| Previous changeset 1:21a0f28aea68 (2019-04-12) |
|
Commit message:
Uploaded |
|
added:
biobb_cluster.xml biobb_editconf.xml biobb_fix_side_chain.xml biobb_genion.xml biobb_genrestr.xml biobb_grompp.xml biobb_make_ndx.xml biobb_mdrun.xml biobb_mutate.xml biobb_ndx2resttop.xml biobb_pdb.xml biobb_pdb2gmx.xml biobb_pdb_cluster.xml biobb_pdb_variants.xml biobb_rms.xml biobb_solvate.xml test-data/1.pdb_Download_initial_structure.json test-data/11.grompp_preprocess_temperature_eq.json test-data/13.grompp_preprocess_pressure_eq.json test-data/15.grompp_preprocess_free_dynamics.json test-data/3.mutate_modelling_mutation_list.json test-data/7.grompp_preprocess_iongeneration.json test-data/8.genion_iongeneration.json test-data/9.grompp_preprocess_energymin.json test-data/GNUSparseFile.0/biobb_genion_input.tpr test-data/GNUSparseFile.0/biobb_grompp_myGrompp.tpr test-data/GNUSparseFile.0/biobb_make-ndx_input.tpr test-data/biobb_cluster_input.gro test-data/biobb_cluster_input.trr test-data/biobb_cluster_myCluster.pdb test-data/biobb_editconf_input.gro test-data/biobb_editconf_myEdit_conf.gro test-data/biobb_fix_side_chain_input.pdb test-data/biobb_fix_side_chain_myFixSideChain.pdb test-data/biobb_genion_input.zip test-data/biobb_genion_myGenion.gro test-data/biobb_genion_myGenion.zip test-data/biobb_genrestr_input.gro test-data/biobb_genrestr_input.ndx test-data/biobb_genrestr_input.zip test-data/biobb_genrestr_myGenrestr.zip test-data/biobb_grompp_input.gro test-data/biobb_grompp_input.zip test-data/biobb_make-ndx_myMake_ndx.ndx test-data/biobb_mdrun_input.tpr test-data/biobb_mdrun_mdrun.trr test-data/biobb_mutate_input.pdb test-data/biobb_mutate_mutate.pdb test-data/biobb_ndx2resttop_input.ndx test-data/biobb_ndx2resttop_input.zip test-data/biobb_ndx2resttop_myNdx2resttop.zip test-data/biobb_pdb2gmx_input.pdb test-data/biobb_pdb_cluster_myCluster.zip test-data/biobb_pdb_myStructure.pdb test-data/biobb_pdb_variants_myMutants.txt test-data/biobb_rms_input.gro test-data/biobb_rms_input.trr test-data/biobb_rms_rms.xvg test-data/biobb_solvate_input.gro test-data/biobb_solvate_input.zip test-data/biobb_solvate_mySolvate.gro test-data/biobb_solvate_solvate.zip |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde biobb_cluster.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/biobb_cluster.xml Fri Apr 12 07:18:48 2019 -0400 |
| [ |
| @@ -0,0 +1,80 @@ +<tool id="biobb_cluster" name="Cluster" version="0.1.3"> + <description>: creates cluster structures from a given input trajectory. </description> + <requirements> + <requirement type="binary">docker</requirement> + </requirements> + <command detect_errors="aggressive"> + ln -f -s ${inputname} ${inputname}.${inputname.ext}; + ln -f -s ${inputtraj} ${inputtraj}.${inputtraj.ext}; + #if $config.sele == "option1": + ln -s -f ${config.properties} ${config.properties}.${config.properties.ext}; + #end if + docker run -v $__root_dir__/database/files:$__root_dir__/database/files mmbirb/biobb_analysis:0.1.3 cluster --input_gro_path $inputname.${inputname.ext} --input_traj_path ${inputtraj}.${inputtraj.ext} + #if $config.sele == "option1": + --config ${config.properties}.${config.properties.ext} + #else if $config.sele == "option2": + --config ${config.jsonstr} + #end if + --output_pdb_path $__root_dir__/database/files/000/$outname; + #if $config.sele == "option1": + rm -f ${config.properties}.${config.properties.ext}; + #end if + rm -f ${inputname}.${inputname.ext} ${inputtraj}.${inputtraj.ext}; + mv $__root_dir__/database/files/000/$outname $output + </command> + <inputs> + <param name="outname" type="text" value="myCluster.pdb" label="Output PDB name" help="Name for the Output PDB. Format: [output].pdb "/> + <param name="inputname" type="data" format="gro" label="Structure file" help="Select your GROMACS structure file. Format: [input].gro"/> + <param name="inputtraj" type="data" format="trr,xtc" label="Trajectory file" help="Select your input GROMACS trajectory file. Format: [input].trr or [input].xtc"/> + <conditional name="config"> + <param name="sele" type="select" label="Take tool settings:" help="Select where tool settings are to be read from"> + <option value="option1">from configuration file</option> + <option value="option2">from JSON string</option> + <option value="option3" selected="true">by default</option> + </param> + <when value="option1"> + <param name="properties" type="data" format="yml,json" optional="false" label="Configuration file" help="File containing tool settings. See below for the syntax"/> + </when> + <when value="option2"> + <param name="jsonstr" type="text" value="{}" optional="false" label="JSON string" help="JSON string containing tool settings. See below for the syntax"/> + </when> + <when value="option3"> + </when> + + </conditional> + </inputs> + <outputs> + <data name="output" format="pdb" label="${outname}"/> + + </outputs> + <tests> + <test> + </test> + </tests> + <help> +.. class:: warningmark + + +Check the syntax for setting the tool parameters at the original library documentation: https://biobb-analysis.readthedocs.io/en/latest/gromacs.html#module-gromacs.cluster + +----- + +.. image:: ${static_path}/images/biobb.png + :height: 57 + :width: 150 + + +**https://bioexcel.eu** + </help> + <citations> + <citation type="bibtex"> +@misc{githubbiobb, + author = {Andrio P, Hospital A, Gelpi JL}, + year = {2019}, + title = {biobb: BioExcel building blocks }, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/bioexcel/biobb_io}, +}</citation> + </citations> +</tool> |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde biobb_editconf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/biobb_editconf.xml Fri Apr 12 07:18:48 2019 -0400 |
| [ |
| @@ -0,0 +1,77 @@ +<tool id="biobb_editconf" name="EditConf" version="0.1.5" > + <description>: creates a Gromacs file adding the information of the solvent box to the input</description> + <requirements> + <requirement type="binary">docker</requirement> + </requirements> + <command detect_errors="aggressive"> + ln -f -s ${inputname} ${inputname}.${inputname.ext}; + #if $config.sele == "option1": + ln -s -f ${config.properties} ${config.properties}.${config.properties.ext}; + #end if + docker run -v $__root_dir__/database/files:$__root_dir__/database/files quay.io/biocontainers/biobb_md:0.1.5--py_0 editconf --input_gro_path $inputname.${inputname.ext} + #if $config.sele == "option1": + --config ${config.properties}.${config.properties.ext} + #else if $config.sele == "option2": + --config ${config.jsonstr} + #end if + --output_gro_path $__root_dir__/database/files/000/$outname; + #if $config.sele == "option1": + rm -f ${config.properties}.${config.properties.ext}; + #end if + rm -f ${inputname}.${inputname.ext}; + mv $__root_dir__/database/files/000/$outname $output + </command> + <inputs> + <param name="outname" type="text" value="myEdit_conf.gro" label="Output GRO name" help="Name for the Output list. Format: [output].gro "/> + <param name="inputname" type="data" format="gro" label="Input GRO file" help="Select your input GRO file. Format: [input].gro"/> + <conditional name="config"> + <param name="sele" type="select" label="Take tool settings:" help="Select where tool settings are to be read from"> + <option value="option1">from configuration file</option> + <option value="option2">from JSON string</option> + <option value="option3" selected="true">by default</option> + </param> + <when value="option1"> + <param name="properties" type="data" format="yml,json" optional="false" label="Configuration file" help="File containing tool settings. See below for the syntax"/> + </when> + <when value="option2"> + <param name="jsonstr" type="text" value="{}" optional="false" label="JSON string" help="JSON string containing tool settings. See below for the syntax"/> + </when> + <when value="option3"> + </when> + + </conditional> + </inputs> + <outputs> + <data name="output" format="gro" label="${outname}"/> + </outputs> + <tests> + <test> + </test> + </tests> + <help> +.. class:: warningmark + + +Check the syntax for setting the tool parameters at the original library documentation: https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.editconf + +----- + +.. image:: ${static_path}/images/biobb.png + :height: 57 + :width: 150 + + +**https://bioexcel.eu** + </help> + <citations> + <citation type="bibtex"> +@misc{githubbiobb, + author = {Andrio P, Hospital A, Gelpi JL}, + year = {2019}, + title = {biobb: BioExcel building blocks }, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/bioexcel/biobb_io}, +}</citation> + </citations> +</tool> |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde biobb_fix_side_chain.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/biobb_fix_side_chain.xml Fri Apr 12 07:18:48 2019 -0400 |
| [ |
| @@ -0,0 +1,78 @@ +<tool id="biobb_fix_side_chain" name="Fix Side Chain" version="0.1.5" > + <description>: reconstructs the missing side chains and heavy atoms.</description> + <requirements> + <requirement type="binary">docker</requirement> + </requirements> + <command detect_errors="aggressive"> + ln -f -s ${inputname} ${inputname}.${inputname.ext}; + #if $config.sele == "option1": + ln -s -f ${config.properties} ${config.properties}.${config.properties.ext}; + #end if + docker run -v $__root_dir__/database/files:$__root_dir__/database/files quay.io/biocontainers/biobb_model:0.1.5--py_0 fix_side_chain --input_pdb_path $inputname.${inputname.ext} + #if $config.sele == "option1": + --config ${config.properties}.${config.properties.ext} + #else if $config.sele == "option2": + --config ${config.jsonstr} + #end if + --output_pdb_path $output; + #if $config.sele == "option1": + rm -f ${config.properties}.${config.properties.ext}; + #end if + rm -f ${inputname}.${inputname.ext} + </command> + <inputs> + <param name="outname" type="text" value="myFixSideChain.pdb" label="Output PDB name" help="Name for the Output list. Format: [output].pdb "/> + <param name="inputname" type="data" format="pdb" label="Input PDB file" help="Select your input PDB file. Format: [input].pdb"/> + <conditional name="config"> + <param name="sele" type="select" label="Take tool settings:" help="Select where tool settings are to be read from"> + <option value="option1">from configuration file</option> + <option value="option2">from JSON string</option> + <option value="option3" selected="true">by default</option> + </param> + <when value="option1"> + <param name="properties" type="data" format="yml,json" optional="false" label="Configuration file" help="File containing tool settings. See below for the syntax"/> + </when> + <when value="option2"> + <param name="jsonstr" type="text" value="{}" optional="false" label="JSON string" help="JSON string containing tool settings. See below for the syntax"/> + </when> + <when value="option3"> + </when> + + </conditional> + </inputs> + <outputs> + <data name="output" format="pdb" label="${outname}"/> + </outputs> + <tests> + <test> + <param name="inputname" value="../test-data/2ki5.pdb"/> + <output name="output" file="../test-data/biobb_fix_side_chain_myFixSideChain.pdb"/> + </test> + </tests> + <help> +.. class:: warningmark + + +Check the syntax for setting the tool parameters at the original library documentation: https://biobb-model.readthedocs.io/en/latest/model.html#module-model.fix_side_chain + +----- + +.. image:: ${static_path}/images/biobb.png + :height: 57 + :width: 150 + + +**https://bioexcel.eu** + </help> + <citations> + <citation type="bibtex"> +@misc{githubbiobb, + author = {Andrio P, Hospital A, Gelpi JL}, + year = {2019}, + title = {biobb: BioExcel building blocks }, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/bioexcel/biobb_io}, +}</citation> + </citations> +</tool> |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde biobb_genion.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/biobb_genion.xml Fri Apr 12 07:18:48 2019 -0400 |
| [ |
| @@ -0,0 +1,85 @@ +<tool id="biobb_genion" name="Genion" version="0.1.5"> + <description>: adding ions to Gromacs topology</description> + <requirements> + <requirement type="binary">docker</requirement> + </requirements> + <command detect_errors="aggressive"> + ln -f -s ${inputname} ${inputname}.${inputname.ext}; + ln -f -s ${inputzip} ${inputzip}.${inputzip.ext}; + #if $config.sele == "option1": + ln -s -f ${config.properties} ${config.properties}.${config.properties.ext}; + #end if + docker run -v $__root_dir__/database/files:$__root_dir__/database/files quay.io/biocontainers/biobb_md:0.1.5--py_0 genion --input_tpr_path $inputname.${inputname.ext} --input_top_zip_path ${inputzip}.${inputzip.ext} + #if $config.sele == "option1": + --config ${config.properties}.${config.properties.ext} + #else if $config.sele == "option2": + --config ${config.jsonstr} + #end if + --output_gro_path $__root_dir__/database/files/000/$outname + --output_top_zip_path $outputzip; + #if $config.sele == "option1": + rm -f ${config.properties}.${config.properties.ext}; + #end if + rm -f ${inputname}.${inputname.ext} ${inputzip}.${inputzip.ext}; + mv $__root_dir__/database/files/000/$outname $output + </command> + <inputs> + <param name="outname" type="text" value="myGenion.gro" label="Output GRO name" help="Name for the Output. Format: [output].gro "/> + <param name="outnamezip" type="text" value="myGenion.zip" label="Output ZIP name" help="Name for the Output topology TOP and ITP files. Format: [output].zip "/> + <param name="inputname" type="data" format="tpr" label="Input TPR file" help="Select your input portable run TPR file. Format: [input].tpr"/> + <param name="inputzip" type="data" format="zip" label="Input ZIP file" help="Select your input topology TOP and ITP files zipball. Format: [input].zip"/> + <conditional name="config"> + <param name="sele" type="select" label="Take tool settings:" help="Select where tool settings are to be read from"> + <option value="option1">from configuration file</option> + <option value="option2">from JSON string</option> + <option value="option3" selected="true">by default</option> + </param> + <when value="option1"> + <param name="properties" type="data" format="yml,json" optional="false" label="Configuration file" help="File containing tool settings. See below for the syntax"/> + </when> + <when value="option2"> + <param name="jsonstr" type="text" value="{}" optional="false" label="JSON string" help="JSON string containing tool settings. See below for the syntax"/> + </when> + <when value="option3"> + </when> + + </conditional> + </inputs> + <outputs> + <data name="output" format="gro" label="${outname}"/> + <data name="outputzip" format="zip" label="${outnamezip}"/> + + </outputs> + <tests> + <test> + </test> + </tests> + <help> +.. class:: warningmark + + +Check the syntax for setting the tool parameters at the original library documentation: https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.genion + +----- + +The main output of this BB will be an updated post-procesed Gromacs structure file (.gro) and a zip file containing the updated topology file (.top) and the restriction files (.itp). + +.. image:: ${static_path}/images/biobb.png + :height: 57 + :width: 150 + + +**https://bioexcel.eu** + </help> + <citations> + <citation type="bibtex"> +@misc{githubbiobb, + author = {Andrio P, Hospital A, Gelpi JL}, + year = {2019}, + title = {biobb: BioExcel building blocks }, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/bioexcel/biobb_io}, +}</citation> + </citations> +</tool> |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde biobb_genrestr.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/biobb_genrestr.xml Fri Apr 12 07:18:48 2019 -0400 |
| [ |
| @@ -0,0 +1,79 @@ +<tool id="biobb_genrestr" name="Genrestr" version="0.1.5" > + <description>: creates a new zip Gromacs topology applying the indicated force restrains</description> + <requirements> + <requirement type="binary">docker</requirement> + </requirements> + <command detect_errors="aggressive"> + ln -f -s ${inputname} ${inputname}.${inputname.ext}; + ln -f -s ${inputzip} ${inputzip}.${inputzip.ext}; + ln -f -s ${inputstr} ${inputstr}.${inputstr.ext}; + #if $config.sele == "option1": + ln -s -f ${config.properties} ${config.properties}.${config.properties.ext}; + #end if + docker run -v $__root_dir__/database/files:$__root_dir__/database/files quay.io/biocontainers/biobb_md:0.1.5--py_0 genrestr --input_ndx_path $inputname.${inputname.ext} --input_top_zip_path ${inputzip}.${inputzip.ext} --input_structure_path ${inputstr}.${inputstr.ext} + #if $config.sele == "option1": + --config ${config.properties}.${config.properties.ext} + #else if $config.sele == "option2": + --config ${config.jsonstr} + #end if + --output_top_zip_path $outputzip; + #if $config.sele == "option1": + rm -f ${config.properties}.${config.properties.ext}; + #end if + rm -f ${inputname}.${inputname.ext} ${inputzip}.${inputzip.ext} ${inputstr}.${inputstr.ext} + </command> + <inputs> + <param name="outnamezip" type="text" value="myGenrestr.zip" label="Output ZIP name" help="Name for the Output TOP topology. Format: [output].zip "/> + <param name="inputstr" type="data" format="pdb,gro,tpr" label="Structure file" help="Select your input structure. Format: [input].pdb or [input].gro or [input].tpr"/> + <param name="inputname" type="data" format="ndx" label="Index file" help="Select your input GROMACS index file. Format: [input].ndx"/> + <param name="inputzip" type="data" format="zip" label="ZIP file" help="Select your input ZIP file. Format: [input].zip"/> + <conditional name="config"> + <param name="sele" type="select" label="Take tool settings:" help="Select where tool settings are to be read from"> + <option value="option1">from configuration file</option> + <option value="option2">from JSON string</option> + <option value="option3" selected="true">by default</option> + </param> + <when value="option1"> + <param name="properties" type="data" format="yml,json" optional="false" label="Configuration file" help="File containing tool settings. See below for the syntax"/> + </when> + <when value="option2"> + <param name="jsonstr" type="text" value="{}" optional="false" label="JSON string" help="JSON string containing tool settings. See below for the syntax"/> + </when> + <when value="option3"> + </when> + </conditional> + </inputs> + <outputs> + <data name="outputzip" format="zip" label="${outnamezip}"/> + </outputs> + <tests> + <test> + </test> + </tests> + <help> +.. class:: warningmark + + +Check the syntax for setting the tool parameters at the original library documentation: https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.genrestr + +----- + +.. image:: ${static_path}/images/biobb.png + :height: 57 + :width: 150 + + +**https://bioexcel.eu** + </help> + <citations> + <citation type="bibtex"> +@misc{githubbiobb, + author = {Andrio P, Hospital A, Gelpi JL}, + year = {2019}, + title = {biobb: BioExcel building blocks }, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/bioexcel/biobb_io}, +}</citation> + </citations> +</tool> |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde biobb_grompp.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/biobb_grompp.xml Fri Apr 12 07:18:48 2019 -0400 |
| [ |
| @@ -0,0 +1,80 @@ +<tool id="biobb_grompp" name="Grompp" version="0.1.5" > + <description>:Gromacs preprocessor. Reads topology file to create TPR atomic description</description> + <requirements> + <requirement type="binary">docker</requirement> + </requirements> + <command detect_errors="aggressive"> + ln -f -s ${inputname} ${inputname}.${inputname.ext}; + ln -f -s ${inputzip} ${inputzip}.${inputzip.ext}; + ln -f -s ${inputgro} ${inputgro}.${inputgro.ext}; + #if $config.sele == "option1": + ln -s -f ${config.properties} ${config.properties}.${config.properties.ext}; + #end if + docker run -v $__root_dir__/database/files:$__root_dir__/database/files quay.io/biocontainers/biobb_md:0.1.5--py_0 grompp --input_cpt_path $inputname.${inputname.ext} --input_top_zip_path ${inputzip}.${inputzip.ext} --input_gro_path ${inputgro}.${inputgro.ext} + #if $config.sele == "option1": + --config ${config.properties}.${config.properties.ext} + #else if $config.sele == "option2": + --config ${config.jsonstr} + #end if + --output_tpr_path $__root_dir__/database/files/000/$outname; + #if $config.sele == "option1": + rm -f ${config.properties}.${config.properties.ext}; + #end if + rm -f ${inputname}.${inputname.ext} ${inputzip}.${inputzip.ext} ${inputgro}.${inputgro.ext}; + mv $__root_dir__/database/files/000/$outname $output_tpr + </command> + <inputs> + <param name="inputgro" type="data" format="gro" label="Structure file" help="Select your input GROMACS structure file. Format: [input].gro"/> + <param name="inputzip" type="data" format="zip" label="Topology file" help="Select your input GROMACS topology TOP and ITP file. Format: [input].zip"/> + <param name="inputname" type="data" format="cpt" label="Check point file" optional="True" help="Select your input GROMACS checkpoint file. Format: [input].cpt"/> + <param name="outname" type="text" value="myGrompp.tpr" label="Output TPR name" help="Name for the Output binary run file. Format: [output].tpr "/> + <conditional name="config"> + <param name="sele" type="select" label="Take tool settings:" help="Select where tool settings are to be read from"> + <option value="option1">from configuration file</option> + <option value="option2">from JSON string</option> + <option value="option3" selected="true">by default</option> + </param> + <when value="option1"> + <param name="properties" type="data" format="yml,json" optional="false" label="Configuration file" help="File containing tool settings. See below for the syntax"/> + </when> + <when value="option2"> + <param name="jsonstr" type="text" value="{}" optional="false" label="JSON string" help="JSON string containing tool settings. See below for the syntax"/> + </when> + <when value="option3"> + </when> + </conditional> + </inputs> + <outputs> + <data name="output_tpr" format="tpr" label="${outname}"/> + </outputs> + <tests> + <test> + </test> + </tests> + <help> +.. class:: warningmark + + +Check the syntax for setting the tool parameters at the original library documentation: https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.grompp + +----- + +.. image:: ${static_path}/images/biobb.png + :height: 57 + :width: 150 + + +**https://bioexcel.eu** + </help> + <citations> + <citation type="bibtex"> +@misc{githubbiobb, + author = {Andrio P, Hospital A, Gelpi JL}, + year = {2019}, + title = {biobb: BioExcel building blocks }, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/bioexcel/biobb_io}, +}</citation> + </citations> +</tool> |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde biobb_make_ndx.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/biobb_make_ndx.xml Fri Apr 12 07:18:48 2019 -0400 |
