http://wiki.docking.org/api.php?action=feedcontributions&feedformat=atom&user=Shuogu 2026-04-05T09:32:59Z User contributions MediaWiki 1.39.1 http://wiki.docking.org/index.php?title=Interaction_Filtering&diff=13658 2021-08-18T01:54:17Z

<p>Shuogu: </p> <hr /> <div>This is Interaction Filtering version 1.1 (20200601). Please copy the code to your current directory.<br /> <br /> $ cp -r /mnt/nfs/home/sgu/code/interfilter .<br /> <br /> '''FIRST AND FOREMOST, if you find any version conflicts between python3 and python2, you need to comment out inside ~/.cshrc:''' # source /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/env.csh<br /> <br /> To run the code, you need to install OpenEye (version 2019.Oct.2) by following the instruction: https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html<br /> <br /> On our cluster, you may source my environment.<br /> $ source /nfs/home/sgu/anaconda3/etc/profile.d/conda.sh<br /> $ conda activate oepython<br /> $ source /nfs/soft/openeye/OpenEye-toolkits-python3-linux-x64-2019.10.2/env.sh<br /> <br /> Running the code:<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2<br /> If you want to have/avoid the interaction (hydrogen bond or salt bridge) for a specific residue (e.g. ASP115A, A means chain A):<br /> <br /> In rec.crg.pdb, some residue like HIS is converted to HID or HIE. Please use the converted name instead of HIS.<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A<br /> If you want to plot the paired/unpaired interaction (figure generation can be slow, but tens of thousands should be fine):<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A -plot<br /> <br /> [[File: Pair.png|thumb|center|500px|An example of paired interaction plot]]<br /> [[File: Unpair.png|thumb|center|500px|An example of unpaired interaction plot]]<br /> <br /> The output is a txt file, containing 15 columns:<br /> 1ligand 2clash 3hbond_clash+sbridge_clash 4unpairedl_donor+unpairedl_sbridge 5unpairedl_acceptor 6unpairedp_donor+unpairedp_acceptor 7unpairedp_sbridge 8contact 9hbond+hbond_nonideal 10hbond_ligand 11sbridge 12stacking 13cationpi 14halogen 15residue<br /> <br /> To filter out compounds, you may be interested in:<br /> <br /> '''Column3: #hydrogen bond clash + #salt bridge clash'''<br /> <br /> '''Column4: #unpaired ligand donor + #unpaired ligand salt bridge'''<br /> <br /> '''Column5: #unpaired ligand acceptor'''<br /> <br /> '''Column9: #hydrogen bond'''<br /> <br /> '''Column11: #salt bridge'''<br /> <br /> '''Column15: interaction (hydrogen bond or salt bridge) for you specified residue (0 means no, 1 means yes)'''<br /> <br /> $ awk '$3==0 &amp;&amp; $4==0 &amp;&amp; $5&lt;=3 &amp;&amp; $9+$11&gt;0' poses_noResidue_interaction_analysis.txt &gt; filtered.txt<br /> $ awk '$3==0 &amp;&amp; $4==0 &amp;&amp; $5&lt;=3 &amp;&amp; $9+$11&gt;0 &amp;&amp; $15&gt;0' poses_ASP115A_interaction_analysis.txt &gt; filtered.txt<br /> <br /> ---------------------------------------------------------------------------------------------------------------------------------------------<br /> 8/5/2020 Ying<br /> <br /> Collect 2D interaction plots into a html file:<br /> <br /> cd &lt;folder with png files&gt;<br /> python /nfs/home/yingyangg/scripts/plot_2Dinteraction_html.py<br /> <br /> 2Dinteraciton.html will be generated, and can be further converted to PDF via print.<br /> [[File: 2d_html.png|thumb|center|500px|2Dinteraction_html plot]]</div>

Shuogu http://wiki.docking.org/index.php?title=GPCR_Waiver_Wire&diff=13041 2020-10-22T05:40:06Z

<p>Shuogu: </p> <hr /> <div>When new projects come into the lab, the person on the top of the order gets first choice to either take or pass the project. The project will be moved down the order until it is claimed. Once a person claims a project, they will be moved to the bottom of the order. This process ideally ensures a fair process for determining who gets new projects and allows those that don't speak up as much to have a fair chance of getting a new, great project. Passing on a project will not effect the position in the order since not all projects are suitable for all persons. <br /> <br /> '''Brian reserves the right to change the order at any time for any reason, e.g. passing on too many projects, new member in lab getting bumped up, etc...'''<br /> <br /> == Updated guidelines: ==<br /> a. People get first refusal for projects in the order they are listed. If they choose and are placed on a project they go to the bottom of the list.<br /> <br /> b. Occasionally projects will come along where Brian feels someone has particular expertise or history. Brian reserves the right to over-rule the waiver list order in these circumstances.<br /> <br /> c. On the GPCR projects teams have worked out very well. There must be a more senior partner and a more junior partner in these collaborations, if only because there is only one first co-first author. To encourage collaboration, anyone who volunteers to be the more junior partner in a project will not lose their place on the waiver list. Please discuss with the senior partner first to ensure compatibility. <br /> <br /> ----<br /> <br /> == Project waiver order: ==<br /> <br /> *Chase Webb<br /> *Elissa Fink<br /> *Tia Tummino<br /> *Isha Singh<br /> *Shuo Gu<br /> *Anat Levit<br /> *Jiankun Lyu<br /> *Shiming Peng<br /> *Fangyu Liu<br /> *Matt Smith<br /> *Ying Yang<br /> *Brian Bender<br /> *Stefan Gahbauer<br /> <br /> [[Category:Obsolete]]</div>

Shuogu http://wiki.docking.org/index.php?title=GPCR_Waiver_Wire&diff=12926 2020-09-15T21:37:25Z

<p>Shuogu: /* Project waiver order: */</p> <hr /> <div>When new projects come into the lab, the person on the top of the order gets first choice to either take or pass the project. The project will be moved down the order until it is claimed. Once a person claims a project, they will be moved to the bottom of the order. This process ideally ensures a fair process for determining who gets new projects and allows those that don't speak up as much to have a fair chance of getting a new, great project. Passing on a project will not effect the position in the order since not all projects are suitable for all persons. <br /> <br /> '''Brian reserves the right to change the order at any time for any reason, e.g. passing on too many projects, new member in lab getting bumped up, etc...'''<br /> <br /> == Updated guidelines: ==<br /> a. People get first refusal for projects in the order they are listed. If they choose and are placed on a project they go to the bottom of the list.<br /> <br /> b. Occasionally projects will come along where Brian feels someone has particular expertise or history. Brian reserves the right to over-rule the waiver list order in these circumstances.<br /> <br /> c. On the GPCR projects teams have worked out very well. There must be a more senior partner and a more junior partner in these collaborations, if only because there is only one first co-first author. To encourage collaboration, anyone who volunteers to be the more junior partner in a project will not lose their place on the waiver list. Please discuss with the senior partner first to ensure compatibility. <br /> <br /> ----<br /> <br /> == Project waiver order: ==<br /> <br /> *Stefan Gahbauer<br /> *Chase Webb<br /> *Elissa Fink<br /> *Tia Tummino<br /> *Isha Singh<br /> *Shuo Gu<br /> *Anat Levit<br /> *Jiankun Lyu<br /> *Shiming Peng<br /> *Fangyu Liu<br /> *Matt Smith<br /> *Ying Yang<br /> *Brian Bender<br /> <br /> [[Category:Obsolete]]</div>

Shuogu http://wiki.docking.org/index.php?title=GPCR_Waiver_Wire&diff=12753 2020-07-08T20:45:48Z

<p>Shuogu: /* Project waiver order: */</p> <hr /> <div>When new projects come into the lab, the person on the top of the order gets first choice to either take or pass the project. The project will be moved down the order until it is claimed. Once a person claims a project, they will be moved to the bottom of the order. This process ideally ensures a fair process for determining who gets new projects and allows those that don't speak up as much to have a fair chance of getting a new, great project. Passing on a project will not effect the position in the order since not all projects are suitable for all persons. <br /> <br /> '''Brian reserves the right to change the order at any time for any reason, e.g. passing on too many projects, new member in lab getting bumped up, etc...'''<br /> <br /> == Updated guidelines: ==<br /> a. People get first refusal for projects in the order they are listed. If they choose and are placed on a project they go to the bottom of the list.<br /> <br /> b. Occasionally projects will come along where Brian feels someone has particular expertise or history. Brian reserves the right to over-rule the waiver list order in these circumstances.<br /> <br /> c. On the GPCR projects teams have worked out very well. There must be a more senior partner and a more junior partner in these collaborations, if only because there is only one first co-first author. To encourage collaboration, anyone who volunteers to be the more junior partner in a project will not lose their place on the waiver list. Please discuss with the senior partner first to ensure compatibility. <br /> <br /> ----<br /> <br /> == Project waiver order: ==<br /> <br /> *Stefan Gahbauer<br /> *Chase Webb<br /> *Elissa Fink<br /> *Tia Tummino<br /> *Isha Singh<br /> *Shuo Gu<br /> *Anat Levit<br /> *Jiankun Lyu<br /> *Shiming Peng<br /> *Matt Smith<br /> *Ying Yang<br /> *Brian Bender<br /> <br /> [[Category:Obsolete]]</div>

Shuogu http://wiki.docking.org/index.php?title=Interaction_Filtering&diff=12714 2020-06-18T09:33:23Z

<p>Shuogu: </p> <hr /> <div>This is Interaction Filtering version 1.1 (20200601). Please copy the code to your current directory.<br /> <br /> $ cp -r /mnt/nfs/home/sgu/code/interfilter .<br /> <br /> '''FIRST AND FOREMOST, if you find any version conflicts between python3 and python2, you need to comment out inside ~/.cshrc:''' # source /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/env.csh<br /> <br /> To run the code, you need to install OpenEye (version 2019.Oct.2) by following the instruction: https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html<br /> <br /> On our cluster, you may source my environment.<br /> $ source /nfs/home/sgu/anaconda3/etc/profile.d/conda.csh<br /> $ conda activate oepython<br /> $ source /nfs/soft/openeye/license.csh<br /> <br /> Running the code:<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2<br /> If you want to have/avoid the interaction (hydrogen bond or salt bridge) for a specific residue (e.g. ASP115A, A means chain A):<br /> <br /> In rec.crg.pdb, some residue like HIS is converted to HID or HIE. Please use the converted name instead of HIS.<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A<br /> If you want to plot the paired/unpaired interaction (figure generation can be slow, but tens of thousands should be fine):<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A -plot<br /> <br /> [[File: Pair.png|thumb|center|500px|An example of paired interaction plot]]<br /> [[File: Unpair.png|thumb|center|500px|An example of unpaired interaction plot]]<br /> <br /> The output is a txt file, containing 15 columns:<br /> 1ligand 2clash 3hbond_clash+sbridge_clash 4unpairedl_donor+unpairedl_sbridge 5unpairedl_acceptor 6unpairedp_donor+unpairedp_acceptor 7unpairedp_sbridge 8contact 9hbond+hbond_nonideal 10hbond_ligand 11sbridge 12stacking 13cationpi 14halogen 15residue<br /> <br /> To filter out compounds, you may be interested in:<br /> <br /> '''Column3: #hydrogen bond clash + #salt bridge clash'''<br /> <br /> '''Column4: #unpaired ligand donor + #unpaired ligand salt bridge'''<br /> <br /> '''Column5: #unpaired ligand acceptor'''<br /> <br /> '''Column9: #hydrogen bond'''<br /> <br /> '''Column11: #salt bridge'''<br /> <br /> '''Column15: interaction (hydrogen bond or salt bridge) for you specified residue (0 means no, 1 means yes)'''<br /> <br /> $ awk '$3==0 &amp;&amp; $4==0 &amp;&amp; $5&lt;=3 &amp;&amp; $9+$11&gt;0' poses_noResidue_interaction_analysis.txt &gt; filtered.txt<br /> $ awk '$3==0 &amp;&amp; $4==0 &amp;&amp; $5&lt;=3 &amp;&amp; $9+$11&gt;0 &amp;&amp; $15&gt;0' poses_ASP115A_interaction_analysis.txt &gt; filtered.txt</div>

Shuogu http://wiki.docking.org/index.php?title=Strain_Filtering&diff=12713 2020-06-17T21:55:25Z

<p>Shuogu: </p> <hr /> <div>This is Strain Filtering version 1.1 (20200218). Please copy the code to your current directory.<br /> $ cp -r /mnt/nfs/home/sgu/code/strainfilter .<br /> <br /> Furthermore, if you don't want to include the strain from hydrogens, you can try this version:<br /> $ cp -r /mnt/nfs/home/sgu/code/noh .<br /> <br /> <br /> To run the code, you need to install RDKit by following the instruction: https://www.rdkit.org/docs/Install.html<br /> <br /> On our cluster, you may source my environment.<br /> $ source /nfs/home/sgu/anaconda3/etc/profile.d/conda.csh<br /> $ conda activate my-rdkit-env<br /> <br /> Currently, the code can handle db2/db2.gz and mol2 inputs. For example:<br /> $ python Torsion_Strain.py test1.db2.gz<br /> $ python Torsion_Strain.py test2.mol2<br /> <br /> The output is a csv file, containing the total strain energy and detailed information of each dihedral sorted by its torsion energy.<br /> <br /> You may be interested in '''Column 2 (total strain energy) and Column 6 (the maximum dihedral torsion energy)''', from which you can choose different thresholds to filter compounds. e.g.<br /> $ awk -F&quot;,&quot; '$2&gt;0 &amp;&amp; $2&lt;6.5 &amp;&amp; $6&lt;1.8' test2_Torsion_Strain.csv &gt; filtered.csv<br /> This example uses awk to output all the compounds with total strain energy &lt;6.5 and every torsion energy &lt;1.8.</div>

