Detailed Timeline

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This work took place in the Summer of 2011. The detailed timeline of the work is presented below in reverse chronological order.

Contents

Phase 4: Publication of Workflows as Linked Data and Demo application

Phase 3: Mapping of the workflow template and execution to OPM

Phase 2: Implementation of Five Core Workflow Steps

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On purple we can see the components that have been added to ensure the reproducibility of the workflow avoiding manual steps. I have avoided adding one additional component (getSMAPAlignementFolder), because it is not necessary for the global understanding of the workflow.

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./autodock_vina -i1 /Users/danielgarijo/WORK_ISI/DOCKING/Steps_Before_Docking/TESTSCRIPT/sig_results_1e-5_fatcat_filtered -i2 /Users/
danielgarijo/WORK_ISI/DOCKING/Steps_Before_Docking/TESTSCRIPT/align_struct_output/ -i3 /Users/danielgarijo/WORK_ISI/DOCKING/Steps_Before_Docking
/TESTSCRIPT/ideal_ligs/ -i4 /Users/danielgarijo/WORK_ISI/DOCKING/Steps_Before_Docking/TESTSCRIPT/749_mtb_structures/ -o output

1,2 .-We execute the clip file scripts+the lig scripts to have all the inputs available.

3.-Initial Line: 1K0R_A nusA 1HK3_LIG.T44 SERUM ALBUMIN P02768 T44 2.586E-08 80.39 0.75 2.23A

4.- We extract the coordinates using the script and the SMAP aligned output: ./ligand_center.csh 1HK3_LIG.T44-1K0R_A.pdb T44.

Results: (Example Dani) center_x = -42.625 center_y = 62.5417 center_z = 16.125

we redirect the output to a file csh ./ligand_center.csh 1HK3_LIG.T44-1K0R_A.pdb T44 > COORD_1HK3_LIG.T44-1K03_A

4a,b: test if the prepare receptor and ligand work (Sarah' s example): ./prepare_ligand4.py -l VDN.pdb ./prepare_receptor4.py -r 1BVR_F.pdb ./vina --receptor 1BVR_F.pdbqt --ligand VDN.pdbqt --center_x 20.34 --center_y -16.11 --center_z 53.21 --size_x 20 --size_y 20 --size_z 20

Example Dani ./prepare_ligand4.py -l T44.pdb OUTPUT:error. It looks like the PDB file is not right. I cannot do anything else here

./prepare_receptor4.py -r 1K0R_A.pdb LLamada real: /Users/danielgarijo/Downloads/mgltools_i86Darwin9_1.5.4/bin/pythonsh /Users/danielgarijo/Downloads/mgltools_i86Darwin9_1.5.4/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_receptor4.py -r 1K0R.pdb (NOTA: there is no _A file) OUTPUT: 1K0R.pdbqt

Error creating thumbnail: convert: unable to open image `/lfs1/www/html/site/wings/drugome/images/0/04/Script&ResultsConnection2.0.png': @ error/blob.c/OpenBlob/2588.
convert: unable to open file `/lfs1/www/html/site/wings/drugome/images/0/04/Script&ResultsConnection2.0.png' @ error/png.c/ReadPNGImage/3636.
convert: missing an image filename `/lfs1/www/html/site/wings/drugome/images/thumb/0/04/Script&ResultsConnection2.0.png/800px-Script&ResultsConnection2.0.png' @ error/convert.c/ConvertImageCommand/3015.

Legend: Green boxes are the steps already executed properly in WINGS. The FatCat needs a URL checker to make sure the packages in the list generated in the previous step have not been superseeded. Red boxes mean that there is something missing or that there is no script currently.

   1BVR_C-D-E-F	inhA	1UHO_LIG.VDN	CGMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE ....
   ./ligand_center.csh 1UHO_LIG.VDN-1BVR_CDEF.pdb VDN
   ./prepare_ligand4.py -l VDN.pdb (file obtained from step 4)
   ./prepare_receptor4.py -r 1BVR_F.pdb
A

In green are represented the sub workflows already working on Wings. In red the missing/scripts (or to do scripts). Note that some of the tools will not work in the Wings with mac (due to some compatibility issues), but the final version will be tested in Linux, where I have already tested all the scripts.

sudo csh ligand_center.csh 1BVR.pdb THT 

Output:

center_x =  27.1258
center_y =  -1.97632
center_z =  28.3574

This output is not written to a file, maybe additional scripts are needed?