| [ |
| @@ -0,0 +1,77 @@ +<tool id="biobb_make_ndx" name="Make NDX" version="0.1.5" > + <description>: creates a Gromacs index file (NDX).</description> + <requirements> + <requirement type="binary">docker</requirement> + </requirements> + <command detect_errors="aggressive"> + ln -f -s ${inputname} ${inputname}.${inputname.ext}; + #if $config.sele == "option1": + ln -s -f ${config.properties} ${config.properties}.${config.properties.ext}; + #end if + docker run -v $__root_dir__/database/files:$__root_dir__/database/files quay.io/biocontainers/biobb_md:0.1.5--py_0 make_ndx --input_structure_path $inputname.${inputname.ext} + #if $config.sele == "option1": + --config ${config.properties}.${config.properties.ext} + #else if $config.sele == "option2": + --config ${config.jsonstr} + #end if + --output_ndx_path $__root_dir__/database/files/000/$outname; + #if $config.sele == "option1": + rm -f ${config.properties}.${config.properties.ext}; + #end if + rm -f ${inputname}.${inputname.ext}; + mv $__root_dir__/database/files/000/$outname $output + </command> + <inputs> + <param name="outname" type="text" value="myMake_ndx.ndx" label="Output NDX name" help="Name for the Output index file. Format: [output].ndx "/> + <param name="inputname" type="data" format="gro,pdb,tpr" label="Input GRO/PDB/TPR file" help="Select your input GRO/PDB/TPR file. Format: [input].gro or [input].pdb or [input].tpr"/> + <conditional name="config"> + <param name="sele" type="select" label="Take tool settings:" help="Select where tool settings are to be read from"> + <option value="option1">from configuration file</option> + <option value="option2">from JSON string</option> + <option value="option3" selected="true">by default</option> + </param> + <when value="option1"> + <param name="properties" type="data" format="yml,json" optional="false" label="Configuration file" help="File containing tool settings. See below for the syntax"/> + </when> + <when value="option2"> + <param name="jsonstr" type="text" value="{}" optional="false" label="JSON string" help="JSON string containing tool settings. See below for the syntax"/> + </when> + <when value="option3"> + </when> + + </conditional> + </inputs> + <outputs> + <data name="output" format="ndx" label="${outname}"/> + </outputs> + <tests> + <test> + </test> + </tests> + <help> +.. class:: warningmark + + +Check the syntax for setting the tool parameters at the original library documentation: https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.make_ndx + +----- + +.. image:: ${static_path}/images/biobb.png + :height: 57 + :width: 150 + + +**https://bioexcel.eu** + </help> + <citations> + <citation type="bibtex"> +@misc{githubbiobb, + author = {Andrio P, Hospital A, Gelpi JL}, + year = {2019}, + title = {biobb: BioExcel building blocks }, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/bioexcel/biobb_io}, +}</citation> + </citations> +</tool> |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde biobb_mdrun.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/biobb_mdrun.xml Fri Apr 12 07:18:48 2019 -0400 |
| [ |
| @@ -0,0 +1,96 @@ +<tool id="biobb_mdrun" name="Mdrun" version="0.1.5" > + <description>: performs molecular dynamics simulations from an input Gromacs TPR file. </description> + <requirements> + <requirement type="binary">docker</requirement> + </requirements> + <command detect_errors="aggressive"> + ln -f -s ${inputname} ${inputname}.${inputname.ext}; + #if $config.sele == "option1": + ln -s -f ${config.properties} ${config.properties}.${config.properties.ext}; + #end if + docker run -v $__root_dir__/database/files:$__root_dir__/database/files quay.io/biocontainers/biobb_md:0.1.5--py_0 mdrun --input_tpr_path $inputname.${inputname.ext} + #if $config.sele == "option1": + --config ${config.properties}.${config.properties.ext} + #else if $config.sele == "option2": + --config ${config.jsonstr} + #end if + --output_log_path $__root_dir__/database/files/000/$outname_log + --output_gro_path $__root_dir__/database/files/000/$outname + --output_trr_path $__root_dir__/database/files/000/$outname_trr + --output_edr_path $__root_dir__/database/files/000//$outname_edr + --output_xtc_path $__root_dir__/database/files/000/$outname_xtc + --output_cpt_path $__root_dir__/database/files/000/$outname_cpt; + #if $config.sele == "option1": + rm -f ${config.properties}.${config.properties.ext}; + #end if +rm -f ${inputname}.${inputname.ext}; +mv $__root_dir__/database/files/000/$outname $output; +mv $__root_dir__/database/files/000/$outname_trr $output_trr; +mv $__root_dir__/database/files/000//$outname_edr $output_edr; +mv $__root_dir__/database/files/000/$outname_xtc $output_xtc; +mv $__root_dir__/database/files/000/$outname_cpt $output_cpt; +mv $__root_dir__/database/files/000/$outname_log $output_log + </command> + <inputs> + <param name="inputname" type="data" format="tpr" label="TPR file" help="Select your portable binary run input file. Format: [input].tpr"/> + <param name="outname" type="text" value="mdrun.gro" label="Output GRO name" help="Name for the Output GROMACS structure. Format: [output].gro "/> + <param name="outname_trr" type="text" value="mdrun.trr" label="Output TRR name" help="Name for the Output GROMACS uncompressed raw. Format: [output].trr"/> + <param name="outname_edr" type="text" value="mdrun.edr" label="Output EDR name" help="Name for the Output GROMACS portable energy file. Format: [output].edr"/> + <param name="outname_xtc" type="text" value="mdrun.xtc" optional="True" label="Output XTC name" help="Name for the Output GROMACS compressed trajectory file. Format: [output].xtc"/> + <param name="outname_cpt" type="text" value="mdrun.cpt" optional="True" label="Output CPT name" help="Name for the Output GROMACS checkpoint file. Format: [output].cpt"/> + <param name="outname_log" type="text" value="mdrun.log" label="Output LOG name" help="Name for the Output GROMACS trajectory file. Format: [output].log"/> + <conditional name="config"> + <param name="sele" type="select" label="Take tool settings:" help="Select where tool settings are to be read from"> + <option value="option1">from configuration file</option> + <option value="option2">from JSON string</option> + <option value="option3" selected="true">by default</option> + </param> + <when value="option1"> + <param name="properties" type="data" format="yml,json" optional="false" label="Configuration file" help="File containing tool settings. See below for the syntax"/> + </when> + <when value="option2"> + <param name="jsonstr" type="text" value="{}" optional="false" label="JSON string" help="JSON string containing tool settings. See below for the syntax"/> + </when> + <when value="option3"> + </when> + </conditional> + </inputs> + <outputs> + <data name="output" format="gro" label="${outname}"/> + <data name="output_trr" format="trr" label="${outname_trr}"/> + <data name="output_edr" format="edr" label="${outname_edr}"/> + <data name="output_xtc" format="xtc" label="${outname_xtc}"/> + <data name="output_cpt" format="cpt" label="${outname_cpt}"/> + <data name="output_log" format="log" label="${outname_log}"/> + </outputs> + <tests> + <test> + </test> + </tests> + <help> +.. class:: warningmark + + +Check the syntax for setting the tool parameters at the original library documentation: https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.mdrun + +----- + +.. image:: ${static_path}/images/biobb.png + :height: 57 + :width: 150 + + +**https://bioexcel.eu** + </help> + <citations> + <citation type="bibtex"> +@misc{githubbiobb, + author = {Andrio P, Hospital A, Gelpi JL}, + year = {2019}, + title = {biobb: BioExcel building blocks }, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/bioexcel/biobb_io}, +}</citation> + </citations> +</tool> |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde biobb_mutate.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/biobb_mutate.xml Fri Apr 12 07:18:48 2019 -0400 |
| [ |
| @@ -0,0 +1,76 @@ +<tool id="biobb_mutate" name="Mutate" version="0.1.5" > + <description>: mutate one aminoacid by another</description> + <requirements> + <requirement type="binary">docker</requirement> + </requirements> + <command detect_errors="aggressive"> + ln -f -s ${inputname} ${inputname}.${inputname.ext}; + #if $config.sele == "option1": + ln -s -f ${config.properties} ${config.properties}.${config.properties.ext}; + #end if + docker run -v $__root_dir__/database/files:$__root_dir__/database/files quay.io/biocontainers/biobb_model:0.1.5--py_0 mutate --input_pdb_path $inputname.${inputname.ext} + #if $config.sele == "option1": + --config ${config.properties}.${config.properties.ext} + #else if $config.sele == "option2": + --config ${config.jsonstr} + #end if + --output_pdb_path $output; + #if $config.sele == "option1": + rm -f ${config.properties}.${config.properties.ext}; + #end if + rm -f ${inputname}.${inputname.ext} + </command> + <inputs> + <param name="outname" type="text" value="myMutate.pdb" label="Output PDB name" help="Name for the Output list. Format: [output].pdb "/> + <param name="inputname" type="data" format="pdb" label="Input PDB file" help="Select your input file. Format: [input].pdb"/> + <conditional name="config"> + <param name="sele" type="select" label="Take tool settings:" help="Select where tool settings are to be read from"> + <option value="option1">from configuration file</option> + <option value="option2">from JSON string</option> + <option value="option3" selected="true">by default</option> + </param> + <when value="option1"> + <param name="properties" type="data" format="yml,json" optional="false" label="Configuration file" help="File containing tool settings. See below for the syntax"/> + </when> + <when value="option2"> + <param name="jsonstr" type="text" value="{}" optional="false" label="JSON string" help="JSON string containing tool settings. See below for the syntax"/> + </when> + <when value="option3"> + </when> + + </conditional> + </inputs> + <outputs> + <data name="output" format="pdb" label="${outname}"/> + </outputs> + <tests> + <test> + </test> + </tests> + <help> +.. class:: warningmark + + +Check the syntax for setting the tool parameters at the original library documentation: https://biobb-model.readthedocs.io/en/latest/model.html#module-model.mutate + +----- + +.. image:: ${static_path}/images/biobb.png + :height: 57 + :width: 150 + + +**https://bioexcel.eu** + </help> + <citations> + <citation type="bibtex"> +@misc{githubbiobb, + author = {Andrio P, Hospital A, Gelpi JL}, + year = {2019}, + title = {biobb: BioExcel building blocks }, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/bioexcel/biobb_io}, +}</citation> + </citations> +</tool> |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde biobb_ndx2resttop.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/biobb_ndx2resttop.xml Fri Apr 12 07:18:48 2019 -0400 |
| [ |
| @@ -0,0 +1,78 @@ +<tool id="biobb_ndx2resttop" name="Ndx2resttop" version="0.1.5" > + <description>: creates a Gromacs topology applying the force restrains</description> + <requirements> + <requirement type="binary">docker</requirement> + </requirements> + <command detect_errors="aggressive"> + ln -f -s ${inputname} ${inputname}.${inputname.ext}; + ln -f -s ${inputzip} ${inputzip}.${inputzip.ext}; + #if $config.sele == "option1": + ln -s -f ${config.properties} ${config.properties}.${config.properties.ext}; + #end if + docker run -v $__root_dir__/database/files:$__root_dir__/database/files quay.io/biocontainers/biobb_md:0.1.5--py_0 ndx2resttop --input_ndx_path $inputname.${inputname.ext} --input_top_zip_path ${inputzip}.${inputzip.ext} + #if $config.sele == "option1": + --config ${config.properties}.${config.properties.ext} + #else if $config.sele == "option2": + --config ${config.jsonstr} + #end if + --output_top_zip_path $output; + #if $config.sele == "option1": + rm -f ${config.properties}.${config.properties.ext}; + #end if + rm -f ${inputname}.${inputname.ext} ${inputzip}.${inputzip.ext} + </command> + <inputs> + <param name="outname" type="text" value="myNdx2resttop.zip" label="Output ZIP name" help="Name for the Output TOP topology. Format: [output].zip "/> + <param name="inputname" type="data" format="ndx" label="Index file" help="Select your input index file. Format: [input].ndx"/> + <param name="inputzip" type="data" format="zip" label="Input TOP file" help="Select your input TOP topology. Format: [input].zip"/> + <conditional name="config"> + <param name="sele" type="select" label="Take tool settings:" help="Select where tool settings are to be read from"> + <option value="option1">from configuration file</option> + <option value="option2">from JSON string</option> + <option value="option3" selected="true">by default</option> + </param> + <when value="option1"> + <param name="properties" type="data" format="yml,json" optional="false" label="Configuration file" help="File containing tool settings. See below for the syntax"/> + </when> + <when value="option2"> + <param name="jsonstr" type="text" value="{}" optional="false" label="JSON string" help="JSON string containing tool settings. See below for the syntax"/> + </when> + <when value="option3"> + </when> + + </conditional> + </inputs> + <outputs> + <data name="output" format="zip" label="${outname}"/> + </outputs> + <tests> + <test> + </test> + </tests> + <help> +.. class:: warningmark + + +Check the syntax for setting the tool parameters at the original library documentation: https//biobb-md.readthedocs.io/en/latest/gromacs_extra.html#gromacs-extra-ndx2resttop-module + +----- + +.. image:: ${static_path}/images/biobb.png + :height: 57 + :width: 150 + + +**https://bioexcel.eu** + </help> + <citations> + <citation type="bibtex"> +@misc{githubbiobb, + author = {Andrio P, Hospital A, Gelpi JL}, + year = {2019}, + title = {biobb: BioExcel building blocks }, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/bioexcel/biobb_io}, +}</citation> + </citations> +</tool> |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde biobb_pdb.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/biobb_pdb.xml Fri Apr 12 07:18:48 2019 -0400 |
| [ |
| @@ -0,0 +1,72 @@ +<tool id="biobb_pdb" name="pdb" version="0.1.3" > + <description>: get PDB from rcsb.org</description> + <requirements> + <requirement type="binary">docker</requirement> + </requirements> + <command detect_errors="aggressive"> + #if $config.sele == "option1": + ln -s -f ${config.properties} ${config.properties}.${config.properties.ext}; + #end if + docker run -v $__root_dir__/database/files:$__root_dir__/database/files quay.io/biocontainers/biobb_io:0.1.3--py_0 pdb + #if $config.sele == "option1": + --config ${config.properties}.${config.properties.ext} + #else if $config.sele == "option2": + --config ${config.jsonstr} + #end if + --output_pdb_path $output; + #if $config.sele == "option1": + rm -f ${config.properties}.${config.properties.ext}; + #end if + </command> + <inputs> + <param name="outname" type="text" value="myStructure.pdb" label="Output PDB name" help="Name for the Output list. Format: [output].pdb "/> + <conditional name="config"> + <param name="sele" type="select" label="Take tool settings:" help="Select where tool settings are to be read from"> + <option value="option1">from configuration file</option> + <option value="option2">from JSON string</option> + <option value="option3" selected="true">by default</option> + </param> + <when value="option1"> + <param name="properties" type="data" format="yml,json" optional="false" label="Configuration file" help="File containing tool settings. See below for the syntax"/> + </when> + <when value="option2"> + <param name="jsonstr" type="text" value="{}" optional="false" label="JSON string" help="JSON string containing tool settings. See below for the syntax"/> + </when> + <when value="option3"> + </when> + </conditional> + </inputs> + <outputs> + <data name="output" format="pdb" label="${outname}"/> + </outputs> + <tests> + <test> + </test> + </tests> + <help> +.. class:: warningmark + + +Check the syntax for setting the tool parameters at the original library documentation: https://biobb-io.readthedocs.io/en/latest/mmb_api.html#module-mmb_api.pdb_variants + +----- + +.. image:: ${static_path}/images/biobb.png + :height: 57 + :width: 150 + + +**https://bioexcel.eu** + </help> + <citations> + <citation type="bibtex"> +@misc{githubbiobb, + author = {Andrio P, Hospital A, Gelpi JL}, + year = {2019}, + title = {biobb: BioExcel building blocks }, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/bioexcel/biobb_io}, +}</citation> + </citations> +</tool> |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde biobb_pdb2gmx.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/biobb_pdb2gmx.xml Fri Apr 12 07:18:48 2019 -0400 |
| [ |
| @@ -0,0 +1,80 @@ +<tool id="biobb_pdb2gmx" name="Pdb2gmx" version="0.1.5" > + <description>: creates a ZIP Gromacs topology from a given PDB file. </description> + <requirements> + <requirement type="binary">docker</requirement> + </requirements> + <command detect_errors="aggressive"> + ln -f -s ${inputname} ${inputname}.${inputname.ext}; + #if $config.sele == "option1": + ln -s -f ${config.properties} ${config.properties}.${config.properties.ext}; + #end if + docker run -v $__root_dir__/database/files:$__root_dir__/database/files quay.io/biocontainers/biobb_md:0.1.5--py_0 pdb2gmx --input_pdb_path $inputname.${inputname.ext} + #if $config.sele == "option1": + --config ${config.properties}.${config.properties.ext} + #else if $config.sele == "option2": + --config ${config.jsonstr} + #end if + --output_gro_path $__root_dir__/database/files/000/$outname + --output_top_zip_path $outputzip; + #if $config.sele == "option1": + rm -f ${config.properties}.${config.properties.ext}; + #end if + rm -f ${inputname}.${inputname.ext}; + mv $__root_dir__/database/files/000/$outname $output + </command> + <inputs> + <param name="outname" type="text" value="myPdb2gmx.gro" label="Output GRO name" help="Name for the Output GRO. Format: [output].gro "/> + <param name="outzip" type="text" value="myPdb2gmx.zip" label="Output ZIP name" help="Name for the Output TOP topology. Format: [output].zip"/> + <param name="inputname" type="data" format="pdb" label="Input PDB file" help="Select your input PDB file. Format: [input].pdb"/> + <conditional name="config"> + <param name="sele" type="select" label="Take tool settings:" help="Select where tool settings are to be read from"> + <option value="option1">from configuration file</option> + <option value="option2">from JSON string</option> + <option value="option3" selected="true">by default</option> + </param> + <when value="option1"> + <param name="properties" type="data" format="yml,json" optional="false" label="Configuration file" help="File containing tool settings. See below for the syntax"/> + </when> + <when value="option2"> + <param name="jsonstr" type="text" value="{}" optional="false" label="JSON string" help="JSON string containing tool settings. See below for the syntax"/> + </when> + <when value="option3"> + </when> + + </conditional> + </inputs> + <outputs> + <data name="output" format="gro" label="${outname}"/> + <data name="outputzip" format="zip" label="${outzip}"/> + </outputs> + <tests> + <test> + </test> + </tests> + <help> +.. class:: warningmark + + +Check the syntax for setting the tool parameters at the original library documentation: https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.pdb2gmx + +----- + +.. image:: ${static_path}/images/biobb.png + :height: 57 + :width: 150 + + +**https://bioexcel.eu** + </help> + <citations> + <citation type="bibtex"> +@misc{githubbiobb, + author = {Andrio P, Hospital A, Gelpi JL}, + year = {2019}, + title = {biobb: BioExcel building blocks }, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/bioexcel/biobb_io}, +}</citation> + </citations> +</tool> |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde biobb_pdb_cluster.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/biobb_pdb_cluster.xml Fri Apr 12 07:18:48 2019 -0400 |
| [ |
| @@ -0,0 +1,72 @@ +<tool id="biobb_pdb_cluster" name="pdb cluster" version="0.1.3" > + <description>: get zip from mmb.irbbarcelona.org</description> + <requirements> + <requirement type="binary">docker</requirement> + </requirements> + <command detect_errors="aggressive"> + #if $config.sele == "option1": + ln -s -f ${config.properties} ${config.properties}.${config.properties.ext}; + #end if + docker run -v $__root_dir__/database/files:$__root_dir__/database/files quay.io/biocontainers/biobb_io:0.1.3--py_0 pdb_cluster_zip + #if $config.sele == "option1": + --config ${config.properties}.${config.properties.ext} + #else if $config.sele == "option2": + --config ${config.jsonstr} + #end if + --output_pdb_zip_path $output; + #if $config.sele == "option1": + rm -f ${config.properties}.${config.properties.ext}; + #end if + </command> + <inputs> + <param name="outname" type="text" value="myCluster.zip" label="Output ZIP name" help="Name for the Output list. Format: [output].zip "/> + <conditional name="config"> + <param name="sele" type="select" label="Take tool settings:" help="Select where tool settings are to be read from"> + <option value="option1">from configuration file</option> + <option value="option2">from JSON string</option> + <option value="option3" selected="true">by default</option> + </param> + <when value="option1"> + <param name="properties" type="data" format="yml,json" optional="false" label="Configuration file" help="File containing tool settings. See below for the syntax"/> + </when> + <when value="option2"> + <param name="jsonstr" type="text" value="{}" optional="false" label="JSON string" help="JSON string containing tool settings. See below for the syntax"/> + </when> + <when value="option3"> + </when> + </conditional> + </inputs> + <outputs> + <data name="output" format="zip" label="${outname}"/> + </outputs> + <tests> + <test> + </test> + </tests> + <help> +.. class:: warningmark + + +Check the syntax for setting the tool parameters at the original library documentation: https://biobb-io.readthedocs.io/en/latest/mmb_api.html#module-mmb_api.pdb_cluster_zip + +----- + +.. image:: ${static_path}/images/biobb.png + :height: 57 + :width: 150 + + +**https://bioexcel.eu** + </help> + <citations> + <citation type="bibtex"> +@misc{githubbiobb, + author = {Andrio P, Hospital A, Gelpi JL}, + year = {2019}, + title = {biobb: BioExcel building blocks }, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/bioexcel/biobb_io}, +}</citation> + </citations> +</tool> |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde biobb_pdb_variants.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/biobb_pdb_variants.xml Fri Apr 12 07:18:48 2019 -0400 |