Shuogu http://wiki.docking.org/index.php?title=Interaction_Filtering&diff=12712 2020-06-17T08:11:54Z

<p>Shuogu: </p> <hr /> <div>This is the 1st version (20200210) of Interaction Filtering. Please copy the code to your current directory.<br /> <br /> $ cp -r /mnt/nfs/home/sgu/code/interfilter .<br /> <br /> '''FIRST AND FOREMOST, if you find any version conflicts between python3 and python2, you need to comment out inside ~/.cshrc:''' # source /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/env.csh<br /> <br /> To run the code, you need to install OpenEye (version 2019.Oct.2) by following the instruction: https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html<br /> <br /> On our cluster, you may source my environment.<br /> $ source /nfs/home/sgu/anaconda3/etc/profile.d/conda.csh<br /> $ conda activate oepython<br /> $ source /nfs/soft/openeye/license.csh<br /> <br /> Running the code:<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2<br /> If you want to have/avoid the interaction (hydrogen bond or salt bridge) for a specific residue (e.g. ASP115A, A means chain A):<br /> <br /> In rec.crg.pdb, some residue like HIS is converted to HID or HIE. Please use the converted name instead of HIS.<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A<br /> If you want to plot the paired/unpaired interaction (figure generation can be slow, but tens of thousands should be fine):<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A -plot<br /> <br /> [[File: Pair.png|thumb|center|500px|An example of paired interaction plot]]<br /> [[File: Unpair.png|thumb|center|500px|An example of unpaired interaction plot]]<br /> <br /> The output is a txt file, containing 15 columns:<br /> 1ligand 2clash 3hbond_clash+sbridge_clash 4unpairedl_donor+unpairedl_sbridge 5unpairedl_acceptor 6unpairedp_donor+unpairedp_acceptor 7unpairedp_sbridge 8contact 9hbond+hbond_nonideal 10hbond_ligand 11sbridge 12stacking 13cationpi 14halogen 15residue<br /> <br /> To filter out compounds, you may be interested in:<br /> <br /> '''Column3: #hydrogen bond clash + #salt bridge clash'''<br /> <br /> '''Column4: #unpaired ligand donor + #unpaired ligand salt bridge'''<br /> <br /> '''Column9: #hydrogen bond'''<br /> <br /> '''Column11: #salt bridge'''<br /> <br /> '''Column15: interaction (hydrogen bond or salt bridge) for you specified residue (0 means no, 1 means yes)'''<br /> <br /> $ awk '$3==0 &amp;&amp; $4==0 &amp;&amp; $9+$11&gt;0' poses_noResidue_interaction_analysis.txt &gt; filtered.txt<br /> $ awk '$3==0 &amp;&amp; $4==0 &amp;&amp; $9+$11&gt;0 &amp;&amp; $15&gt;0' poses_ASP115A_interaction_analysis.txt &gt; filtered.txt</div>

Shuogu http://wiki.docking.org/index.php?title=GPCR_Waiver_Wire&diff=12693 2020-06-13T00:43:10Z

<p>Shuogu: </p> <hr /> <div>When new projects come into the lab, the person on the top of the order gets first choice to either take or pass the project. The project will be moved down the order until it is claimed. Once a person claims a project, they will be moved to the bottom of the order. This process ideally ensures a fair process for determining who gets new projects and allows those that don't speak up as much to have a fair chance of getting a new, great project. Passing on a project will not effect the position in the order since not all projects are suitable for all persons. <br /> <br /> '''Brian reserves the right to change the order at any time for any reason, e.g. passing on too many projects, new member in lab getting bumped up, etc...'''<br /> <br /> == Updated guidelines: ==<br /> a. People get first refusal for projects in the order they are listed. If they choose and are placed on a project they go to the bottom of the list.<br /> <br /> b. Occasionally projects will come along where Brian feels someone has particular expertise or history. Brian reserves the right to over-rule the waiver list order in these circumstances.<br /> <br /> c. On the GPCR projects teams have worked out very well. There must be a more senior partner and a more junior partner in these collaborations, if only because there is only one first co-first author. To encourage collaboration, anyone who volunteers to be the more junior partner in a project will not lose their place on the waiver list. Please discuss with the senior partner first to ensure compatibility. <br /> <br /> ----<br /> <br /> == Project waiver order: ==<br /> <br /> <br /> *Ying Yang<br /> *Brian Bender<br /> *Stefan Gahbauer<br /> *Chase Webb<br /> *Elissa Fink<br /> *Tia Tummino<br /> *Xiaobo Wan<br /> *Isha Singh<br /> *Shuo Gu<br /> *Anat Levit<br /> *Jiankun Lyu<br /> *Shiming Peng<br /> *Matt Smith<br /> <br /> <br /> [[Category:Obsolete]]</div>

Shuogu http://wiki.docking.org/index.php?title=GPCR_Waiver_Wire&diff=12497 2020-05-01T23:49:18Z

<p>Shuogu: </p> <hr /> <div>When new projects come into the lab, the person on the top of the order gets first choice to either take or pass the project. The project will be moved down the order until it is claimed. Once a person claims a project, they will be moved to the bottom of the order. This process ideally ensures a fair process for determining who gets new projects and allows those that don't speak up as much to have a fair chance of getting a new, great project. Passing on a project will not effect the position in the order since not all projects are suitable for all persons. <br /> <br /> '''Brian reserves the right to change the order at any time for any reason, e.g. passing on too many projects, new member in lab getting bumped up, etc...'''<br /> <br /> == Updated guidelines: ==<br /> a. People get first refusal for projects in the order they are listed. If they choose and are placed on a project they go to the bottom of the list.<br /> <br /> b. Occasionally projects will come along where Brian feels someone has particular expertise or history. Brian reserves the right to over-rule the waiver list order in these circumstances.<br /> <br /> c. On the GPCR projects teams have worked out very well. There must be a more senior partner and a more junior partner in these collaborations, if only because there is only one first co-first author. To encourage collaboration, anyone who volunteers to be the more junior partner in a project will not lose their place on the waiver list. Please discuss with the senior partner first to ensure compatibility. <br /> <br /> ----<br /> <br /> == Project waiver order: ==<br /> <br /> <br /> *Ying Yang<br /> *Shiming Peng<br /> *Chase Webb<br /> *Brian Bender<br /> *Stefan Gahbauer<br /> *Elissa Fink<br /> *Tia Tummino<br /> *Reed Stein<br /> *Xiaobo Wan<br /> *Isha Singh<br /> *Shuo Gu<br /> *Anat Levit<br /> *Jiankun Lyu<br /> <br /> <br /> [[Category:Obsolete]]</div>

Shuogu http://wiki.docking.org/index.php?title=Interaction_Filtering&diff=12302 2020-03-02T08:13:07Z

<p>Shuogu: </p> <hr /> <div>This is the 1st version (20200210) of Interaction Filtering. Please copy the code to your current directory.<br /> <br /> $ cp -r /mnt/nfs/home/sgu/code/interfilter .<br /> <br /> '''FIRST AND FOREMOST, if you find any version conflicts between python3 and python2, you need to comment out inside ~/.cshrc:''' # source /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/env.csh<br /> <br /> To run the code, you need to install OpenEye (version 2019.Oct.2) by following the instruction: https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html<br /> <br /> On our cluster, you may source my environment.<br /> $ source /nfs/home/sgu/anaconda3/etc/profile.d/conda.csh<br /> $ conda activate oepython<br /> $ source /nfs/soft/openeye/license.csh<br /> <br /> Running the code:<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2<br /> If you want to have/avoid the interaction (hydrogen bond or salt bridge) for a specific residue (e.g. ASP115A, A means chain A):<br /> <br /> In rec.crg.pdb, some residue like HIS is converted to HID or HIE. Please use the converted name instead of HIS.<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A<br /> If you want to plot the paired/unpaired interaction (figure generation can be slow, but tens of thousands should be fine):<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A -plot<br /> <br /> [[File: Pair.png|thumb|center|500px|An example of paired interaction plot]]<br /> [[File: Unpair.png|thumb|center|500px|An example of unpaired interaction plot]]<br /> <br /> The output is a txt file, containing 15 columns:<br /> 1ligand 2clash 3hbond_clash+sbridge_clash 4unpairedl_donor+unpairedl_sbridge 5unpairedl_acceptor 6unpairedp_donor+unpairedp_acceptor 7unpairedp_sbridge 8contact 9hbond+hbond_nonideal 10hbond_ligand 11sbridge 12stacking 13cationpi 14halogen 15residue<br /> <br /> To filter out compounds, you may be interested in:<br /> <br /> '''Column3: #hydrogen bond clash + #salt bridge clash'''<br /> <br /> '''Column4: #unpaired ligand donor + #unpaired ligand salt bridge'''<br /> <br /> '''Column9: #hydrogen bond + #non-ideal hydrogen bond'''<br /> <br /> '''Column11: #salt bridge'''<br /> <br /> '''Column15: interaction (hydrogen bond or salt bridge) for you specified residue (0 means no, 1 means yes)'''<br /> <br /> $ awk '$3==0 &amp;&amp; $4==0 &amp;&amp; $9+$11&gt;0' poses_noResidue_interaction_analysis.txt &gt; filtered.txt<br /> $ awk '$3==0 &amp;&amp; $4==0 &amp;&amp; $9+$11&gt;0 &amp;&amp; $15&gt;0' poses_ASP115A_interaction_analysis.txt &gt; filtered.txt</div>

Shuogu http://wiki.docking.org/index.php?title=Interaction_Filtering&diff=12301 2020-03-02T08:12:36Z

<p>Shuogu: </p> <hr /> <div>This is the 1st version (20200210) of Interaction Filtering. Please copy the code to your current directory.<br /> <br /> '''FIRST AND FOREMOST, if you find any version conflicts between python3 and python2, you need to comment out inside ~/.cshrc:''' # source /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/env.csh<br /> <br /> $ cp -r /mnt/nfs/home/sgu/code/interfilter .<br /> <br /> To run the code, you need to install OpenEye (version 2019.Oct.2) by following the instruction: https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html<br /> <br /> On our cluster, you may source my environment.<br /> $ source /nfs/home/sgu/anaconda3/etc/profile.d/conda.csh<br /> $ conda activate oepython<br /> $ source /nfs/soft/openeye/license.csh<br /> <br /> Running the code:<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2<br /> If you want to have/avoid the interaction (hydrogen bond or salt bridge) for a specific residue (e.g. ASP115A, A means chain A):<br /> <br /> In rec.crg.pdb, some residue like HIS is converted to HID or HIE. Please use the converted name instead of HIS.<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A<br /> If you want to plot the paired/unpaired interaction (figure generation can be slow, but tens of thousands should be fine):<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A -plot<br /> <br /> [[File: Pair.png|thumb|center|500px|An example of paired interaction plot]]<br /> [[File: Unpair.png|thumb|center|500px|An example of unpaired interaction plot]]<br /> <br /> The output is a txt file, containing 15 columns:<br /> 1ligand 2clash 3hbond_clash+sbridge_clash 4unpairedl_donor+unpairedl_sbridge 5unpairedl_acceptor 6unpairedp_donor+unpairedp_acceptor 7unpairedp_sbridge 8contact 9hbond+hbond_nonideal 10hbond_ligand 11sbridge 12stacking 13cationpi 14halogen 15residue<br /> <br /> To filter out compounds, you may be interested in:<br /> <br /> '''Column3: #hydrogen bond clash + #salt bridge clash'''<br /> <br /> '''Column4: #unpaired ligand donor + #unpaired ligand salt bridge'''<br /> <br /> '''Column9: #hydrogen bond + #non-ideal hydrogen bond'''<br /> <br /> '''Column11: #salt bridge'''<br /> <br /> '''Column15: interaction (hydrogen bond or salt bridge) for you specified residue (0 means no, 1 means yes)'''<br /> <br /> $ awk '$3==0 &amp;&amp; $4==0 &amp;&amp; $9+$11&gt;0' poses_noResidue_interaction_analysis.txt &gt; filtered.txt<br /> $ awk '$3==0 &amp;&amp; $4==0 &amp;&amp; $9+$11&gt;0 &amp;&amp; $15&gt;0' poses_ASP115A_interaction_analysis.txt &gt; filtered.txt</div>

Shuogu http://wiki.docking.org/index.php?title=Interaction_Filtering&diff=12300 2020-02-24T04:57:24Z