./pythonsh /Users/danielgarijo/Downloads/mgltools_i86Darwin9_1.5.4/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_receptor.py -r
/Users/danielgarijo/Downloads/1BVR.pdb 
java -Xmx512M -jar cytoscape.jar -N /Users/danielgarijo/Desktop/graph_1e-5.gml
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The package that solves the problem with 3i3k is 3ld6. (Thanks to Sarah for her help with this issue)

All the results of this step have been reproduced

I've spent some time gathering and connecting all the scripts, inputs and outputs to know how the different steps are connected to each other. Also to identify the missing scripts between steps. The file can be watched below:

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FatCat is run with the next command:

sudo sh ./runFatcat.sh -alignPairs fatcat_list -pdbFilePath pdb_files -autoFetch true -outFile fatcat_output -printFatCat true

Input: fatcat_list: I have to investigate how the smap_output gets converted into this list.

Output: fatcat_output: I assume that this list is the one to go to the eHITS step

I think there are some necessary preprocessing steps. For the moment, the subworkflow looks like this figure:

FatCat Method.png

SMAP tested in Windows and in Linux, repeating successfully the first results in table S2 (2VBW_A-B with 1SN5_LIG.T3 and 2VBX_A-B with 1SN5_LIG.T3). In Linux it is required to install the qhull package and create soft links in the SMAP folder replacing the current ones (which don't work). In Mac I've tried to apply the same thing but it is still not working. However, since WINGs Marbles is in Linux, we don't need this step to be running on a Mac. Thus, we can conclude that the SMAP step is done.

sudo perl calc_lig_tanimotos 

Example:

Table value:

M.tb PDB code: 2VBW

Chains:A,B

Drug target PDB code: 1SN5

SMAP P-value: 6.08E-011

SMAP result: No hit found. Log:

SCORE_MATRIX = McLACHLAN
CONFORMER_UNIT_DIR = /Users/danielgarijo/WORK_ISI/smap_v2_0/conformerUnit
LIGAND_CONTACT_DISTANCE_CUTOFF = 10.0
Warn: PVALUE_CUTOFF is unknown. Set default value of 0.02
PRINT_PDB = false
Warn: PRINT_TEMPLATE_LIGAND is unknown. Set default true
Warn: PRINT_QUERY_LIGAND is unknown. Set default false
TEMPLATE_LIGAND_SITE_ONLY = true
Warn: QUERY_LIGAND_SITE_ONLY is unknown. Set default true
/Users/danielgarijo/WORK_ISI/smap_v2_0/conformerUnit/2VBW_.object
PdbLogger setting log level to: warn
/Users/danielgarijo/WORK_ISI/smap_v2_0/conformerUnit/1SN5_.object
No hit found

Command used:

sudo sh ./smap_comp.sh 2VBW 1SN5 outputprueba

I separated and fixed the sorting part from the SMAP perl script. Now the processing occurs according to the figure below.

The call to the script is made through the command line this way:

sudo perl  ./testDaniSORT.pl -l InputFromSarah/solved_tb_structures_listREDUCED.txt -d InputFromSarah/drug_binding_sites_listREDUCED.txt 
-o Output/smap_output_REDUCED -p 1e-5

Note: It can be optimized removing the drug binding sites list.

OpenBabel2.1.1 successfully installed: I just need the input parameters and datasets. Until I get more information about the process, inputs and outputs, the next figure explains this step.

Method8.png

Therefore, the SMAP subworkflow would be modified as follows:

Method 3v1.3.png

In WINGS it would be translated to 3 different components: SMAP for files, SMAP for chains and sorter.

SMAP seems to work with the command ./smap_comp.sh 1M44 1M44 output, but when running the perl script included in the file (after correcting a couple things in the syntax and libraries) it produces a exception. Still to be fixed. Also, the tables provided by Sarah look like the output of some preprocessing step. I still have to get the scripts form her.

SMAPS works. The script must be executed with admin permission

Therefore, the complete SMAP step is as follows:

Method 3v1.2.png

sudo perl ./run_smap.pl -l solved_tb_structures_list.txt -d drug_binding_sites_list.txt -o smap_output -p 1e-5
./smap_comp.sh 1M44 1M44 output

1M44 are the codes to be compared, and "output" is the name of the output file where the solution is stored. There is a perl script to run a lot of comparations, but I haven't figured out yet how should I pass the lists of codes.

Phase 1: Project Scoping

We will focus on 5 steps right now:

The next figure illustrates the modified subworkflow connection after the meeting:

ConnectionOfTheMethodsFIX.png

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