| [ |
| @@ -0,0 +1,72 @@ +<tool id="biobb_pdb_variants" name="pdb variants" version="0.1.3" > + <description>: get list of mutants from mmb.irbbarcelona.org</description> + <requirements> + <requirement type="binary">docker</requirement> + </requirements> + <command detect_errors="aggressive"> + #if $config.sele == "option1": + ln -s -f ${config.properties} ${config.properties}.${config.properties.ext}; + #end if + docker run -v $__root_dir__/database/files:$__root_dir__/database/files quay.io/biocontainers/biobb_io:0.1.3--py_0 pdb_variants + #if $config.sele == "option1": + --config ${config.properties}.${config.properties.ext} + #else if $config.sele == "option2": + --config ${config.jsonstr} + #end if + --output_mutations_list_txt $output; + #if $config.sele == "option1": + rm -f ${config.properties}.${config.properties.ext}; + #end if + </command> + <inputs> + <param name="outname" type="text" value="myMutants.txt" label="Output TXT name" help="Name for the Output list. Format: [output].txt "/> + <conditional name="config"> + <param name="sele" type="select" label="Take tool settings:" help="Select where tool settings are to be read from"> + <option value="option1">from configuration file</option> + <option value="option2">from JSON string</option> + <option value="option3" selected="true">by default</option> + </param> + <when value="option1"> + <param name="properties" type="data" format="yml,json" optional="false" label="Configuration file" help="File containing tool settings. See below for the syntax"/> + </when> + <when value="option2"> + <param name="jsonstr" type="text" value="{}" optional="false" label="JSON string" help="JSON string containing tool settings. See below for the syntax"/> + </when> + <when value="option3"> + </when> + </conditional> + </inputs> + <outputs> + <data name="output" format="txt" label="${outname}"/> + </outputs> + <tests> + <test> + </test> + </tests> + <help> +.. class:: warningmark + + +Check the syntax for setting the tool parameters at the original library documentation: https://biobb-io.readthedocs.io/en/latest/mmb_api.html#module-mmb_api.pdb_variants + +----- + +.. image:: ${static_path}/images/biobb.png + :height: 57 + :width: 150 + + +**https://bioexcel.eu** + </help> + <citations> + <citation type="bibtex"> +@misc{githubbiobb, + author = {Andrio P, Hospital A, Gelpi JL}, + year = {2019}, + title = {biobb: BioExcel building blocks }, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/bioexcel/biobb_io}, +}</citation> + </citations> +</tool> |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde biobb_rms.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/biobb_rms.xml Fri Apr 12 07:18:48 2019 -0400 |
| [ |
| @@ -0,0 +1,80 @@ +<tool id="biobb_rms" name="RMS" version="0.1.3"> + <description>: performs a RMSD analysis. </description> + <requirements> + <requirement type="binary">docker</requirement> + </requirements> + <command detect_errors="aggressive"> + ln -f -s ${inputname} ${inputname}.${inputname.ext}; + ln -f -s ${inputtraj} ${inputtraj}.${inputtraj.ext}; + #if $config.sele == "option1": + ln -s -f ${config.properties} ${config.properties}.${config.properties.ext}; + #end if + docker run -v $__root_dir__/database/files:$__root_dir__/database/files mmbirb/biobb_analysis:0.1.3 rms --input_structure_path $inputname.${inputname.ext} --input_traj_path ${inputtraj}.${inputtraj.ext} + #if $config.sele == "option1": + --config ${config.properties}.${config.properties.ext} + #else if $config.sele == "option2": + --config ${config.jsonstr} + #end if + --output_xvg_path $__root_dir__/database/files/000/$outname; + #if $config.sele == "option1": + rm -f ${config.properties}.${config.properties.ext}; + #end if + rm -f ${inputname}.${inputname.ext} ${inputtraj}.${inputtraj.ext}; + mv $__root_dir__/database/files/000/$outname $output + </command> + <inputs> + <param name="inputname" type="data" format="gro,pdb,tpr" label="Structure file" help="Select your input structure file. Format: [input].gro or [input].pdb or [input].tpr"/> + <param name="inputtraj" type="data" format="trr,xtc" label="Trajectory file" help="Select your input GROMACS trajectory. Format: [input].trr or [input].xtc"/> + <param name="outname" type="text" value="rms.xvg" label="Output XVG name" help="Name for the XVG Output. Format: [output].xvg "/> + <conditional name="config"> + <param name="sele" type="select" label="Take tool settings:" help="Select where tool settings are to be read from"> + <option value="option1">from configuration file</option> + <option value="option2">from JSON string</option> + <option value="option3" selected="true">by default</option> + </param> + <when value="option1"> + <param name="properties" type="data" format="yml,json" optional="false" label="Configuration file" help="File containing tool settings. See below for the syntax"/> + </when> + <when value="option2"> + <param name="jsonstr" type="text" value="{}" optional="false" label="JSON string" help="JSON string containing tool settings. See below for the syntax"/> + </when> + <when value="option3"> + </when> + + </conditional> + </inputs> + <outputs> + <data name="output" format="xvg" label="${outname}"/> + + </outputs> + <tests> + <test> + </test> + </tests> + <help> +.. class:: warningmark + + +Check the syntax for setting the tool parameters at the original library documentation: https://biobb-analysis.readthedocs.io/en/latest/gromacs.html#module-gromacs.rms + +----- + +.. image:: ${static_path}/images/biobb.png + :height: 57 + :width: 150 + + +**https://bioexcel.eu** + </help> + <citations> + <citation type="bibtex"> +@misc{githubbiobb, + author = {Andrio P, Hospital A, Gelpi JL}, + year = {2019}, + title = {biobb: BioExcel building blocks }, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/bioexcel/biobb_io}, +}</citation> + </citations> +</tool> |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde biobb_solvate.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/biobb_solvate.xml Fri Apr 12 07:18:48 2019 -0400 |
| [ |
| @@ -0,0 +1,83 @@ +<tool id="biobb_solvate" name="Solvate" version="0.1.5"> + <description>: creates a Gromacs topology file adding solvent molecules to a given input. </description> + <requirements> + <requirement type="binary">docker</requirement> + </requirements> + <command detect_errors="aggressive"> + ln -f -s ${inputname} ${inputname}.${inputname.ext}; + ln -f -s ${inputzip} ${inputzip}.${inputzip.ext}; + #if $config.sele == "option1": + ln -s -f ${config.properties} ${config.properties}.${config.properties.ext}; + #end if + docker run -v $__root_dir__/database/files:$__root_dir__/database/files quay.io/biocontainers/biobb_md:0.1.5--py_0 solvate --input_solute_gro_path $inputname.${inputname.ext} --input_top_zip_path ${inputzip}.${inputzip.ext} + #if $config.sele == "option1": + --config ${config.properties}.${config.properties.ext} + #else if $config.sele == "option2": + --config ${config.jsonstr} + #end if + --output_gro_path $__root_dir__/database/files/000/$outname + --output_top_zip_path $outputzip; + #if $config.sele == "option1": + rm -f ${config.properties}.${config.properties.ext}; + #end if + rm -f ${inputname}.${inputname.ext} ${inputzip}.${inputzip.ext}; + mv $__root_dir__/database/files/000/$outname $output + </command> + <inputs> + <param name="outname" type="text" value="mySolvate.gro" label="Output GRO name" help="Name for the Output GRO. Format: [output].gro "/> + <param name="outnamezip" type="text" value="solvate.zip" label="Output ZIP name" help="Name for the Output topology in ZIP. Format: [output].zip "/> + <param name="inputname" type="data" format="gro" label="Input GRO file" help="Select your input GRO file. Format: [input].gro"/> + <param name="inputzip" type="data" format="zip" label="Topology file" help="Select your input TOP topology ZIP. Format: [input].zip"/> + <conditional name="config"> + <param name="sele" type="select" label="Take tool settings:" help="Select where tool settings are to be read from"> + <option value="option1">from configuration file</option> + <option value="option2">from JSON string</option> + <option value="option3" selected="true">by default</option> + </param> + <when value="option1"> + <param name="properties" type="data" format="yml,json" optional="false" label="Configuration file" help="File containing tool settings. See below for the syntax"/> + </when> + <when value="option2"> + <param name="jsonstr" type="text" value="{}" optional="false" label="JSON string" help="JSON string containing tool settings. See below for the syntax"/> + </when> + <when value="option3"> + </when> + + </conditional> + </inputs> + <outputs> + <data name="output" format="gro" label="${outname}"/> + <data name="outputzip" format="zip" label="${outnamezip}"/> + + </outputs> + <tests> + <test> + </test> + </tests> + <help> +.. class:: warningmark + + +Check the syntax for setting the tool parameters at the original library documentation: https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.solvate + +----- + +.. image:: ${static_path}/images/biobb.png + :height: 57 + :width: 150 + + +**https://bioexcel.eu** + </help> + <citations> + <citation type="bibtex"> +@misc{githubbiobb, + author = {Andrio P, Hospital A, Gelpi JL}, + year = {2019}, + title = {biobb: BioExcel building blocks }, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/bioexcel/biobb_io}, +}</citation> + </citations> +</tool> |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde test-data/1.pdb_Download_initial_structure.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1.pdb_Download_initial_structure.json Fri Apr 12 07:18:48 2019 -0400 |
| b |
| @@ -0,0 +1,2 @@ +{"pdb_code" : "1aki"} + |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde test-data/11.grompp_preprocess_temperature_eq.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/11.grompp_preprocess_temperature_eq.json Fri Apr 12 07:18:48 2019 -0400 |
| b |
| @@ -0,0 +1,1 @@ +{"mdp": {"type":"nvt", "nsteps":"500"}} |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde test-data/13.grompp_preprocess_pressure_eq.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/13.grompp_preprocess_pressure_eq.json Fri Apr 12 07:18:48 2019 -0400 |
| b |
| @@ -0,0 +1,1 @@ +{"mdp": {"type":"npt", "nsteps":"500"}} |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde test-data/15.grompp_preprocess_free_dynamics.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/15.grompp_preprocess_free_dynamics.json Fri Apr 12 07:18:48 2019 -0400 |
| b |
| @@ -0,0 +1,1 @@ +{"mdp": {"type":"free", "nsteps":"5000"}} |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde test-data/3.mutate_modelling_mutation_list.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/3.mutate_modelling_mutation_list.json Fri Apr 12 07:18:48 2019 -0400 |
| b |
| @@ -0,0 +1,2 @@ +{"mutation_list": "A:Val2Ala"} + |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde test-data/7.grompp_preprocess_iongeneration.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/7.grompp_preprocess_iongeneration.json Fri Apr 12 07:18:48 2019 -0400 |
| b |
| @@ -0,0 +1,2 @@ +{"mdp": {"type":"minimization", "nsteps":"500"}} + |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde test-data/8.genion_iongeneration.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/8.genion_iongeneration.json Fri Apr 12 07:18:48 2019 -0400 |
| b |
| @@ -0,0 +1,1 @@ +{"neutral": "True", "concentration": 0.05} |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde test-data/9.grompp_preprocess_energymin.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/9.grompp_preprocess_energymin.json Fri Apr 12 07:18:48 2019 -0400 |
| b |
| @@ -0,0 +1,1 @@ +{"mdp": {"type":"minimization", "nsteps":"500", "emtol":"500"}} |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde test-data/GNUSparseFile.0/biobb_genion_input.tpr |
| b |
| Binary file test-data/GNUSparseFile.0/biobb_genion_input.tpr has changed |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde test-data/GNUSparseFile.0/biobb_grompp_myGrompp.tpr |
| b |
| Binary file test-data/GNUSparseFile.0/biobb_grompp_myGrompp.tpr has changed |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde test-data/GNUSparseFile.0/biobb_make-ndx_input.tpr |
| b |
| Binary file test-data/GNUSparseFile.0/biobb_make-ndx_input.tpr has changed |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde test-data/biobb_cluster_input.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/biobb_cluster_input.gro Fri Apr 12 07:18:48 2019 -0400 |
| b |
| b'@@ -0,0 +1,71693 @@\n+Protein in water\n+71690\n+ 1SER N 1 2.406 1.298 5.582 0.1451 -0.0207 0.9647\n+ 1SER H1 2 2.431 1.330 5.489 1.4799 -0.0517 1.2833\n+ 1SER H2 3 2.480 1.328 5.644 2.3000 -2.1141 -0.4143\n+ 1SER H3 4 2.400 1.197 5.585 -1.2202 -0.1270 -1.8923\n+ 1SER CA 5 2.279 1.359 5.622 -0.1113 0.2348 -0.2099\n+ 1SER HA 6 2.202 1.343 5.546 -0.8951 1.3824 0.3191\n+ 1SER CB 7 2.232 1.279 5.743 0.1444 0.0378 -0.2400\n+ 1SER HB1 8 2.317 1.266 5.810 2.1329 -0.4234 -2.6959\n+ 1SER HB2 9 2.203 1.181 5.708 0.6973 0.2813 -1.4227\n+ 1SER OG 10 2.124 1.343 5.808 0.0490 -0.2760 -0.0882\n+ 1SER HG 11 2.042 1.315 5.766 0.1020 0.9942 -1.1044\n+ 1SER C 12 2.293 1.509 5.639 -0.0784 0.2445 -0.3220\n+ 1SER O 13 2.382 1.557 5.711 -0.0905 -0.0437 -0.1128\n+ 2GLU N 14 2.204 1.579 5.569 -1.0101 0.0027 0.6049\n+ 2GLU H 15 2.128 1.528 5.525 -2.0684 1.3046 0.8673\n+ 2GLU CA 16 2.204 1.722 5.550 -0.2983 -0.0434 0.2569\n+ 2GLU HA 17 2.252 1.765 5.638 1.1870 -2.0755 0.5050\n+ 2GLU CB 18 2.294 1.743 5.428 -0.1253 0.2022 0.4263\n+ 2GLU HB1 19 2.278 1.668 5.351 -2.1944 1.3930 -0.3946\n+ 2GLU HB2 20 2.397 1.748 5.464 -0.4181 0.4755 1.2592\n+ 2GLU CG 21 2.271 1.873 5.351 -0.4888 0.1839 0.5036\n+ 2GLU HG1 22 2.286 1.954 5.421 0.6005 1.7489 -1.4349\n+ 2GLU HG2 23 2.168 1.877 5.316 -0.6776 -0.9532 0.8790\n+ 2GLU CD 24 2.366 1.890 5.233 0.2542 -0.1468 1.0479\n+ 2GLU OE1 25 2.395 1.788 5.168 -0.5433 0.1057 0.2680\n+ 2GLU OE2 26 2.413 2.002 5.202 0.0681 -0.3192 0.1180\n+ 2GLU C 27 2.068 1.783 5.519 -0.0257 0.3115 -0.2626\n+ 2GLU O 28 1.985 1.718 5.456 0.7467 -0.9611 0.0011\n+ 3ALA N 29 2.044 1.908 5.559 0.1424 0.5057 -0.7696\n+ 3ALA H 30 2.120 1.956 5.604 1.2585 -1.4156 -0.4991\n+ 3ALA CA 31 1.915 1.973 5.542 -0.3063 -0.1742 -0.0501\n+ 3ALA HA 32 1.842 1.915 5.598 -0.5349 0.0937 -0.0698\n+ 3ALA CB 33 1.934 2.109 5.609 0.1593 -0.3039 0.0866\n+ 3ALA HB1 34 1.842 2.166 5.595 -0.8598 -1.9311 -0.1555\n+ 3ALA HB2 35 1.948 2.097 5.717 0.4126 -0.3115 0.0529\n+ 3ALA HB3 36 2.018 2.168 5.574 0.2273 0.6963 1.8346\n+ 3ALA C 37 1.879 2.003 5.397 -0.1969 0.1352 -0.0142\n+ 3ALA O 38 1.963 2.054 5.323 0.2950 -0.3282 0.2209\n+ 4GLU N 39 1.766 1.951 5.347 -0.2742 0.1302 0.1667\n+ 4GLU H 40 1.707 1.898 5.410 1.3132 -3.1774 -0.8993\n+ 4GLU CA 41 1.730 1.964 5.208 0.4733 -0.0473 -0.0502\n+ 4GLU HA 42 1.811 1.951 5.136 -0.8231 0.5521 -1.7124\n+ 4GLU CB 43 1.635 1.849 5.174 0.3897 -0.0603 0.2262\n+ 4GLU HB1 44 1.625 1.849 5.065 0.6754 -0.9757 0.1863\n+ 4GLU HB2 45 1.541 1.864 5.226 0.9600 -1.7750 1.8698\n+ 4GLU CG 46 1.684 1.709 5.210 -0.1734 -0.2366 0.3133\n+ 4GLU HG1 47 1.661 1.688 5.315 -0.3792 1.2707 0.5866\n+ 4GLU HG2 48 1.793 1.719 5.206 -0.2614 1.3652 1.0880\n+ 4GLU CD 49 1.614 1.604 5.125 -0.1008 -0.2047 0.2148\n+ 4GLU OE1 50 1.492 1.621 5.107 0.1106 0.3637 -0.7477\n+ 4GLU OE2 51 1.672 1.504 5.076 0.2933 0.2410 -0.2501\n+ 4GLU C 52 1.672 2.101 5.175 0.7932 0.1248 0.1062\n+ 4GLU O 53 1.660 2.137 5.058 0.0637 -0.2787 0.0555\n+ 5ASP N 54 1.645 2.186 5.274 0.0271 -0.2312 0.2104\n+ 5ASP H 55 1.654 2.152 5.369 -0.2937 3.4754 1.7602\n+ 5ASP CA 56 1.599 2.322 5.253 0.2833 -0.1433 0.2011\n+ 5ASP HA 57 1.510 2.'..b' 8.760 7.631 7.921 0.5593 0.1717 0.2566\n+23559SOL HW171635 8.661 7.630 7.913 0.6365 -0.4233 -0.7690\n+23559SOL HW271636 8.795 7.722 7.900 0.1537 0.7297 1.8880\n+23560SOL OW71637 7.837 7.960 8.333 -0.4486 -0.5402 0.0292\n+23560SOL HW171638 7.896 8.022 8.383 -0.8773 -1.5228 1.8158\n+23560SOL HW271639 7.876 7.942 8.243 1.0337 0.2127 0.4971\n+23561SOL OW71640 8.411 8.827 7.990 0.4208 -0.7506 0.4511\n+23561SOL HW171641 8.408 8.925 7.969 0.4629 -0.9522 -0.5672\n+23561SOL HW271642 8.332 8.803 8.047 1.0158 0.0691 1.6592\n+23562SOL OW71643 8.869 0.828 0.215 0.1582 0.3802 0.0503\n+23562SOL HW171644 8.966 0.844 0.197 0.3755 0.7389 1.3553\n+23562SOL HW271645 8.853 0.730 0.228 0.0564 0.1438 -1.6595\n+23563SOL OW71646 8.724 7.902 8.696 0.1021 -0.2398 -0.5517\n+23563SOL HW171647 8.671 7.986 8.683 -0.3050 -0.5996 -1.2700\n+23563SOL HW271648 8.714 7.843 8.615 2.3687 0.1016 -1.1532\n+23564SOL OW71649 8.382 7.918 7.447 -0.7326 -0.3587 -0.4197\n+23564SOL HW171650 8.469 7.888 7.487 -1.0150 -1.5562 -0.6705\n+23564SOL HW271651 8.395 8.007 7.404 -0.0076 0.1643 0.8398\n+23565SOL OW71652 7.570 8.202 8.519 -0.5501 -0.5421 -0.3418\n+23565SOL HW171653 7.533 8.135 8.584 0.5780 0.8218 1.8413\n+23565SOL HW271654 7.509 8.281 8.513 -0.0011 -0.0680 0.1491\n+23566SOL OW71655 7.367 7.479 7.788 0.2635 -0.4986 -0.4955\n+23566SOL HW171656 7.365 7.462 7.887 0.4491 -1.0854 -0.5912\n+23566SOL HW271657 7.275 7.467 7.750 -0.1408 1.1966 -0.1670\n+23567SOL OW71658 0.259 8.926 8.302 -0.0226 0.2050 -0.1480\n+23567SOL HW171659 0.300 8.990 8.367 -0.9011 -0.7849 1.4453\n+23567SOL HW271660 0.178 8.968 8.261 1.8957 1.8348 -2.6196\n+23568SOL OW71661 7.612 8.246 8.928 -0.3914 0.6939 -0.6676\n+23568SOL HW171662 7.519 8.211 8.936 -0.6597 1.2091 -1.4028\n+23568SOL HW271663 7.625 8.320 8.994 -0.9109 1.4300 -1.3524\n+23569SOL OW71664 8.550 7.575 8.654 -0.4971 0.0420 -0.3353\n+23569SOL HW171665 8.513 7.653 8.703 -1.6166 0.7822 -2.2616\n+23569SOL HW271666 8.502 7.564 8.566 3.2901 0.6002 -2.6835\n+23570SOL OW71667 8.891 7.142 8.741 -0.1219 -0.1925 1.0420\n+23570SOL HW171668 8.939 7.213 8.690 0.1491 -0.0887 1.4354\n+23570SOL HW271669 8.889 7.167 8.838 -1.3352 0.0107 0.9815\n+23571SOL OW71670 8.346 8.771 7.737 -0.2423 -0.5274 -0.0890\n+23571SOL HW171671 8.390 8.793 7.824 1.9320 1.2827 -1.5160\n+23571SOL HW271672 8.392 8.821 7.663 -2.2201 -1.7134 -2.2566\n+23572SOL OW71673 8.510 8.572 8.670 -0.0452 0.4206 -0.1934\n+23572SOL HW171674 8.486 8.625 8.589 -1.3447 2.2662 1.3221\n+23572SOL HW271675 8.452 8.599 8.746 0.0283 -2.4207 0.9892\n+23573SOL OW71676 8.729 7.473 7.700 0.0078 0.7352 0.0363\n+23573SOL HW171677 8.808 7.411 7.705 2.7949 4.0038 0.1462\n+23573SOL HW271678 8.730 7.535 7.779 -1.3491 2.3378 -1.1236\n+23574SOL OW71679 8.291 8.003 8.202 0.6695 -0.1348 -0.0296\n+23574SOL HW171680 8.339 8.067 8.142 0.6374 -1.1772 -1.2300\n+23574SOL HW271681 8.288 8.040 8.295 1.1542 1.3154 -0.5522\n+23575SOL OW71682 7.758 8.125 7.216 0.6581 0.1185 -0.3065\n+23575SOL HW171683 7.663 8.097 7.204 1.0699 -0.8943 -1.4143\n+23575SOL HW271684 7.807 8.055 7.269 0.6739 0.9038 0.7535\n+23576NA NA71685 1.504 4.959 3.101 -0.4335 -0.1540 0.8201\n+23577NA NA71686 1.650 6.672 7.136 0.2832 0.1370 -0.6779\n+23578NA NA71687 2.449 1.554 0.493 -0.0285 0.1871 0.0169\n+23579NA NA71688 1.808 3.155 4.161 -0.6016 -0.5202 0.0713\n+23580NA NA71689 7.900 5.218 2.045 0.4164 -0.1648 0.2341\n+23581NA NA71690 0.021 4.797 8.133 -0.0029 -0.4022 -0.2441\n+ 8.95366 8.95366 8.95366\n' |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde test-data/biobb_cluster_input.trr |
| b |
| Binary file test-data/biobb_cluster_input.trr has changed |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde test-data/biobb_cluster_myCluster.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/biobb_cluster_myCluster.pdb Fri Apr 12 07:18:48 2019 -0400 |
| b |