<p>Shuogu: </p> <hr /> <div>This is the 1st version (20200210) of Interaction Filtering. Please copy the code to your current directory.<br /> <br /> '''FIRST AND FOREMOST, if you find any version conflicts between python3 and python2, you need to comment out inside ~/.cshrc:''' # source /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/env.csh<br /> <br /> $ cp -r /mnt/nfs/home/sgu/code/interfilter .<br /> <br /> To run the code, you need to install OpenEye (version 2019.Oct.2) by following the instruction: https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html<br /> <br /> On our cluster, you may source my environment.<br /> $ source /nfs/home/sgu/anaconda3/etc/profile.d/conda.csh<br /> $ conda activate oepython<br /> $ source /nfs/soft/openeye/license.csh<br /> <br /> Running the code:<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2<br /> If you want to know the interaction (hydrogen bond or salt bridge) for a specific residue (e.g. ASP115A, A means chain A):<br /> <br /> In rec.crg.pdb, some residue like HIS is converted to HID or HIE. Please use the converted name instead of HIS.<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A<br /> If you want to plot the paired/unpaired interaction (figure generation can be slow, but tens of thousands should be fine):<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A -plot<br /> <br /> [[File: Pair.png|thumb|center|500px|An example of paired interaction plot]]<br /> [[File: Unpair.png|thumb|center|500px|An example of unpaired interaction plot]]<br /> <br /> The output is a txt file, containing 15 columns:<br /> 1ligand 2clash 3hbond_clash+sbridge_clash 4unpairedl_donor+unpairedl_sbridge 5unpairedl_acceptor 6unpairedp_donor+unpairedp_acceptor 7unpairedp_sbridge 8contact 9hbond+hbond_nonideal 10hbond_ligand 11sbridge 12stacking 13cationpi 14halogen 15residue<br /> <br /> To filter out compounds, you may be interested in:<br /> <br /> '''Column3: #hydrogen bond clash + #salt bridge clash'''<br /> <br /> '''Column4: #unpaired ligand donor + #unpaired ligand salt bridge'''<br /> <br /> '''Column9: #hydrogen bond + #non-ideal hydrogen bond'''<br /> <br /> '''Column11: #salt bridge'''<br /> <br /> '''Column15: interaction (hydrogen bond or salt bridge) for you specified residue (0 means no, 1 means yes)'''<br /> <br /> $ awk '$3==0 &amp;&amp; $4==0 &amp;&amp; $9+$11&gt;0' poses_noResidue_interaction_analysis.txt &gt; filtered.txt<br /> $ awk '$3==0 &amp;&amp; $4==0 &amp;&amp; $9+$11&gt;0 &amp;&amp; $15&gt;0' poses_ASP115A_interaction_analysis.txt &gt; filtered.txt</div>

Shuogu http://wiki.docking.org/index.php?title=Interaction_Filtering&diff=12299 2020-02-24T04:55:21Z

<p>Shuogu: </p> <hr /> <div>This is the 1st version (20200210) of Interaction Filtering. Please copy the code to your current directory.<br /> <br /> '''FIRST AND FOREMOST, if you find any version conflicts between python3 and python2, you need to comment out inside ~/.cshrc:''' # source /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/env.csh<br /> <br /> $ cp -r /mnt/nfs/home/sgu/code/interfilter .<br /> <br /> To run the code, you need to install OpenEye (version 2019.Oct.2) by following the instruction: https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html<br /> <br /> On our cluster, you may source my environment.<br /> $ source /nfs/home/sgu/anaconda3/etc/profile.d/conda.csh<br /> $ conda activate oepython<br /> $ source /nfs/soft/openeye/license.csh<br /> <br /> Running the code:<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2<br /> If you want to know the interaction (hydrogen bond or salt bridge) for a specific residue (e.g. ASP115A, A means chain A):<br /> <br /> In rec.crg.pdb, some residue like HIS is converted to HID or HIE. Please use the converted name instead of HIS.<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A<br /> If you want to plot the paired/unpaired interaction (figure generation can be slow, but tens of thousands should be fine):<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A -plot<br /> <br /> [[File: Pair.png|thumb|center|500px|An example of paired interaction plot]]<br /> [[File: Unpair.png|thumb|center|500px|An example of unpaired interaction plot]]<br /> <br /> The output is a txt file, containing 15 columns:<br /> 1ligand 2clash 3hbond_clash+sbridge_clash 4unpairedl_donor+unpairedl_sbridge 5unpairedl_acceptor 6unpairedp_donor+unpairedp_acceptor 7unpairedp_sbridge 8contact 9hbond+hbond_nonideal 10hbond_ligand 11sbridge 12stacking 13cationpi 14halogen 15residue<br /> <br /> To filter out compounds, you may be interested in:<br /> <br /> '''Column3: #hydrogen bond clash + #salt bridge clash'''<br /> <br /> '''Column4: #unpaired ligand donor + #unpaired ligand salt bridge'''<br /> <br /> '''Column9: #hydrogen bond + #non-ideal hydrogen bond'''<br /> <br /> '''Column11: #salt bridge'''<br /> <br /> '''Column15: interaction (hydrogen bond or salt bridge) for you specified residue (0 means no, 1 means yes)'''<br /> <br /> $ awk '$3==0 &amp;&amp; $4==0 &amp;&amp; $9+$11&gt;0 {print $0}' poses_noResidue_interaction_analysis.txt &gt; filtered.txt<br /> $ awk '$3==0 &amp;&amp; $4==0 &amp;&amp; $9+$11&gt;0 &amp;&amp; $15&gt;0 {print $0}' poses_ASP115A_interaction_analysis.txt &gt; filtered.txt</div>

Shuogu http://wiki.docking.org/index.php?title=Interaction_Filtering&diff=12298 2020-02-24T04:52:42Z

<p>Shuogu: </p> <hr /> <div>This is the 1st version (20200210) of Interaction Filtering. Please copy the code to your current directory.<br /> <br /> '''FIRST AND FOREMOST, if you find any version conflicts between python3 and python2, you need to comment out inside ~/.cshrc:''' # source /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/env.csh<br /> <br /> $ cp -r /mnt/nfs/home/sgu/code/interfilter .<br /> <br /> To run the code, you need to install OpenEye (version 2019.Oct.2) by following the instruction: https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html<br /> <br /> On our cluster, you may source my environment.<br /> $ source /nfs/home/sgu/anaconda3/etc/profile.d/conda.csh<br /> $ conda activate oepython<br /> $ source /nfs/soft/openeye/license.csh<br /> <br /> Running the code:<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2<br /> If you want to know the interaction (hydrogen bond or salt bridge) for a specific residue (e.g. ASP115A, A means chain A):<br /> <br /> In rec.crg.pdb, some residue like HIS is converted to HID or HIE. Please use the converted name instead of HIS.<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A<br /> If you want to plot the paired/unpaired interaction (figure generation can be slow, but tens of thousands should be fine):<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A -plot<br /> <br /> [[File: Pair.png|thumb|center|500px|An example of paired interaction plot]]<br /> [[File: Unpair.png|thumb|center|500px|An example of unpaired interaction plot]]<br /> <br /> The output is a txt file, containing 15 columns:<br /> 1ligand 2clash 3hbond_clash+sbridge_clash 4unpairedl_donor+unpairedl_sbridge 5unpairedl_acceptor 6unpairedp_donor+unpairedp_acceptor 7unpairedp_sbridge 8contact 9hbond+hbond_nonideal 10hbond_ligand 11sbridge 12stacking 13cationpi 14halogen 15residue<br /> <br /> To filter out compounds, you may be interested in:<br /> <br /> '''Column3: #hydrogen bond clash + #salt bridge clash'''<br /> <br /> '''Column4: #unpaired ligand donor + #unpaired ligand salt bridge'''<br /> <br /> '''Column9: #hydrogen bond + #non-ideal hydrogen bond'''<br /> <br /> '''Column11: #salt bridge'''<br /> <br /> '''Column15: interaction (hydrogen bond or salt bridge) for you specified residue (0 means no, 1 means yes)'''<br /> <br /> $ awk '$3==0 &amp;&amp; $4==0 &amp;&amp; $9+$11&gt;0 {print $0}'<br /> $ awk '$3==0 &amp;&amp; $4==0 &amp;&amp; $9+$11&gt;0 &amp;&amp; $15&gt;0 {print $0}' (if you provided residue)</div>

Shuogu http://wiki.docking.org/index.php?title=Interaction_Filtering&diff=12297 2020-02-24T04:52:14Z

<p>Shuogu: </p> <hr /> <div>This is the 1st version (20200210) of Interaction Filtering. Please copy the code to your current directory.<br /> <br /> '''FIRST AND FOREMOST, if you find any version conflicts between python3 and python2, you need to comment out inside ~/.cshrc:''' # source /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/env.csh<br /> <br /> $ cp -r /mnt/nfs/home/sgu/code/interfilter .<br /> <br /> To run the code, you need to install OpenEye (version 2019.Oct.2) by following the instruction: https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html<br /> <br /> On our cluster, you may source my environment.<br /> $ source /nfs/home/sgu/anaconda3/etc/profile.d/conda.csh<br /> $ conda activate oepython<br /> $ source /nfs/soft/openeye/license.csh<br /> <br /> Running the code:<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2<br /> If you want to know the interaction (hydrogen bond or salt bridge) for a specific residue (e.g. ASP115A, A means chain A):<br /> <br /> In rec.crg.pdb, some residue like HIS is converted to HID or HIE. Please use the converted name instead of HIS.<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A<br /> If you want to plot the paired/unpaired interaction (figure generation can be slow, but tens of thousands should be fine):<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A -plot<br /> <br /> [[File: Pair.png|thumb|center|500px|An example of paired interaction plot]]<br /> [[File: Unpair.png|thumb|center|500px|An example of unpaired interaction plot]]<br /> <br /> The output is a txt file, containing 15 columns:<br /> 1ligand 2clash 3hbond_clash+sbridge_clash 4unpairedl_donor+unpairedl_sbridge 5unpairedl_acceptor 6unpairedp_donor+unpairedp_acceptor 7unpairedp_sbridge 8contact 9hbond+hbond_nonideal 10hbond_ligand 11sbridge 12stacking 13cationpi 14halogen 15residue<br /> <br /> To filter out compounds, you may be interested in:<br /> <br /> '''Column3: #hydrogen bond clash + #salt bridge clash'''<br /> <br /> '''Column4: #unpaired ligand donor + #unpaired ligand salt bridge'''<br /> <br /> '''Column9: #hydrogen bond + #non-ideal hydrogen bond'''<br /> <br /> '''Column11: #salt bridge'''<br /> <br /> '''Column15: interaction (hydrogen bond or salt bridge) for you specified residue (0 means no, 1 means yes)'''<br /> <br /> $ awk '$3==0 &amp;&amp; $4==0 &amp;&amp; $9+$11&gt;0 {print $0}'<br /> $ awk '$3==0 &amp;&amp; $4==0 &amp;&amp; $9+$11&gt;0 &amp;&amp; $15&gt;0 {print $0}' (if you provided residue)</div>

Shuogu http://wiki.docking.org/index.php?title=Interaction_Filtering&diff=12296 2020-02-24T04:51:57Z

<p>Shuogu: </p> <hr /> <div>This is the 1st version (20200210) of Interaction Filtering. Please copy the code to your current directory.<br /> <br /> '''FIRST AND FOREMOST, if you find any version conflicts between python3 and python2, you need to comment out inside ~/.cshrc:''' # source /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/env.csh<br /> <br /> $ cp -r /mnt/nfs/home/sgu/code/interfilter .<br /> <br /> To run the code, you need to install OpenEye (version 2019.Oct.2) by following the instruction: https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html<br /> <br /> On our cluster, you may source my environment.<br /> $ source /nfs/home/sgu/anaconda3/etc/profile.d/conda.csh<br /> $ conda activate oepython<br /> $ source /nfs/soft/openeye/license.csh<br /> <br /> Running the code:<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2<br /> If you want to know the interaction (hydrogen bond or salt bridge) for a specific residue (e.g. ASP115A, A means chain A):<br /> <br /> In rec.crg.pdb, some residue like HIS is converted to HID or HIE. Please use the converted name instead of HIS.<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A<br /> If you want to plot the paired/unpaired interaction (figure generation can be slow, but tens of thousands should be fine):<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A -plot<br /> <br /> [[File: Pair.png|thumb|center|500px|An example of paired interaction plot]]<br /> [[File: Unpair.png|thumb|center|500px|An example of unpaired interaction plot]]<br /> <br /> The output is a txt file, containing 15 columns:<br /> 1ligand 2clash 3hbond_clash+sbridge_clash 4unpairedl_donor+unpairedl_sbridge 5unpairedl_acceptor 6unpairedp_donor+unpairedp_acceptor 7unpairedp_sbridge 8contact 9hbond+hbond_nonideal 10hbond_ligand 11sbridge 12stacking 13cationpi 14halogen 15residue<br /> <br /> To filter out compounds, you may be interested in:<br /> <br /> '''Column3: #hydrogen bond clash + #salt bridge clash'''<br /> <br /> '''Column4: #unpaired ligand donor + #unpaired ligand salt bridge'''<br /> <br /> '''Column9: #hydrogen bond + #non-ideal hydrogen bond'''<br /> <br /> '''Column11: #salt bridge'''<br /> <br /> '''Column15: interaction (hydrogen bond or salt bridge) for you specified residue (0 means no, 1 means yes)'''<br /> $ awk '$3==0 &amp;&amp; $4==0 &amp;&amp; $9+$11&gt;0 {print $0}'<br /> $ awk '$3==0 &amp;&amp; $4==0 &amp;&amp; $9+$11&gt;0 &amp;&amp; $15&gt;0 {print $0}' (if you provided residue)</div>

