action="store_true", - default=False, - help="Write header line.") + default=False, + help="Write header line.") args = parser.parse_args() @@ -315,15 +325,18 @@ print "Error: ", ifile, " is not readable." sys.exit(1) - filetype = check_filetype(ifile) + if not args.iformat: + # try to guess the filetype + filetype = check_filetype( ifile ) + else: + filetype = args.iformat # sdf or smi """ We want to store the original SMILES in the output. So in case of a SMILES file iterate over the file and convert each line separate. """ - if filetype == 'sdf': - supplier = Chem.SDMolSupplier(ifile) + supplier = Chem.SDMolSupplier( ifile ) # Process file if args.header: args.outfile.write("MW\tALOGP\tHBA\tHBD\tPSA\tROTB\tAROM\tALERTS\tLRo5\tQED\tNAME\n") @@ -356,7 +369,7 @@ mol.GetProp("_Name"), )) elif filetype == 'smi': - supplier = Chem.SmilesMolSupplier(ifile, " \t", 0, 1, False, True) + supplier = Chem.SmilesMolSupplier( ifile, " \t", 0, 1, False, True ) # Process file if args.header: @@ -397,9 +410,5 @@ title, smiles )) - else: - print "Error: unknown file extension: ", extension - sys.exit(1) - - sys.exit(0) + sys.exit("Error: unknown file-type: ", filetype)
--- a/qed/silicos_qed.xml Sat May 25 12:56:15 2013 -0400 +++ b/qed/silicos_qed.xml Sun May 26 16:50:00 2013 +0200 @@ -6,7 +6,12 @@ <requirement type="package" version="2012_12_1">rdkit</requirement> <requirement type="package" version="1.7.1">numpy</requirement> </requirements> - <command interpreter="python">qed.py -i "${infile}" --method "${method}" -o "${outfile}" $header 2>&1</command> + <command interpreter="python"> + qed.py -i "${infile}" + --method "${method}" + --iformat ${infile.ext} + -o "${outfile}" $header 2>&1 + </command> <inputs> <param format="smi,sdf" name="infile" type="data" label="Molecule data in SD- or SMILES-format" help="Dataset missing? See TIP below"/> <param name="method" type="select" label="Method">
--- a/repository_dependencies.xml Sat May 25 12:56:15 2013 -0400 +++ b/repository_dependencies.xml Sun May 26 16:50:00 2013 +0200 @@ -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="c5383bd4d006" name="molecule_datatypes" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" /> -</repositories> + <repository name="molecule_datatypes" owner="bgruening" /> +</repositories>
--- a/shape-it/shape-it.xml Sat May 25 12:56:15 2013 -0400 +++ b/shape-it/shape-it.xml Sun May 26 16:50:00 2013 +0200 @@ -31,10 +31,10 @@ **What it does** -Shape-it is a program for the alignment of a reference molecule against a -database of molecules using the shape of the molecules. It is based on -the use of Gaussian volumes as descriptor for molecular shape as it was -introduced by Grant and Pickup1 . +Shape-it_ is a tool that aligns a reference molecule against a set of database +molecules using the shape of the molecules as the align criterion. +It is based on the use of Gaussian volumes as descriptor for molecular +shape as it was introduced by `Grant and Pickup`_. The program expects one reference molecule with its three-dimensional coordinates and one database files containing one @@ -42,6 +42,10 @@ of all database molecules and their respective scores or the N best scoring molecules from the complete database. + +.. _Shape-it: http://silicos-it.com/software/shape-it/1.0.1/shape-it.html +.. _`Grant and Pickup`: http://onlinelibrary.wiley.com/doi/10.1002/(SICI)1096-987X(19961115)17:14%3C1653::AID-JCC7%3E3.0.CO;2-K/abstract + ----- **Example**
--- a/tool_dependencies.xml Sat May 25 12:56:15 2013 -0400 +++ b/tool_dependencies.xml Sun May 26 16:50:00 2013 +0200 @@ -1,13 +1,12 @@ -<?xml version="1.0"?> <tool_dependency> <package name="numpy" version="1.7.1"> - <repository changeset_revision="7283651b62fe" name="package_numpy_1_7" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository name="package_numpy_1_7" owner="bgruening" prior_installation_required="True" /> </package> <package name="openbabel" version="2.3.2"> - <repository changeset_revision="ccda1b8ebc72" name="package_openbabel_2_3" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository name="package_openbabel_2_3" owner="bgruening" prior_installation_required="True" /> </package> <package name="rdkit" version="2012_12_1"> - <repository changeset_revision="87b2d2831a31" name="package_rdkit_2012_12" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository name="package_rdkit_2012_12" owner="bgruening" prior_installation_required="True" /> </package> <package name="silicos_it" version="1.0.0"> <install version="1.0"> @@ -19,7 +18,7 @@ $OPENBABEL_INCLUDE_DIR and $OPENBABEL_LIB_DIR --> <action type="set_environment_for_install"> - <repository changeset_revision="ccda1b8ebc72" name="package_openbabel_2_3" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu"> + <repository name="package_openbabel_2_3" owner="bgruening"> <package name="openbabel" version="2.3.2" /> </repository> </action> @@ -31,7 +30,7 @@ make && make install</action> <action type="set_environment"> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/strip-it/bin</environment_variable> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/strip-it/bin</environment_variable> </action> <!-- compiling align-it --> @@ -42,7 +41,7 @@ make && make install</action> <action type="set_environment"> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/align-it/bin</environment_variable> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/align-it/bin</environment_variable> </action> <!-- compiling shape-it --> @@ -53,7 +52,7 @@ make && make install</action> <action type="set_environment"> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/shape-it/bin</environment_variable> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/shape-it/bin</environment_variable> </action> </actions>