| b'@@ -0,0 +1,1202 @@\n+TITLE frame t= 0.000\n+REMARK THIS IS A SIMULATION BOX\n+CRYST1 89.435 89.435 89.435 90.00 90.00 90.00 P 1 1\n+MODEL 1\n+ATOM 1 N SER 1 -21.611 -32.909 10.197 1.00 0.00 \n+ATOM 2 H1 SER 1 -21.611 -32.849 9.189 1.00 0.00 \n+ATOM 3 H2 SER 1 -20.758 -32.491 10.541 1.00 0.00 \n+ATOM 4 H3 SER 1 -21.489 -33.900 10.350 1.00 0.00 \n+ATOM 5 CA SER 1 -22.830 -32.317 10.768 1.00 0.00 \n+ATOM 6 HA SER 1 -23.603 -32.507 10.024 1.00 0.00 \n+ATOM 7 CB SER 1 -23.182 -32.831 12.161 1.00 0.00 \n+ATOM 8 HB1 SER 1 -22.322 -32.804 12.831 1.00 0.00 \n+ATOM 9 HB2 SER 1 -23.445 -33.880 12.024 1.00 0.00 \n+ATOM 10 OG SER 1 -24.281 -32.125 12.690 1.00 0.00 \n+ATOM 11 HG SER 1 -25.061 -32.410 12.210 1.00 0.00 \n+ATOM 12 C SER 1 -22.594 -30.813 10.800 1.00 0.00 \n+ATOM 13 O SER 1 -21.537 -30.420 11.288 1.00 0.00 \n+ATOM 14 N GLU 2 -23.521 -30.006 10.280 1.00 0.00 \n+ATOM 15 H GLU 2 -24.418 -30.392 10.021 1.00 0.00 \n+ATOM 16 CA GLU 2 -23.461 -28.562 10.168 1.00 0.00 \n+ATOM 17 HA GLU 2 -23.016 -28.199 11.094 1.00 0.00 \n+ATOM 18 CB GLU 2 -22.554 -28.262 8.978 1.00 0.00 \n+ATOM 19 HB1 GLU 2 -23.116 -28.765 8.191 1.00 0.00 \n+ATOM 20 HB2 GLU 2 -21.578 -28.700 9.186 1.00 0.00 \n+ATOM 21 CG GLU 2 -22.249 -26.811 8.618 1.00 0.00 \n+ATOM 22 HG1 GLU 2 -21.969 -26.311 9.545 1.00 0.00 \n+ATOM 23 HG2 GLU 2 -23.213 -26.493 8.219 1.00 0.00 \n+ATOM 24 CD GLU 2 -21.202 -26.749 7.515 1.00 0.00 \n+ATOM 25 OE1 GLU 2 -20.979 -27.689 6.721 1.00 0.00 \n+ATOM 26 OE2 GLU 2 -20.434 -25.769 7.413 1.00 0.00 \n+ATOM 27 C GLU 2 -24.819 -27.896 9.999 1.00 0.00 \n+ATOM 28 O GLU 2 -25.673 -28.423 9.290 1.00 0.00 \n+ATOM 29 N ALA 3 -25.023 -26.736 10.628 1.00 0.00 \n+ATOM 30 H ALA 3 -24.296 -26.383 11.233 1.00 0.00 \n+ATOM 31 CA ALA 3 -25.951 -25.683 10.264 1.00 0.00 \n+ATOM 32 HA ALA 3 -26.909 -25.972 10.695 1.00 0.00 \n+ATOM 33 CB ALA 3 -25.410 -24.443 10.969 1.00 0.00 \n+ATOM 34 HB1 ALA 3 -25.968 -23.557 10.667 1.00 0.00 \n+ATOM 35 HB2 ALA 3 -25.591 -24.483 12.044 1.00 0.00 \n+ATOM 36 HB3 ALA 3 -24.331 -24.353 10.843 1.00 0.00 \n+ATOM 37 C ALA 3 -26.076 -25.444 8.767 1.00 0.00 \n+ATOM 38 O ALA 3 -25.175 -24.993 8.063 1.00 0.00 \n+ATOM 39 N GLU 4 -27.317 -25.650 8.319 1.00 0.00 \n+ATOM 40 H GLU 4 -28.063 -25.803 8.982 1.00 0.00 \n+ATOM 41 CA GLU 4 -27.610 -25.457 6.913 1.00 0.00 \n+ATOM 42 HA GLU 4 -26.759 -25.633 6.255 1.00 0.00 \n+ATOM 43 CB GLU 4 -28.683 -26.442 6.458 1.00 0.00 \n+ATOM 44 HB1 GLU 4 -28.735 -26.379 5.371 1.00 0.00 \n+ATOM 45 HB2 GLU 4 -29.687 -26.341 6.872 1.00 0.00 \n+ATOM 46 CG GLU 4 -28.183 -27.864 6.699 1.00 0.00 \n+ATOM 47 HG1 GLU 4 -28.158 -27.966 7.784 1.00 0.00 \n+ATOM 48 HG2 GLU 4 -27.243 -28.008 6.167 1.00 0.00 '..b'HG SER 75 -14.563 22.814 -15.470 1.00 0.00 \n+ATOM 1148 C SER 75 -11.171 20.633 -14.583 1.00 0.00 \n+ATOM 1149 O SER 75 -10.130 20.700 -15.233 1.00 0.00 \n+ATOM 1150 N ALA 76 -11.150 20.195 -13.321 1.00 0.00 \n+ATOM 1151 H ALA 76 -12.007 20.150 -12.789 1.00 0.00 \n+ATOM 1152 CA ALA 76 -9.957 19.809 -12.595 1.00 0.00 \n+ATOM 1153 HA ALA 76 -9.205 20.597 -12.627 1.00 0.00 \n+ATOM 1154 CB ALA 76 -10.339 19.430 -11.167 1.00 0.00 \n+ATOM 1155 HB1 ALA 76 -9.481 19.232 -10.525 1.00 0.00 \n+ATOM 1156 HB2 ALA 76 -10.995 20.148 -10.675 1.00 0.00 \n+ATOM 1157 HB3 ALA 76 -10.850 18.479 -11.316 1.00 0.00 \n+ATOM 1158 C ALA 76 -9.244 18.618 -13.219 1.00 0.00 \n+ATOM 1159 O ALA 76 -8.080 18.358 -12.924 1.00 0.00 \n+ATOM 1160 N VAL 77 -9.915 17.810 -14.043 1.00 0.00 \n+ATOM 1161 H VAL 77 -10.885 18.042 -14.206 1.00 0.00 \n+ATOM 1162 CA VAL 77 -9.378 16.664 -14.749 1.00 0.00 \n+ATOM 1163 HA VAL 77 -8.371 16.417 -14.414 1.00 0.00 \n+ATOM 1164 CB VAL 77 -10.358 15.501 -14.628 1.00 0.00 \n+ATOM 1165 HB VAL 77 -11.315 15.912 -14.950 1.00 0.00 \n+ATOM 1166 CG1 VAL 77 -9.944 14.280 -15.445 1.00 0.00 \n+ATOM 1167 1HG1 VAL 77 -10.698 13.496 -15.503 1.00 0.00 \n+ATOM 1168 2HG1 VAL 77 -9.774 14.535 -16.491 1.00 0.00 \n+ATOM 1169 3HG1 VAL 77 -9.051 13.770 -15.080 1.00 0.00 \n+ATOM 1170 CG2 VAL 77 -10.503 15.104 -13.162 1.00 0.00 \n+ATOM 1171 1HG2 VAL 77 -11.175 14.256 -13.024 1.00 0.00 \n+ATOM 1172 2HG2 VAL 77 -9.551 14.723 -12.793 1.00 0.00 \n+ATOM 1173 3HG2 VAL 77 -10.965 15.896 -12.572 1.00 0.00 \n+ATOM 1174 C VAL 77 -9.000 17.087 -16.162 1.00 0.00 \n+ATOM 1175 O VAL 77 -7.955 16.713 -16.689 1.00 0.00 \n+ATOM 1176 N ALA 78 -9.846 17.918 -16.776 1.00 0.00 \n+ATOM 1177 H ALA 78 -10.730 18.020 -16.300 1.00 0.00 \n+ATOM 1178 CA ALA 78 -9.643 18.342 -18.147 1.00 0.00 \n+ATOM 1179 HA ALA 78 -9.508 17.399 -18.677 1.00 0.00 \n+ATOM 1180 CB ALA 78 -10.944 18.945 -18.670 1.00 0.00 \n+ATOM 1181 HB1 ALA 78 -10.960 18.838 -19.755 1.00 0.00 \n+ATOM 1182 HB2 ALA 78 -11.843 18.534 -18.212 1.00 0.00 \n+ATOM 1183 HB3 ALA 78 -10.999 20.022 -18.513 1.00 0.00 \n+ATOM 1184 C ALA 78 -8.534 19.355 -18.395 1.00 0.00 \n+ATOM 1185 O ALA 78 -7.944 19.313 -19.473 1.00 0.00 \n+ATOM 1186 N ALA 79 -8.136 20.090 -17.355 1.00 0.00 \n+ATOM 1187 H ALA 79 -8.570 19.886 -16.466 1.00 0.00 \n+ATOM 1188 CA ALA 79 -7.009 20.998 -17.264 1.00 0.00 \n+ATOM 1189 HA ALA 79 -6.357 20.752 -18.102 1.00 0.00 \n+ATOM 1190 CB ALA 79 -7.465 22.414 -17.602 1.00 0.00 \n+ATOM 1191 HB1 ALA 79 -6.529 22.907 -17.865 1.00 0.00 \n+ATOM 1192 HB2 ALA 79 -8.099 22.354 -18.486 1.00 0.00 \n+ATOM 1193 HB3 ALA 79 -7.977 22.795 -16.718 1.00 0.00 \n+ATOM 1194 C ALA 79 -6.263 20.915 -15.940 1.00 0.00 \n+ATOM 1195 OC1 ALA 79 -6.737 21.560 -14.979 1.00 0.00 \n+ATOM 1196 OC2 ALA 79 -5.202 20.262 -15.848 1.00 0.00 \n+TER\n+ENDMDL\n' |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde test-data/biobb_editconf_input.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/biobb_editconf_input.gro Fri Apr 12 07:18:48 2019 -0400 |
| b |
| b'@@ -0,0 +1,1199 @@\n+Created with pdb2gmx building block\n+ 1196\n+ 1SER N 1 2.270 1.214 5.506\n+ 1SER H1 2 2.288 1.242 5.411\n+ 1SER H2 3 2.354 1.220 5.559\n+ 1SER H3 4 2.237 1.120 5.507\n+ 1SER CA 5 2.167 1.304 5.566\n+ 1SER HA 6 2.083 1.294 5.512\n+ 1SER CB 7 2.138 1.263 5.710\n+ 1SER HB1 8 2.222 1.264 5.765\n+ 1SER HB2 9 2.097 1.172 5.713\n+ 1SER OG 10 2.046 1.352 5.771\n+ 1SER HG 11 2.029 1.323 5.865\n+ 1SER C 12 2.215 1.448 5.559\n+ 1SER O 13 2.326 1.480 5.601\n+ 2GLU N 14 2.130 1.536 5.505\n+ 2GLU H 15 2.041 1.504 5.472\n+ 2GLU CA 16 2.165 1.677 5.493\n+ 2GLU HA 17 2.205 1.702 5.581\n+ 2GLU CB 18 2.267 1.697 5.381\n+ 2GLU HB1 19 2.224 1.670 5.294\n+ 2GLU HB2 20 2.346 1.639 5.399\n+ 2GLU CG 21 2.315 1.841 5.367\n+ 2GLU HG1 22 2.354 1.870 5.454\n+ 2GLU HG2 23 2.237 1.899 5.343\n+ 2GLU CD 24 2.421 1.856 5.259\n+ 2GLU OE1 25 2.456 1.755 5.196\n+ 2GLU OE2 26 2.469 1.970 5.239\n+ 2GLU C 27 2.040 1.761 5.467\n+ 2GLU O 28 1.946 1.716 5.400\n+ 3ALA N 29 2.039 1.882 5.522\n+ 3ALA H 30 2.118 1.912 5.575\n+ 3ALA CA 31 1.926 1.971 5.505\n+ 3ALA HA 32 1.846 1.920 5.536\n+ 3ALA CB 33 1.944 2.096 5.591\n+ 3ALA HB1 34 1.865 2.157 5.578\n+ 3ALA HB2 35 1.951 2.070 5.687\n+ 3ALA HB3 36 2.027 2.144 5.563\n+ 3ALA C 37 1.909 2.009 5.359\n+ 3ALA O 38 1.988 2.085 5.303\n+ 4GLU N 39 1.805 1.955 5.299\n+ 4GLU H 40 1.745 1.894 5.351\n+ 4GLU CA 41 1.775 1.982 5.159\n+ 4GLU HA 42 1.859 1.961 5.108\n+ 4GLU CB 43 1.662 1.890 5.110\n+ 4GLU HB1 44 1.635 1.920 5.018\n+ 4GLU HB2 45 1.584 1.900 5.172\n+ 4GLU CG 46 1.700 1.743 5.102\n+ 4GLU HG1 47 1.727 1.713 5.194\n+ 4GLU HG2 48 1.777 1.733 5.040\n+ 4GLU CD 49 1.586 1.656 5.054\n+ 4GLU OE1 50 1.475 1.710 5.031\n+ 4GLU OE2 51 1.607 1.534 5.038\n+ 4GLU C 52 1.737 2.128 5.139\n+ 4GLU O 53 1.740 2.180 5.028\n+ 5ASP N 54 1.702 2.195 5.249\n+ 5ASP H 55 1.702 2.148 5.337\n+ 5ASP CA 56 1.664 2.336 5.242\n+ 5ASP HA 57 1.589 2.341 5.177\n+ 5ASP CB 58 1.618 2.385 5.380\n+ 5ASP HB1 59 1.612 2.485 5.378\n+ 5ASP HB2 60 1.686 2.358 5.448\n+ 5ASP CG 61 1.483 2.329 5.420\n+ 5ASP OD1 62 1.413 2.276 5.331\n+ 5ASP OD2 63 1.448 2.340 5.539\n+ 5ASP C 64 1.781 2.419 5.192\n+ 5ASP O 65 1.762 2.515 5.116\n+ 6ALA N 66 1.901 2.385 5.235\n+ 6ALA H 67 1.911 2.306 5.296\n+ 6ALA CA 68 2.019 2.460 5.196\n+ 6ALA HA 69 2.007 2.552 5.233\n+ 6ALA CB 70 2.144 2.396 5.254\n+ 6ALA HB1 71 2.224 2.449 5.226\n+ 6ALA HB2 72 2.138 2.396 5.354\n+ 6ALA HB3 73 2.153 2.302 5.221\n+ 6ALA C 74 2.028 2.466 5.044\n+ 6ALA O 75 2.029 2.364 4.976\n+ 7SER N 76 2.033 2.588 4.995\n+ 7SER H 77 2.031 2.666 5.057\n+ 7SER CA 78 2.041 2.612 4.852\n+ 7SER HA 79 1.973 2.552 4.811\n+ 7SER CB 80 2.008 2.758 4.820\n+ 7SER HB1 81 1.922 2.785 4.864\n+ 7SER HB2 82 2.001 2.772 4.722\n+ 7SER OG 83 2.109 2.845 4.868\n+ 7SER HG 84 2.085 2.940 4.846\n+ 7SER C 85 2.180 2.577 4.800\n+ 7SER O 86 2.'..b'53 3.381\n+ 73PRO N 1111 3.036 6.339 3.408\n+ 73PRO CD 1112 2.901 6.311 3.463\n+ 73PRO HD1 1113 2.835 6.379 3.431\n+ 73PRO HD2 1114 2.902 6.310 3.563\n+ 73PRO CG 1115 2.868 6.175 3.408\n+ 73PRO HG1 1116 2.823 6.183 3.320\n+ 73PRO HG2 1117 2.810 6.125 3.472\n+ 73PRO CB 1118 2.999 6.105 3.392\n+ 73PRO HB1 1119 2.993 6.035 3.320\n+ 73PRO HB2 1120 3.026 6.061 3.478\n+ 73PRO CA 1121 3.097 6.215 3.353\n+ 73PRO HA 1122 3.189 6.200 3.390\n+ 73PRO C 1123 3.113 6.226 3.201\n+ 73PRO O 1124 3.187 6.148 3.140\n+ 74THR N 1125 3.041 6.320 3.140\n+ 74THR H 1126 2.982 6.380 3.194\n+ 74THR CA 1127 3.046 6.336 2.994\n+ 74THR HA 1128 3.053 6.242 2.961\n+ 74THR CB 1129 2.918 6.405 2.941\n+ 74THR HB 1130 2.904 6.493 2.987\n+ 74THR CG2 1131 2.927 6.424 2.791\n+ 74THR HG21 1132 2.844 6.469 2.758\n+ 74THR HG22 1133 3.006 6.481 2.768\n+ 74THR HG23 1134 2.936 6.335 2.746\n+ 74THR OG1 1135 2.804 6.325 2.971\n+ 74THR HG1 1136 2.722 6.370 2.937\n+ 74THR C 1137 3.167 6.416 2.949\n+ 74THR O 1138 3.255 6.363 2.882\n+ 75SER N 1139 3.168 6.543 2.984\n+ 75SER H 1140 3.093 6.580 3.039\n+ 75SER CA 1141 3.277 6.631 2.943\n+ 75SER HA 1142 3.276 6.629 2.843\n+ 75SER CB 1143 3.253 6.773 2.994\n+ 75SER HB1 1144 3.332 6.832 2.973\n+ 75SER HB2 1145 3.236 6.773 3.092\n+ 75SER OG 1146 3.140 6.831 2.931\n+ 75SER HG 1147 3.126 6.924 2.966\n+ 75SER C 1148 3.410 6.578 2.994\n+ 75SER O 1149 3.511 6.585 2.925\n+ 76ALA N 1150 3.410 6.524 3.116\n+ 76ALA H 1151 3.325 6.521 3.168\n+ 76ALA CA 1152 3.532 6.470 3.173\n+ 76ALA HA 1153 3.595 6.547 3.184\n+ 76ALA CB 1154 3.504 6.408 3.309\n+ 76ALA HB1 1155 3.589 6.371 3.347\n+ 76ALA HB2 1156 3.468 6.478 3.370\n+ 76ALA HB3 1157 3.437 6.334 3.299\n+ 76ALA C 1158 3.593 6.366 3.078\n+ 76ALA O 1159 3.705 6.384 3.030\n+ 77VAL N 1160 3.520 6.258 3.055\n+ 77VAL H 1161 3.430 6.249 3.097\n+ 77VAL CA 1162 3.570 6.152 2.968\n+ 77VAL HA 1163 3.656 6.122 3.009\n+ 77VAL CB 1164 3.472 6.033 2.962\n+ 77VAL HB 1165 3.381 6.067 2.938\n+ 77VAL CG1 1166 3.514 5.934 2.855\n+ 77VAL HG11 1167 3.450 5.858 2.852\n+ 77VAL HG12 1168 3.516 5.979 2.766\n+ 77VAL HG13 1169 3.606 5.900 2.876\n+ 77VAL CG2 1170 3.462 5.965 3.098\n+ 77VAL HG21 1171 3.398 5.888 3.092\n+ 77VAL HG22 1172 3.553 5.931 3.124\n+ 77VAL HG23 1173 3.430 6.031 3.166\n+ 77VAL C 1174 3.595 6.206 2.827\n+ 77VAL O 1175 3.702 6.185 2.771\n+ 78ALA N 1176 3.497 6.277 2.772\n+ 78ALA H 1177 3.412 6.291 2.823\n+ 78ALA CA 1178 3.512 6.335 2.639\n+ 78ALA HA 1179 3.543 6.261 2.580\n+ 78ALA CB 1180 3.379 6.388 2.589\n+ 78ALA HB1 1181 3.390 6.427 2.498\n+ 78ALA HB2 1182 3.313 6.312 2.585\n+ 78ALA HB3 1183 3.345 6.458 2.651\n+ 78ALA C 1184 3.616 6.447 2.641\n+ 78ALA O 1185 3.657 6.497 2.537\n+ 79ALA N 1186 3.659 6.483 2.762\n+ 79ALA H 1187 3.622 6.438 2.843\n+ 79ALA CA 1188 3.758 6.589 2.778\n+ 79ALA HA 1189 3.839 6.559 2.727\n+ 79ALA CB 1190 3.706 6.720 2.720\n+ 79ALA HB1 1191 3.775 6.791 2.732\n+ 79ALA HB2 1192 3.687 6.708 2.622\n+ 79ALA HB3 1193 3.622 6.746 2.767\n+ 79ALA C 1194 3.794 6.608 2.925\n+ 79ALA OC1 1195 3.732 6.692 2.989\n+ 79ALA OC2 1196 3.881 6.537 2.972\n+ 9.00078 9.00078 9.00078\n' |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde test-data/biobb_editconf_myEdit_conf.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/biobb_editconf_myEdit_conf.gro Fri Apr 12 07:18:48 2019 -0400 |
| b |
| b'@@ -0,0 +1,1199 @@\n+Created with pdb2gmx building block\n+ 1196\n+ 1SER N 1 2.270 1.214 5.506\n+ 1SER H1 2 2.288 1.242 5.411\n+ 1SER H2 3 2.354 1.220 5.559\n+ 1SER H3 4 2.237 1.120 5.507\n+ 1SER CA 5 2.167 1.304 5.566\n+ 1SER HA 6 2.083 1.294 5.512\n+ 1SER CB 7 2.138 1.263 5.710\n+ 1SER HB1 8 2.222 1.264 5.765\n+ 1SER HB2 9 2.097 1.172 5.713\n+ 1SER OG 10 2.046 1.352 5.771\n+ 1SER HG 11 2.029 1.323 5.865\n+ 1SER C 12 2.215 1.448 5.559\n+ 1SER O 13 2.326 1.480 5.601\n+ 2GLU N 14 2.130 1.536 5.505\n+ 2GLU H 15 2.041 1.504 5.472\n+ 2GLU CA 16 2.165 1.677 5.493\n+ 2GLU HA 17 2.205 1.702 5.581\n+ 2GLU CB 18 2.267 1.697 5.381\n+ 2GLU HB1 19 2.224 1.670 5.294\n+ 2GLU HB2 20 2.346 1.639 5.399\n+ 2GLU CG 21 2.315 1.841 5.367\n+ 2GLU HG1 22 2.354 1.870 5.454\n+ 2GLU HG2 23 2.237 1.899 5.343\n+ 2GLU CD 24 2.421 1.856 5.259\n+ 2GLU OE1 25 2.456 1.755 5.196\n+ 2GLU OE2 26 2.469 1.970 5.239\n+ 2GLU C 27 2.040 1.761 5.467\n+ 2GLU O 28 1.946 1.716 5.400\n+ 3ALA N 29 2.039 1.882 5.522\n+ 3ALA H 30 2.118 1.912 5.575\n+ 3ALA CA 31 1.926 1.971 5.505\n+ 3ALA HA 32 1.846 1.920 5.536\n+ 3ALA CB 33 1.944 2.096 5.591\n+ 3ALA HB1 34 1.865 2.157 5.578\n+ 3ALA HB2 35 1.951 2.070 5.687\n+ 3ALA HB3 36 2.027 2.144 5.563\n+ 3ALA C 37 1.909 2.009 5.359\n+ 3ALA O 38 1.988 2.085 5.303\n+ 4GLU N 39 1.805 1.955 5.299\n+ 4GLU H 40 1.745 1.894 5.351\n+ 4GLU CA 41 1.775 1.982 5.159\n+ 4GLU HA 42 1.859 1.961 5.108\n+ 4GLU CB 43 1.662 1.890 5.110\n+ 4GLU HB1 44 1.635 1.920 5.018\n+ 4GLU HB2 45 1.584 1.900 5.172\n+ 4GLU CG 46 1.700 1.743 5.102\n+ 4GLU HG1 47 1.727 1.713 5.194\n+ 4GLU HG2 48 1.777 1.733 5.040\n+ 4GLU CD 49 1.586 1.656 5.054\n+ 4GLU OE1 50 1.475 1.710 5.031\n+ 4GLU OE2 51 1.607 1.534 5.038\n+ 4GLU C 52 1.737 2.128 5.139\n+ 4GLU O 53 1.740 2.180 5.028\n+ 5ASP N 54 1.702 2.195 5.249\n+ 5ASP H 55 1.702 2.148 5.337\n+ 5ASP CA 56 1.664 2.336 5.242\n+ 5ASP HA 57 1.589 2.341 5.177\n+ 5ASP CB 58 1.618 2.385 5.380\n+ 5ASP HB1 59 1.612 2.485 5.378\n+ 5ASP HB2 60 1.686 2.358 5.448\n+ 5ASP CG 61 1.483 2.329 5.420\n+ 5ASP OD1 62 1.413 2.276 5.331\n+ 5ASP OD2 63 1.448 2.340 5.539\n+ 5ASP C 64 1.781 2.419 5.192\n+ 5ASP O 65 1.762 2.515 5.116\n+ 6ALA N 66 1.901 2.385 5.235\n+ 6ALA H 67 1.911 2.306 5.296\n+ 6ALA CA 68 2.019 2.460 5.196\n+ 6ALA HA 69 2.007 2.552 5.233\n+ 6ALA CB 70 2.144 2.396 5.254\n+ 6ALA HB1 71 2.224 2.449 5.226\n+ 6ALA HB2 72 2.138 2.396 5.354\n+ 6ALA HB3 73 2.153 2.302 5.221\n+ 6ALA C 74 2.028 2.466 5.044\n+ 6ALA O 75 2.029 2.364 4.976\n+ 7SER N 76 2.033 2.588 4.995\n+ 7SER H 77 2.031 2.666 5.057\n+ 7SER CA 78 2.041 2.612 4.852\n+ 7SER HA 79 1.973 2.552 4.811\n+ 7SER CB 80 2.008 2.758 4.820\n+ 7SER HB1 81 1.922 2.785 4.864\n+ 7SER HB2 82 2.001 2.772 4.722\n+ 7SER OG 83 2.109 2.845 4.868\n+ 7SER HG 84 2.085 2.940 4.846\n+ 7SER C 85 2.180 2.577 4.800\n+ 7SER O 86 2.'..b'53 3.381\n+ 73PRO N 1111 3.036 6.339 3.408\n+ 73PRO CD 1112 2.901 6.311 3.463\n+ 73PRO HD1 1113 2.835 6.379 3.431\n+ 73PRO HD2 1114 2.902 6.310 3.563\n+ 73PRO CG 1115 2.868 6.175 3.408\n+ 73PRO HG1 1116 2.823 6.183 3.320\n+ 73PRO HG2 1117 2.810 6.125 3.472\n+ 73PRO CB 1118 2.999 6.105 3.392\n+ 73PRO HB1 1119 2.993 6.035 3.320\n+ 73PRO HB2 1120 3.026 6.061 3.478\n+ 73PRO CA 1121 3.097 6.215 3.353\n+ 73PRO HA 1122 3.189 6.200 3.390\n+ 73PRO C 1123 3.113 6.226 3.201\n+ 73PRO O 1124 3.187 6.148 3.140\n+ 74THR N 1125 3.041 6.320 3.140\n+ 74THR H 1126 2.982 6.380 3.194\n+ 74THR CA 1127 3.046 6.336 2.994\n+ 74THR HA 1128 3.053 6.242 2.961\n+ 74THR CB 1129 2.918 6.405 2.941\n+ 74THR HB 1130 2.904 6.493 2.987\n+ 74THR CG2 1131 2.927 6.424 2.791\n+ 74THR HG21 1132 2.844 6.469 2.758\n+ 74THR HG22 1133 3.006 6.481 2.768\n+ 74THR HG23 1134 2.936 6.335 2.746\n+ 74THR OG1 1135 2.804 6.325 2.971\n+ 74THR HG1 1136 2.722 6.370 2.937\n+ 74THR C 1137 3.167 6.416 2.949\n+ 74THR O 1138 3.255 6.363 2.882\n+ 75SER N 1139 3.168 6.543 2.984\n+ 75SER H 1140 3.093 6.580 3.039\n+ 75SER CA 1141 3.277 6.631 2.943\n+ 75SER HA 1142 3.276 6.629 2.843\n+ 75SER CB 1143 3.253 6.773 2.994\n+ 75SER HB1 1144 3.332 6.832 2.973\n+ 75SER HB2 1145 3.236 6.773 3.092\n+ 75SER OG 1146 3.140 6.831 2.931\n+ 75SER HG 1147 3.126 6.924 2.966\n+ 75SER C 1148 3.410 6.578 2.994\n+ 75SER O 1149 3.511 6.585 2.925\n+ 76ALA N 1150 3.410 6.524 3.116\n+ 76ALA H 1151 3.325 6.521 3.168\n+ 76ALA CA 1152 3.532 6.470 3.173\n+ 76ALA HA 1153 3.595 6.547 3.184\n+ 76ALA CB 1154 3.504 6.408 3.309\n+ 76ALA HB1 1155 3.589 6.371 3.347\n+ 76ALA HB2 1156 3.468 6.478 3.370\n+ 76ALA HB3 1157 3.437 6.334 3.299\n+ 76ALA C 1158 3.593 6.366 3.078\n+ 76ALA O 1159 3.705 6.384 3.030\n+ 77VAL N 1160 3.520 6.258 3.055\n+ 77VAL H 1161 3.430 6.249 3.097\n+ 77VAL CA 1162 3.570 6.152 2.968\n+ 77VAL HA 1163 3.656 6.122 3.009\n+ 77VAL CB 1164 3.472 6.033 2.962\n+ 77VAL HB 1165 3.381 6.067 2.938\n+ 77VAL CG1 1166 3.514 5.934 2.855\n+ 77VAL HG11 1167 3.450 5.858 2.852\n+ 77VAL HG12 1168 3.516 5.979 2.766\n+ 77VAL HG13 1169 3.606 5.900 2.876\n+ 77VAL CG2 1170 3.462 5.965 3.098\n+ 77VAL HG21 1171 3.398 5.888 3.092\n+ 77VAL HG22 1172 3.553 5.931 3.124\n+ 77VAL HG23 1173 3.430 6.031 3.166\n+ 77VAL C 1174 3.595 6.206 2.827\n+ 77VAL O 1175 3.702 6.185 2.771\n+ 78ALA N 1176 3.497 6.277 2.772\n+ 78ALA H 1177 3.412 6.291 2.823\n+ 78ALA CA 1178 3.512 6.335 2.639\n+ 78ALA HA 1179 3.543 6.261 2.580\n+ 78ALA CB 1180 3.379 6.388 2.589\n+ 78ALA HB1 1181 3.390 6.427 2.498\n+ 78ALA HB2 1182 3.313 6.312 2.585\n+ 78ALA HB3 1183 3.345 6.458 2.651\n+ 78ALA C 1184 3.616 6.447 2.641\n+ 78ALA O 1185 3.657 6.497 2.537\n+ 79ALA N 1186 3.659 6.483 2.762\n+ 79ALA H 1187 3.622 6.438 2.843\n+ 79ALA CA 1188 3.758 6.589 2.778\n+ 79ALA HA 1189 3.839 6.559 2.727\n+ 79ALA CB 1190 3.706 6.720 2.720\n+ 79ALA HB1 1191 3.775 6.791 2.732\n+ 79ALA HB2 1192 3.687 6.708 2.622\n+ 79ALA HB3 1193 3.622 6.746 2.767\n+ 79ALA C 1194 3.794 6.608 2.925\n+ 79ALA OC1 1195 3.732 6.692 2.989\n+ 79ALA OC2 1196 3.881 6.537 2.972\n+ 9.00078 9.00078 9.00078\n' |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde test-data/biobb_fix_side_chain_input.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/biobb_fix_side_chain_input.pdb Fri Apr 12 07:18:48 2019 -0400 |
| b |
| b'@@ -0,0 +1,5648 @@\n+HEADER TRANSFERASE 12-FEB-99 2KI5 \n+TITLE HERPES SIMPLEX TYPE-1 THYMIDINE KINASE IN COMPLEX WITH THE \n+TITLE 2 DRUG ACICLOVIR AT 1.9A RESOLUTION \n+COMPND MOL_ID: 1; \n+COMPND 2 MOLECULE: PROTEIN (THYMIDINE KINASE); \n+COMPND 3 CHAIN: A, B; \n+COMPND 4 SYNONYM: TK; \n+COMPND 5 EC: 2.7.1.21; \n+COMPND 6 ENGINEERED: YES; \n+COMPND 7 OTHER_DETAILS: ACICLOVIR, ANTIVIRAL DRUG AS DEPOSITED IN \n+COMPND 8 1KI5 \n+SOURCE MOL_ID: 1; \n+SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN HERPESVIRUS 1; \n+SOURCE 3 ORGANISM_COMMON: HERPES SIMPLEX VIRUS TYPE 1; \n+SOURCE 4 ORGANISM_TAXID: 10298; \n+SOURCE 5 STRAIN: SY211; \n+SOURCE 6 GENE: TK; \n+SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; \n+SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; \n+SOURCE 9 EXPRESSION_SYSTEM_STRAIN: SY211; \n+SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PT7:HSVTK; \n+SOURCE 11 EXPRESSION_SYSTEM_GENE: TK \n+KEYWDS TRANSFERASE (PHOSPHOTRANSFERASE) THYMID, TRANSFERASE \n+KEYWDS 2 (PHOSPHOTRANSFERASE) THYMIDINE KINASE; VIRIDAE; DS-DNA \n+KEYWDS 3 ENVELOPED VIRUSES; HERPESVIRIDAE; ALPHAHERPESVIRINAE \n+KEYWDS 4 ANTIVIRAL DRUG (ACICLOVIR) \n+EXPDTA X-RAY DIFFRACTION \n+AUTHOR M.S.BENNETT,F.WIEN,J.N.CHAMPNESS,T.BATUWANGALA,T.RUTHERFORD, \n+AUTHOR 2 W.C.SUMMERS,H.SUN,G.WRIGHT,M.R.SANDERSON \n+REVDAT 4 24-FEB-09 2KI5 1 VERSN \n+REVDAT 3 01-APR-03 2KI5 1 JRNL \n+REVDAT 2 17-MAY-99 2KI5 1 TITLE \n+REVDAT 1 04-MAR-99 2KI5 0 \n+SPRSDE 02-MAR-99 2KI5 1KI5 \n+JRNL AUTH M.S.BENNETT,F.WIEN,J.N.CHAMPNESS,T.BATUWANGALA, \n+JRNL AUTH 2 T.RUTHERFORD,W.C.SUMMERS,H.SUN,G.WRIGHT, \n+JRNL AUTH 3 M.R.SANDERSON \n+JRNL TITL STRUCTURE TO 1.9 A RESOLUTION OF A COMPLEX WITH \n+JRNL TITL 2 HERPES SIMPLEX VIRUS TYPE-1 THYMIDINE KINASE OF A \n+JRNL TITL 3 NOVEL, NON-SUBSTRATE INHIBITOR: X-RAY \n+JRNL TITL 4 CRYSTALLOGRAPHIC COMPARISON WITH BINDING OF \n+JRNL TITL 5 ACICLOVIR. \n+JRNL REF FEBS LETT. V. 443 121 1999 \n+JRNL REFN ISSN 0014-5793 \n+JRNL PMID 9989588 \n+JRNL DOI 10.1016/S0014-5793(98)01619-6 \n+REMARK 1 \n+REMARK 2 \n+REMARK 2 RESOLUTION. 1.90 ANGSTROMS. '..b'632 4633 4634 \n+CONECT 4631 4630 \n+CONECT 4632 4630 \n+CONECT 4633 4630 \n+CONECT 4634 4630 \n+CONECT 4635 4637 4639 \n+CONECT 4636 4638 4640 \n+CONECT 4637 4635 \n+CONECT 4638 4636 \n+CONECT 4639 4635 4641 \n+CONECT 4640 4636 4642 \n+CONECT 4641 4639 4643 \n+CONECT 4642 4640 4644 \n+CONECT 4643 4641 4645 \n+CONECT 4644 4642 4645 \n+CONECT 4645 4643 4644 4646 4655 \n+CONECT 4646 4645 4647 \n+CONECT 4647 4646 4648 \n+CONECT 4648 4647 4649 4655 \n+CONECT 4649 4648 4650 4651 \n+CONECT 4650 4649 \n+CONECT 4651 4649 4652 \n+CONECT 4652 4651 4653 4654 \n+CONECT 4653 4652 \n+CONECT 4654 4652 4655 \n+CONECT 4655 4645 4648 4654 \n+CONECT 4656 4657 4658 4659 4660 \n+CONECT 4657 4656 \n+CONECT 4658 4656 \n+CONECT 4659 4656 \n+CONECT 4660 4656 \n+CONECT 4661 4662 4663 \n+CONECT 4662 4661 \n+CONECT 4663 4661 4664 \n+CONECT 4664 4663 4665 \n+CONECT 4665 4664 4666 \n+CONECT 4666 4665 4667 4676 \n+CONECT 4667 4666 4668 \n+CONECT 4668 4667 4669 \n+CONECT 4669 4668 4670 4676 \n+CONECT 4670 4669 4671 4672 \n+CONECT 4671 4670 \n+CONECT 4672 4670 4673 \n+CONECT 4673 4672 4674 4675 \n+CONECT 4674 4673 \n+CONECT 4675 4673 4676 \n+CONECT 4676 4666 4669 4675 \n+MASTER 453 0 4 32 10 0 14 6 4966 2 47 58 \n+END \n' |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde test-data/biobb_fix_side_chain_myFixSideChain.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/biobb_fix_side_chain_myFixSideChain.pdb Fri Apr 12 07:18:48 2019 -0400 |
| b |
| b'@@ -0,0 +1,4987 @@\n+ATOM 1 N MET A 46 42.224 58.491 28.031 1.00 31.76 N \n+ATOM 2 CA MET A 46 42.964 59.788 28.172 1.00 34.85 C \n+ATOM 3 C MET A 46 43.978 59.649 29.317 1.00 36.75 C \n+ATOM 4 O MET A 46 43.755 58.843 30.241 1.00 40.33 O \n+ATOM 5 CB MET A 46 41.991 60.929 28.438 1.00 32.51 C \n+ATOM 6 CG MET A 46 42.765 62.235 28.577 1.00 99.00 C \n+ATOM 7 SD MET A 46 41.622 63.602 28.894 1.00 99.00 S \n+ATOM 8 CE MET A 46 42.777 64.952 29.007 1.00 99.00 C \n+ATOM 9 N PRO A 47 45.116 60.391 29.265 1.00 36.24 N \n+ATOM 10 CA PRO A 47 46.136 60.304 30.323 1.00 33.42 C \n+ATOM 11 C PRO A 47 45.604 60.613 31.701 1.00 30.60 C \n+ATOM 12 O PRO A 47 44.457 61.023 31.857 1.00 29.75 O \n+ATOM 13 CB PRO A 47 47.188 61.331 29.889 1.00 34.73 C \n+ATOM 14 CG PRO A 47 46.417 62.315 29.035 1.00 35.61 C \n+ATOM 15 CD PRO A 47 45.505 61.394 28.250 1.00 36.31 C \n+ATOM 16 N THR A 48 46.458 60.431 32.698 1.00 30.18 N \n+ATOM 17 CA THR A 48 46.072 60.672 34.071 1.00 26.68 C \n+ATOM 18 C THR A 48 46.809 61.829 34.705 1.00 25.13 C \n+ATOM 19 O THR A 48 47.953 62.141 34.335 1.00 23.66 O \n+ATOM 20 CB THR A 48 46.294 59.428 34.915 1.00 26.86 C \n+ATOM 21 OG1 THR A 48 47.641 58.977 34.737 1.00 28.95 O \n+ATOM 22 CG2 THR A 48 45.339 58.337 34.511 1.00 25.93 C \n+ATOM 23 N LEU A 49 46.136 62.465 35.661 1.00 21.74 N \n+ATOM 24 CA LEU A 49 46.680 63.586 36.393 1.00 20.12 C \n+ATOM 25 C LEU A 49 46.548 63.304 37.881 1.00 20.56 C \n+ATOM 26 O LEU A 49 45.645 62.578 38.325 1.00 19.49 O \n+ATOM 27 CB LEU A 49 45.904 64.859 36.050 1.00 17.69 C \n+ATOM 28 CG LEU A 49 46.191 66.129 36.843 1.00 15.68 C \n+ATOM 29 CD1 LEU A 49 47.563 66.629 36.545 1.00 17.87 C \n+ATOM 30 CD2 LEU A 49 45.192 67.206 36.538 1.00 16.05 C \n+ATOM 31 N LEU A 50 47.500 63.810 38.643 1.00 21.96 N \n+ATOM 32 CA LEU A 50 47.457 63.674 40.089 1.00 21.20 C \n+ATOM 33 C LEU A 50 47.627 65.096 40.622 1.00 20.37 C \n+ATOM 34 O LEU A 50 48.614 65.721 40.349 1.00 22.88 O \n+ATOM 35 CB LEU A 50 48.569 62.750 40.575 1.00 20.38 C \n+ATOM 36 CG LEU A 50 48.698 62.327 42.051 1.00 23.98 C \n+ATOM 37 CD1 LEU A 50 49.683 63.182 42.761 1.00 22.07 C \n+ATOM 38 CD2 LEU A 50 47.362 62.340 42.770 1.00 23.15 C \n+ATOM 39 N ARG A 51 46.593 65.649 41.253 1.00 18.59 N \n+ATOM 40 CA ARG A 51 46.675 66.995 41.810 1.00 17.55 C \n+ATOM 41 C ARG A 51 46.870 66.866 43.318 1.00 17.00 C \n+ATOM 42 O ARG A 51 46.252 65.996 43.965 1.00 17.03 O \n+ATOM 43 CB ARG A 51 45.398 67.765 41.532 1.00 18.02 C \n+ATOM 44 CG ARG A 51 45.275 68.303 40.123 1.00 20.14 C \n+ATOM 45 CD ARG A 51 43.927 68.949 39.958 1.00 21.12 C \n+ATOM 46 NE ARG A 51 42.877 67.959 40.171 1.00 24.39 N \n+ATOM 47 CZ ARG A 51 41.853 68.101 41.001 1.00 21.53 C \n+ATOM 48 NH1 ARG A 51 41.710 69.196 41.719 1.00 23.06 N \n+ATOM 49 NH2 ARG A 51 40.979 67.'..b'05 6.270 82.517 47.565 1.00 31.93 O \n+HETATM 4938 O HOH B 706 5.857 88.669 24.803 1.00 25.08 O \n+HETATM 4939 O HOH B 707 3.718 78.699 30.773 1.00 55.75 O \n+HETATM 4940 O HOH B 709 2.353 79.693 34.112 1.00 41.98 O \n+HETATM 4941 O HOH B 710 26.563 76.882 43.357 1.00 18.46 O \n+HETATM 4942 O HOH B 713 2.247 79.965 44.762 1.00 30.21 O \n+HETATM 4943 O HOH B 714 3.396 78.328 47.460 1.00 31.20 O \n+HETATM 4944 O HOH B 716 29.900 100.169 25.531 1.00 35.22 O \n+HETATM 4945 O HOH B 717 39.508 89.834 15.307 1.00 36.16 O \n+HETATM 4946 O HOH B 718 41.208 99.764 46.839 1.00 36.34 O \n+HETATM 4947 O HOH B 722 46.146 101.401 27.996 1.00 41.26 O \n+HETATM 4948 O HOH B 724 18.779 95.945 61.261 1.00 28.00 O \n+HETATM 4949 O HOH B 726 6.577 101.398 46.248 1.00 34.71 O \n+HETATM 4950 O HOH B 727 23.776 75.396 30.958 1.00 24.31 O \n+HETATM 4951 O HOH B 731 0.732 81.480 35.666 1.00 45.32 O \n+HETATM 4952 O HOH B 732 10.702 90.064 49.390 1.00 28.67 O \n+HETATM 4953 O HOH B 735 9.897 82.965 24.164 1.00 28.83 O \n+HETATM 4954 O HOH B 739 21.168 111.301 40.601 1.00 26.38 O \n+HETATM 4955 O HOH B 740 13.088 94.113 58.697 1.00 41.36 O \n+HETATM 4956 O HOH B 743 35.181 104.131 45.821 1.00 56.22 O \n+HETATM 4957 O HOH B 746 13.304 87.909 60.368 1.00 31.96 O \n+HETATM 4958 O HOH B 748 16.588 110.077 48.074 1.00 43.94 O \n+HETATM 4959 O HOH B 749 42.246 106.520 50.126 1.00 39.16 O \n+HETATM 4960 O HOH B 750 38.865 101.910 42.169 1.00 48.46 O \n+HETATM 4961 O HOH B 751 40.714 108.701 46.369 1.00 33.86 O \n+HETATM 4962 O HOH B 752 9.660 94.289 45.733 1.00 38.22 O \n+HETATM 4963 O HOH B 753 47.600 95.570 38.981 1.00 32.59 O \n+HETATM 4964 O HOH B 754 4.261 74.375 36.569 1.00 26.76 O \n+HETATM 4965 O HOH B 755 13.163 90.429 39.514 1.00 33.46 O \n+HETATM 4966 O HOH B 756 5.557 95.092 23.874 1.00 50.25 O \n+HETATM 4967 O HOH B 761 10.311 90.259 45.491 1.00 36.89 O \n+HETATM 4968 O HOH B 763 26.508 106.710 34.666 1.00 25.80 O \n+HETATM 4969 O HOH B 764 6.249 106.003 34.370 1.00 27.75 O \n+HETATM 4970 O HOH B 767 13.747 87.697 23.984 1.00 46.31 O \n+HETATM 4971 O HOH B 768 41.046 101.834 52.490 1.00 41.04 O \n+HETATM 4972 O HOH B 769 20.482 95.631 23.868 1.00 36.96 O \n+HETATM 4973 O HOH B 770 32.254 109.242 42.071 1.00 35.06 O \n+HETATM 4974 O HOH B 772 23.353 115.199 50.789 1.00 38.86 O \n+HETATM 4975 O HOH B 773 26.818 79.120 44.718 1.00 27.83 O \n+HETATM 4976 O HOH B 774 12.865 99.935 25.528 1.00 25.37 O \n+HETATM 4977 O HOH B 778 19.756 94.242 43.430 1.00 41.39 O \n+HETATM 4978 O HOH B 780 23.930 113.884 53.741 1.00 40.75 O \n+HETATM 4979 O HOH B 784 21.068 92.013 43.768 1.00 37.38 O \n+HETATM 4980 O HOH B 785 3.187 96.240 24.851 1.00 33.43 O \n+HETATM 4981 O HOH B 786 4.113 82.010 45.454 1.00 27.14 O \n+HETATM 4982 O HOH B 787 48.863 97.909 35.568 1.00 23.24 O \n+HETATM 4983 O HOH B 790 15.430 92.039 43.798 1.00 26.19 O \n+HETATM 4984 O HOH B 792 38.780 103.293 38.129 1.00 46.73 O \n+TER 4985 HOH B 792 \n+END\n' |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde test-data/biobb_genion_input.zip |