Shuogu http://wiki.docking.org/index.php?title=Interaction_Filtering&diff=12295 2020-02-24T02:16:24Z

<p>Shuogu: </p> <hr /> <div>This is the 1st version (20200210) of Interaction Filtering. Please copy the code to your current directory.<br /> <br /> '''FIRST AND FOREMOST, if you find any version conflicts between python3 and python2, you need to comment out inside ~/.cshrc:''' # source /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/env.csh<br /> <br /> $ cp -r /mnt/nfs/home/sgu/code/interfilter .<br /> <br /> To run the code, you need to install OpenEye (version 2019.Oct.2) by following the instruction: https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html<br /> <br /> On our cluster, you may source my environment.<br /> $ source /nfs/home/sgu/anaconda3/etc/profile.d/conda.csh<br /> $ conda activate oepython<br /> $ source /nfs/soft/openeye/license.csh<br /> <br /> Running the code:<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2<br /> If you want to know the interaction (hydrogen bond or salt bridge) for a specific residue (e.g. ASP115A, A means chain A):<br /> <br /> In rec.crg.pdb, some residue like HIS is converted to HID or HIE. Please use the converted name instead of HIS.<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A<br /> If you want to plot the paired/unpaired interaction (figure generation can be slow, but tens of thousands should be fine):<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A -plot<br /> <br /> [[File: Pair.png|thumb|center|500px|An example of paired interaction plot]]<br /> [[File: Unpair.png|thumb|center|500px|An example of unpaired interaction plot]]<br /> <br /> The output is a txt file, containing 15 columns:<br /> 1ligand 2clash 3hbond_clash+sbridge_clash 4unpairedl_donor+unpairedl_sbridge 5unpairedl_acceptor 6unpairedp_donor+unpairedp_acceptor 7unpairedp_sbridge 8contact 9hbond+hbond_nonideal 10hbond_ligand 11sbridge 12stacking 13cationpi 14halogen 15residue<br /> <br /> To filter out compounds, you may be interested in:<br /> <br /> '''Column3: #hydrogen bond clash + #salt bridge clash'''<br /> <br /> '''Column4: #unpaired ligand donor + #unpaired ligand salt bridge'''<br /> <br /> '''Column9: #hydrogen bond + #non-ideal hydrogen bond'''<br /> <br /> '''Column11: #salt bridge'''<br /> <br /> '''Column15: interaction (hydrogen bond or salt bridge) for you specified residue (0 means no, 1 means yes)'''</div>

Shuogu http://wiki.docking.org/index.php?title=Strain_Filtering&diff=12291 2020-02-18T23:01:28Z

<p>Shuogu: </p> <hr /> <div>This is Strain Filtering version 1.1 (20200218). Please copy the code to your current directory.<br /> $ cp -r /mnt/nfs/home/sgu/code/strainfilter .<br /> <br /> To run the code, you need to install RDKit by following the instruction: https://www.rdkit.org/docs/Install.html<br /> <br /> On our cluster, you may source my environment.<br /> $ source /nfs/home/sgu/anaconda3/etc/profile.d/conda.csh<br /> $ conda activate my-rdkit-env<br /> <br /> Currently, the code can handle db2/db2.gz and mol2 inputs. For example:<br /> $ python Torsion_Strain.py test1.db2.gz<br /> $ python Torsion_Strain.py test2.mol2<br /> <br /> The output is a csv file, containing the total strain energy and detailed information of each dihedral sorted by its torsion energy.<br /> <br /> You may be interested in '''Column 2 (total strain energy) and Column 6 (the maximum dihedral torsion energy)''', from which you can choose different thresholds to filter compounds. e.g.<br /> $ awk -F&quot;,&quot; '$2&gt;0 &amp;&amp; $2&lt;6.5 &amp;&amp; $6&lt;1.8' test2_Torsion_Strain.csv &gt; filtered.csv<br /> This example uses awk to output all the compounds with total strain energy &lt;6.5 and every torsion energy &lt;1.8.</div>

Shuogu http://wiki.docking.org/index.php?title=Interaction_Filtering&diff=12290 2020-02-18T22:59:08Z

<p>Shuogu: </p> <hr /> <div>This is the 1st version (20200210) of Interaction Filtering. Please copy the code to your current directory.<br /> <br /> '''FIRST AND FOREMOST, if you find any version conflicts between python3 and python2, you need to comment out inside ~/.cshrc:''' # source /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/env.csh<br /> <br /> $ cp -r /mnt/nfs/home/sgu/code/interfilter .<br /> <br /> To run the code, you need to install OpenEye (version 2019.Oct.2) by following the instruction: https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html<br /> <br /> On our cluster, you may source my environment.<br /> $ source /nfs/home/sgu/anaconda3/etc/profile.d/conda.csh<br /> $ conda activate oepython<br /> $ setenv OE_LICENSE /nfs/soft/openeye/oe_license.txt<br /> <br /> Running the code:<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2<br /> If you want to know the interaction (hydrogen bond or salt bridge) for a specific residue (e.g. ASP115A, A means chain A):<br /> <br /> In rec.crg.pdb, some residue like HIS is converted to HID or HIE. Please use the converted name instead of HIS.<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A<br /> If you want to plot the paired/unpaired interaction (figure generation can be slow, but tens of thousands should be fine):<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A -plot<br /> <br /> [[File: Pair.png|thumb|center|500px|An example of paired interaction plot]]<br /> [[File: Unpair.png|thumb|center|500px|An example of unpaired interaction plot]]<br /> <br /> The output is a txt file, containing 15 columns:<br /> 1ligand 2clash 3hbond_clash+sbridge_clash 4unpairedl_donor+unpairedl_sbridge 5unpairedl_acceptor 6unpairedp_donor+unpairedp_acceptor 7unpairedp_sbridge 8contact 9hbond+hbond_nonideal 10hbond_ligand 11sbridge 12stacking 13cationpi 14halogen 15residue<br /> <br /> To filter out compounds, you may be interested in:<br /> <br /> '''Column3: #hydrogen bond clash + #salt bridge clash'''<br /> <br /> '''Column4: #unpaired ligand donor + #unpaired ligand salt bridge'''<br /> <br /> '''Column9: #hydrogen bond + #non-ideal hydrogen bond'''<br /> <br /> '''Column11: #salt bridge'''<br /> <br /> '''Column15: interaction (hydrogen bond or salt bridge) for you specified residue (0 means no, 1 means yes)'''</div>

Shuogu http://wiki.docking.org/index.php?title=Strain_Filtering&diff=12289 2020-02-18T08:45:24Z

<p>Shuogu: </p> <hr /> <div>This is Strain Filtering version 1.1 (20200211). Please copy the code to your current directory.<br /> $ cp -r /mnt/nfs/home/sgu/code/strainfilter .<br /> <br /> To run the code, you need to install RDKit by following the instruction: https://www.rdkit.org/docs/Install.html<br /> <br /> On our cluster, you may source my environment.<br /> $ source /nfs/home/sgu/anaconda3/etc/profile.d/conda.csh<br /> $ conda activate my-rdkit-env<br /> <br /> Currently, the code can handle db2/db2.gz and mol2 inputs. For example:<br /> $ python Torsion_Strain.py test1.db2.gz<br /> $ python Torsion_Strain.py test2.mol2<br /> <br /> The output is a csv file, containing the total strain energy and detailed information of each dihedral sorted by its torsion energy.<br /> <br /> You may be interested in '''Column 2 (total strain energy) and Column 6 (the maximum dihedral torsion energy)''', from which you can choose different thresholds to filter compounds. e.g.<br /> $ awk -F&quot;,&quot; '$2&gt;0 &amp;&amp; $2&lt;6.5 &amp;&amp; $6&lt;1.8' test2_Torsion_Strain.csv &gt; filtered.csv<br /> This example uses awk to output all the compounds with total strain energy &lt;6.5 and every torsion energy &lt;1.8.</div>

Shuogu http://wiki.docking.org/index.php?title=Strain_Filtering&diff=12288 2020-02-18T08:44:46Z

<p>Shuogu: </p> <hr /> <div>This is Strain Filtering version 1.1 (20200211). Please copy the code to your current directory.<br /> $ cp -r /mnt/nfs/home/sgu/code/strainfilter .<br /> <br /> To run the code, you need to install RDKit by following the instruction: https://www.rdkit.org/docs/Install.html<br /> <br /> On our cluster, you may source my environment.<br /> $ source /nfs/home/sgu/anaconda3/etc/profile.d/conda.csh<br /> $ conda activate my-rdkit-env<br /> <br /> Currently, the code can handle db2/db2.gz and mol2 inputs. For example:<br /> $ python Torsion_Strain.py test1.db2.gz<br /> $ python Torsion_Strain.py test2.mol2<br /> <br /> The output is a csv file, containing the total strain energy and detailed information of each dihedral sorted by its torsion energy.<br /> <br /> You may be interested in '''Column 2 (total strain energy) and Column 6 (the maximum dihedral torsion energy)''', from which you can choose different thresholds to filter compounds. e.g.<br /> $ awk -F&quot;,&quot; '$2&gt;0 &amp;&amp; $2&lt;6.5 &amp;&amp; $6&lt;1.8' test2_Torsion_Strain.csv<br /> This example uses awk to output all the compounds with total strain energy &lt;6.5 and every torsion energy &lt;1.8.</div>

Shuogu http://wiki.docking.org/index.php?title=Strain_Filtering&diff=12287 2020-02-18T08:44:32Z

<p>Shuogu: </p> <hr /> <div>This is Strain Filtering version 1.1 (20200211). Please copy the code to your current directory.<br /> $ cp -r /mnt/nfs/home/sgu/code/strainfilter .<br /> <br /> To run the code, you need to install RDKit by following the instruction: https://www.rdkit.org/docs/Install.html<br /> <br /> On our cluster, you may source my environment.<br /> $ source /nfs/home/sgu/anaconda3/etc/profile.d/conda.csh<br /> $ conda activate my-rdkit-env<br /> <br /> Currently, the code can handle db2/db2.gz and mol2 inputs. For example:<br /> $ python Torsion_Strain.py test1.db2.gz<br /> $ python Torsion_Strain.py test2.mol2<br /> <br /> The output is a csv file, containing the total strain energy and detailed information of each dihedral sorted by its torsion energy.<br /> <br /> You may be interested in '''Column 2 (total strain energy) and Column 6 (the maximum dihedral torsion energy)''', from which you can choose different thresholds to filter compounds. e.g.<br /> $ awk -F&quot;,&quot; '$2 &gt; 0 &amp;&amp; $2&lt;6.5 &amp;&amp; $6&lt;1.8' test2_Torsion_Strain.csv<br /> This example uses awk to output all the compounds with total strain energy &lt;6.5 and every torsion energy &lt;1.8.</div>

Shuogu http://wiki.docking.org/index.php?title=Interaction_Filtering&diff=12286 2020-02-18T07:40:02Z

<p>Shuogu: </p> <hr /> <div>This is the 1st version (20200210) of Interaction Filtering. Please copy the code to your current directory.<br /> <br /> '''FIRST AND FOREMOST, if you find any version conflicts between python3 and python2, you need to comment out inside ~/.cshrc:''' # source /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/env.csh<br /> <br /> $ cp -r /mnt/nfs/home/sgu/code/interfilter .<br /> <br /> To run the code, you need to install OpenEye (version 2019.Oct.2) by following the instruction: https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html<br /> <br /> On our cluster, you may source my environment.<br /> $ source /nfs/home/sgu/anaconda3/etc/profile.d/conda.csh<br /> $ conda activate oepython<br /> $ setenv OE_LICENSE /nfs/soft/openeye/oe_license.txt<br /> <br /> Running the code:<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2<br /> If you want to know the interaction (hydrogen bond or salt bridge) for a specific residue (e.g. ASP115A, A means chain A):<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A<br /> If you want to plot the paired/unpaired interaction (figure generation can be slow, but tens of thousands should be fine):<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A -plot<br /> <br /> [[File: Pair.png|thumb|center|500px|An example of paired interaction plot]]<br /> [[File: Unpair.png|thumb|center|500px|An example of unpaired interaction plot]]<br /> <br /> The output is a txt file, containing 15 columns:<br /> 1ligand 2clash 3hbond_clash+sbridge_clash 4unpairedl_donor+unpairedl_sbridge 5unpairedl_acceptor 6unpairedp_donor+unpairedp_acceptor 7unpairedp_sbridge 8contact 9hbond+hbond_nonideal 10hbond_ligand 11sbridge 12stacking 13cationpi 14halogen 15residue<br /> <br /> To filter out compounds, you may be interested in:<br /> <br /> '''Column3: #hydrogen bond clash + #salt bridge clash'''<br /> <br /> '''Column4: #unpaired ligand donor + #unpaired ligand salt bridge'''<br /> <br /> '''Column9: #hydrogen bond + #non-ideal hydrogen bond'''<br /> <br /> '''Column11: #salt bridge'''<br /> <br /> '''Column15: interaction for you specified residue (0 means no, 1 means yes)'''</div>

Shuogu http://wiki.docking.org/index.php?title=Strain_Filtering&diff=12285 2020-02-15T10:10:21Z

<p>Shuogu: </p> <hr /> <div>This is Strain Filtering version 1.1 (20200211). Please copy the code to your current directory.<br /> $ cp -r /mnt/nfs/home/sgu/code/strainfilter .<br /> <br /> To run the code, you need to install RDKit by following the instruction: https://www.rdkit.org/docs/Install.html<br /> <br /> On our cluster, you may source my environment.<br /> $ source /nfs/home/sgu/anaconda3/etc/profile.d/conda.csh<br /> $ conda activate my-rdkit-env<br /> <br /> Currently, the code can handle db2/db2.gz and mol2 inputs. For example:<br /> $ python Torsion_Strain.py test1.db2.gz<br /> $ python Torsion_Strain.py test2.mol2<br /> <br /> The output is a csv file, containing the total strain energy and detailed information of each dihedral sorted by its torsion energy.<br /> <br /> You may be interested in '''Column 2 (total strain energy) and Column 6 (the maximum dihedral torsion energy)''', from which you can choose different thresholds to filter compounds. e.g.<br /> $ awk -F&quot;,&quot; '$2&lt;6.5 &amp;&amp; $6&lt;1.8' test2_Torsion_Strain.csv<br /> This example uses awk to output all the compounds with total strain energy &lt;6.5 and every torsion energy &lt;1.8.</div>

Shuogu http://wiki.docking.org/index.php?title=Interaction_Filtering&diff=12284 2020-02-15T10:06:50Z

<p>Shuogu: </p> <hr /> <div>This is the 1st version (20200210) of Interaction Filtering. Please copy the code to your current directory.<br /> <br /> '''FIRST AND FOREMOST, if you find any version conflicts between python3 and python2, you need to comment out inside ~/.cshrc:''' # source /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/env.csh<br /> <br /> $ cp -r /mnt/nfs/home/sgu/code/interfilter .<br /> <br /> To run the code, you need to install OpenEye (version 2019.Oct.2) by following the instruction: https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html<br /> <br /> On our cluster, you may source my environment.<br /> $ source /nfs/home/sgu/anaconda3/etc/profile.d/conda.csh<br /> $ conda activate oepython<br /> $ setenv OE_LICENSE /nfs/soft/openeye/oe_license.txt<br /> <br /> Running the code:<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2<br /> If you want to know the interaction for a specific residue (e.g. ASP115A, A means chain A):<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A<br /> If you want to plot the paired/unpaired interaction (figure generation can be slow, but tens of thousands should be fine):<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A -plot<br /> <br /> [[File: Pair.png|thumb|center|500px|An example of paired interaction plot]]<br /> [[File: Unpair.png|thumb|center|500px|An example of unpaired interaction plot]]<br /> <br /> The output is a txt file, containing 15 columns:<br /> 1ligand 2clash 3hbond_clash+sbridge_clash 4unpairedl_donor+unpairedl_sbridge 5unpairedl_acceptor 6unpairedp_donor+unpairedp_acceptor 7unpairedp_sbridge 8contact 9hbond+hbond_nonideal 10hbond_ligand 11sbridge 12stacking 13cationpi 14halogen 15residue<br /> <br /> To filter out compounds, you may be interested in:<br /> <br /> '''Column3: #hydrogen bond clash + #salt bridge clash'''<br /> <br /> '''Column4: #unpaired ligand donor + #unpaired ligand salt bridge'''<br /> <br /> '''Column9: #hydrogen bond + #non-ideal hydrogen bond'''<br /> <br /> '''Column11: #salt bridge'''<br /> <br /> '''Column15: interaction for you specified residue (0 means no, 1 means yes)'''</div>

Shuogu http://wiki.docking.org/index.php?title=Interaction_Filtering&diff=12283 2020-02-15T03:13:08Z

<p>Shuogu: </p> <hr /> <div>This is the 1st version (20200210) of Interaction Filtering. Please copy the code to your current directory.<br /> <br /> '''FIRST AND FOREMOST, If you find any version conflicts between python3 and python2, you need to comment out inside ~/.cshrc:''' # source /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/env.csh<br /> <br /> $ cp -r /mnt/nfs/home/sgu/code/interfilter .<br /> <br /> To run the code, you need OpenEye (version 2019.Oct.2). You can follow the instruction to install: https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html<br /> <br /> On our cluster, you may source my environment.<br /> $ source /nfs/home/sgu/anaconda3/etc/profile.d/conda.csh<br /> $ conda activate oepython<br /> $ setenv OE_LICENSE /nfs/soft/openeye/oe_license.txt<br /> <br /> Running the code:<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2<br /> If you want to know the interaction for a specific residue (e.g. ASP115A, A means chain A):<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A<br /> If you want to plot the paired/unpaired interaction (figure generation can be slow, but tens of thousands should be fine):<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A -plot<br /> <br /> [[File: Pair.png|thumb|center|500px|An example of paired interaction plot]]<br /> [[File: Unpair.png|thumb|center|500px|An example of unpaired interaction plot]]<br /> <br /> The output is a txt file, containing 15 columns:<br /> 1ligand 2clash 3hbond_clash+sbridge_clash 4unpairedl_donor+unpairedl_sbridge 5unpairedl_acceptor 6unpairedp_donor+unpairedp_acceptor 7unpairedp_sbridge 8contact 9hbond+hbond_nonideal 10hbond_ligand 11sbridge 12stacking 13cationpi 14halogen 15residue<br /> <br /> To filter out compounds, you may be interested in:<br /> <br /> '''Column3: #hydrogen bond clash + #salt bridge clash'''<br /> <br /> '''Column4: #unpaired ligand donor + #unpaired ligand salt bridge'''<br /> <br /> '''Column9: #hydrogen bond + #non-ideal hydrogen bond'''<br /> <br /> '''Column11: #salt bridge'''<br /> <br /> '''Column15: interaction for you specified residue (0 means no, 1 means yes)'''</div>

Shuogu http://wiki.docking.org/index.php?title=Interaction_Filtering&diff=12282 2020-02-15T03:12:45Z

<p>Shuogu: </p> <hr /> <div>This is the 1st version (20200210) of Interaction Filtering. Please copy the code to your current directory.<br /> <br /> '''FIRST AND FOREMOST, If you find any version conflicts between python3 and python2, you need to comment out inside ~/.cshrc:''' # source /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/env.csh<br /> <br /> $ cp -r /mnt/nfs/home/sgu/code/interfilter .<br /> <br /> To run the code, you need OpenEye (version 2019.Oct.2). You can follow the instruction to install: https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html<br /> <br /> On our cluster, you may source my environment.<br /> $ source /nfs/home/sgu/anaconda3/etc/profile.d/conda.csh<br /> $ conda activate oepython<br /> $ setenv OE_LICENSE /nfs/soft/openeye/oe_license.txt<br /> <br /> Running the code:<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2<br /> If you want to know the interaction for a specific residue (e.g. ASP115A, A means chain A):<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A<br /> If you want to plot the paired/unpaired interaction (figure generation can be slow, but tens of thousands should be fine):<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A -plot<br /> <br /> [[File: Pair.png|thumb|center|500px|An example of paired interaction plot]]<br /> [[File: Unpair.png|thumb|center|500px|An example of unpaired interaction plot]]<br /> <br /> The output is a txt file, containing 15 columns:<br /> 1ligand 2clash 3hbond_clash+sbridge_clash 4unpairedl_donor+unpairedl_sbridge 5unpairedl_acceptor 6unpairedp_donor+unpairedp_acceptor 7unpairedp_sbridge 8contact 9hbond+hbond_nonideal 10hbond_ligand 11sbridge 12stacking 13cationpi 14halogen 15residue<br /> <br /> To filter out compounds, you may be interested in:<br /> <br /> '''Column3: #hydrogen bond clash + #salt bridge clash<br /> <br /> Column4: #unpaired ligand donor + #unpaired ligand salt bridge<br /> <br /> Column9: #hydrogen bond + #non-ideal hydrogen bond<br /> <br /> Column11: #salt bridge<br /> <br /> Column15: interaction for you specified residue (0 means no, 1 means yes)'''</div>

Shuogu http://wiki.docking.org/index.php?title=Interaction_Filtering&diff=12281 2020-02-15T03:11:34Z

<p>Shuogu: </p> <hr /> <div>This is the 1st version (20200210) of Interaction Filtering. Please copy the code to your current directory.<br /> <br /> '''FIRST AND FOREMOST, If you find any version conflicts between python3 and python2, you need to comment out inside ~/.cshrc:''' # source /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/env.csh<br /> <br /> $ cp -r /mnt/nfs/home/sgu/code/interfilter .<br /> <br /> To run the code, you need OpenEye (version 2019.Oct.2). You can follow the instruction to install: https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html<br /> <br /> On our cluster, you may source my environment.<br /> $ source /nfs/home/sgu/anaconda3/etc/profile.d/conda.csh<br /> $ conda activate oepython<br /> $ setenv OE_LICENSE /nfs/soft/openeye/oe_license.txt<br /> <br /> Running the code:<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2<br /> If you want to know the interaction for a specific residue (e.g. ASP115A, A means chain A):<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A<br /> If you want to plot the paired/unpaired interaction (figure generation can be slow, but tens of thousands should be fine):<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A -plot<br /> <br /> [[File: Pair.png|thumb|center|500px|An example of paired interaction plot]]<br /> [[File: Unpair.png|thumb|center|500px|An example of unpaired interaction plot]]<br /> <br /> The output is a txt file, containing 15 columns:<br /> 1ligand 2clash 3hbond_clash+sbridge_clash 4unpairedl_donor+unpairedl_sbridge 5unpairedl_acceptor 6unpairedp_donor+unpairedp_acceptor 7unpairedp_sbridge 8contact 9hbond+hbond_nonideal 10hbond_ligand 11sbridge 12stacking 13cationpi 14halogen 15residue<br /> <br /> To filter out compounds, you may be interested in:<br /> <br /> '''Column3''': #hydrogen bond clash + #salt bridge clash<br /> <br /> '''Column4''': #unpaired ligand donor + #unpaired ligand salt bridge<br /> <br /> '''Column9''': #hydrogen bond + #non-ideal hydrogen bond<br /> <br /> '''Column11''': #salt bridge<br /> <br /> '''Column15''': interaction for you specified residue (0 means no, 1 means yes)</div>

Shuogu http://wiki.docking.org/index.php?title=Strain_Filtering&diff=12280 2020-02-15T03:10:46Z

<p>Shuogu: </p> <hr /> <div>This is Strain Filtering version 1.1 (20200211). Please copy the code to your current directory.<br /> $ cp -r /mnt/nfs/home/sgu/code/strainfilter .<br /> <br /> To run the code, you need RDKit. You can follow the instruction to install RDKit: https://www.rdkit.org/docs/Install.html<br /> <br /> On our cluster, you may source my environment.<br /> $ source /nfs/home/sgu/anaconda3/etc/profile.d/conda.csh<br /> $ conda activate my-rdkit-env<br /> <br /> Currently, the code can handle db2/db2.gz and mol2 inputs. For example:<br /> $ python Torsion_Strain.py test1.db2.gz<br /> $ python Torsion_Strain.py test2.mol2<br /> <br /> The output is a csv file, containing the total strain energy and detailed information of each dihedral sorted by its torsion energy.<br /> <br /> You may be interested in '''Column 2 (total strain energy) and Column 6 (the maximum dihedral torsion energy)''', from which you can choose different thresholds to filter compounds. e.g.<br /> $ awk -F&quot;,&quot; '$2&lt;6.5 &amp;&amp; $6&lt;1.8' test2_Torsion_Strain.csv<br /> This example uses awk to output all the compounds with total strain energy &lt;6.5 and every torsion energy &lt;1.8.</div>

Shuogu http://wiki.docking.org/index.php?title=Interaction_Filtering&diff=12279 2020-02-15T03:09:56Z

<p>Shuogu: </p> <hr /> <div>This is the 1st version (20200210) of Interaction Filtering. Please copy the code to your current directory.<br /> <br /> '''FIRST AND FOREMOST, If you find any version conflicts between python3 and python2, you need to comment out inside ~/.cshrc: # source /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/env.csh'''<br /> <br /> $ cp -r /mnt/nfs/home/sgu/code/interfilter .<br /> <br /> To run the code, you need OpenEye (version 2019.Oct.2). You can follow the instruction to install: https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html<br /> <br /> On our cluster, you may source my environment.<br /> $ source /nfs/home/sgu/anaconda3/etc/profile.d/conda.csh<br /> $ conda activate oepython<br /> $ setenv OE_LICENSE /nfs/soft/openeye/oe_license.txt<br /> <br /> Running the code:<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2<br /> If you want to know the interaction for a specific residue (e.g. ASP115A, A means chain A):<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A<br /> If you want to plot the paired/unpaired interaction (figure generation can be slow, but tens of thousands should be fine):<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A -plot<br /> <br /> [[File: Pair.png|thumb|center|500px|An example of paired interaction plot]]<br /> [[File: Unpair.png|thumb|center|500px|An example of unpaired interaction plot]]<br /> <br /> The output is a txt file, containing 15 columns:<br /> 1ligand 2clash 3hbond_clash+sbridge_clash 4unpairedl_donor+unpairedl_sbridge 5unpairedl_acceptor 6unpairedp_donor+unpairedp_acceptor 7unpairedp_sbridge 8contact 9hbond+hbond_nonideal 10hbond_ligand 11sbridge 12stacking 13cationpi 14halogen 15residue<br /> <br /> To filter out compounds, you may be interested in:<br /> <br /> '''Column3''': #hydrogen bond clash + #salt bridge clash<br /> <br /> '''Column4''': #unpaired ligand donor + #unpaired ligand salt bridge<br /> <br /> '''Column9''': #hydrogen bond + #non-ideal hydrogen bond<br /> <br /> '''Column11''': #salt bridge<br /> <br /> '''Column15''': interaction for you specified residue (0 means no, 1 means yes)</div>