| b |
| Binary file test-data/biobb_genion_input.zip has changed |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde test-data/biobb_genion_myGenion.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/biobb_genion_myGenion.gro Fri Apr 12 07:18:48 2019 -0400 |
| b |
| b'@@ -0,0 +1,71617 @@\n+Protein in water\n+71614\n+ 1SER N 1 2.270 1.214 5.506\n+ 1SER H1 2 2.288 1.242 5.411\n+ 1SER H2 3 2.354 1.220 5.559\n+ 1SER H3 4 2.237 1.120 5.507\n+ 1SER CA 5 2.167 1.304 5.566\n+ 1SER HA 6 2.083 1.294 5.512\n+ 1SER CB 7 2.138 1.263 5.710\n+ 1SER HB1 8 2.222 1.264 5.765\n+ 1SER HB2 9 2.097 1.172 5.713\n+ 1SER OG 10 2.046 1.352 5.771\n+ 1SER HG 11 2.029 1.323 5.865\n+ 1SER C 12 2.215 1.448 5.559\n+ 1SER O 13 2.326 1.480 5.601\n+ 2GLU N 14 2.130 1.536 5.505\n+ 2GLU H 15 2.041 1.504 5.472\n+ 2GLU CA 16 2.165 1.677 5.493\n+ 2GLU HA 17 2.205 1.702 5.581\n+ 2GLU CB 18 2.267 1.697 5.381\n+ 2GLU HB1 19 2.224 1.670 5.294\n+ 2GLU HB2 20 2.346 1.639 5.399\n+ 2GLU CG 21 2.315 1.841 5.367\n+ 2GLU HG1 22 2.354 1.870 5.454\n+ 2GLU HG2 23 2.237 1.899 5.343\n+ 2GLU CD 24 2.421 1.856 5.259\n+ 2GLU OE1 25 2.456 1.755 5.196\n+ 2GLU OE2 26 2.469 1.970 5.239\n+ 2GLU C 27 2.040 1.761 5.467\n+ 2GLU O 28 1.946 1.716 5.400\n+ 3ALA N 29 2.039 1.882 5.522\n+ 3ALA H 30 2.118 1.912 5.575\n+ 3ALA CA 31 1.926 1.971 5.505\n+ 3ALA HA 32 1.846 1.920 5.536\n+ 3ALA CB 33 1.944 2.096 5.591\n+ 3ALA HB1 34 1.865 2.157 5.578\n+ 3ALA HB2 35 1.951 2.070 5.687\n+ 3ALA HB3 36 2.027 2.144 5.563\n+ 3ALA C 37 1.909 2.009 5.359\n+ 3ALA O 38 1.988 2.085 5.303\n+ 4GLU N 39 1.805 1.955 5.299\n+ 4GLU H 40 1.745 1.894 5.351\n+ 4GLU CA 41 1.775 1.982 5.159\n+ 4GLU HA 42 1.859 1.961 5.108\n+ 4GLU CB 43 1.662 1.890 5.110\n+ 4GLU HB1 44 1.635 1.920 5.018\n+ 4GLU HB2 45 1.584 1.900 5.172\n+ 4GLU CG 46 1.700 1.743 5.102\n+ 4GLU HG1 47 1.727 1.713 5.194\n+ 4GLU HG2 48 1.777 1.733 5.040\n+ 4GLU CD 49 1.586 1.656 5.054\n+ 4GLU OE1 50 1.475 1.710 5.031\n+ 4GLU OE2 51 1.607 1.534 5.038\n+ 4GLU C 52 1.737 2.128 5.139\n+ 4GLU O 53 1.740 2.180 5.028\n+ 5ASP N 54 1.702 2.195 5.249\n+ 5ASP H 55 1.702 2.148 5.337\n+ 5ASP CA 56 1.664 2.336 5.242\n+ 5ASP HA 57 1.589 2.341 5.177\n+ 5ASP CB 58 1.618 2.385 5.380\n+ 5ASP HB1 59 1.612 2.485 5.378\n+ 5ASP HB2 60 1.686 2.358 5.448\n+ 5ASP CG 61 1.483 2.329 5.420\n+ 5ASP OD1 62 1.413 2.276 5.331\n+ 5ASP OD2 63 1.448 2.340 5.539\n+ 5ASP C 64 1.781 2.419 5.192\n+ 5ASP O 65 1.762 2.515 5.116\n+ 6ALA N 66 1.901 2.385 5.235\n+ 6ALA H 67 1.911 2.306 5.296\n+ 6ALA CA 68 2.019 2.460 5.196\n+ 6ALA HA 69 2.007 2.552 5.233\n+ 6ALA CB 70 2.144 2.396 5.254\n+ 6ALA HB1 71 2.224 2.449 5.226\n+ 6ALA HB2 72 2.138 2.396 5.354\n+ 6ALA HB3 73 2.153 2.302 5.221\n+ 6ALA C 74 2.028 2.466 5.044\n+ 6ALA O 75 2.029 2.364 4.976\n+ 7SER N 76 2.033 2.588 4.995\n+ 7SER H 77 2.031 2.666 5.057\n+ 7SER CA 78 2.041 2.612 4.852\n+ 7SER HA 79 1.973 2.552 4.811\n+ 7SER CB 80 2.008 2.758 4.820\n+ 7SER HB1 81 1.922 2.785 4.864\n+ 7SER HB2 82 2.001 2.772 4.722\n+ 7SER OG 83 2.109 2.845 4.868\n+ 7SER HG 84 2.085 2.940 4.846\n+ 7SER C 85 2.180 2.577 4.800\n+ 7SER O 86 2.270 2.543 4.87'..b'07 7.434\n+23524SOL OW71529 8.856 9.299 9.168\n+23524SOL HW171530 8.760 9.288 9.141\n+23524SOL HW271531 8.912 9.232 9.120\n+23525SOL OW71532 8.307 8.404 8.309\n+23525SOL HW171533 8.361 8.335 8.357\n+23525SOL HW271534 8.275 8.473 8.375\n+23526SOL OW71535 8.531 8.432 7.535\n+23526SOL HW171536 8.508 8.485 7.453\n+23526SOL HW271537 8.612 8.376 7.516\n+23527SOL OW71538 7.527 8.688 8.101\n+23527SOL HW171539 7.526 8.641 8.189\n+23527SOL HW271540 7.609 8.660 8.050\n+23528SOL OW71541 7.876 7.872 7.968\n+23528SOL HW171542 7.906 7.800 7.906\n+23528SOL HW271543 7.837 7.832 8.051\n+23529SOL OW71544 9.153 8.935 8.552\n+23529SOL HW171545 9.060 8.910 8.525\n+23529SOL HW271546 9.179 8.885 8.634\n+23530SOL OW71547 7.765 7.995 8.728\n+23530SOL HW171548 7.803 7.936 8.800\n+23530SOL HW271549 7.805 7.969 8.640\n+23531SOL OW71550 8.872 7.662 8.560\n+23531SOL HW171551 8.924 7.597 8.615\n+23531SOL HW271552 8.823 7.725 8.621\n+23532SOL OW71553 8.449 7.482 8.602\n+23532SOL HW171554 8.386 7.410 8.571\n+23532SOL HW271555 8.542 7.446 8.602\n+23533SOL OW71556 8.218 8.778 7.749\n+23533SOL HW171557 8.172 8.691 7.766\n+23533SOL HW271558 8.309 8.775 7.790\n+23534SOL OW71559 8.066 9.015 8.732\n+23534SOL HW171560 8.061 9.097 8.789\n+23534SOL HW271561 8.155 9.012 8.687\n+23535SOL OW71562 8.800 7.500 7.616\n+23535SOL HW171563 8.835 7.459 7.532\n+23535SOL HW271564 8.710 7.462 7.636\n+23536SOL OW71565 8.748 7.901 8.139\n+23536SOL HW171566 8.689 7.981 8.143\n+23536SOL HW271567 8.763 7.866 8.232\n+23537SOL OW71568 7.487 8.525 7.748\n+23537SOL HW171569 7.586 8.514 7.739\n+23537SOL HW271570 7.447 8.439 7.780\n+23538NA NA71571 1.434 1.188 7.489\n+23539NA NA71572 1.041 2.563 7.877\n+23540NA NA71573 1.300 4.177 6.277\n+23541NA NA71574 0.231 5.437 7.931\n+23542NA NA71575 1.902 2.406 8.562\n+23543NA NA71576 1.992 5.518 3.713\n+23544NA NA71577 2.550 5.386 5.440\n+23545NA NA71578 2.423 5.808 1.147\n+23546NA NA71579 1.901 8.525 7.748\n+23547NA NA71580 3.829 4.737 1.726\n+23548NA NA71581 4.546 4.726 3.234\n+23549NA NA71582 5.005 7.793 2.806\n+23550NA NA71583 4.737 7.553 5.494\n+23551NA NA71584 6.367 0.264 5.473\n+23552NA NA71585 5.699 6.323 5.321\n+23553NA NA71586 5.662 6.397 8.237\n+23554NA NA71587 6.192 8.412 0.123\n+23555NA NA71588 7.445 8.966 1.605\n+23556NA NA71589 6.318 8.082 8.512\n+23557NA NA71590 8.038 1.487 6.077\n+23558NA NA71591 8.307 6.960 7.464\n+23559NA NA71592 8.480 7.997 1.878\n+23560CL CL71593 1.187 3.654 7.202\n+23561CL CL71594 0.561 7.670 4.871\n+23562CL CL71595 0.221 8.762 7.430\n+23563CL CL71596 3.291 1.173 8.315\n+23564CL CL71597 2.201 2.371 1.006\n+23565CL CL71598 2.853 5.996 3.104\n+23566CL CL71599 3.536 6.469 8.702\n+23567CL CL71600 3.639 7.790 7.228\n+23568CL CL71601 2.728 7.902 8.090\n+23569CL CL71602 4.911 1.792 1.616\n+23570CL CL71603 4.737 0.105 3.632\n+23571CL CL71604 5.279 3.373 2.565\n+23572CL CL71605 4.212 5.109 7.622\n+23573CL CL71606 5.190 8.865 2.815\n+23574CL CL71607 6.445 0.956 2.723\n+23575CL CL71608 6.445 0.956 4.585\n+23576CL CL71609 5.903 2.113 9.249\n+23577CL CL71610 6.780 7.198 7.479\n+23578CL CL71611 5.665 8.688 6.239\n+23579CL CL71612 7.520 0.166 0.318\n+23580CL CL71613 8.428 2.978 7.305\n+23581CL CL71614 7.607 2.999 7.052\n+ 9.00078 9.00078 9.00078\n' |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde test-data/biobb_genion_myGenion.zip |
| b |
| Binary file test-data/biobb_genion_myGenion.zip has changed |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde test-data/biobb_genrestr_input.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/biobb_genrestr_input.gro Fri Apr 12 07:18:48 2019 -0400 |
| b |
| b'@@ -0,0 +1,71693 @@\n+Protein in water\n+71690\n+ 1SER N 1 2.270 1.214 5.506\n+ 1SER H1 2 2.288 1.242 5.411\n+ 1SER H2 3 2.354 1.220 5.559\n+ 1SER H3 4 2.237 1.120 5.507\n+ 1SER CA 5 2.167 1.304 5.566\n+ 1SER HA 6 2.083 1.294 5.512\n+ 1SER CB 7 2.138 1.263 5.710\n+ 1SER HB1 8 2.222 1.264 5.765\n+ 1SER HB2 9 2.097 1.172 5.713\n+ 1SER OG 10 2.046 1.352 5.771\n+ 1SER HG 11 2.029 1.323 5.865\n+ 1SER C 12 2.215 1.448 5.559\n+ 1SER O 13 2.326 1.480 5.601\n+ 2GLU N 14 2.130 1.536 5.505\n+ 2GLU H 15 2.041 1.504 5.472\n+ 2GLU CA 16 2.165 1.677 5.493\n+ 2GLU HA 17 2.205 1.702 5.581\n+ 2GLU CB 18 2.267 1.697 5.381\n+ 2GLU HB1 19 2.224 1.670 5.294\n+ 2GLU HB2 20 2.346 1.639 5.399\n+ 2GLU CG 21 2.315 1.841 5.367\n+ 2GLU HG1 22 2.354 1.870 5.454\n+ 2GLU HG2 23 2.237 1.899 5.343\n+ 2GLU CD 24 2.421 1.856 5.259\n+ 2GLU OE1 25 2.456 1.755 5.196\n+ 2GLU OE2 26 2.469 1.970 5.239\n+ 2GLU C 27 2.040 1.761 5.467\n+ 2GLU O 28 1.946 1.716 5.400\n+ 3ALA N 29 2.039 1.882 5.522\n+ 3ALA H 30 2.118 1.912 5.575\n+ 3ALA CA 31 1.926 1.971 5.505\n+ 3ALA HA 32 1.846 1.920 5.536\n+ 3ALA CB 33 1.944 2.096 5.591\n+ 3ALA HB1 34 1.865 2.157 5.578\n+ 3ALA HB2 35 1.951 2.070 5.687\n+ 3ALA HB3 36 2.027 2.144 5.563\n+ 3ALA C 37 1.909 2.009 5.359\n+ 3ALA O 38 1.988 2.085 5.303\n+ 4GLU N 39 1.805 1.955 5.299\n+ 4GLU H 40 1.745 1.894 5.351\n+ 4GLU CA 41 1.775 1.982 5.159\n+ 4GLU HA 42 1.859 1.961 5.108\n+ 4GLU CB 43 1.662 1.890 5.110\n+ 4GLU HB1 44 1.635 1.920 5.018\n+ 4GLU HB2 45 1.584 1.900 5.172\n+ 4GLU CG 46 1.700 1.743 5.102\n+ 4GLU HG1 47 1.727 1.713 5.194\n+ 4GLU HG2 48 1.777 1.733 5.040\n+ 4GLU CD 49 1.586 1.656 5.054\n+ 4GLU OE1 50 1.475 1.710 5.031\n+ 4GLU OE2 51 1.607 1.534 5.038\n+ 4GLU C 52 1.737 2.128 5.139\n+ 4GLU O 53 1.740 2.180 5.028\n+ 5ASP N 54 1.702 2.195 5.249\n+ 5ASP H 55 1.702 2.148 5.337\n+ 5ASP CA 56 1.664 2.336 5.242\n+ 5ASP HA 57 1.589 2.341 5.177\n+ 5ASP CB 58 1.618 2.385 5.380\n+ 5ASP HB1 59 1.612 2.485 5.378\n+ 5ASP HB2 60 1.686 2.358 5.448\n+ 5ASP CG 61 1.483 2.329 5.420\n+ 5ASP OD1 62 1.413 2.276 5.331\n+ 5ASP OD2 63 1.448 2.340 5.539\n+ 5ASP C 64 1.781 2.419 5.192\n+ 5ASP O 65 1.762 2.515 5.116\n+ 6ALA N 66 1.901 2.385 5.235\n+ 6ALA H 67 1.911 2.306 5.296\n+ 6ALA CA 68 2.019 2.460 5.196\n+ 6ALA HA 69 2.007 2.552 5.233\n+ 6ALA CB 70 2.144 2.396 5.254\n+ 6ALA HB1 71 2.224 2.449 5.226\n+ 6ALA HB2 72 2.138 2.396 5.354\n+ 6ALA HB3 73 2.153 2.302 5.221\n+ 6ALA C 74 2.028 2.466 5.044\n+ 6ALA O 75 2.029 2.364 4.976\n+ 7SER N 76 2.033 2.588 4.995\n+ 7SER H 77 2.031 2.666 5.057\n+ 7SER CA 78 2.041 2.612 4.852\n+ 7SER HA 79 1.973 2.552 4.811\n+ 7SER CB 80 2.008 2.758 4.820\n+ 7SER HB1 81 1.922 2.785 4.864\n+ 7SER HB2 82 2.001 2.772 4.722\n+ 7SER OG 83 2.109 2.845 4.868\n+ 7SER HG 84 2.085 2.940 4.846\n+ 7SER C 85 2.180 2.577 4.800\n+ 7SER O 86 2.270 2.543 4.87'..b'58 7.739\n+23549SOL HW171605 8.427 8.396 7.671\n+23549SOL HW271606 8.404 8.275 7.778\n+23550SOL OW71607 7.820 8.736 8.938\n+23550SOL HW171608 7.807 8.829 8.904\n+23550SOL HW271609 7.736 8.684 8.925\n+23551SOL OW71610 8.487 8.546 8.144\n+23551SOL HW171611 8.417 8.499 8.198\n+23551SOL HW271612 8.546 8.478 8.101\n+23552SOL OW71613 8.462 7.684 8.419\n+23552SOL HW171614 8.454 7.648 8.326\n+23552SOL HW271615 8.460 7.608 8.484\n+23553SOL OW71616 7.703 8.796 7.738\n+23553SOL HW171617 7.607 8.797 7.711\n+23553SOL HW271618 7.715 8.849 7.822\n+23554SOL OW71619 7.523 7.793 7.481\n+23554SOL HW171620 7.431 7.765 7.452\n+23554SOL HW271621 7.554 7.870 7.425\n+23555SOL OW71622 8.888 8.304 8.846\n+23555SOL HW171623 8.831 8.356 8.783\n+23555SOL HW271624 8.984 8.316 8.822\n+23556SOL OW71625 7.520 7.614 7.766\n+23556SOL HW171626 7.503 7.697 7.712\n+23556SOL HW271627 7.610 7.577 7.744\n+23557SOL OW71628 8.631 8.783 7.567\n+23557SOL HW171629 8.532 8.772 7.569\n+23557SOL HW271630 8.665 8.798 7.660\n+23558SOL OW71631 8.061 8.290 8.879\n+23558SOL HW171632 8.117 8.371 8.862\n+23558SOL HW271633 8.120 8.210 8.882\n+23559SOL OW71634 8.673 7.773 7.897\n+23559SOL HW171635 8.738 7.699 7.886\n+23559SOL HW271636 8.693 7.823 7.981\n+23560SOL OW71637 8.042 8.193 8.100\n+23560SOL HW171638 8.092 8.278 8.081\n+23560SOL HW271639 7.954 8.195 8.052\n+23561SOL OW71640 8.307 8.822 7.464\n+23561SOL HW171641 8.261 8.837 7.552\n+23561SOL HW271642 8.351 8.907 7.434\n+23562SOL OW71643 8.856 9.299 9.168\n+23562SOL HW171644 8.760 9.288 9.141\n+23562SOL HW271645 8.912 9.232 9.120\n+23563SOL OW71646 8.307 8.404 8.309\n+23563SOL HW171647 8.361 8.335 8.357\n+23563SOL HW271648 8.275 8.473 8.375\n+23564SOL OW71649 8.531 8.432 7.535\n+23564SOL HW171650 8.508 8.485 7.453\n+23564SOL HW271651 8.612 8.376 7.516\n+23565SOL OW71652 7.527 8.688 8.101\n+23565SOL HW171653 7.526 8.641 8.189\n+23565SOL HW271654 7.609 8.660 8.050\n+23566SOL OW71655 7.876 7.872 7.968\n+23566SOL HW171656 7.906 7.800 7.906\n+23566SOL HW271657 7.837 7.832 8.051\n+23567SOL OW71658 9.153 8.935 8.552\n+23567SOL HW171659 9.060 8.910 8.525\n+23567SOL HW271660 9.179 8.885 8.634\n+23568SOL OW71661 7.765 7.995 8.728\n+23568SOL HW171662 7.803 7.936 8.800\n+23568SOL HW271663 7.805 7.969 8.640\n+23569SOL OW71664 8.872 7.662 8.560\n+23569SOL HW171665 8.924 7.597 8.615\n+23569SOL HW271666 8.823 7.725 8.621\n+23570SOL OW71667 8.449 7.482 8.602\n+23570SOL HW171668 8.386 7.410 8.571\n+23570SOL HW271669 8.542 7.446 8.602\n+23571SOL OW71670 8.218 8.778 7.749\n+23571SOL HW171671 8.172 8.691 7.766\n+23571SOL HW271672 8.309 8.775 7.790\n+23572SOL OW71673 8.066 9.015 8.732\n+23572SOL HW171674 8.061 9.097 8.789\n+23572SOL HW271675 8.155 9.012 8.687\n+23573SOL OW71676 8.800 7.500 7.616\n+23573SOL HW171677 8.835 7.459 7.532\n+23573SOL HW271678 8.710 7.462 7.636\n+23574SOL OW71679 8.748 7.901 8.139\n+23574SOL HW171680 8.689 7.981 8.143\n+23574SOL HW271681 8.763 7.866 8.232\n+23575SOL OW71682 7.487 8.525 7.748\n+23575SOL HW171683 7.586 8.514 7.739\n+23575SOL HW271684 7.447 8.439 7.780\n+23576NA NA71685 1.272 5.169 3.004\n+23577NA NA71686 1.293 6.814 7.009\n+23578NA NA71687 2.674 1.586 0.687\n+23579NA NA71688 1.901 2.939 4.024\n+23580NA NA71689 8.120 5.340 2.016\n+23581NA NA71690 8.808 4.586 8.493\n+ 9.00078 9.00078 9.00078\n' |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde test-data/biobb_genrestr_input.ndx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/biobb_genrestr_input.ndx Fri Apr 12 07:18:48 2019 -0400 |
| [ |
| b'@@ -0,0 +1,9662 @@\n+[ System ]\n+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 \n+ 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 \n+ 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 \n+ 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 \n+ 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 \n+ 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 \n+ 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 \n+ 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 \n+ 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 \n+ 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 \n+ 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 \n+ 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 \n+ 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 \n+ 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 \n+ 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 \n+ 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 \n+ 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 \n+ 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 \n+ 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 \n+ 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 \n+ 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 \n+ 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 \n+ 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 \n+ 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 \n+ 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 \n+ 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 \n+ 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 \n+ 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 \n+ 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 \n+ 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 \n+ 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 \n+ 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 \n+ 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 \n+ 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 \n+ 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 \n+ 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 \n+ 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 \n+ 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 \n+ 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 \n+ 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 \n+ 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 \n+ 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 \n+ 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 \n+ 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 \n+ 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 \n+ 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 \n+ 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 \n+ 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 \n+ 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 \n+ 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 \n+ 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 \n+ 766 767 768 769 770 771 772 773 '..b'8 29089 29090 29099 29102 29103 29105 29107 29109 29111 29116 29119 29122 29133 \n+29135 29139 29149 29152 29155 29156 29157 29164 29174 29176 29180 29190 29193 29196 29199 \n+29202 29212 29215 29218 29219 29229 29232 29235 29236 29237 29246 29249 29250 29251 29253 \n+29255 29263 29273 29275 29279 29282 29292 29302 29305 29308 29311 29313 29314 29317 29326 \n+29329 29332 29333 29334 29341 29351 29354 29357 29358 29359 29366 29376 29386 29388 29392 \n+29402 29405 29406 29408 29410 29411 29413 29415 29423 29426 29427 29428 29430 29432 29440 \n+29443 29446 29449 29451 29452 29455 29464 29467 29470 29471 29472 29481 29484 29486 29490 \n+29500 29503 29504 29506 29508 29510 29512 29520 29523 29526 29527 29528 29535 29538 29541 \n+29542 29543 29550 29553 29555 29559 29569 29572 29575 29578 29580 29581 29584 29593 29596 \n+29599 29602 29604 29605 29608 29617 29627 29634 29637 29640 29651 29654 29656 29660 29670 \n+29673 29681 29684 29687 29690 29692 29693 29696 29705 29708 29709 29710 29714 29717 29720 \n+29731 29733 29737 29745 29748 29751 29752 29753 29760 29762 29766 29776 29778 29782 29790 \n+29800 29802 29806 29809 29826 29836 29838 29842 29852 29855 29858 29859 29860 29867 29877 \n+29887 29890 29891 29893 29895 29897 29899 29907 29910 29913 29916 29919 29929 29932 29940 \n+29943 29951 29961 29971 29981 29983 29987 29990 30000 30002 30006 30009 30019 30021 30025 \n+30035 30038 30040 30044 30054 30056 30060 30068 30070 30074 30082 30084 30088 30103 30106 \n+30109 30112 30114 30115 30118 30127 30130 30138 30148 30151 30154 30155 30156 30165 30168 \n+30170 30174 30184 30187 30189 30193 30203 30206 30214 30217 30220 30223 30225 30226 30229 \n+30238 30241 30242 30244 30246 30247 30249 30251 30259 30262 30265 30268 30270 30271 30274 \n+30280 30283 30286 30297 30300 30303 30306 30308 30309 30312 30321 30331 30341 30343 30347 \n+30357 30359 30363 30366 30376 30386 30388 30392 30402 30404 30408 30416 30419 30422 30425 \n+30427 30428 30431 30440 30443 30451 30461 30464 30467 30468 30469 30478 30488 30498 30501 \n+30504 30507 30509 30510 30513 30522 30525 30528 30529 30530 30539 30541 30545 30555 30558 \n+30559 30560 30562 30564 30572 30575 30577 30581 30591 30594 30602 30605 30608 30611 30613 \n+30614 30617 30633 30635 30639 30649 30652 30653 30655 30657 30659 30661 30666 30669 30672 \n+30683 30686 30688 30692 30702 30705 30707 30711 30721 30724 30725 30727 30729 30730 30732 \n+30734 30742 30745 30748 30751 30753 30754 30757 30766 30769 30772 30773 30774 30778 30781 \n+30784 30792 30795 30798 30809 30812 30815 30816 30817 30824 30834 30836 30840 30843 30853 \n+30856 30857 30859 30861 30862 30864 30866 30868 30870 30877 30887 30890 30891 30892 30899 \n+30902 30903 30904 30911 30913 30917 30927 30930 30931 30932 30939 30942 30945 30948 30950 \n+30951 30954 30963 30966 30969 30972 30974 30975 30978 30987 30989 30993 31003 31006 31009 \n+31010 31011 31020 31023 31024 31026 31028 31030 31032 31047 31049 31053 31056 31066 31069 \n+31072 31073 31074 31081 31084 31099 31102 31105 31108 31111 31121 31124 31126 31130 31140 \n+31143 31146 31149 31151 31152 31155 31171 31174 31175 31177 31179 31181 31183 31191 31194 \n+31196 31200 31210 31213 31216 31219 31221 31222 31225 31234 31236 31240 31257 31260 31261 \n+31262 31269 31272 31274 31278 31288 31290 31294 31304 31306 31310 31313 31323 31325 31329 \n+31339 31341 31345 31355 31357 31361 31376 31379 31380 31382 31384 31385 31387 31389 31391 \n+31393 31400 31403 31406 31409 31411 31412 31415 31421 31424 31427 31445 31448 31463 31466 \n+31467 31469 31471 31472 31474 31476 31484 31486 31490 31498 31501 31502 31503 31512 31514 \n+31518 31521 31531 31534 31537 31538 31548 31551 31554 31557 31559 31560 31563 31572 31574 \n+31578 31588 31591 31593 31597 31607 31610 31618 31620 31624 31627 \n+[ chA_&_r_513 ]\n+6920 6921 6922 6923 6924 6925 6926 6927 6928 6929 6930 6931 6932 6933 6934 \n+6935 6936 6937 6938 6939 \n+[ chB_&_r_513 ]\n+14828 14829 14830 14831 14832 14833 14834 14835 14836 14837 14838 14839 14840 14841 14842 \n+14843 14844 14845 14846 14847 \n' |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde test-data/biobb_genrestr_input.zip |