Shuogu http://wiki.docking.org/index.php?title=Strain_Filtering&diff=12278 2020-02-15T03:08:15Z

<p>Shuogu: </p> <hr /> <div>This is Strain Filtering version 1.1 (20200211). Please copy the code to your current directory.<br /> $ cp -r /mnt/nfs/home/sgu/code/strainfilter .<br /> <br /> To run the code, you need RDKit. You can follow the instruction to install RDKit: https://www.rdkit.org/docs/Install.html<br /> <br /> On our cluster, you may source my environment.<br /> $ source /nfs/home/sgu/anaconda3/etc/profile.d/conda.csh<br /> $ conda activate my-rdkit-env<br /> <br /> Currently, the code can handle db2/db2.gz and mol2 inputs. For example:<br /> $ python Torsion_Strain.py test1.db2.gz<br /> $ python Torsion_Strain.py test2.mol2<br /> <br /> The output is a csv file, containing the total strain energy and detailed information of each dihedral sorted by its torsion energy.<br /> <br /> You may be interested in column 2 (total strain energy) and column 6 (the maximum dihedral torsion energy), from which you can choose different thresholds to filter compounds. e.g.<br /> $ awk -F&quot;,&quot; '$2&lt;6.5 &amp;&amp; $6&lt;1.8' test2_Torsion_Strain.csv<br /> This example uses awk to output all the compounds with total strain energy &lt;6.5 and every torsion energy &lt;1.8.</div>

Shuogu http://wiki.docking.org/index.php?title=Interaction_Filtering&diff=12277 2020-02-15T02:57:01Z

<p>Shuogu: </p> <hr /> <div>This is the 1st version (20200210) of Interaction Filtering. Please copy the code to your current directory.<br /> <br /> FIRST AND FOREMOST, If you find any version conflicts between python3 and python2, you need to comment out inside ~/.cshrc: # source /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/env.csh<br /> <br /> $ cp -r /mnt/nfs/home/sgu/code/interfilter .<br /> <br /> To run the code, you need OpenEye (version 2019.Oct.2). You can follow the instruction to install: https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html<br /> <br /> On our cluster, you may source my environment.<br /> $ source /nfs/home/sgu/anaconda3/etc/profile.d/conda.csh<br /> $ conda activate oepython<br /> $ setenv OE_LICENSE /nfs/soft/openeye/oe_license.txt<br /> <br /> Running the code:<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2<br /> If you want to know the interaction for a specific residue (e.g. ASP115A, A means chain A):<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A<br /> If you want to plot the paired/unpaired interaction (figure generation can be slow, but tens of thousands should be fine):<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A -plot<br /> <br /> [[File: Pair.png|thumb|center|500px|An example of paired interaction plot]]<br /> [[File: Unpair.png|thumb|center|500px|An example of unpaired interaction plot]]<br /> <br /> The output is a txt file, containing 15 columns:<br /> 1ligand 2clash 3hbond_clash+sbridge_clash 4unpairedl_donor+unpairedl_sbridge 5unpairedl_acceptor 6unpairedp_donor+unpairedp_acceptor 7unpairedp_sbridge 8contact 9hbond+hbond_nonideal 10hbond_ligand 11sbridge 12stacking 13cationpi 14halogen 15residue<br /> <br /> To filter out compounds, you may be interested in:<br /> <br /> Column3: #hydrogen bond clash + #salt bridge clash<br /> <br /> Column4: #unpaired ligand donor + #unpaired ligand salt bridge<br /> <br /> Column9: #hydrogen bond + #non-ideal hydrogen bond<br /> <br /> Column11: #salt bridge<br /> <br /> Column15: interaction for you specified residue (0 means no, 1 means yes)</div>

Shuogu http://wiki.docking.org/index.php?title=Interaction_Filtering&diff=12276 2020-02-15T02:56:24Z

<p>Shuogu: </p> <hr /> <div>This is the 1st version (20200210) of Interaction Filtering. Please copy the code to your current directory.<br /> <br /> FIRST AND FOREMOST, If you find any version conflicts between python3 and python2, you need to comment out inside ~/.cshrc: # source /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/env.csh<br /> <br /> $ cp -r /mnt/nfs/home/sgu/code/interfilter .<br /> <br /> To run the code, you need OpenEye (version 2019.Oct.2). You can follow the instruction to install: https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html<br /> <br /> On our cluster, you may source my environment.<br /> $ source /nfs/home/sgu/anaconda3/etc/profile.d/conda.csh<br /> $ conda activate oepython<br /> $ setenv OE_LICENSE /nfs/soft/openeye/oe_license.txt<br /> <br /> Running the code:<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2<br /> If you want to know the interaction for a specific residue (e.g. ASP115A, A means chain A):<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A<br /> If you want to plot the paired/unpaired interaction (figure generation can be slow, but tens of thousands should be fine):<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A -plot<br /> <br /> [[File: Pair.png|thumb|left|500px|An example of paired interaction plot]]<br /> [[File: Unpair.png|thumb|right|500px|An example of unpaired interaction plot]]<br /> <br /> The output is a txt file, containing 15 columns:<br /> 1ligand 2clash 3hbond_clash+sbridge_clash 4unpairedl_donor+unpairedl_sbridge 5unpairedl_acceptor 6unpairedp_donor+unpairedp_acceptor 7unpairedp_sbridge 8contact 9hbond+hbond_nonideal 10hbond_ligand 11sbridge 12stacking 13cationpi 14halogen 15residue<br /> <br /> To filter out compounds, you may be interested in:<br /> <br /> Column3: #hydrogen bond clash + #salt bridge clash<br /> <br /> Column4: #unpaired ligand donor + #unpaired ligand salt bridge<br /> <br /> Column9: #hydrogen bond + #non-ideal hydrogen bond<br /> <br /> Column11: #salt bridge<br /> <br /> Column15: interaction for you specified residue (0 means no, 1 means yes)</div>

Shuogu http://wiki.docking.org/index.php?title=Interaction_Filtering&diff=12275 2020-02-15T02:56:03Z

<p>Shuogu: </p> <hr /> <div>This is the 1st version (20200210) of Interaction Filtering. Please copy the code to your current directory.<br /> <br /> FIRST AND FOREMOST, If you find any version conflicts between python3 and python2, you need to comment out inside ~/.cshrc: # source /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/env.csh<br /> <br /> $ cp -r /mnt/nfs/home/sgu/code/interfilter .<br /> <br /> To run the code, you need OpenEye (version 2019.Oct.2). You can follow the instruction to install: https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html<br /> <br /> On our cluster, you may source my environment.<br /> $ source /nfs/home/sgu/anaconda3/etc/profile.d/conda.csh<br /> $ conda activate oepython<br /> $ setenv OE_LICENSE /nfs/soft/openeye/oe_license.txt<br /> <br /> Running the code:<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2<br /> If you want to know the interaction for a specific residue (e.g. ASP115A, A means chain A):<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A<br /> If you want to plot the paired/unpaired interaction (figure generation can be slow, but tens of thousands should be fine):<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A -plot<br /> <br /> [[File: Pair.png|thumb|center|500px|An example of paired interaction plot]]<br /> [[File: Unpair.png|thumb|center|500px|An example of unpaired interaction plot]]<br /> <br /> The output is a txt file, containing 15 columns:<br /> 1ligand 2clash 3hbond_clash+sbridge_clash 4unpairedl_donor+unpairedl_sbridge 5unpairedl_acceptor 6unpairedp_donor+unpairedp_acceptor 7unpairedp_sbridge 8contact 9hbond+hbond_nonideal 10hbond_ligand 11sbridge 12stacking 13cationpi 14halogen 15residue<br /> <br /> To filter out compounds, you may be interested in:<br /> <br /> Column3: #hydrogen bond clash + #salt bridge clash<br /> <br /> Column4: #unpaired ligand donor + #unpaired ligand salt bridge<br /> <br /> Column9: #hydrogen bond + #non-ideal hydrogen bond<br /> <br /> Column11: #salt bridge<br /> <br /> Column15: interaction for you specified residue (0 means no, 1 means yes)</div>

Shuogu http://wiki.docking.org/index.php?title=Interaction_Filtering&diff=12274 2020-02-15T02:54:39Z

<p>Shuogu: </p> <hr /> <div>This is the 1st version (20200210) of Interaction Filtering. Please copy the code to your current directory.<br /> <br /> FIRST AND FOREMOST, If you find any version conflicts between python3 and python2, you need to comment out inside ~/.cshrc: # source /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/env.csh<br /> <br /> $ cp -r /mnt/nfs/home/sgu/code/interfilter .<br /> <br /> To run the code, you need OpenEye (version 2019.Oct.2). You can follow the instruction to install: https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html<br /> <br /> On our cluster, you may source my environment.<br /> $ source /nfs/home/sgu/anaconda3/etc/profile.d/conda.csh<br /> $ conda activate oepython<br /> $ setenv OE_LICENSE /nfs/soft/openeye/oe_license.txt<br /> <br /> Running the code:<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2<br /> If you want to know the interaction for a specific residue (e.g. ASP115A, A means chain A):<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A<br /> If you want to plot the paired/unpaired interaction (figure generation can be slow, but several thousand should be fine):<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A -plot<br /> <br /> [[File: Pair.png|thumb|center|500px|An example of paired interaction plot]]<br /> [[File: Unpair.png|thumb|center|500px|An example of unpaired interaction plot]]<br /> <br /> The output is a txt file, containing 15 columns:<br /> 1ligand 2clash 3hbond_clash+sbridge_clash 4unpairedl_donor+unpairedl_sbridge 5unpairedl_acceptor 6unpairedp_donor+unpairedp_acceptor 7unpairedp_sbridge 8contact 9hbond+hbond_nonideal 10hbond_ligand 11sbridge 12stacking 13cationpi 14halogen 15residue<br /> <br /> To filter out compounds, you may be interested in:<br /> <br /> Column3: #hydrogen bond clash + #salt bridge clash<br /> <br /> Column4: #unpaired ligand donor + #unpaired ligand salt bridge<br /> <br /> Column9: #hydrogen bond + #non-ideal hydrogen bond<br /> <br /> Column11: #salt bridge<br /> <br /> Column15: interaction for you specified residue (0 means no, 1 means yes)</div>

Shuogu http://wiki.docking.org/index.php?title=Interaction_Filtering&diff=12273 2020-02-15T02:54:08Z

<p>Shuogu: </p> <hr /> <div>This is the 1st version (20200210) of Interaction Filtering. Please copy the code to your current directory.<br /> <br /> FIRST AND FOREMOST, If you find any version conflicts between python3 and python2. You need to comment out inside ~/.cshrc: # source /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/env.csh<br /> <br /> $ cp -r /mnt/nfs/home/sgu/code/interfilter .<br /> <br /> To run the code, you need OpenEye (version 2019.Oct.2). You can follow the instruction to install: https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html<br /> <br /> On our cluster, you may source my environment.<br /> $ source /nfs/home/sgu/anaconda3/etc/profile.d/conda.csh<br /> $ conda activate oepython<br /> $ setenv OE_LICENSE /nfs/soft/openeye/oe_license.txt<br /> <br /> Running the code:<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2<br /> If you want to know the interaction for a specific residue (e.g. ASP115A, A means chain A):<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A<br /> If you want to plot the paired/unpaired interaction (figure generation can be slow, but several thousand should be fine):<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A -plot<br /> <br /> [[File: Pair.png|thumb|center|500px|An example of paired interaction plot]]<br /> [[File: Unpair.png|thumb|center|500px|An example of unpaired interaction plot]]<br /> <br /> The output is a txt file, containing 15 columns:<br /> 1ligand 2clash 3hbond_clash+sbridge_clash 4unpairedl_donor+unpairedl_sbridge 5unpairedl_acceptor 6unpairedp_donor+unpairedp_acceptor 7unpairedp_sbridge 8contact 9hbond+hbond_nonideal 10hbond_ligand 11sbridge 12stacking 13cationpi 14halogen 15residue<br /> <br /> To filter out compounds, you may be interested in:<br /> <br /> Column3: #hydrogen bond clash + #salt bridge clash<br /> <br /> Column4: #unpaired ligand donor + #unpaired ligand salt bridge<br /> <br /> Column9: #hydrogen bond + #non-ideal hydrogen bond<br /> <br /> Column11: #salt bridge<br /> <br /> Column15: interaction for you specified residue (0 means no, 1 means yes)</div>

Shuogu http://wiki.docking.org/index.php?title=Interaction_Filtering&diff=12272 2020-02-15T02:53:32Z

<p>Shuogu: </p> <hr /> <div>This is the 1st version (20200210) of Interaction Filtering. Please copy the code to your current directory.<br /> <br /> FIRST AND FOREMOST, If you find any version conflicts between python 3.7 and 2.7. You need to comment out inside ~/.cshrc: # source /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/env.csh<br /> <br /> $ cp -r /mnt/nfs/home/sgu/code/interfilter .<br /> <br /> To run the code, you need OpenEye (version 2019.Oct.2). You can follow the instruction to install: https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html<br /> <br /> On our cluster, you may source my environment.<br /> $ source /nfs/home/sgu/anaconda3/etc/profile.d/conda.csh<br /> $ conda activate oepython<br /> $ setenv OE_LICENSE /nfs/soft/openeye/oe_license.txt<br /> <br /> Running the code:<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2<br /> If you want to know the interaction for a specific residue (e.g. ASP115A, A means chain A):<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A<br /> If you want to plot the paired/unpaired interaction (figure generation can be slow, but several thousand should be fine):<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A -plot<br /> <br /> [[File: Pair.png|thumb|center|500px|An example of paired interaction plot]]<br /> [[File: Unpair.png|thumb|center|500px|An example of unpaired interaction plot]]<br /> <br /> The output is a txt file, containing 15 columns:<br /> 1ligand 2clash 3hbond_clash+sbridge_clash 4unpairedl_donor+unpairedl_sbridge 5unpairedl_acceptor 6unpairedp_donor+unpairedp_acceptor 7unpairedp_sbridge 8contact 9hbond+hbond_nonideal 10hbond_ligand 11sbridge 12stacking 13cationpi 14halogen 15residue<br /> <br /> To filter out compounds, you may be interested in:<br /> <br /> Column3: #hydrogen bond clash + #salt bridge clash<br /> <br /> Column4: #unpaired ligand donor + #unpaired ligand salt bridge<br /> <br /> Column9: #hydrogen bond + #non-ideal hydrogen bond<br /> <br /> Column11: #salt bridge<br /> <br /> Column15: interaction for you specified residue (0 means no, 1 means yes)</div>

Shuogu http://wiki.docking.org/index.php?title=Strain_Filtering&diff=12271 2020-02-13T09:40:08Z

<p>Shuogu: </p> <hr /> <div>This is Strain Filtering version 1.1 (20200211). Please copy the code to your current directory.<br /> $ cp -r /mnt/nfs/home/sgu/code/strainfilter .<br /> <br /> To run the code, you need RDKit. You can follow the instruction to install RDKit: https://www.rdkit.org/docs/Install.html<br /> $ conda create -c rdkit -n my-rdkit-env rdkit<br /> $ conda activate my-rdkit-env<br /> <br /> Currently, the code can handle db2/db2.gz and mol2 inputs. For example:<br /> $ python Torsion_Strain.py test1.db2.gz<br /> $ python Torsion_Strain.py test2.mol2<br /> <br /> The output is a csv file, containing the total strain energy and detailed information of each dihedral sorted by its torsion energy.<br /> <br /> You may be interested in column 2 (total strain energy) and column 6 (the maximum dihedral torsion energy), from which you can choose different thresholds to filter compounds. e.g.<br /> $ awk -F&quot;,&quot; '$2&lt;6.5 &amp;&amp; $6&lt;1.8' test2_Torsion_Strain.csv<br /> This example uses awk to output all the compounds with total strain energy &lt;6.5 and every torsion energy &lt;1.8.</div>

Shuogu http://wiki.docking.org/index.php?title=Strain_Filtering&diff=12270 2020-02-13T09:39:20Z

<p>Shuogu: </p> <hr /> <div>This is Strain Filtering version 1.1 (20200211). Please copy the code to your current directory.<br /> $ cp -r /mnt/nfs/home/sgu/code/strainfilter .<br /> <br /> To run the code, you need RDKit. You can follow the instruction to install RDKit: https://www.rdkit.org/docs/Install.html<br /> $ conda create -c rdkit -n my-rdkit-env rdkit<br /> $ conda activate my-rdkit-env<br /> <br /> Currently, the code can handle db2/db2.gz and mol2 inputs. For example:<br /> $ python Torsion_Strain.py test1.db2.gz<br /> $ python Torsion_Strain.py test2.mol2<br /> <br /> The output is a csv file, containing the total strain energy and detailed information of each dihedral sorted by its torsion energy.<br /> <br /> You may be interested in column 2 (total strain energy) and column 6 (the maximum dihedral torsion energy), from which you can choose different thresholds to filter compounds. e.g.<br /> $ awk -F&quot;,&quot; '$2&lt;6.5&amp;&amp;$6&lt;1.8' test2_Torsion_Strain.csv<br /> This example uses awk to output all the compounds with total strain energy &lt;6.5 and every torsion energy &lt;1.8.</div>

Shuogu http://wiki.docking.org/index.php?title=Strain_Filtering&diff=12268 2020-02-12T04:49:07Z

<p>Shuogu: </p> <hr /> <div>This is Strain Filtering version 1.1 (20200211). Please copy the code to your current directory.<br /> $ cp -r /mnt/nfs/home/sgu/code/strainfilter .<br /> <br /> To run the code, you need RDKit. You can follow the instruction to install RDKit: https://www.rdkit.org/docs/Install.html<br /> $ conda create -c rdkit -n my-rdkit-env rdkit<br /> $ conda activate my-rdkit-env<br /> <br /> Please use python3 to run the code. Currently, the code can handle db2/db2.gz and mol2 inputs. For example:<br /> $ python3 Torsion_Strain.py test1.db2.gz<br /> $ python3 Torsion_Strain.py test2.mol2<br /> <br /> The output is a csv file, containing the total strain energy and detailed information of each dihedral sorted by its torsion energy.<br /> <br /> You may be interested in column 2 (total strain energy) and column 11 (the maximum dihedral torsion energy), from which you can choose different thresholds to filter compounds. e.g.<br /> $ csvcut -c 1,2,11 test2_Torsion_Strain.csv | awk -F&quot;,&quot; '$2&lt;6.5&amp;&amp;$3&lt;1.8 {print $1&quot; &quot;$2&quot; &quot;$3}'<br /> This example uses csvkit and awk to output all the compounds with total strain energy &lt;6.5 and every torsion energy &lt;1.8.</div>

Shuogu http://wiki.docking.org/index.php?title=UCSF_Strain_Filtering&diff=12267 2020-02-12T04:39:31Z

<p>Shuogu: </p> <hr /> <div>NOTE: This version is deprecated. The new version is 1.1<br /> <br /> This is the 1st version of UCSF strain filtering. Please copy the code to your current directory.<br /> $ cp -r /mnt/nfs/home/sgu/code/ucsf .<br /> <br /> To run the code, you need RDKit. You can follow the instruction to install RDKit: https://www.rdkit.org/docs/Install.html<br /> On our cluster, you only need to type:<br /> $ conda create -c rdkit -n my-rdkit-env rdkit<br /> $ conda activate my-rdkit-env<br /> <br /> Please use python3 to run the code. Currently, the code can handle db2/db2.gz and mol2 inputs. For example:<br /> $ python3 Torsion_Strain.py test1.db2.gz<br /> $ python3 Torsion_Strain.py test2.mol2<br /> <br /> The output is a csv file, containing the strain energy and detailed information for each compound in mol2 or each conformation in db2.<br /> You may be most interested in the first two columns of the output, otherwise please refer to the detailed comments in the Torsion_Strain.py.</div>

Shuogu http://wiki.docking.org/index.php?title=UCSF_Strain_Filtering&diff=12266 2020-02-12T04:39:05Z

<p>Shuogu: </p> <hr /> <div>###This version is deprecated. The new version is 1.1###<br /> <br /> This is the 1st version of UCSF strain filtering. Please copy the code to your current directory.<br /> $ cp -r /mnt/nfs/home/sgu/code/ucsf .<br /> <br /> To run the code, you need RDKit. You can follow the instruction to install RDKit: https://www.rdkit.org/docs/Install.html<br /> On our cluster, you only need to type:<br /> $ conda create -c rdkit -n my-rdkit-env rdkit<br /> $ conda activate my-rdkit-env<br /> <br /> Please use python3 to run the code. Currently, the code can handle db2/db2.gz and mol2 inputs. For example:<br /> $ python3 Torsion_Strain.py test1.db2.gz<br /> $ python3 Torsion_Strain.py test2.mol2<br /> <br /> The output is a csv file, containing the strain energy and detailed information for each compound in mol2 or each conformation in db2.<br /> You may be most interested in the first two columns of the output, otherwise please refer to the detailed comments in the Torsion_Strain.py.</div>

Shuogu http://wiki.docking.org/index.php?title=UCSF_Strain_Filtering&diff=12265 2020-02-12T04:37:35Z

<p>Shuogu: Undo revision 12260 by Shuogu (talk)</p> <hr /> <div>This is the 1st version of UCSF strain filtering. Please copy the code to your current directory.<br /> $ cp -r /mnt/nfs/home/sgu/code/ucsf .<br /> <br /> To run the code, you need RDKit. You can follow the instruction to install RDKit: https://www.rdkit.org/docs/Install.html<br /> On our cluster, you only need to type:<br /> $ conda create -c rdkit -n my-rdkit-env rdkit<br /> $ conda activate my-rdkit-env<br /> <br /> Please use python3 to run the code. Currently, the code can handle db2/db2.gz and mol2 inputs. For example:<br /> $ python3 Torsion_Strain.py test1.db2.gz<br /> $ python3 Torsion_Strain.py test2.mol2<br /> <br /> The output is a csv file, containing the strain energy and detailed information for each compound in mol2 or each conformation in db2.<br /> You may be most interested in the first two columns of the output, otherwise please refer to the detailed comments in the Torsion_Strain.py.</div>

Shuogu http://wiki.docking.org/index.php?title=Strain_Filtering&diff=12264 2020-02-12T04:34:40Z

<p>Shuogu: </p> <hr /> <div>This is Strain Filtering version 1.1 (20200211). Please copy the code to your current directory.<br /> $ cp -r /mnt/nfs/home/sgu/code/strainfilter .<br /> <br /> To run the code, you need RDKit. You can follow the instruction to install RDKit: https://www.rdkit.org/docs/Install.html<br /> $ conda create -c rdkit -n my-rdkit-env rdkit<br /> $ conda activate my-rdkit-env<br /> <br /> Please use python3 to run the code. Currently, the code can handle db2/db2.gz and mol2 inputs. For example:<br /> $ python3 Torsion_Strain.py test1.db2.gz<br /> $ python3 Torsion_Strain.py test2.mol2<br /> <br /> The output is a csv file, containing the total strain energy and detailed information of each dihedral sorted by its torsion energy.<br /> <br /> You may be interested in column 2 (total strain energy) and column 11 (the maximum dihedral torsion energy), from which you can choose different levels to filter compounds, e.g.<br /> $ csvcut -c 1,2,11 test2_Torsion_Strain.csv | awk -F&quot;,&quot; '$2&lt;6.5&amp;&amp;$3&lt;1.8 {print $1&quot; &quot;$2&quot; &quot;$3}'<br /> This example uses csvkit and awk to output all the compounds with total strain energy &lt;6.5 and every torsion energy &lt;1.8.</div>

Shuogu http://wiki.docking.org/index.php?title=Strain_Filtering&diff=12263 2020-02-12T04:29:51Z

<p>Shuogu: </p> <hr /> <div>This is Strain Filtering version 1.1. Please copy the code to your current directory.<br /> $ cp -r /mnt/nfs/home/sgu/code/strainfilter .<br /> <br /> To run the code, you need RDKit. You can follow the instruction to install RDKit: https://www.rdkit.org/docs/Install.html<br /> $ conda create -c rdkit -n my-rdkit-env rdkit<br /> $ conda activate my-rdkit-env<br /> <br /> Please use python3 to run the code. Currently, the code can handle db2/db2.gz and mol2 inputs. For example:<br /> $ python3 Torsion_Strain.py test1.db2.gz<br /> $ python3 Torsion_Strain.py test2.mol2<br /> <br /> The output is a csv file, containing the total strain energy and detailed information of each dihedral sorted by its torsion energy.<br /> <br /> You may be interested in column 2 (total strain energy) and column 11 (the maximum dihedral torsion energy), from which you can choose different levels to filter compounds, e.g.<br /> $ csvcut -c 1,2,11 test2_Torsion_Strain.csv | awk -F&quot;,&quot; '$2&lt;6.5&amp;&amp;$3&lt;1.8 {print $1&quot; &quot;$2&quot; &quot;$3}'<br /> This example uses csvkit and awk to output all the compounds with total strain energy &lt;6.5 and every torsion energy &lt;1.8.</div>

Shuogu http://wiki.docking.org/index.php?title=Strain_Filtering&diff=12262 2020-02-12T04:25:00Z