| b |
| Binary file test-data/biobb_genrestr_input.zip has changed |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde test-data/biobb_genrestr_myGenrestr.zip |
| b |
| Binary file test-data/biobb_genrestr_myGenrestr.zip has changed |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde test-data/biobb_grompp_input.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/biobb_grompp_input.gro Fri Apr 12 07:18:48 2019 -0400 |
| b |
| b'@@ -0,0 +1,71705 @@\n+Created with pdb2gmx building block\n+71702\n+ 1SER N 1 2.270 1.214 5.506\n+ 1SER H1 2 2.288 1.242 5.411\n+ 1SER H2 3 2.354 1.220 5.559\n+ 1SER H3 4 2.237 1.120 5.507\n+ 1SER CA 5 2.167 1.304 5.566\n+ 1SER HA 6 2.083 1.294 5.512\n+ 1SER CB 7 2.138 1.263 5.710\n+ 1SER HB1 8 2.222 1.264 5.765\n+ 1SER HB2 9 2.097 1.172 5.713\n+ 1SER OG 10 2.046 1.352 5.771\n+ 1SER HG 11 2.029 1.323 5.865\n+ 1SER C 12 2.215 1.448 5.559\n+ 1SER O 13 2.326 1.480 5.601\n+ 2GLU N 14 2.130 1.536 5.505\n+ 2GLU H 15 2.041 1.504 5.472\n+ 2GLU CA 16 2.165 1.677 5.493\n+ 2GLU HA 17 2.205 1.702 5.581\n+ 2GLU CB 18 2.267 1.697 5.381\n+ 2GLU HB1 19 2.224 1.670 5.294\n+ 2GLU HB2 20 2.346 1.639 5.399\n+ 2GLU CG 21 2.315 1.841 5.367\n+ 2GLU HG1 22 2.354 1.870 5.454\n+ 2GLU HG2 23 2.237 1.899 5.343\n+ 2GLU CD 24 2.421 1.856 5.259\n+ 2GLU OE1 25 2.456 1.755 5.196\n+ 2GLU OE2 26 2.469 1.970 5.239\n+ 2GLU C 27 2.040 1.761 5.467\n+ 2GLU O 28 1.946 1.716 5.400\n+ 3ALA N 29 2.039 1.882 5.522\n+ 3ALA H 30 2.118 1.912 5.575\n+ 3ALA CA 31 1.926 1.971 5.505\n+ 3ALA HA 32 1.846 1.920 5.536\n+ 3ALA CB 33 1.944 2.096 5.591\n+ 3ALA HB1 34 1.865 2.157 5.578\n+ 3ALA HB2 35 1.951 2.070 5.687\n+ 3ALA HB3 36 2.027 2.144 5.563\n+ 3ALA C 37 1.909 2.009 5.359\n+ 3ALA O 38 1.988 2.085 5.303\n+ 4GLU N 39 1.805 1.955 5.299\n+ 4GLU H 40 1.745 1.894 5.351\n+ 4GLU CA 41 1.775 1.982 5.159\n+ 4GLU HA 42 1.859 1.961 5.108\n+ 4GLU CB 43 1.662 1.890 5.110\n+ 4GLU HB1 44 1.635 1.920 5.018\n+ 4GLU HB2 45 1.584 1.900 5.172\n+ 4GLU CG 46 1.700 1.743 5.102\n+ 4GLU HG1 47 1.727 1.713 5.194\n+ 4GLU HG2 48 1.777 1.733 5.040\n+ 4GLU CD 49 1.586 1.656 5.054\n+ 4GLU OE1 50 1.475 1.710 5.031\n+ 4GLU OE2 51 1.607 1.534 5.038\n+ 4GLU C 52 1.737 2.128 5.139\n+ 4GLU O 53 1.740 2.180 5.028\n+ 5ASP N 54 1.702 2.195 5.249\n+ 5ASP H 55 1.702 2.148 5.337\n+ 5ASP CA 56 1.664 2.336 5.242\n+ 5ASP HA 57 1.589 2.341 5.177\n+ 5ASP CB 58 1.618 2.385 5.380\n+ 5ASP HB1 59 1.612 2.485 5.378\n+ 5ASP HB2 60 1.686 2.358 5.448\n+ 5ASP CG 61 1.483 2.329 5.420\n+ 5ASP OD1 62 1.413 2.276 5.331\n+ 5ASP OD2 63 1.448 2.340 5.539\n+ 5ASP C 64 1.781 2.419 5.192\n+ 5ASP O 65 1.762 2.515 5.116\n+ 6ALA N 66 1.901 2.385 5.235\n+ 6ALA H 67 1.911 2.306 5.296\n+ 6ALA CA 68 2.019 2.460 5.196\n+ 6ALA HA 69 2.007 2.552 5.233\n+ 6ALA CB 70 2.144 2.396 5.254\n+ 6ALA HB1 71 2.224 2.449 5.226\n+ 6ALA HB2 72 2.138 2.396 5.354\n+ 6ALA HB3 73 2.153 2.302 5.221\n+ 6ALA C 74 2.028 2.466 5.044\n+ 6ALA O 75 2.029 2.364 4.976\n+ 7SER N 76 2.033 2.588 4.995\n+ 7SER H 77 2.031 2.666 5.057\n+ 7SER CA 78 2.041 2.612 4.852\n+ 7SER HA 79 1.973 2.552 4.811\n+ 7SER CB 80 2.008 2.758 4.820\n+ 7SER HB1 81 1.922 2.785 4.864\n+ 7SER HB2 82 2.001 2.772 4.722\n+ 7SER OG 83 2.109 2.845 4.868\n+ 7SER HG 84 2.085 2.940 4.846\n+ 7SER C 85 2.180 2.577 4.800\n+ 7SER O 86 2'..b'74 8.168\n+23553SOL HW171617 7.632 7.825 8.134\n+23553SOL HW271618 7.702 7.759 8.266\n+23554SOL OW71619 8.270 8.450 8.820\n+23554SOL HW171620 8.310 8.449 8.728\n+23554SOL HW271621 8.280 8.542 8.860\n+23555SOL OW71622 8.364 8.358 7.739\n+23555SOL HW171623 8.427 8.396 7.671\n+23555SOL HW271624 8.404 8.275 7.778\n+23556SOL OW71625 7.820 8.736 8.938\n+23556SOL HW171626 7.807 8.829 8.904\n+23556SOL HW271627 7.736 8.684 8.925\n+23557SOL OW71628 8.487 8.546 8.144\n+23557SOL HW171629 8.417 8.499 8.198\n+23557SOL HW271630 8.546 8.478 8.101\n+23558SOL OW71631 8.462 7.684 8.419\n+23558SOL HW171632 8.454 7.648 8.326\n+23558SOL HW271633 8.460 7.608 8.484\n+23559SOL OW71634 7.703 8.796 7.738\n+23559SOL HW171635 7.607 8.797 7.711\n+23559SOL HW271636 7.715 8.849 7.822\n+23560SOL OW71637 7.523 7.793 7.481\n+23560SOL HW171638 7.431 7.765 7.452\n+23560SOL HW271639 7.554 7.870 7.425\n+23561SOL OW71640 8.888 8.304 8.846\n+23561SOL HW171641 8.831 8.356 8.783\n+23561SOL HW271642 8.984 8.316 8.822\n+23562SOL OW71643 7.520 7.614 7.766\n+23562SOL HW171644 7.503 7.697 7.712\n+23562SOL HW271645 7.610 7.577 7.744\n+23563SOL OW71646 8.631 8.783 7.567\n+23563SOL HW171647 8.532 8.772 7.569\n+23563SOL HW271648 8.665 8.798 7.660\n+23564SOL OW71649 8.061 8.290 8.879\n+23564SOL HW171650 8.117 8.371 8.862\n+23564SOL HW271651 8.120 8.210 8.882\n+23565SOL OW71652 8.673 7.773 7.897\n+23565SOL HW171653 8.738 7.699 7.886\n+23565SOL HW271654 8.693 7.823 7.981\n+23566SOL OW71655 8.042 8.193 8.100\n+23566SOL HW171656 8.092 8.278 8.081\n+23566SOL HW271657 7.954 8.195 8.052\n+23567SOL OW71658 8.307 8.822 7.464\n+23567SOL HW171659 8.261 8.837 7.552\n+23567SOL HW271660 8.351 8.907 7.434\n+23568SOL OW71661 8.856 9.299 9.168\n+23568SOL HW171662 8.760 9.288 9.141\n+23568SOL HW271663 8.912 9.232 9.120\n+23569SOL OW71664 8.307 8.404 8.309\n+23569SOL HW171665 8.361 8.335 8.357\n+23569SOL HW271666 8.275 8.473 8.375\n+23570SOL OW71667 8.531 8.432 7.535\n+23570SOL HW171668 8.508 8.485 7.453\n+23570SOL HW271669 8.612 8.376 7.516\n+23571SOL OW71670 7.527 8.688 8.101\n+23571SOL HW171671 7.526 8.641 8.189\n+23571SOL HW271672 7.609 8.660 8.050\n+23572SOL OW71673 7.876 7.872 7.968\n+23572SOL HW171674 7.906 7.800 7.906\n+23572SOL HW271675 7.837 7.832 8.051\n+23573SOL OW71676 9.153 8.935 8.552\n+23573SOL HW171677 9.060 8.910 8.525\n+23573SOL HW271678 9.179 8.885 8.634\n+23574SOL OW71679 7.765 7.995 8.728\n+23574SOL HW171680 7.803 7.936 8.800\n+23574SOL HW271681 7.805 7.969 8.640\n+23575SOL OW71682 8.872 7.662 8.560\n+23575SOL HW171683 8.924 7.597 8.615\n+23575SOL HW271684 8.823 7.725 8.621\n+23576SOL OW71685 8.449 7.482 8.602\n+23576SOL HW171686 8.386 7.410 8.571\n+23576SOL HW271687 8.542 7.446 8.602\n+23577SOL OW71688 8.218 8.778 7.749\n+23577SOL HW171689 8.172 8.691 7.766\n+23577SOL HW271690 8.309 8.775 7.790\n+23578SOL OW71691 8.066 9.015 8.732\n+23578SOL HW171692 8.061 9.097 8.789\n+23578SOL HW271693 8.155 9.012 8.687\n+23579SOL OW71694 8.800 7.500 7.616\n+23579SOL HW171695 8.835 7.459 7.532\n+23579SOL HW271696 8.710 7.462 7.636\n+23580SOL OW71697 8.748 7.901 8.139\n+23580SOL HW171698 8.689 7.981 8.143\n+23580SOL HW271699 8.763 7.866 8.232\n+23581SOL OW71700 7.487 8.525 7.748\n+23581SOL HW171701 7.586 8.514 7.739\n+23581SOL HW271702 7.447 8.439 7.780\n+ 9.00078 9.00078 9.00078\n' |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde test-data/biobb_grompp_input.zip |
| b |
| Binary file test-data/biobb_grompp_input.zip has changed |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde test-data/biobb_make-ndx_myMake_ndx.ndx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/biobb_make-ndx_myMake_ndx.ndx Fri Apr 12 07:18:48 2019 -0400 |
| [ |
| b'@@ -0,0 +1,10209 @@\n+[ System ]\n+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15\n+ 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30\n+ 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45\n+ 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60\n+ 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75\n+ 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90\n+ 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105\n+ 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120\n+ 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135\n+ 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150\n+ 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165\n+ 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180\n+ 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195\n+ 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210\n+ 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225\n+ 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240\n+ 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255\n+ 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270\n+ 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285\n+ 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300\n+ 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315\n+ 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330\n+ 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345\n+ 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360\n+ 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375\n+ 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390\n+ 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405\n+ 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420\n+ 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435\n+ 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450\n+ 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465\n+ 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480\n+ 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495\n+ 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510\n+ 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525\n+ 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540\n+ 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555\n+ 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570\n+ 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585\n+ 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600\n+ 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615\n+ 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630\n+ 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645\n+ 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660\n+ 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675\n+ 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690\n+ 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705\n+ 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720\n+ 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735\n+ 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750\n+ 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765\n+ 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780\n+ 781 782 783'..b' 29042 29044 29050 29051 29052 29054 29072 29073 29074 29076 29079\n+29080 29081 29083 29093 29094 29095 29097 29113 29114 29115 29125 29127 29128 29129 29131\n+29143 29144 29145 29147 29158 29159 29160 29162 29168 29169 29170 29172 29184 29185 29186\n+29188 29206 29207 29208 29210 29223 29224 29225 29227 29240 29241 29242 29244 29257 29258\n+29259 29261 29267 29268 29269 29271 29286 29287 29288 29290 29296 29297 29298 29300 29320\n+29321 29322 29324 29335 29336 29337 29339 29345 29346 29347 29349 29360 29361 29362 29364\n+29370 29371 29372 29374 29380 29381 29382 29384 29396 29397 29398 29400 29417 29418 29419\n+29421 29434 29435 29436 29438 29458 29459 29460 29462 29475 29476 29477 29479 29494 29495\n+29496 29498 29514 29515 29516 29518 29529 29530 29531 29533 29544 29545 29546 29548 29563\n+29564 29565 29567 29587 29588 29589 29591 29611 29612 29613 29615 29621 29622 29623 29625\n+29631 29632 29633 29643 29645 29646 29647 29649 29664 29665 29666 29668 29675 29676 29677\n+29679 29699 29700 29701 29703 29711 29712 29713 29723 29725 29726 29727 29729 29739 29740\n+29741 29743 29754 29755 29756 29758 29770 29771 29772 29774 29784 29785 29786 29788 29794\n+29795 29796 29798 29813 29814 29815 29817 29820 29821 29822 29824 29830 29831 29832 29834\n+29846 29847 29848 29850 29861 29862 29863 29865 29871 29872 29873 29875 29881 29882 29883\n+29885 29901 29902 29903 29905 29923 29924 29925 29927 29934 29935 29936 29938 29945 29946\n+29947 29949 29955 29956 29957 29959 29965 29966 29967 29969 29975 29976 29977 29979 29994\n+29995 29996 29998 30013 30014 30015 30017 30029 30030 30031 30033 30048 30049 30050 30052\n+30062 30063 30064 30066 30076 30077 30078 30080 30090 30091 30092 30094 30097 30098 30099\n+30101 30121 30122 30123 30125 30132 30133 30134 30136 30142 30143 30144 30146 30159 30160\n+30161 30163 30178 30179 30180 30182 30197 30198 30199 30201 30208 30209 30210 30212 30232\n+30233 30234 30236 30253 30254 30255 30257 30277 30278 30279 30289 30291 30292 30293 30295\n+30315 30316 30317 30319 30325 30326 30327 30329 30335 30336 30337 30339 30351 30352 30353\n+30355 30370 30371 30372 30374 30380 30381 30382 30384 30396 30397 30398 30400 30410 30411\n+30412 30414 30434 30435 30436 30438 30445 30446 30447 30449 30455 30456 30457 30459 30472\n+30473 30474 30476 30482 30483 30484 30486 30492 30493 30494 30496 30516 30517 30518 30520\n+30533 30534 30535 30537 30549 30550 30551 30553 30566 30567 30568 30570 30585 30586 30587\n+30589 30596 30597 30598 30600 30620 30621 30622 30624 30627 30628 30629 30631 30643 30644\n+30645 30647 30663 30664 30665 30675 30677 30678 30679 30681 30696 30697 30698 30700 30715\n+30716 30717 30719 30736 30737 30738 30740 30760 30761 30762 30764 30775 30776 30777 30787\n+30789 30790 30791 30801 30803 30804 30805 30807 30818 30819 30820 30822 30828 30829 30830\n+30832 30847 30848 30849 30851 30871 30872 30873 30875 30881 30882 30883 30885 30893 30894\n+30895 30897 30905 30906 30907 30909 30921 30922 30923 30925 30933 30934 30935 30937 30957\n+30958 30959 30961 30981 30982 30983 30985 30997 30998 30999 31001 31014 31015 31016 31018\n+31034 31035 31036 31038 31041 31042 31043 31045 31060 31061 31062 31064 31075 31076 31077\n+31079 31086 31087 31088 31090 31093 31094 31095 31097 31115 31116 31117 31119 31134 31135\n+31136 31138 31158 31159 31160 31162 31165 31166 31167 31169 31185 31186 31187 31189 31204\n+31205 31206 31208 31228 31229 31230 31232 31244 31245 31246 31248 31251 31252 31253 31255\n+31263 31264 31265 31267 31282 31283 31284 31286 31298 31299 31300 31302 31317 31318 31319\n+31321 31333 31334 31335 31337 31349 31350 31351 31353 31363 31364 31365 31367 31370 31371\n+31372 31374 31394 31395 31396 31398 31418 31419 31420 31430 31432 31433 31434 31436 31439\n+31440 31441 31443 31450 31451 31452 31454 31457 31458 31459 31461 31478 31479 31480 31482\n+31492 31493 31494 31496 31506 31507 31508 31510 31525 31526 31527 31529 31542 31543 31544\n+31546 31566 31567 31568 31570 31582 31583 31584 31586 31601 31602 31603 31605 31612 31613\n+31614 31616 31631\n' |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde test-data/biobb_mdrun_input.tpr |
| b |
| Binary file test-data/biobb_mdrun_input.tpr has changed |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde test-data/biobb_mdrun_mdrun.trr |
| b |
| Binary file test-data/biobb_mdrun_mdrun.trr has changed |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde test-data/biobb_mutate_input.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/biobb_mutate_input.pdb Fri Apr 12 07:18:48 2019 -0400 |
| b |
| b'@@ -0,0 +1,5648 @@\n+HEADER TRANSFERASE 12-FEB-99 2KI5 \n+TITLE HERPES SIMPLEX TYPE-1 THYMIDINE KINASE IN COMPLEX WITH THE \n+TITLE 2 DRUG ACICLOVIR AT 1.9A RESOLUTION \n+COMPND MOL_ID: 1; \n+COMPND 2 MOLECULE: PROTEIN (THYMIDINE KINASE); \n+COMPND 3 CHAIN: A, B; \n+COMPND 4 SYNONYM: TK; \n+COMPND 5 EC: 2.7.1.21; \n+COMPND 6 ENGINEERED: YES; \n+COMPND 7 OTHER_DETAILS: ACICLOVIR, ANTIVIRAL DRUG AS DEPOSITED IN \n+COMPND 8 1KI5 \n+SOURCE MOL_ID: 1; \n+SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN HERPESVIRUS 1; \n+SOURCE 3 ORGANISM_COMMON: HERPES SIMPLEX VIRUS TYPE 1; \n+SOURCE 4 ORGANISM_TAXID: 10298; \n+SOURCE 5 STRAIN: SY211; \n+SOURCE 6 GENE: TK; \n+SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; \n+SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; \n+SOURCE 9 EXPRESSION_SYSTEM_STRAIN: SY211; \n+SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PT7:HSVTK; \n+SOURCE 11 EXPRESSION_SYSTEM_GENE: TK \n+KEYWDS TRANSFERASE (PHOSPHOTRANSFERASE) THYMID, TRANSFERASE \n+KEYWDS 2 (PHOSPHOTRANSFERASE) THYMIDINE KINASE; VIRIDAE; DS-DNA \n+KEYWDS 3 ENVELOPED VIRUSES; HERPESVIRIDAE; ALPHAHERPESVIRINAE \n+KEYWDS 4 ANTIVIRAL DRUG (ACICLOVIR) \n+EXPDTA X-RAY DIFFRACTION \n+AUTHOR M.S.BENNETT,F.WIEN,J.N.CHAMPNESS,T.BATUWANGALA,T.RUTHERFORD, \n+AUTHOR 2 W.C.SUMMERS,H.SUN,G.WRIGHT,M.R.SANDERSON \n+REVDAT 4 24-FEB-09 2KI5 1 VERSN \n+REVDAT 3 01-APR-03 2KI5 1 JRNL \n+REVDAT 2 17-MAY-99 2KI5 1 TITLE \n+REVDAT 1 04-MAR-99 2KI5 0 \n+SPRSDE 02-MAR-99 2KI5 1KI5 \n+JRNL AUTH M.S.BENNETT,F.WIEN,J.N.CHAMPNESS,T.BATUWANGALA, \n+JRNL AUTH 2 T.RUTHERFORD,W.C.SUMMERS,H.SUN,G.WRIGHT, \n+JRNL AUTH 3 M.R.SANDERSON \n+JRNL TITL STRUCTURE TO 1.9 A RESOLUTION OF A COMPLEX WITH \n+JRNL TITL 2 HERPES SIMPLEX VIRUS TYPE-1 THYMIDINE KINASE OF A \n+JRNL TITL 3 NOVEL, NON-SUBSTRATE INHIBITOR: X-RAY \n+JRNL TITL 4 CRYSTALLOGRAPHIC COMPARISON WITH BINDING OF \n+JRNL TITL 5 ACICLOVIR. \n+JRNL REF FEBS LETT. V. 443 121 1999 \n+JRNL REFN ISSN 0014-5793 \n+JRNL PMID 9989588 \n+JRNL DOI 10.1016/S0014-5793(98)01619-6 \n+REMARK 1 \n+REMARK 2 \n+REMARK 2 RESOLUTION. 1.90 ANGSTROMS. '..b'632 4633 4634 \n+CONECT 4631 4630 \n+CONECT 4632 4630 \n+CONECT 4633 4630 \n+CONECT 4634 4630 \n+CONECT 4635 4637 4639 \n+CONECT 4636 4638 4640 \n+CONECT 4637 4635 \n+CONECT 4638 4636 \n+CONECT 4639 4635 4641 \n+CONECT 4640 4636 4642 \n+CONECT 4641 4639 4643 \n+CONECT 4642 4640 4644 \n+CONECT 4643 4641 4645 \n+CONECT 4644 4642 4645 \n+CONECT 4645 4643 4644 4646 4655 \n+CONECT 4646 4645 4647 \n+CONECT 4647 4646 4648 \n+CONECT 4648 4647 4649 4655 \n+CONECT 4649 4648 4650 4651 \n+CONECT 4650 4649 \n+CONECT 4651 4649 4652 \n+CONECT 4652 4651 4653 4654 \n+CONECT 4653 4652 \n+CONECT 4654 4652 4655 \n+CONECT 4655 4645 4648 4654 \n+CONECT 4656 4657 4658 4659 4660 \n+CONECT 4657 4656 \n+CONECT 4658 4656 \n+CONECT 4659 4656 \n+CONECT 4660 4656 \n+CONECT 4661 4662 4663 \n+CONECT 4662 4661 \n+CONECT 4663 4661 4664 \n+CONECT 4664 4663 4665 \n+CONECT 4665 4664 4666 \n+CONECT 4666 4665 4667 4676 \n+CONECT 4667 4666 4668 \n+CONECT 4668 4667 4669 \n+CONECT 4669 4668 4670 4676 \n+CONECT 4670 4669 4671 4672 \n+CONECT 4671 4670 \n+CONECT 4672 4670 4673 \n+CONECT 4673 4672 4674 4675 \n+CONECT 4674 4673 \n+CONECT 4675 4673 4676 \n+CONECT 4676 4666 4669 4675 \n+MASTER 453 0 4 32 10 0 14 6 4966 2 47 58 \n+END \n' |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde test-data/biobb_mutate_mutate.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/biobb_mutate_mutate.pdb Fri Apr 12 07:18:48 2019 -0400 |
| b |
| b'@@ -0,0 +1,4967 @@\n+ATOM 1 N MET A 46 42.224 58.491 28.031 1.00 31.76 N \n+ATOM 2 CA MET A 46 42.964 59.788 28.172 1.00 34.85 C \n+ATOM 3 C MET A 46 43.978 59.649 29.317 1.00 36.75 C \n+ATOM 4 O MET A 46 43.755 58.843 30.241 1.00 40.33 O \n+ATOM 5 CB MET A 46 41.991 60.929 28.438 1.00 32.51 C \n+ATOM 6 N PRO A 47 45.116 60.391 29.265 1.00 36.24 N \n+ATOM 7 CA PRO A 47 46.136 60.304 30.323 1.00 33.42 C \n+ATOM 8 C PRO A 47 45.604 60.613 31.701 1.00 30.60 C \n+ATOM 9 O PRO A 47 44.457 61.023 31.857 1.00 29.75 O \n+ATOM 10 CB PRO A 47 47.188 61.331 29.889 1.00 34.73 C \n+ATOM 11 CG PRO A 47 46.417 62.315 29.035 1.00 35.61 C \n+ATOM 12 CD PRO A 47 45.505 61.394 28.250 1.00 36.31 C \n+ATOM 13 N THR A 48 46.458 60.431 32.698 1.00 30.18 N \n+ATOM 14 CA THR A 48 46.072 60.672 34.071 1.00 26.68 C \n+ATOM 15 C THR A 48 46.809 61.829 34.705 1.00 25.13 C \n+ATOM 16 O THR A 48 47.953 62.141 34.335 1.00 23.66 O \n+ATOM 17 CB THR A 48 46.294 59.428 34.915 1.00 26.86 C \n+ATOM 18 OG1 THR A 48 47.641 58.977 34.737 1.00 28.95 O \n+ATOM 19 CG2 THR A 48 45.339 58.337 34.511 1.00 25.93 C \n+ATOM 20 N ILE A 49 46.136 62.465 35.661 1.00 21.74 N \n+ATOM 21 CA ILE A 49 46.680 63.586 36.393 1.00 20.12 C \n+ATOM 22 C ILE A 49 46.548 63.304 37.881 1.00 20.56 C \n+ATOM 23 O ILE A 49 45.645 62.578 38.325 1.00 19.49 O \n+ATOM 24 CB ILE A 49 45.904 64.859 36.050 1.00 17.69 C \n+ATOM 25 CD1 ILE A 49 47.563 66.629 36.545 1.00 17.87 C \n+ATOM 26 CG1 ILE A 49 46.191 66.129 36.843 1.00 15.68 C \n+ATOM 27 CG2 ILE A 49 44.437 64.677 36.426 1.00 99.00 C \n+ATOM 28 N LEU A 50 47.500 63.810 38.643 1.00 21.96 N \n+ATOM 29 CA LEU A 50 47.457 63.674 40.089 1.00 21.20 C \n+ATOM 30 C LEU A 50 47.627 65.096 40.622 1.00 20.37 C \n+ATOM 31 O LEU A 50 48.614 65.721 40.349 1.00 22.88 O \n+ATOM 32 CB LEU A 50 48.569 62.750 40.575 1.00 20.38 C \n+ATOM 33 CG LEU A 50 48.698 62.327 42.051 1.00 23.98 C \n+ATOM 34 CD1 LEU A 50 49.683 63.182 42.761 1.00 22.07 C \n+ATOM 35 CD2 LEU A 50 47.362 62.340 42.770 1.00 23.15 C \n+ATOM 36 N ARG A 51 46.593 65.649 41.253 1.00 18.59 N \n+ATOM 37 CA ARG A 51 46.675 66.995 41.810 1.00 17.55 C \n+ATOM 38 C ARG A 51 46.870 66.866 43.318 1.00 17.00 C \n+ATOM 39 O ARG A 51 46.252 65.996 43.965 1.00 17.03 O \n+ATOM 40 CB ARG A 51 45.398 67.765 41.532 1.00 18.02 C \n+ATOM 41 CG ARG A 51 45.275 68.303 40.123 1.00 20.14 C \n+ATOM 42 CD ARG A 51 43.927 68.949 39.958 1.00 21.12 C \n+ATOM 43 NE ARG A 51 42.877 67.959 40.171 1.00 24.39 N \n+ATOM 44 CZ ARG A 51 41.853 68.101 41.001 1.00 21.53 C \n+ATOM 45 NH1 ARG A 51 41.710 69.196 41.719 1.00 23.06 N \n+ATOM 46 NH2 ARG A 51 40.979 67.127 41.116 1.00 23.24 N \n+ATOM 47 N VAL A 52 47.729 67.705 43.877 1.00 16.51 N \n+ATOM 48 CA VAL A 52 48.029 67.656 45.319 1.00 18.88 C \n+ATOM 49 C VAL A 52 48.045 69.'..b'05 6.270 82.517 47.565 1.00 31.93 O \n+HETATM 4918 O HOH B 706 5.857 88.669 24.803 1.00 25.08 O \n+HETATM 4919 O HOH B 707 3.718 78.699 30.773 1.00 55.75 O \n+HETATM 4920 O HOH B 709 2.353 79.693 34.112 1.00 41.98 O \n+HETATM 4921 O HOH B 710 26.563 76.882 43.357 1.00 18.46 O \n+HETATM 4922 O HOH B 713 2.247 79.965 44.762 1.00 30.21 O \n+HETATM 4923 O HOH B 714 3.396 78.328 47.460 1.00 31.20 O \n+HETATM 4924 O HOH B 716 29.900 100.169 25.531 1.00 35.22 O \n+HETATM 4925 O HOH B 717 39.508 89.834 15.307 1.00 36.16 O \n+HETATM 4926 O HOH B 718 41.208 99.764 46.839 1.00 36.34 O \n+HETATM 4927 O HOH B 722 46.146 101.401 27.996 1.00 41.26 O \n+HETATM 4928 O HOH B 724 18.779 95.945 61.261 1.00 28.00 O \n+HETATM 4929 O HOH B 726 6.577 101.398 46.248 1.00 34.71 O \n+HETATM 4930 O HOH B 727 23.776 75.396 30.958 1.00 24.31 O \n+HETATM 4931 O HOH B 731 0.732 81.480 35.666 1.00 45.32 O \n+HETATM 4932 O HOH B 732 10.702 90.064 49.390 1.00 28.67 O \n+HETATM 4933 O HOH B 735 9.897 82.965 24.164 1.00 28.83 O \n+HETATM 4934 O HOH B 739 21.168 111.301 40.601 1.00 26.38 O \n+HETATM 4935 O HOH B 740 13.088 94.113 58.697 1.00 41.36 O \n+HETATM 4936 O HOH B 743 35.181 104.131 45.821 1.00 56.22 O \n+HETATM 4937 O HOH B 746 13.304 87.909 60.368 1.00 31.96 O \n+HETATM 4938 O HOH B 748 16.588 110.077 48.074 1.00 43.94 O \n+HETATM 4939 O HOH B 749 42.246 106.520 50.126 1.00 39.16 O \n+HETATM 4940 O HOH B 750 38.865 101.910 42.169 1.00 48.46 O \n+HETATM 4941 O HOH B 751 40.714 108.701 46.369 1.00 33.86 O \n+HETATM 4942 O HOH B 752 9.660 94.289 45.733 1.00 38.22 O \n+HETATM 4943 O HOH B 753 47.600 95.570 38.981 1.00 32.59 O \n+HETATM 4944 O HOH B 754 4.261 74.375 36.569 1.00 26.76 O \n+HETATM 4945 O HOH B 755 13.163 90.429 39.514 1.00 33.46 O \n+HETATM 4946 O HOH B 756 5.557 95.092 23.874 1.00 50.25 O \n+HETATM 4947 O HOH B 761 10.311 90.259 45.491 1.00 36.89 O \n+HETATM 4948 O HOH B 763 26.508 106.710 34.666 1.00 25.80 O \n+HETATM 4949 O HOH B 764 6.249 106.003 34.370 1.00 27.75 O \n+HETATM 4950 O HOH B 767 13.747 87.697 23.984 1.00 46.31 O \n+HETATM 4951 O HOH B 768 41.046 101.834 52.490 1.00 41.04 O \n+HETATM 4952 O HOH B 769 20.482 95.631 23.868 1.00 36.96 O \n+HETATM 4953 O HOH B 770 32.254 109.242 42.071 1.00 35.06 O \n+HETATM 4954 O HOH B 772 23.353 115.199 50.789 1.00 38.86 O \n+HETATM 4955 O HOH B 773 26.818 79.120 44.718 1.00 27.83 O \n+HETATM 4956 O HOH B 774 12.865 99.935 25.528 1.00 25.37 O \n+HETATM 4957 O HOH B 778 19.756 94.242 43.430 1.00 41.39 O \n+HETATM 4958 O HOH B 780 23.930 113.884 53.741 1.00 40.75 O \n+HETATM 4959 O HOH B 784 21.068 92.013 43.768 1.00 37.38 O \n+HETATM 4960 O HOH B 785 3.187 96.240 24.851 1.00 33.43 O \n+HETATM 4961 O HOH B 786 4.113 82.010 45.454 1.00 27.14 O \n+HETATM 4962 O HOH B 787 48.863 97.909 35.568 1.00 23.24 O \n+HETATM 4963 O HOH B 790 15.430 92.039 43.798 1.00 26.19 O \n+HETATM 4964 O HOH B 792 38.780 103.293 38.129 1.00 46.73 O \n+TER 4965 HOH B 792 \n+END\n' |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde test-data/biobb_ndx2resttop_input.ndx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/biobb_ndx2resttop_input.ndx Fri Apr 12 07:18:48 2019 -0400 |