<p>Shuogu: Created page with &quot;This is Strain Filtering version 1.1. Please copy the code to your current directory. $ cp -r /mnt/nfs/home/sgu/code/ucsf . To run the code, you need RDKit. You can follow t...&quot;</p> <hr /> <div>This is Strain Filtering version 1.1. Please copy the code to your current directory.<br /> $ cp -r /mnt/nfs/home/sgu/code/ucsf .<br /> <br /> To run the code, you need RDKit. You can follow the instruction to install RDKit: https://www.rdkit.org/docs/Install.html<br /> $ conda create -c rdkit -n my-rdkit-env rdkit<br /> $ conda activate my-rdkit-env<br /> <br /> Please use python3 to run the code. Currently, the code can handle db2/db2.gz and mol2 inputs. For example:<br /> $ python3 Torsion_Strain.py test1.db2.gz<br /> $ python3 Torsion_Strain.py test2.mol2<br /> <br /> The output is a csv file, containing the total strain energy and detailed information of each dihedral sorted by its torsion energy.<br /> <br /> You may be interested in column 2 (total strain energy) and column 11 (the maximum dihedral torsion energy), from which you can choose different levels to filter compounds, e.g.<br /> $ csvcut -c 1,2,11 test2_Torsion_Strain.csv | awk -F&quot;,&quot; '$2&lt;6.5&amp;&amp;$3&lt;1.8 {print $1&quot; &quot;$2&quot; &quot;$3}'<br /> This example uses csvkit and awk to output all the compounds with total strain energy &lt;6.5 and every torsion energy &lt;1.8.</div>

Shuogu http://wiki.docking.org/index.php?title=DOCK_3.7&diff=12261 2020-02-12T04:24:17Z

<p>Shuogu: /* Post Docking Filters */</p> <hr /> <div>= About = <br /> <br /> DOCK 3.7 the current version in the [[DOCK 3]] series of docking programs developed and used by the [[Shoichet Lab]]. Please read and cite the DOCK 3.7 paper<br /> [http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075992 Coleman, Carchia, Sterling, Irwin &amp; Shoichet, PLOS ONE 2013.]<br /> <br /> DOCK 3.7 is written in Fortran and some C. It is an update of [[DOCK 3.6]] with many improved features. DOCK 3.7 comes with all the tools necessary to prepare a <br /> protein for docking and some tools necessary to build ligands, though some tools must be obtained externally. It uses new Flexibase/DB2 files found in [[ZINC15]]. It includes tools to prepare receptors, and several auxiliary scripts.<br /> <br /> DOCK 3.7 is available at [http://dock.compbio.ucsf.edu/DOCK3.7/ http://dock.compbio.ucsf.edu/DOCK3.7/].<br /> <br /> {{TOCright}}<br /> <br /> = Start here =<br /> * [[So you want to set up a lab]] - only if you don't already have hardware ready.<br /> * [[Install DOCK 3.7]]<br /> * [[DOCK 3.7 2014/09/25 FXa Tutorial]]<br /> * [[DOCK 3.7 2015/04/15 abl1 Tutorial]] superseded<br /> * [[DOCK 3.7 2018/06/05 abl1 Tutorial]]<br /> * [[DOCK 3.7 2016/09/16 Tutorial for Enrichment Calculations (Trent &amp; Jiankun)]]<br /> * [[DOCK 3.7 tutorial (Anat)]]<br /> * [[DOCK 3.7 with GIST tutorials]]<br /> * [[DOCK 3.7 tutorial based on Webinar 2017/06/28]]<br /> * [[Getting started with DOCK 3.7]]<br /> * [[Blastermaster]] - Prepare input for and then run [[DOCK 3.7]].<br /> * [[Ligand preparation 3.7]] - Create dockable databases for [[DOCK 3.7]].<br /> * [[Ligand preparation]] - different version. <br /> * [[Ligand prep Irwin Nov 2016]] - John's current version<br /> * [[Mol2db2 Format 2]] - details on the database formate.<br /> * [[Running docking 3.7]] - how to actually run docking.<br /> * [[DOCK 3.7 Development]] - for software developers<br /> === For DOCKovalent, start here ===<br /> * [[DOCKovalent_3.7]]<br /> * [[DOCKovalent lysine inhibitor design tutorial]]<br /> * [[DOCKovalent cysteine inhibitor design tutorial]]<br /> <br /> = Prepare Receptor = <br /> * [[Protein Target Preparation]]<br /> * [[Protein Target Preparation Updated]]<br /> * [[Using_thin_spheres_in_DOCK3.7]]<br /> * [[Adding Static Waters to the Protein Structure]]<br /> * [[Flexible Docking]]<br /> * [[Visualize docking grids]]<br /> * [[Minimize protein-ligand complex with AMBER]]<br /> * [[Minimize protein-covalent ligand complex with AMBER]]<br /> <br /> = Prepare Screening Library =<br /> * [[mol2db2]] is the program that creates [[mol2db2 format]] database files which are read by [[DOCK 3.7]]<br /> * [[ligand preparation 3.7]]<br /> * [[generating decoys (Reed's way)]]<br /> * [[generating extrema set]]<br /> <br /> = Running Docking =<br /> * [[Running docking 3.7]] - JJI currently working on this.<br /> * [[Running DOCK 3.7]] - this seems to be slightly dated.<br /> * [[INDOCK 3.7]] - file format used by [[DOCK 3.7]]<br /> * [[DOCK3.7_INDOCK_Minimization_Parameter]] - How to run DOCK 3.7.1rc1 (and latter versions) with the minimization.<br /> * Interpreting the [[OUTDOCK 3.7]] file.<br /> <br /> = Analysis =<br /> * [[Analyzing DOCK Results]]<br /> * [http://autodude.docking.org/ Auto-DUD-E Test Set] (external site) <br /> * [[Other Useful Stuff]]<br /> * [[Bootstrap AUC]]<br /> * [[Converting SMILES to Kekule Format]]<br /> <br /> = Post Docking Clustering=<br /> * [[How to process results from a large-scale docking]] <br /> * [[Large-scale SMILES Requesting and Fingerprints Converting]]<br /> * [[ECFP4 Best First Clustering]]<br /> * [[Bemis-Murcko Scaffold Analysis]]<br /> <br /> = Post Docking Filters=<br /> * [[Large-scale TC Calculations]]<br /> * [[Whole Library TC to Knowns Calculations]]<br /> * [[Filtering ligands for novelty]]<br /> * [[Strain Filtering]]<br /> * [[Interaction Filtering]]<br /> <br /> = Redocking with Enhanced Sampling =<br /> *[[Sample Additional Ring Puckers ]]<br /> = Rescoring =<br /> *[[Rescoring_with_DOCK_3.7]]<br /> <br /> = Available Libraries = <br /> * [[ZINC Subset DB2 file locations]]<br /> * how to get db2 files from zinc15.docking.org<br /> <br /> = Analog by Catalog= <br /> * [[Substructure searching]]<br /> * [[TC analog searching in ZINC]]<br /> <br /> = Previous verisons and compatibility = <br /> DOCK 3.7 is part of the [[DOCK 3]] series. It differs substantially from its immediate predecessor [[DOCK 3.6]],<br /> which uses a different format of database files that cannot be read by [[DOCK 3.7]], and vice versa. <br /> <br /> = How to Cite = <br /> To cite the DOCK 3.7 paper, please use<br /> [http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075992 Coleman, Carchia, Sterling, Irwin &amp; Shoichet, PLOS ONE 2013.]<br /> <br /> = How to Download = <br /> DOCK 3.7 is available at [http://dock.compbio.ucsf.edu/DOCK3.7/ http://dock.compbio.ucsf.edu/DOCK3.7/].<br /> <br /> = Implementation = <br /> DOCK 3.7 is written in Fortran and some C. Scripts are mostly in [[python]] and [[perl]].<br /> <br /> {{Template:CC-BY-SA-30}}<br /> {{Template:Coleman}}<br /> <br /> [[Category:DOCK 3.7]]<br /> [[Category:Software]]<br /> [[Category:Freecom]]</div>

Shuogu http://wiki.docking.org/index.php?title=UCSF_Strain_Filtering&diff=12260 2020-02-12T04:23:39Z

<p>Shuogu: </p> <hr /> <div>This is Strain Filtering version 1.1. Please copy the code to your current directory.<br /> $ cp -r /mnt/nfs/home/sgu/code/ucsf .<br /> <br /> To run the code, you need RDKit. You can follow the instruction to install RDKit: https://www.rdkit.org/docs/Install.html<br /> $ conda create -c rdkit -n my-rdkit-env rdkit<br /> $ conda activate my-rdkit-env<br /> <br /> Please use python3 to run the code. Currently, the code can handle db2/db2.gz and mol2 inputs. For example:<br /> $ python3 Torsion_Strain.py test1.db2.gz<br /> $ python3 Torsion_Strain.py test2.mol2<br /> <br /> The output is a csv file, containing the total strain energy and detailed information of each dihedral sorted by its torsion energy.<br /> <br /> You may be interested in column 2 (total strain energy) and column 11 (the maximum dihedral torsion energy), from which you can choose different levels to filter compounds, e.g.<br /> $ csvcut -c 1,2,11 test2_Torsion_Strain.csv | awk -F&quot;,&quot; '$2&lt;6.5&amp;&amp;$3&lt;1.8 {print $1&quot; &quot;$2&quot; &quot;$3}'<br /> This example uses csvkit and awk to output all the compounds with total strain energy &lt;6.5 and every torsion energy &lt;1.8.</div>

Shuogu http://wiki.docking.org/index.php?title=Interaction_Filtering&diff=12259 2020-02-12T00:23:03Z

<p>Shuogu: </p> <hr /> <div>This is the 1st version (20200210) of Interaction Filtering. Please copy the code to your current directory.<br /> $ cp -r /mnt/nfs/home/sgu/code/interfilter .<br /> <br /> To run the code, you need OpenEye (version 2019.Oct.2). You can follow the instruction to install: https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html<br /> <br /> On our cluster, you may source my environment.<br /> $ source /nfs/home/sgu/anaconda3/etc/profile.d/conda.csh<br /> $ conda activate oepython<br /> $ setenv OE_LICENSE /nfs/soft/openeye/oe_license.txt<br /> If you find any version conflicts between python 3.7 and 2.7. You may comment in the ~/.cshrc: # source /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/env.csh<br /> <br /> Running the code:<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2<br /> If you want to know the interaction for a specific residue (e.g. ASP115A, A means chain A):<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A<br /> If you want to plot the paired/unpaired interaction (figure generation can be slow, but several thousand should be fine):<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A -plot<br /> <br /> [[File: Pair.png|thumb|center|500px|An example of paired interaction plot]]<br /> [[File: Unpair.png|thumb|center|500px|An example of unpaired interaction plot]]<br /> <br /> The output is a txt file, containing 15 columns:<br /> 1ligand 2clash 3hbond_clash+sbridge_clash 4unpairedl_donor+unpairedl_sbridge 5unpairedl_acceptor 6unpairedp_donor+unpairedp_acceptor 7unpairedp_sbridge 8contact 9hbond+hbond_nonideal 10hbond_ligand 11sbridge 12stacking 13cationpi 14halogen 15residue<br /> <br /> To filter out compounds, you may be interested in:<br /> <br /> Column3: #hydrogen bond clash + #salt bridge clash<br /> <br /> Column4: #unpaired ligand donor + #unpaired ligand salt bridge<br /> <br /> Column9: #hydrogen bond + #non-ideal hydrogen bond<br /> <br /> Column11: #salt bridge<br /> <br /> Column15: interaction for you specified residue (0 means no, 1 means yes)</div>

Shuogu http://wiki.docking.org/index.php?title=Interaction_Filtering&diff=12258 2020-02-12T00:19:55Z

<p>Shuogu: </p> <hr /> <div>This is the 1st version (20200210) of Interaction Filtering. Please copy the code to your current directory.<br /> $ cp -r /mnt/nfs/home/sgu/code/interfilter .<br /> <br /> To run the code, you need OpenEye (version 2019.Oct.2). You can follow the instruction to install: https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html<br /> <br /> On our cluster, you may source my environment.<br /> $ source /nfs/home/sgu/anaconda3/etc/profile.d/conda.csh<br /> $ conda activate oepython<br /> $ setenv OE_LICENSE /nfs/soft/openeye/oe_license.txt<br /> If you find any version conflicts between python 3.7 and 2.7. You may comment in the ~/.cshrc: # source /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/env.csh<br /> <br /> Running the code:<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2<br /> If you want to know the interaction for a specific residue (e.g. ASP115A, A means chain A):<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A<br /> If you want to plot the paired/unpaired interaction (figure generation can be slow, but several thousand should be fine):<br /> $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A -plot<br /> <br /> [[File: Pair.png|thumb|center|500px|An example of paired interaction plot]]<br /> [[File: Unpair.png|thumb|center|500px|An example of unpaired interaction plot]]<br /> <br /> The output is a txt file, containing 15 columns:<br /> 1ligand 2clash 3hbond_clash+sbridge_clash 4unpairedl_donor+unpairedl_sbridge 5unpairedl_acceptor 6unpairedp_donor+unpairedp_acceptor 7unpairedp_sbridge 8contact 9hbond+hbond_nonideal 10hbond_ligand 11sbridge 12stacking 13cationpi 14halogen 15residue<br /> <br /> To filter out compounds, you may be interested in:<br /> <br /> Column3: # of hydrogen bond clash + # of salt bridge clash<br /> <br /> Column4: # of unpaired ligand donor + # of unpaired ligand salt bridge<br /> <br /> Column9: # of hydrogen bond + non-ideal hydrogen bond<br /> <br /> Column11: # of salt bridge<br /> <br /> Column15: interaction for you specified residue (0 means no, 1 means yes)</div>

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