| [ |
| b'@@ -0,0 +1,141537 @@\n+[ System ]\n+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 \n+ 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 \n+ 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 \n+ 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 \n+ 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 \n+ 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 \n+ 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 \n+ 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 \n+ 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 \n+ 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 \n+ 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 \n+ 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 \n+ 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 \n+ 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 \n+ 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 \n+ 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 \n+ 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 \n+ 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 \n+ 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 \n+ 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 \n+ 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 \n+ 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 \n+ 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 \n+ 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 \n+ 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 \n+ 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 \n+ 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 \n+ 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 \n+ 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 \n+ 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 \n+ 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 \n+ 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 \n+ 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 \n+ 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 \n+ 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 \n+ 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 \n+ 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 \n+ 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 \n+ 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 \n+ 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 \n+ 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 \n+ 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 \n+ 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 \n+ 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 \n+ 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 \n+ 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 \n+ 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 \n+ 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 \n+ 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 \n+ 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 \n+ 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 \n+ 766 767 768 769 770 771 772 77'..b'327 30330 30331 30332 30334 30336 30340 \n+30341 30342 30344 30346 30350 30351 30352 30354 30356 30358 30362 30366 30367 30368 30370 \n+30372 30374 30378 30381 30385 30386 30387 30389 30391 30395 30396 30397 30399 30401 30403 \n+30407 30411 30412 30413 30415 30417 30419 30423 30425 30426 30427 30429 30431 30434 30437 \n+30440 30442 30443 30446 30449 30450 30451 30453 30455 30458 30460 30461 30462 30464 30466 \n+30470 30471 30472 30474 30476 30479 30482 30483 30484 30487 30488 30489 30491 30493 30497 \n+30498 30499 30501 30503 30507 30508 30509 30511 30513 30516 30519 30522 30524 30525 30528 \n+30531 30532 30533 30535 30537 30540 30543 30544 30545 30548 30549 30550 30552 30554 30556 \n+30560 30564 30565 30566 30568 30570 30573 30574 30575 30577 30579 30581 30582 30583 30585 \n+30587 30590 30592 30596 30600 30601 30602 30604 30606 30609 30611 30612 30613 30615 30617 \n+30620 30623 30626 30628 30629 30632 30635 30636 30637 30639 30642 30643 30644 30646 30648 \n+30650 30654 30658 30659 30660 30662 30664 30667 30668 30670 30672 30674 30676 30678 30679 \n+30680 30681 30684 30687 30690 30692 30693 30694 30696 30698 30701 30703 30707 30711 30712 \n+30713 30715 30717 30720 30722 30726 30730 30731 30732 30734 30736 30739 30740 30742 30744 \n+30745 30747 30749 30751 30752 30753 30755 30757 30760 30763 30766 30768 30769 30772 30775 \n+30776 30777 30779 30781 30784 30787 30788 30789 30790 30791 30792 30793 30796 30799 30802 \n+30804 30805 30806 30807 30810 30813 30816 30818 30819 30820 30822 30824 30827 30830 30831 \n+30832 30833 30834 30835 30837 30839 30843 30844 30845 30847 30849 30851 30855 30858 30862 \n+30863 30864 30866 30868 30871 30872 30874 30876 30877 30879 30881 30883 30885 30886 30887 \n+30888 30890 30892 30896 30897 30898 30900 30902 30905 30906 30907 30908 30909 30910 30912 \n+30914 30917 30918 30919 30920 30921 30922 30924 30926 30928 30932 30936 30937 30938 30940 \n+30942 30945 30946 30947 30948 30949 30950 30952 30954 30957 30960 30963 30965 30966 30969 \n+30972 30973 30974 30976 30978 30981 30984 30987 30989 30990 30993 30996 30997 30998 31000 \n+31002 31004 31008 31012 31013 31014 31016 31018 31021 31024 31025 31026 31029 31030 31031 \n+31033 31035 31038 31039 31041 31043 31045 31047 31049 31050 31051 31053 31056 31057 31058 \n+31060 31062 31064 31068 31071 31075 31076 31077 31079 31081 31084 31087 31088 31089 31090 \n+31091 31092 31094 31096 31099 31101 31102 31103 31105 31108 31109 31110 31112 31114 31117 \n+31120 31123 31126 31130 31131 31132 31134 31136 31139 31141 31145 31149 31150 31151 31153 \n+31155 31158 31161 31164 31166 31167 31170 31173 31174 31175 31177 31180 31181 31182 31184 \n+31186 31189 31190 31192 31194 31196 31198 31200 31201 31202 31204 31206 31209 31211 31215 \n+31219 31220 31221 31223 31225 31228 31231 31234 31236 31237 31240 31243 31244 31245 31247 \n+31249 31251 31255 31259 31260 31261 31263 31266 31267 31268 31270 31272 31275 31276 31277 \n+31278 31279 31280 31282 31284 31287 31289 31293 31297 31298 31299 31301 31303 31305 31309 \n+31313 31314 31315 31317 31319 31321 31325 31328 31332 31333 31334 31336 31338 31340 31344 \n+31348 31349 31350 31352 31354 31356 31360 31364 31365 31366 31368 31370 31372 31376 31378 \n+31379 31380 31382 31385 31386 31387 31389 31391 31394 31395 31397 31399 31400 31402 31404 \n+31406 31408 31409 31410 31411 31413 31415 31418 31421 31424 31426 31427 31430 31433 31434 \n+31435 31436 31439 31442 31445 31447 31448 31449 31451 31454 31455 31456 31458 31460 31463 \n+31465 31466 31467 31469 31472 31473 31474 31476 31478 31481 31482 31484 31486 31487 31489 \n+31491 31493 31494 31495 31497 31499 31501 31505 31507 31508 31509 31511 31513 31516 31517 \n+31518 31521 31522 31523 31525 31527 31529 31533 31536 31540 31541 31542 31544 31546 31549 \n+31552 31553 31557 31558 31559 31561 31563 31566 31569 31572 31574 31575 31578 31581 31582 \n+31583 31585 31587 31589 31593 31597 31598 31599 31601 31603 31606 31608 31612 31616 31617 \n+31618 31620 31622 31625 31627 31628 31629 31631 31633 31635 31639 31642 31646 31647 31648 \n+\n' |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde test-data/biobb_ndx2resttop_input.zip |
| b |
| Binary file test-data/biobb_ndx2resttop_input.zip has changed |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde test-data/biobb_ndx2resttop_myNdx2resttop.zip |
| b |
| Binary file test-data/biobb_ndx2resttop_myNdx2resttop.zip has changed |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde test-data/biobb_pdb2gmx_input.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/biobb_pdb2gmx_input.pdb Fri Apr 12 07:18:48 2019 -0400 |
| b |
| b'@@ -0,0 +1,31630 @@\n+TITLE Pyruvate Kinase WT with Gromacs and propKa Setup\n+ATOM 1 N GLN A 57 87.630 71.650 27.610 1.00 0.00 N\n+ATOM 2 H1 GLN A 57 88.450 71.970 27.100 1.00 0.00 H\n+ATOM 3 H2 GLN A 57 87.800 70.710 27.950 1.00 0.00 H\n+ATOM 4 H3 GLN A 57 86.830 71.640 26.990 1.00 0.00 H\n+ATOM 5 CA GLN A 57 87.370 72.550 28.750 1.00 0.00 C\n+ATOM 6 HA GLN A 57 87.210 73.550 28.350 1.00 0.00 H\n+ATOM 7 CB GLN A 57 86.100 72.120 29.510 1.00 0.00 C\n+ATOM 8 HB1 GLN A 57 86.080 72.600 30.490 1.00 0.00 H\n+ATOM 9 HB2 GLN A 57 86.120 71.040 29.670 1.00 0.00 H\n+ATOM 10 CG GLN A 57 84.810 72.510 28.760 1.00 0.00 C\n+ATOM 11 HG1 GLN A 57 83.960 72.110 29.310 1.00 0.00 H\n+ATOM 12 HG2 GLN A 57 84.820 72.040 27.770 1.00 0.00 H\n+ATOM 13 CD GLN A 57 84.620 74.020 28.600 1.00 0.00 C\n+ATOM 14 OE1 GLN A 57 85.290 74.820 29.240 1.00 0.00 O\n+ATOM 15 NE2 GLN A 57 83.690 74.420 27.730 1.00 0.00 N\n+ATOM 16 1HE2 GLN A 57 83.140 73.740 27.220 1.00 0.00 H\n+ATOM 17 2HE2 GLN A 57 83.530 75.400 27.600 1.00 0.00 H\n+ATOM 18 C GLN A 57 88.570 72.620 29.690 1.00 0.00 C\n+ATOM 19 O GLN A 57 89.390 71.710 29.720 1.00 0.00 O\n+ATOM 20 N GLN A 58 88.650 73.720 30.450 1.00 0.00 N\n+ATOM 21 H GLN A 58 87.930 74.420 30.350 1.00 0.00 H\n+ATOM 22 CA GLN A 58 89.700 74.010 31.430 1.00 0.00 C\n+ATOM 23 HA GLN A 58 90.540 73.340 31.270 1.00 0.00 H\n+ATOM 24 CB GLN A 58 90.200 75.450 31.230 1.00 0.00 C\n+ATOM 25 HB1 GLN A 58 91.000 75.640 31.950 1.00 0.00 H\n+ATOM 26 HB2 GLN A 58 89.400 76.150 31.470 1.00 0.00 H\n+ATOM 27 CG GLN A 58 90.760 75.740 29.830 1.00 0.00 C\n+ATOM 28 HG1 GLN A 58 90.960 74.820 29.290 1.00 0.00 H\n+ATOM 29 HG2 GLN A 58 91.720 76.250 29.940 1.00 0.00 H\n+ATOM 30 CD GLN A 58 89.830 76.620 28.980 1.00 0.00 C\n+ATOM 31 OE1 GLN A 58 88.620 76.420 28.940 1.00 0.00 O\n+ATOM 32 NE2 GLN A 58 90.400 77.620 28.290 1.00 0.00 N\n+ATOM 33 1HE2 GLN A 58 91.390 77.760 28.340 1.00 0.00 H\n+ATOM 34 2HE2 GLN A 58 89.820 78.230 27.740 1.00 0.00 H\n+ATOM 35 C GLN A 58 89.180 73.790 32.860 1.00 0.00 C\n+ATOM 36 O GLN A 58 88.000 73.530 33.060 1.00 0.00 O\n+ATOM 37 N GLN A 59 90.070 73.940 33.860 1.00 0.00 N\n+ATOM 38 H GLN A 59 91.030 74.150 33.610 1.00 0.00 H\n+ATOM 39 CA GLN A 59 89.760 73.890 35.300 1.00 0.00 C\n+ATOM 40 HA GLN A 59 90.720 73.970 35.810 1.00 0.00 H\n+ATOM 41 CB GLN A 59 88.920 75.110 35.730 1.00 0.00 C\n+ATOM 42 HB1 GLN A 59 88.780 75.070 36.810 1.00 0.00 H\n+ATOM 43 HB2 GLN A 59 87.940 75.040 35.260 1.00 0.00 H\n+ATOM 44 CG GLN A 59 89.520 76.470 35.390 1.00 0.00 C\n+ATOM 45 HG1 GLN A 59 89.640 76.550 34.310 1.00 0.00 H\n+ATOM 46 HG2 GLN A 59 90.490 76.570 35.870 1.00 0.00 H\n+ATOM 47 CD GLN A 59 88.600 77.590 35.880 1.00 0.00 C\n+ATOM 48 OE1 GLN A 59 88.580 77.910 37.060 1.00 0.00 O\n+ATOM 49 NE2 GLN A 59 87.790 78.160 34.980 1.00 0.00 N'..b' 31582 O VAL D 570 72.070 30.090 40.100 1.00 0.00 O\n+ATOM 31583 N LEU D 571 69.870 30.630 40.080 1.00 0.00 N\n+ATOM 31584 H LEU D 571 69.160 31.250 40.440 1.00 0.00 H\n+ATOM 31585 CA LEU D 571 69.450 29.660 39.070 1.00 0.00 C\n+ATOM 31586 HA LEU D 571 70.310 29.100 38.710 1.00 0.00 H\n+ATOM 31587 CB LEU D 571 68.430 28.660 39.660 1.00 0.00 C\n+ATOM 31588 HB1 LEU D 571 68.200 27.930 38.880 1.00 0.00 H\n+ATOM 31589 HB2 LEU D 571 67.510 29.200 39.870 1.00 0.00 H\n+ATOM 31590 CG LEU D 571 68.840 27.900 40.940 1.00 0.00 C\n+ATOM 31591 HG LEU D 571 68.960 28.610 41.750 1.00 0.00 H\n+ATOM 31592 CD1 LEU D 571 67.720 26.920 41.310 1.00 0.00 C\n+ATOM 31593 1HD1 LEU D 571 67.910 26.490 42.290 1.00 0.00 H\n+ATOM 31594 2HD1 LEU D 571 66.760 27.440 41.330 1.00 0.00 H\n+ATOM 31595 3HD1 LEU D 571 67.660 26.120 40.570 1.00 0.00 H\n+ATOM 31596 CD2 LEU D 571 70.150 27.110 40.780 1.00 0.00 C\n+ATOM 31597 1HD2 LEU D 571 70.360 26.570 41.700 1.00 0.00 H\n+ATOM 31598 2HD2 LEU D 571 70.070 26.400 39.960 1.00 0.00 H\n+ATOM 31599 3HD2 LEU D 571 70.980 27.790 40.590 1.00 0.00 H\n+ATOM 31600 C LEU D 571 68.830 30.380 37.870 1.00 0.00 C\n+ATOM 31601 O LEU D 571 68.330 31.500 38.000 1.00 0.00 O\n+ATOM 31602 N SER D 572 68.830 29.710 36.710 1.00 0.00 N\n+ATOM 31603 H SER D 572 69.270 28.800 36.680 1.00 0.00 H\n+ATOM 31604 CA SER D 572 68.080 30.100 35.520 1.00 0.00 C\n+ATOM 31605 HA SER D 572 67.710 31.120 35.660 1.00 0.00 H\n+ATOM 31606 CB SER D 572 68.990 30.130 34.290 1.00 0.00 C\n+ATOM 31607 HB1 SER D 572 69.790 30.860 34.460 1.00 0.00 H\n+ATOM 31608 HB2 SER D 572 68.420 30.430 33.420 1.00 0.00 H\n+ATOM 31609 OG SER D 572 69.580 28.870 34.050 1.00 0.00 O\n+ATOM 31610 HG SER D 572 70.100 28.920 33.240 1.00 0.00 H\n+ATOM 31611 C SER D 572 66.860 29.190 35.330 1.00 0.00 C\n+ATOM 31612 O SER D 572 66.840 28.050 35.810 1.00 0.00 O\n+ATOM 31613 N ILE D 573 65.840 29.710 34.640 1.00 0.00 N\n+ATOM 31614 H ILE D 573 65.940 30.650 34.270 1.00 0.00 H\n+ATOM 31615 CA ILE D 573 64.530 29.080 34.440 1.00 0.00 C\n+ATOM 31616 HA ILE D 573 64.440 28.250 35.150 1.00 0.00 H\n+ATOM 31617 CB ILE D 573 63.410 30.100 34.730 1.00 0.00 C\n+ATOM 31618 HB ILE D 573 63.510 30.930 34.030 1.00 0.00 H\n+ATOM 31619 CG2 ILE D 573 62.030 29.460 34.490 1.00 0.00 C\n+ATOM 31620 1HG2 ILE D 573 61.240 30.140 34.800 1.00 0.00 H\n+ATOM 31621 2HG2 ILE D 573 61.900 29.240 33.430 1.00 0.00 H\n+ATOM 31622 3HG2 ILE D 573 61.950 28.530 35.060 1.00 0.00 H\n+ATOM 31623 CG1 ILE D 573 63.470 30.700 36.160 1.00 0.00 C\n+ATOM 31624 1HG1 ILE D 573 62.600 31.350 36.300 1.00 0.00 H\n+ATOM 31625 2HG1 ILE D 573 64.350 31.330 36.250 1.00 0.00 H\n+ATOM 31626 CD1 ILE D 573 63.490 29.670 37.300 1.00 0.00 C\n+ATOM 31627 HD1 ILE D 573 63.360 30.190 38.250 1.00 0.00 H\n+ATOM 31628 HD2 ILE D 573 62.690 28.950 37.190 1.00 0.00 H\n+ATOM 31629 HD3 ILE D 573 64.450 29.150 37.320 1.00 0.00 H\n+ATOM 31630 C ILE D 573 64.440 28.480 33.030 1.00 0.00 C\n+ATOM 31632 O ILE D 573 63.980 27.320 32.940 1.00 0.00 O\n+TER\n' |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde test-data/biobb_pdb_cluster_myCluster.zip |
| b |
| Binary file test-data/biobb_pdb_cluster_myCluster.zip has changed |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde test-data/biobb_pdb_myStructure.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/biobb_pdb_myStructure.pdb Fri Apr 12 07:18:48 2019 -0400 |
| b |
| b'@@ -0,0 +1,602 @@\n+ATOM 1 N MET A 1 27.340 24.430 2.614 1.00 9.67 N \n+ATOM 2 CA MET A 1 26.266 25.413 2.842 1.00 10.38 C \n+ATOM 3 C MET A 1 26.913 26.639 3.531 1.00 9.62 C \n+ATOM 4 O MET A 1 27.886 26.463 4.263 1.00 9.62 O \n+ATOM 5 CB MET A 1 25.112 24.880 3.649 1.00 13.77 C \n+ATOM 6 CG MET A 1 25.353 24.860 5.134 1.00 16.29 C \n+ATOM 7 SD MET A 1 23.930 23.959 5.904 1.00 17.17 S \n+ATOM 8 CE MET A 1 24.447 23.984 7.620 1.00 16.11 C \n+ATOM 9 N GLN A 2 26.335 27.770 3.258 1.00 9.27 N \n+ATOM 10 CA GLN A 2 26.850 29.021 3.898 1.00 9.07 C \n+ATOM 11 C GLN A 2 26.100 29.253 5.202 1.00 8.72 C \n+ATOM 12 O GLN A 2 24.865 29.024 5.330 1.00 8.22 O \n+ATOM 13 CB GLN A 2 26.733 30.148 2.905 1.00 14.46 C \n+ATOM 14 CG GLN A 2 26.882 31.546 3.409 1.00 17.01 C \n+ATOM 15 CD GLN A 2 26.786 32.562 2.270 1.00 20.10 C \n+ATOM 16 OE1 GLN A 2 27.783 33.160 1.870 1.00 21.89 O \n+ATOM 17 NE2 GLN A 2 25.562 32.733 1.806 1.00 19.49 N \n+ATOM 18 N ILE A 3 26.849 29.656 6.217 1.00 5.87 N \n+ATOM 19 CA ILE A 3 26.235 30.058 7.497 1.00 5.07 C \n+ATOM 20 C ILE A 3 26.882 31.428 7.862 1.00 4.01 C \n+ATOM 21 O ILE A 3 27.906 31.711 7.264 1.00 4.61 O \n+ATOM 22 CB ILE A 3 26.344 29.050 8.645 1.00 6.55 C \n+ATOM 23 CG1 ILE A 3 27.810 28.748 8.999 1.00 4.72 C \n+ATOM 24 CG2 ILE A 3 25.491 27.771 8.287 1.00 5.58 C \n+ATOM 25 CD1 ILE A 3 27.967 28.087 10.417 1.00 10.83 C \n+ATOM 26 N PHE A 4 26.214 32.097 8.771 1.00 4.55 N \n+ATOM 27 CA PHE A 4 26.772 33.436 9.197 1.00 4.68 C \n+ATOM 28 C PHE A 4 27.151 33.362 10.650 1.00 5.30 C \n+ATOM 29 O PHE A 4 26.350 32.778 11.395 1.00 5.58 O \n+ATOM 30 CB PHE A 4 25.695 34.498 8.946 1.00 4.83 C \n+ATOM 31 CG PHE A 4 25.288 34.609 7.499 1.00 7.97 C \n+ATOM 32 CD1 PHE A 4 24.147 33.966 7.038 1.00 6.69 C \n+ATOM 33 CD2 PHE A 4 26.136 35.346 6.640 1.00 8.34 C \n+ATOM 34 CE1 PHE A 4 23.812 34.031 5.677 1.00 9.10 C \n+ATOM 35 CE2 PHE A 4 25.810 35.392 5.267 1.00 10.61 C \n+ATOM 36 CZ PHE A 4 24.620 34.778 4.853 1.00 8.90 C \n+ATOM 37 N VAL A 5 28.260 33.943 11.096 1.00 4.44 N \n+ATOM 38 CA VAL A 5 28.605 33.965 12.503 1.00 3.87 C \n+ATOM 39 C VAL A 5 28.638 35.461 12.900 1.00 4.93 C \n+ATOM 40 O VAL A 5 29.522 36.103 12.320 1.00 6.84 O \n+ATOM 41 CB VAL A 5 29.963 33.317 12.814 1.00 2.99 C \n+ATOM 42 CG1 VAL A 5 30.211 33.394 14.304 1.00 5.28 C \n+ATOM 43 CG2 VAL A 5 29.957 31.838 12.352 1.00 9.13 C \n+ATOM 44 N LYS A 6 27.751 35.867 13.740 1.00 6.04 N \n+ATOM 45 CA LYS A 6 27.691 37.315 14.143 1.00 6.12 C \n+ATOM 46 C LYS A 6 28.469 37.475 15.420 1.00 6.57 C \n+ATOM 47 O LYS A 6 28.213 36.753 16.411 1.00 5.76 O \n+ATOM 48 CB LYS A 6 26.219 37.684 14.307 1.00 7.45 C \n+ATOM 49 CG LYS A 6 25.884 39.1'..b'AL A 70 29.821 35.957 24.765 1.00 9.76 C \n+ATOM 555 CG2 VAL A 70 28.049 35.454 23.071 1.00 8.54 C \n+ATOM 556 N LEU A 71 32.763 35.831 23.090 1.00 12.71 N \n+ATOM 557 CA LEU A 71 34.145 35.472 23.481 1.00 16.06 C \n+ATOM 558 C LEU A 71 34.239 35.353 24.979 1.00 18.09 C \n+ATOM 559 O LEU A 71 33.707 36.197 25.728 1.00 19.26 O \n+ATOM 560 CB LEU A 71 35.114 36.564 22.907 1.00 17.10 C \n+ATOM 561 CG LEU A 71 35.926 35.979 21.737 1.00 19.37 C \n+ATOM 562 CD1 LEU A 71 35.003 35.084 20.920 1.00 17.51 C \n+ATOM 563 CD2 LEU A 71 36.533 37.087 20.917 1.00 19.57 C \n+ATOM 564 N ARG A 72 34.930 34.384 25.451 1.00 21.47 N \n+ATOM 565 CA ARG A 72 35.161 34.174 26.896 1.00 25.83 C \n+ATOM 566 C ARG A 72 36.671 34.296 27.089 1.00 27.74 C \n+ATOM 567 O ARG A 72 37.305 33.233 26.795 1.00 30.65 O \n+ATOM 568 CB ARG A 72 34.717 32.760 27.286 1.00 28.49 C \n+ATOM 569 CG ARG A 72 35.752 32.054 28.160 1.00 31.79 C \n+ATOM 570 CD ARG A 72 35.612 30.577 28.044 1.00 34.05 C \n+ATOM 571 NE ARG A 72 35.040 30.252 26.730 1.00 35.08 N \n+ATOM 572 CZ ARG A 72 34.338 29.103 26.650 1.00 34.67 C \n+ATOM 573 NH1 ARG A 72 34.110 28.437 27.768 1.00 35.02 N \n+ATOM 574 NH2 ARG A 72 34.014 28.657 25.457 1.00 34.97 N \n+ATOM 575 N LEU A 73 37.197 35.397 27.513 0.45 28.93 N \n+ATOM 576 CA LEU A 73 38.668 35.502 27.680 0.45 30.76 C \n+ATOM 577 C LEU A 73 39.076 34.931 29.031 0.45 32.18 C \n+ATOM 578 O LEU A 73 38.297 34.946 29.996 0.45 32.31 O \n+ATOM 579 CB LEU A 73 39.080 36.941 27.406 0.45 30.53 C \n+ATOM 580 CG LEU A 73 39.502 37.340 26.002 0.45 30.16 C \n+ATOM 581 CD1 LEU A 73 38.684 36.647 24.923 0.45 29.57 C \n+ATOM 582 CD2 LEU A 73 39.337 38.854 25.862 0.45 29.11 C \n+ATOM 583 N ARG A 74 40.294 34.412 29.045 0.45 33.82 N \n+ATOM 584 CA ARG A 74 40.873 33.802 30.253 0.45 35.33 C \n+ATOM 585 C ARG A 74 41.765 34.829 30.944 0.45 36.22 C \n+ATOM 586 O ARG A 74 42.945 34.994 30.583 0.45 36.70 O \n+ATOM 587 CB ARG A 74 41.651 32.529 29.923 0.45 36.91 C \n+ATOM 588 CG ARG A 74 41.608 31.444 30.989 0.45 38.62 C \n+ATOM 589 CD ARG A 74 41.896 30.080 30.456 0.45 39.75 C \n+ATOM 590 NE ARG A 74 43.311 29.735 30.563 0.45 41.13 N \n+ATOM 591 CZ ARG A 74 44.174 29.905 29.554 0.45 41.91 C \n+ATOM 592 NH1 ARG A 74 43.754 30.312 28.356 0.45 42.75 N \n+ATOM 593 NH2 ARG A 74 45.477 29.726 29.763 0.45 41.93 N \n+ATOM 594 N GLY A 75 41.165 35.531 31.898 0.25 36.31 N \n+ATOM 595 CA GLY A 75 41.845 36.550 32.686 0.25 36.07 C \n+ATOM 596 C GLY A 75 41.251 37.941 32.588 0.25 36.16 C \n+ATOM 597 O GLY A 75 41.102 38.523 31.500 0.25 36.26 O \n+ATOM 598 N GLY A 76 40.946 38.472 33.757 0.25 36.05 N \n+ATOM 599 CA GLY A 76 40.373 39.813 33.944 0.25 36.19 C \n+ATOM 600 C GLY A 76 40.031 39.992 35.432 0.25 36.20 C \n+ATOM 601 O GLY A 76 38.933 40.525 35.687 0.25 36.13 O \n+ATOM 602 OXT GLY A 76 40.862 39.575 36.251 0.25 36.27 O \n' |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde test-data/biobb_pdb_variants_myMutants.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/biobb_pdb_variants_myMutants.txt Fri Apr 12 07:18:48 2019 -0400 |
| b |
| @@ -0,0 +1,1 @@ +A.Ala115Pro,A.Ala154Thr,A.Ala295Val,A.Ala336Ser,A.Ala352Asp,A.Ala352Asp,A.Ala392Thr,A.Ala394Asp,A.Ala394Asp,A.Ala394Val,A.Ala431Thr,A.Ala459Val,A.Ala468Gly,A.Ala468Val,A.Ala495Thr,A.Ala495Val,A.Arg163Cys,A.Arg163Leu,A.Arg337Gln,A.Arg337Gln,A.Arg337Pro,A.Arg359Cys,A.Arg359His,A.Arg385Trp,A.Arg426Gln,A.Arg426Trp,A.Arg426Trp,A.Arg479His,A.Arg486Trp,A.Arg488Gln,A.Arg490Trp,A.Arg498Cys,A.Arg498His,A.Arg504Leu,A.Arg510Gln,A.Arg531Cys,A.Arg532Gln,A.Arg532Trp,A.Arg559Gly,A.Arg569Gln,A.Arg86Pro,A.Asn361Asp,A.Asn393Lys,A.Asn393Ser,A.Asn566Lys,A.Asp281Asn,A.Asp293Asn,A.Asp331Asn,A.Asp331Glu,A.Asp339His,A.Asp390Asn,A.Gln421Lys,A.Glu172Gln,A.Glu315Lys,A.Glu387Gly,A.Glu427Ala,A.Glu427Asp,A.Gly111Arg,A.Gly111Arg,A.Gly159Val,A.Gly165Val,A.Gly222Ala,A.Gly263Arg,A.Gly263Trp,A.Gly275Arg,A.Gly332Ser,A.Gly341Ala,A.Gly341Asp,A.Gly358Glu,A.Gly364Asp,A.Gly364Asp,A.Gly458Asp,A.Gly511Arg,A.Gly557Ala,A.Gly95Arg,A.Ile153Thr,A.Ile219Thr,A.Ile310Asn,A.Ile314Thr,A.Ile314Thr,A.Ile342Phe,A.Ile357Thr,A.Ile90Asn,A.Leu155Pro,A.Leu272Val,A.Leu374Pro,A.Leu73Pro,A.Lys348Asn,A.Met107Thr,A.Phe287Val,A.Ser120Phe,A.Ser130Tyr,A.Ser376Ile,A.Ser485Phe,A.Ser80Pro,A.Thr384Met,A.Thr408Ala,A.Thr408Ile,A.Thr477Ala,A.Val134Asp,A.Val288Leu,A.Val320Leu,A.Val335Met,A.Val368Phe,A.Val460Met,A.Val506Ile,A.Val552Met,B.Ala115Pro,B.Ala154Thr,B.Ala295Val,B.Ala336Ser,B.Ala352Asp,B.Ala352Asp,B.Ala392Thr,B.Ala394Asp,B.Ala394Asp,B.Ala394Val,B.Ala431Thr,B.Ala459Val,B.Ala468Gly,B.Ala468Val,B.Ala495Thr,B.Ala495Val,B.Arg163Cys,B.Arg163Leu,B.Arg337Gln,B.Arg337Gln,B.Arg337Pro,B.Arg359Cys,B.Arg359His,B.Arg385Trp,B.Arg426Gln,B.Arg426Trp,B.Arg426Trp,B.Arg479His,B.Arg486Trp,B.Arg488Gln,B.Arg490Trp,B.Arg498Cys,B.Arg498His,B.Arg504Leu,B.Arg510Gln,B.Arg531Cys,B.Arg532Gln,B.Arg532Trp,B.Arg559Gly,B.Arg569Gln,B.Arg86Pro,B.Asn361Asp,B.Asn393Lys,B.Asn393Ser,B.Asn566Lys,B.Asp281Asn,B.Asp293Asn,B.Asp331Asn,B.Asp331Glu,B.Asp339His,B.Asp390Asn,B.Gln421Lys,B.Glu315Lys,B.Glu387Gly,B.Glu427Ala,B.Glu427Asp,B.Gly111Arg,B.Gly111Arg,B.Gly159Val,B.Gly165Val,B.Gly222Ala,B.Gly263Arg,B.Gly263Trp,B.Gly275Arg,B.Gly332Ser,B.Gly341Ala,B.Gly341Asp,B.Gly358Glu,B.Gly364Asp,B.Gly364Asp,B.Gly458Asp,B.Gly511Arg,B.Gly557Ala,B.Gly95Arg,B.Ile153Thr,B.Ile219Thr,B.Ile310Asn,B.Ile314Thr,B.Ile314Thr,B.Ile342Phe,B.Ile357Thr,B.Ile90Asn,B.Leu155Pro,B.Leu272Val,B.Leu374Pro,B.Leu73Pro,B.Lys348Asn,B.Met107Thr,B.Phe287Val,B.Ser120Phe,B.Ser130Tyr,B.Ser376Ile,B.Ser485Phe,B.Ser80Pro,B.Thr384Met,B.Thr408Ala,B.Thr408Ile,B.Thr477Ala,B.Val134Asp,B.Val288Leu,B.Val320Leu,B.Val335Met,B.Val368Phe,B.Val460Met,B.Val506Ile,B.Val552Met,C.Ala115Pro,C.Ala154Thr,C.Ala295Val,C.Ala336Ser,C.Ala352Asp,C.Ala352Asp,C.Ala392Thr,C.Ala394Asp,C.Ala394Asp,C.Ala394Val,C.Ala431Thr,C.Ala459Val,C.Ala468Gly,C.Ala468Val,C.Ala495Thr,C.Ala495Val,C.Arg163Cys,C.Arg163Leu,C.Arg337Gln,C.Arg337Gln,C.Arg337Pro,C.Arg359Cys,C.Arg359His,C.Arg385Trp,C.Arg426Gln,C.Arg426Trp,C.Arg426Trp,C.Arg479His,C.Arg486Trp,C.Arg488Gln,C.Arg490Trp,C.Arg498Cys,C.Arg498His,C.Arg504Leu,C.Arg510Gln,C.Arg531Cys,C.Arg532Gln,C.Arg532Trp,C.Arg559Gly,C.Arg569Gln,C.Arg86Pro,C.Asn361Asp,C.Asn393Lys,C.Asn393Ser,C.Asn566Lys,C.Asp281Asn,C.Asp293Asn,C.Asp331Asn,C.Asp331Glu,C.Asp339His,C.Asp390Asn,C.Gln421Lys,C.Glu172Gln,C.Glu315Lys,C.Glu387Gly,C.Glu427Ala,C.Glu427Asp,C.Gly111Arg,C.Gly111Arg,C.Gly159Val,C.Gly165Val,C.Gly222Ala,C.Gly263Arg,C.Gly263Trp,C.Gly275Arg,C.Gly332Ser,C.Gly341Ala,C.Gly341Asp,C.Gly358Glu,C.Gly364Asp,C.Gly364Asp,C.Gly458Asp,C.Gly511Arg,C.Gly557Ala,C.Gly95Arg,C.Ile153Thr,C.Ile219Thr,C.Ile310Asn,C.Ile314Thr,C.Ile314Thr,C.Ile342Phe,C.Ile357Thr,C.Ile90Asn,C.Leu155Pro,C.Leu272Val,C.Leu374Pro,C.Leu73Pro,C.Lys348Asn,C.Met107Thr,C.Phe287Val,C.Ser120Phe,C.Ser130Tyr,C.Ser376Ile,C.Ser485Phe,C.Ser80Pro,C.Thr384Met,C.Thr408Ala,C.Thr408Ile,C.Thr477Ala,C.Val134Asp,C.Val288Leu,C.Val320Leu,C.Val335Met,C.Val368Phe,C.Val460Met,C.Val506Ile,C.Val552Met,D.Ala115Pro,D.Ala154Thr,D.Ala295Val,D.Ala336Ser,D.Ala352Asp,D.Ala352Asp,D.Ala392Thr,D.Ala394Asp,D.Ala394Asp,D.Ala394Val,D.Ala431Thr,D.Ala459Val,D.Ala468Gly,D.Ala468Val,D.Ala495Thr,D.Ala495Val,D.Arg163Cys,D.Arg163Leu,D.Arg337Gln,D.Arg337Gln,D.Arg337Pro,D.Arg359Cys,D.Arg359His,D.Arg385Trp,D.Arg426Gln,D.Arg426Trp,D.Arg426Trp,D.Arg479His,D.Arg486Trp,D.Arg488Gln,D.Arg490Trp,D.Arg498Cys,D.Arg498His,D.Arg504Leu,D.Arg510Gln,D.Arg531Cys,D.Arg532Gln,D.Arg532Trp,D.Arg559Gly,D.Arg569Gln,D.Arg86Pro,D.Asn361Asp,D.Asn393Lys,D.Asn393Ser,D.Asn566Lys,D.Asp281Asn,D.Asp293Asn,D.Asp331Asn,D.Asp331Glu,D.Asp339His,D.Asp390Asn,D.Gln421Lys,D.Glu172Gln,D.Glu315Lys,D.Glu387Gly,D.Glu427Ala,D.Glu427Asp,D.Gly111Arg,D.Gly111Arg,D.Gly159Val,D.Gly165Val,D.Gly222Ala,D.Gly263Arg,D.Gly263Trp,D.Gly275Arg,D.Gly332Ser,D.Gly341Ala,D.Gly341Asp,D.Gly358Glu,D.Gly364Asp,D.Gly364Asp,D.Gly458Asp,D.Gly511Arg,D.Gly557Ala,D.Gly95Arg,D.Ile153Thr,D.Ile219Thr,D.Ile310Asn,D.Ile314Thr,D.Ile314Thr,D.Ile342Phe,D.Ile357Thr,D.Ile90Asn,D.Leu155Pro,D.Leu272Val,D.Leu374Pro,D.Leu73Pro,D.Lys348Asn,D.Met107Thr,D.Phe287Val,D.Ser120Phe,D.Ser130Tyr,D.Ser376Ile,D.Ser485Phe,D.Ser80Pro,D.Thr384Met,D.Thr408Ala,D.Thr408Ile,D.Thr477Ala,D.Val134Asp,D.Val288Leu,D.Val320Leu,D.Val335Met,D.Val368Phe,D.Val460Met,D.Val506Ile,D.Val552Met \ No newline at end of file |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde test-data/biobb_rms_input.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/biobb_rms_input.gro Fri Apr 12 07:18:48 2019 -0400 |
| b |
| b'@@ -0,0 +1,71693 @@\n+Protein in water\n+71690\n+ 1SER N 1 2.270 1.214 5.506\n+ 1SER H1 2 2.288 1.242 5.411\n+ 1SER H2 3 2.354 1.220 5.559\n+ 1SER H3 4 2.237 1.120 5.507\n+ 1SER CA 5 2.167 1.304 5.566\n+ 1SER HA 6 2.083 1.294 5.512\n+ 1SER CB 7 2.138 1.263 5.710\n+ 1SER HB1 8 2.222 1.264 5.765\n+ 1SER HB2 9 2.097 1.172 5.713\n+ 1SER OG 10 2.046 1.352 5.771\n+ 1SER HG 11 2.029 1.323 5.865\n+ 1SER C 12 2.215 1.448 5.559\n+ 1SER O 13 2.326 1.480 5.601\n+ 2GLU N 14 2.130 1.536 5.505\n+ 2GLU H 15 2.041 1.504 5.472\n+ 2GLU CA 16 2.165 1.677 5.493\n+ 2GLU HA 17 2.205 1.702 5.581\n+ 2GLU CB 18 2.267 1.697 5.381\n+ 2GLU HB1 19 2.224 1.670 5.294\n+ 2GLU HB2 20 2.346 1.639 5.399\n+ 2GLU CG 21 2.315 1.841 5.367\n+ 2GLU HG1 22 2.354 1.870 5.454\n+ 2GLU HG2 23 2.237 1.899 5.343\n+ 2GLU CD 24 2.421 1.856 5.259\n+ 2GLU OE1 25 2.456 1.755 5.196\n+ 2GLU OE2 26 2.469 1.970 5.239\n+ 2GLU C 27 2.040 1.761 5.467\n+ 2GLU O 28 1.946 1.716 5.400\n+ 3ALA N 29 2.039 1.882 5.522\n+ 3ALA H 30 2.118 1.912 5.575\n+ 3ALA CA 31 1.926 1.971 5.505\n+ 3ALA HA 32 1.846 1.920 5.536\n+ 3ALA CB 33 1.944 2.096 5.591\n+ 3ALA HB1 34 1.865 2.157 5.578\n+ 3ALA HB2 35 1.951 2.070 5.687\n+ 3ALA HB3 36 2.027 2.144 5.563\n+ 3ALA C 37 1.909 2.009 5.359\n+ 3ALA O 38 1.988 2.085 5.303\n+ 4GLU N 39 1.805 1.955 5.299\n+ 4GLU H 40 1.745 1.894 5.351\n+ 4GLU CA 41 1.775 1.982 5.159\n+ 4GLU HA 42 1.859 1.961 5.108\n+ 4GLU CB 43 1.662 1.890 5.110\n+ 4GLU HB1 44 1.635 1.920 5.018\n+ 4GLU HB2 45 1.584 1.900 5.172\n+ 4GLU CG 46 1.700 1.743 5.102\n+ 4GLU HG1 47 1.727 1.713 5.194\n+ 4GLU HG2 48 1.777 1.733 5.040\n+ 4GLU CD 49 1.586 1.656 5.054\n+ 4GLU OE1 50 1.475 1.710 5.031\n+ 4GLU OE2 51 1.607 1.534 5.038\n+ 4GLU C 52 1.737 2.128 5.139\n+ 4GLU O 53 1.740 2.180 5.028\n+ 5ASP N 54 1.702 2.195 5.249\n+ 5ASP H 55 1.702 2.148 5.337\n+ 5ASP CA 56 1.664 2.336 5.242\n+ 5ASP HA 57 1.589 2.341 5.177\n+ 5ASP CB 58 1.618 2.385 5.380\n+ 5ASP HB1 59 1.612 2.485 5.378\n+ 5ASP HB2 60 1.686 2.358 5.448\n+ 5ASP CG 61 1.483 2.329 5.420\n+ 5ASP OD1 62 1.413 2.276 5.331\n+ 5ASP OD2 63 1.448 2.340 5.539\n+ 5ASP C 64 1.781 2.419 5.192\n+ 5ASP O 65 1.762 2.515 5.116\n+ 6ALA N 66 1.901 2.385 5.235\n+ 6ALA H 67 1.911 2.306 5.296\n+ 6ALA CA 68 2.019 2.460 5.196\n+ 6ALA HA 69 2.007 2.552 5.233\n+ 6ALA CB 70 2.144 2.396 5.254\n+ 6ALA HB1 71 2.224 2.449 5.226\n+ 6ALA HB2 72 2.138 2.396 5.354\n+ 6ALA HB3 73 2.153 2.302 5.221\n+ 6ALA C 74 2.028 2.466 5.044\n+ 6ALA O 75 2.029 2.364 4.976\n+ 7SER N 76 2.033 2.588 4.995\n+ 7SER H 77 2.031 2.666 5.057\n+ 7SER CA 78 2.041 2.612 4.852\n+ 7SER HA 79 1.973 2.552 4.811\n+ 7SER CB 80 2.008 2.758 4.820\n+ 7SER HB1 81 1.922 2.785 4.864\n+ 7SER HB2 82 2.001 2.772 4.722\n+ 7SER OG 83 2.109 2.845 4.868\n+ 7SER HG 84 2.085 2.940 4.846\n+ 7SER C 85 2.180 2.577 4.800\n+ 7SER O 86 2.270 2.543 4.87'..b'58 7.739\n+23549SOL HW171605 8.427 8.396 7.671\n+23549SOL HW271606 8.404 8.275 7.778\n+23550SOL OW71607 7.820 8.736 8.938\n+23550SOL HW171608 7.807 8.829 8.904\n+23550SOL HW271609 7.736 8.684 8.925\n+23551SOL OW71610 8.487 8.546 8.144\n+23551SOL HW171611 8.417 8.499 8.198\n+23551SOL HW271612 8.546 8.478 8.101\n+23552SOL OW71613 8.462 7.684 8.419\n+23552SOL HW171614 8.454 7.648 8.326\n+23552SOL HW271615 8.460 7.608 8.484\n+23553SOL OW71616 7.703 8.796 7.738\n+23553SOL HW171617 7.607 8.797 7.711\n+23553SOL HW271618 7.715 8.849 7.822\n+23554SOL OW71619 7.523 7.793 7.481\n+23554SOL HW171620 7.431 7.765 7.452\n+23554SOL HW271621 7.554 7.870 7.425\n+23555SOL OW71622 8.888 8.304 8.846\n+23555SOL HW171623 8.831 8.356 8.783\n+23555SOL HW271624 8.984 8.316 8.822\n+23556SOL OW71625 7.520 7.614 7.766\n+23556SOL HW171626 7.503 7.697 7.712\n+23556SOL HW271627 7.610 7.577 7.744\n+23557SOL OW71628 8.631 8.783 7.567\n+23557SOL HW171629 8.532 8.772 7.569\n+23557SOL HW271630 8.665 8.798 7.660\n+23558SOL OW71631 8.061 8.290 8.879\n+23558SOL HW171632 8.117 8.371 8.862\n+23558SOL HW271633 8.120 8.210 8.882\n+23559SOL OW71634 8.673 7.773 7.897\n+23559SOL HW171635 8.738 7.699 7.886\n+23559SOL HW271636 8.693 7.823 7.981\n+23560SOL OW71637 8.042 8.193 8.100\n+23560SOL HW171638 8.092 8.278 8.081\n+23560SOL HW271639 7.954 8.195 8.052\n+23561SOL OW71640 8.307 8.822 7.464\n+23561SOL HW171641 8.261 8.837 7.552\n+23561SOL HW271642 8.351 8.907 7.434\n+23562SOL OW71643 8.856 9.299 9.168\n+23562SOL HW171644 8.760 9.288 9.141\n+23562SOL HW271645 8.912 9.232 9.120\n+23563SOL OW71646 8.307 8.404 8.309\n+23563SOL HW171647 8.361 8.335 8.357\n+23563SOL HW271648 8.275 8.473 8.375\n+23564SOL OW71649 8.531 8.432 7.535\n+23564SOL HW171650 8.508 8.485 7.453\n+23564SOL HW271651 8.612 8.376 7.516\n+23565SOL OW71652 7.527 8.688 8.101\n+23565SOL HW171653 7.526 8.641 8.189\n+23565SOL HW271654 7.609 8.660 8.050\n+23566SOL OW71655 7.876 7.872 7.968\n+23566SOL HW171656 7.906 7.800 7.906\n+23566SOL HW271657 7.837 7.832 8.051\n+23567SOL OW71658 9.153 8.935 8.552\n+23567SOL HW171659 9.060 8.910 8.525\n+23567SOL HW271660 9.179 8.885 8.634\n+23568SOL OW71661 7.765 7.995 8.728\n+23568SOL HW171662 7.803 7.936 8.800\n+23568SOL HW271663 7.805 7.969 8.640\n+23569SOL OW71664 8.872 7.662 8.560\n+23569SOL HW171665 8.924 7.597 8.615\n+23569SOL HW271666 8.823 7.725 8.621\n+23570SOL OW71667 8.449 7.482 8.602\n+23570SOL HW171668 8.386 7.410 8.571\n+23570SOL HW271669 8.542 7.446 8.602\n+23571SOL OW71670 8.218 8.778 7.749\n+23571SOL HW171671 8.172 8.691 7.766\n+23571SOL HW271672 8.309 8.775 7.790\n+23572SOL OW71673 8.066 9.015 8.732\n+23572SOL HW171674 8.061 9.097 8.789\n+23572SOL HW271675 8.155 9.012 8.687\n+23573SOL OW71676 8.800 7.500 7.616\n+23573SOL HW171677 8.835 7.459 7.532\n+23573SOL HW271678 8.710 7.462 7.636\n+23574SOL OW71679 8.748 7.901 8.139\n+23574SOL HW171680 8.689 7.981 8.143\n+23574SOL HW271681 8.763 7.866 8.232\n+23575SOL OW71682 7.487 8.525 7.748\n+23575SOL HW171683 7.586 8.514 7.739\n+23575SOL HW271684 7.447 8.439 7.780\n+23576NA NA71685 1.272 5.169 3.004\n+23577NA NA71686 1.293 6.814 7.009\n+23578NA NA71687 2.674 1.586 0.687\n+23579NA NA71688 1.901 2.939 4.024\n+23580NA NA71689 8.120 5.340 2.016\n+23581NA NA71690 8.808 4.586 8.493\n+ 9.00078 9.00078 9.00078\n' |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde test-data/biobb_rms_input.trr |
| b |
| Binary file test-data/biobb_rms_input.trr has changed |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde test-data/biobb_rms_rms.xvg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/biobb_rms_rms.xvg Fri Apr 12 07:18:48 2019 -0400 |
| b |
| @@ -0,0 +1,2 @@ + 0.0000000 0.0573565 + 1.0000000 0.0963660 |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde test-data/biobb_solvate_input.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/biobb_solvate_input.gro Fri Apr 12 07:18:48 2019 -0400 |
| b |
| b'@@ -0,0 +1,1199 @@\n+Created with pdb2gmx building block\n+ 1196\n+ 1SER N 1 2.270 1.214 5.506\n+ 1SER H1 2 2.288 1.242 5.411\n+ 1SER H2 3 2.354 1.220 5.559\n+ 1SER H3 4 2.237 1.120 5.507\n+ 1SER CA 5 2.167 1.304 5.566\n+ 1SER HA 6 2.083 1.294 5.512\n+ 1SER CB 7 2.138 1.263 5.710\n+ 1SER HB1 8 2.222 1.264 5.765\n+ 1SER HB2 9 2.097 1.172 5.713\n+ 1SER OG 10 2.046 1.352 5.771\n+ 1SER HG 11 2.029 1.323 5.865\n+ 1SER C 12 2.215 1.448 5.559\n+ 1SER O 13 2.326 1.480 5.601\n+ 2GLU N 14 2.130 1.536 5.505\n+ 2GLU H 15 2.041 1.504 5.472\n+ 2GLU CA 16 2.165 1.677 5.493\n+ 2GLU HA 17 2.205 1.702 5.581\n+ 2GLU CB 18 2.267 1.697 5.381\n+ 2GLU HB1 19 2.224 1.670 5.294\n+ 2GLU HB2 20 2.346 1.639 5.399\n+ 2GLU CG 21 2.315 1.841 5.367\n+ 2GLU HG1 22 2.354 1.870 5.454\n+ 2GLU HG2 23 2.237 1.899 5.343\n+ 2GLU CD 24 2.421 1.856 5.259\n+ 2GLU OE1 25 2.456 1.755 5.196\n+ 2GLU OE2 26 2.469 1.970 5.239\n+ 2GLU C 27 2.040 1.761 5.467\n+ 2GLU O 28 1.946 1.716 5.400\n+ 3ALA N 29 2.039 1.882 5.522\n+ 3ALA H 30 2.118 1.912 5.575\n+ 3ALA CA 31 1.926 1.971 5.505\n+ 3ALA HA 32 1.846 1.920 5.536\n+ 3ALA CB 33 1.944 2.096 5.591\n+ 3ALA HB1 34 1.865 2.157 5.578\n+ 3ALA HB2 35 1.951 2.070 5.687\n+ 3ALA HB3 36 2.027 2.144 5.563\n+ 3ALA C 37 1.909 2.009 5.359\n+ 3ALA O 38 1.988 2.085 5.303\n+ 4GLU N 39 1.805 1.955 5.299\n+ 4GLU H 40 1.745 1.894 5.351\n+ 4GLU CA 41 1.775 1.982 5.159\n+ 4GLU HA 42 1.859 1.961 5.108\n+ 4GLU CB 43 1.662 1.890 5.110\n+ 4GLU HB1 44 1.635 1.920 5.018\n+ 4GLU HB2 45 1.584 1.900 5.172\n+ 4GLU CG 46 1.700 1.743 5.102\n+ 4GLU HG1 47 1.727 1.713 5.194\n+ 4GLU HG2 48 1.777 1.733 5.040\n+ 4GLU CD 49 1.586 1.656 5.054\n+ 4GLU OE1 50 1.475 1.710 5.031\n+ 4GLU OE2 51 1.607 1.534 5.038\n+ 4GLU C 52 1.737 2.128 5.139\n+ 4GLU O 53 1.740 2.180 5.028\n+ 5ASP N 54 1.702 2.195 5.249\n+ 5ASP H 55 1.702 2.148 5.337\n+ 5ASP CA 56 1.664 2.336 5.242\n+ 5ASP HA 57 1.589 2.341 5.177\n+ 5ASP CB 58 1.618 2.385 5.380\n+ 5ASP HB1 59 1.612 2.485 5.378\n+ 5ASP HB2 60 1.686 2.358 5.448\n+ 5ASP CG 61 1.483 2.329 5.420\n+ 5ASP OD1 62 1.413 2.276 5.331\n+ 5ASP OD2 63 1.448 2.340 5.539\n+ 5ASP C 64 1.781 2.419 5.192\n+ 5ASP O 65 1.762 2.515 5.116\n+ 6ALA N 66 1.901 2.385 5.235\n+ 6ALA H 67 1.911 2.306 5.296\n+ 6ALA CA 68 2.019 2.460 5.196\n+ 6ALA HA 69 2.007 2.552 5.233\n+ 6ALA CB 70 2.144 2.396 5.254\n+ 6ALA HB1 71 2.224 2.449 5.226\n+ 6ALA HB2 72 2.138 2.396 5.354\n+ 6ALA HB3 73 2.153 2.302 5.221\n+ 6ALA C 74 2.028 2.466 5.044\n+ 6ALA O 75 2.029 2.364 4.976\n+ 7SER N 76 2.033 2.588 4.995\n+ 7SER H 77 2.031 2.666 5.057\n+ 7SER CA 78 2.041 2.612 4.852\n+ 7SER HA 79 1.973 2.552 4.811\n+ 7SER CB 80 2.008 2.758 4.820\n+ 7SER HB1 81 1.922 2.785 4.864\n+ 7SER HB2 82 2.001 2.772 4.722\n+ 7SER OG 83 2.109 2.845 4.868\n+ 7SER HG 84 2.085 2.940 4.846\n+ 7SER C 85 2.180 2.577 4.800\n+ 7SER O 86 2.'..b'53 3.381\n+ 73PRO N 1111 3.036 6.339 3.408\n+ 73PRO CD 1112 2.901 6.311 3.463\n+ 73PRO HD1 1113 2.835 6.379 3.431\n+ 73PRO HD2 1114 2.902 6.310 3.563\n+ 73PRO CG 1115 2.868 6.175 3.408\n+ 73PRO HG1 1116 2.823 6.183 3.320\n+ 73PRO HG2 1117 2.810 6.125 3.472\n+ 73PRO CB 1118 2.999 6.105 3.392\n+ 73PRO HB1 1119 2.993 6.035 3.320\n+ 73PRO HB2 1120 3.026 6.061 3.478\n+ 73PRO CA 1121 3.097 6.215 3.353\n+ 73PRO HA 1122 3.189 6.200 3.390\n+ 73PRO C 1123 3.113 6.226 3.201\n+ 73PRO O 1124 3.187 6.148 3.140\n+ 74THR N 1125 3.041 6.320 3.140\n+ 74THR H 1126 2.982 6.380 3.194\n+ 74THR CA 1127 3.046 6.336 2.994\n+ 74THR HA 1128 3.053 6.242 2.961\n+ 74THR CB 1129 2.918 6.405 2.941\n+ 74THR HB 1130 2.904 6.493 2.987\n+ 74THR CG2 1131 2.927 6.424 2.791\n+ 74THR HG21 1132 2.844 6.469 2.758\n+ 74THR HG22 1133 3.006 6.481 2.768\n+ 74THR HG23 1134 2.936 6.335 2.746\n+ 74THR OG1 1135 2.804 6.325 2.971\n+ 74THR HG1 1136 2.722 6.370 2.937\n+ 74THR C 1137 3.167 6.416 2.949\n+ 74THR O 1138 3.255 6.363 2.882\n+ 75SER N 1139 3.168 6.543 2.984\n+ 75SER H 1140 3.093 6.580 3.039\n+ 75SER CA 1141 3.277 6.631 2.943\n+ 75SER HA 1142 3.276 6.629 2.843\n+ 75SER CB 1143 3.253 6.773 2.994\n+ 75SER HB1 1144 3.332 6.832 2.973\n+ 75SER HB2 1145 3.236 6.773 3.092\n+ 75SER OG 1146 3.140 6.831 2.931\n+ 75SER HG 1147 3.126 6.924 2.966\n+ 75SER C 1148 3.410 6.578 2.994\n+ 75SER O 1149 3.511 6.585 2.925\n+ 76ALA N 1150 3.410 6.524 3.116\n+ 76ALA H 1151 3.325 6.521 3.168\n+ 76ALA CA 1152 3.532 6.470 3.173\n+ 76ALA HA 1153 3.595 6.547 3.184\n+ 76ALA CB 1154 3.504 6.408 3.309\n+ 76ALA HB1 1155 3.589 6.371 3.347\n+ 76ALA HB2 1156 3.468 6.478 3.370\n+ 76ALA HB3 1157 3.437 6.334 3.299\n+ 76ALA C 1158 3.593 6.366 3.078\n+ 76ALA O 1159 3.705 6.384 3.030\n+ 77VAL N 1160 3.520 6.258 3.055\n+ 77VAL H 1161 3.430 6.249 3.097\n+ 77VAL CA 1162 3.570 6.152 2.968\n+ 77VAL HA 1163 3.656 6.122 3.009\n+ 77VAL CB 1164 3.472 6.033 2.962\n+ 77VAL HB 1165 3.381 6.067 2.938\n+ 77VAL CG1 1166 3.514 5.934 2.855\n+ 77VAL HG11 1167 3.450 5.858 2.852\n+ 77VAL HG12 1168 3.516 5.979 2.766\n+ 77VAL HG13 1169 3.606 5.900 2.876\n+ 77VAL CG2 1170 3.462 5.965 3.098\n+ 77VAL HG21 1171 3.398 5.888 3.092\n+ 77VAL HG22 1172 3.553 5.931 3.124\n+ 77VAL HG23 1173 3.430 6.031 3.166\n+ 77VAL C 1174 3.595 6.206 2.827\n+ 77VAL O 1175 3.702 6.185 2.771\n+ 78ALA N 1176 3.497 6.277 2.772\n+ 78ALA H 1177 3.412 6.291 2.823\n+ 78ALA CA 1178 3.512 6.335 2.639\n+ 78ALA HA 1179 3.543 6.261 2.580\n+ 78ALA CB 1180 3.379 6.388 2.589\n+ 78ALA HB1 1181 3.390 6.427 2.498\n+ 78ALA HB2 1182 3.313 6.312 2.585\n+ 78ALA HB3 1183 3.345 6.458 2.651\n+ 78ALA C 1184 3.616 6.447 2.641\n+ 78ALA O 1185 3.657 6.497 2.537\n+ 79ALA N 1186 3.659 6.483 2.762\n+ 79ALA H 1187 3.622 6.438 2.843\n+ 79ALA CA 1188 3.758 6.589 2.778\n+ 79ALA HA 1189 3.839 6.559 2.727\n+ 79ALA CB 1190 3.706 6.720 2.720\n+ 79ALA HB1 1191 3.775 6.791 2.732\n+ 79ALA HB2 1192 3.687 6.708 2.622\n+ 79ALA HB3 1193 3.622 6.746 2.767\n+ 79ALA C 1194 3.794 6.608 2.925\n+ 79ALA OC1 1195 3.732 6.692 2.989\n+ 79ALA OC2 1196 3.881 6.537 2.972\n+ 9.00078 9.00078 9.00078\n' |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde test-data/biobb_solvate_input.zip |
| b |
| Binary file test-data/biobb_solvate_input.zip has changed |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde test-data/biobb_solvate_mySolvate.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/biobb_solvate_mySolvate.gro Fri Apr 12 07:18:48 2019 -0400 |
| b |
| b'@@ -0,0 +1,71705 @@\n+Created with pdb2gmx building block\n+71702\n+ 1SER N 1 2.270 1.214 5.506\n+ 1SER H1 2 2.288 1.242 5.411\n+ 1SER H2 3 2.354 1.220 5.559\n+ 1SER H3 4 2.237 1.120 5.507\n+ 1SER CA 5 2.167 1.304 5.566\n+ 1SER HA 6 2.083 1.294 5.512\n+ 1SER CB 7 2.138 1.263 5.710\n+ 1SER HB1 8 2.222 1.264 5.765\n+ 1SER HB2 9 2.097 1.172 5.713\n+ 1SER OG 10 2.046 1.352 5.771\n+ 1SER HG 11 2.029 1.323 5.865\n+ 1SER C 12 2.215 1.448 5.559\n+ 1SER O 13 2.326 1.480 5.601\n+ 2GLU N 14 2.130 1.536 5.505\n+ 2GLU H 15 2.041 1.504 5.472\n+ 2GLU CA 16 2.165 1.677 5.493\n+ 2GLU HA 17 2.205 1.702 5.581\n+ 2GLU CB 18 2.267 1.697 5.381\n+ 2GLU HB1 19 2.224 1.670 5.294\n+ 2GLU HB2 20 2.346 1.639 5.399\n+ 2GLU CG 21 2.315 1.841 5.367\n+ 2GLU HG1 22 2.354 1.870 5.454\n+ 2GLU HG2 23 2.237 1.899 5.343\n+ 2GLU CD 24 2.421 1.856 5.259\n+ 2GLU OE1 25 2.456 1.755 5.196\n+ 2GLU OE2 26 2.469 1.970 5.239\n+ 2GLU C 27 2.040 1.761 5.467\n+ 2GLU O 28 1.946 1.716 5.400\n+ 3ALA N 29 2.039 1.882 5.522\n+ 3ALA H 30 2.118 1.912 5.575\n+ 3ALA CA 31 1.926 1.971 5.505\n+ 3ALA HA 32 1.846 1.920 5.536\n+ 3ALA CB 33 1.944 2.096 5.591\n+ 3ALA HB1 34 1.865 2.157 5.578\n+ 3ALA HB2 35 1.951 2.070 5.687\n+ 3ALA HB3 36 2.027 2.144 5.563\n+ 3ALA C 37 1.909 2.009 5.359\n+ 3ALA O 38 1.988 2.085 5.303\n+ 4GLU N 39 1.805 1.955 5.299\n+ 4GLU H 40 1.745 1.894 5.351\n+ 4GLU CA 41 1.775 1.982 5.159\n+ 4GLU HA 42 1.859 1.961 5.108\n+ 4GLU CB 43 1.662 1.890 5.110\n+ 4GLU HB1 44 1.635 1.920 5.018\n+ 4GLU HB2 45 1.584 1.900 5.172\n+ 4GLU CG 46 1.700 1.743 5.102\n+ 4GLU HG1 47 1.727 1.713 5.194\n+ 4GLU HG2 48 1.777 1.733 5.040\n+ 4GLU CD 49 1.586 1.656 5.054\n+ 4GLU OE1 50 1.475 1.710 5.031\n+ 4GLU OE2 51 1.607 1.534 5.038\n+ 4GLU C 52 1.737 2.128 5.139\n+ 4GLU O 53 1.740 2.180 5.028\n+ 5ASP N 54 1.702 2.195 5.249\n+ 5ASP H 55 1.702 2.148 5.337\n+ 5ASP CA 56 1.664 2.336 5.242\n+ 5ASP HA 57 1.589 2.341 5.177\n+ 5ASP CB 58 1.618 2.385 5.380\n+ 5ASP HB1 59 1.612 2.485 5.378\n+ 5ASP HB2 60 1.686 2.358 5.448\n+ 5ASP CG 61 1.483 2.329 5.420\n+ 5ASP OD1 62 1.413 2.276 5.331\n+ 5ASP OD2 63 1.448 2.340 5.539\n+ 5ASP C 64 1.781 2.419 5.192\n+ 5ASP O 65 1.762 2.515 5.116\n+ 6ALA N 66 1.901 2.385 5.235\n+ 6ALA H 67 1.911 2.306 5.296\n+ 6ALA CA 68 2.019 2.460 5.196\n+ 6ALA HA 69 2.007 2.552 5.233\n+ 6ALA CB 70 2.144 2.396 5.254\n+ 6ALA HB1 71 2.224 2.449 5.226\n+ 6ALA HB2 72 2.138 2.396 5.354\n+ 6ALA HB3 73 2.153 2.302 5.221\n+ 6ALA C 74 2.028 2.466 5.044\n+ 6ALA O 75 2.029 2.364 4.976\n+ 7SER N 76 2.033 2.588 4.995\n+ 7SER H 77 2.031 2.666 5.057\n+ 7SER CA 78 2.041 2.612 4.852\n+ 7SER HA 79 1.973 2.552 4.811\n+ 7SER CB 80 2.008 2.758 4.820\n+ 7SER HB1 81 1.922 2.785 4.864\n+ 7SER HB2 82 2.001 2.772 4.722\n+ 7SER OG 83 2.109 2.845 4.868\n+ 7SER HG 84 2.085 2.940 4.846\n+ 7SER C 85 2.180 2.577 4.800\n+ 7SER O 86 2'..b'74 8.168\n+23553SOL HW171617 7.632 7.825 8.134\n+23553SOL HW271618 7.702 7.759 8.266\n+23554SOL OW71619 8.270 8.450 8.820\n+23554SOL HW171620 8.310 8.449 8.728\n+23554SOL HW271621 8.280 8.542 8.860\n+23555SOL OW71622 8.364 8.358 7.739\n+23555SOL HW171623 8.427 8.396 7.671\n+23555SOL HW271624 8.404 8.275 7.778\n+23556SOL OW71625 7.820 8.736 8.938\n+23556SOL HW171626 7.807 8.829 8.904\n+23556SOL HW271627 7.736 8.684 8.925\n+23557SOL OW71628 8.487 8.546 8.144\n+23557SOL HW171629 8.417 8.499 8.198\n+23557SOL HW271630 8.546 8.478 8.101\n+23558SOL OW71631 8.462 7.684 8.419\n+23558SOL HW171632 8.454 7.648 8.326\n+23558SOL HW271633 8.460 7.608 8.484\n+23559SOL OW71634 7.703 8.796 7.738\n+23559SOL HW171635 7.607 8.797 7.711\n+23559SOL HW271636 7.715 8.849 7.822\n+23560SOL OW71637 7.523 7.793 7.481\n+23560SOL HW171638 7.431 7.765 7.452\n+23560SOL HW271639 7.554 7.870 7.425\n+23561SOL OW71640 8.888 8.304 8.846\n+23561SOL HW171641 8.831 8.356 8.783\n+23561SOL HW271642 8.984 8.316 8.822\n+23562SOL OW71643 7.520 7.614 7.766\n+23562SOL HW171644 7.503 7.697 7.712\n+23562SOL HW271645 7.610 7.577 7.744\n+23563SOL OW71646 8.631 8.783 7.567\n+23563SOL HW171647 8.532 8.772 7.569\n+23563SOL HW271648 8.665 8.798 7.660\n+23564SOL OW71649 8.061 8.290 8.879\n+23564SOL HW171650 8.117 8.371 8.862\n+23564SOL HW271651 8.120 8.210 8.882\n+23565SOL OW71652 8.673 7.773 7.897\n+23565SOL HW171653 8.738 7.699 7.886\n+23565SOL HW271654 8.693 7.823 7.981\n+23566SOL OW71655 8.042 8.193 8.100\n+23566SOL HW171656 8.092 8.278 8.081\n+23566SOL HW271657 7.954 8.195 8.052\n+23567SOL OW71658 8.307 8.822 7.464\n+23567SOL HW171659 8.261 8.837 7.552\n+23567SOL HW271660 8.351 8.907 7.434\n+23568SOL OW71661 8.856 9.299 9.168\n+23568SOL HW171662 8.760 9.288 9.141\n+23568SOL HW271663 8.912 9.232 9.120\n+23569SOL OW71664 8.307 8.404 8.309\n+23569SOL HW171665 8.361 8.335 8.357\n+23569SOL HW271666 8.275 8.473 8.375\n+23570SOL OW71667 8.531 8.432 7.535\n+23570SOL HW171668 8.508 8.485 7.453\n+23570SOL HW271669 8.612 8.376 7.516\n+23571SOL OW71670 7.527 8.688 8.101\n+23571SOL HW171671 7.526 8.641 8.189\n+23571SOL HW271672 7.609 8.660 8.050\n+23572SOL OW71673 7.876 7.872 7.968\n+23572SOL HW171674 7.906 7.800 7.906\n+23572SOL HW271675 7.837 7.832 8.051\n+23573SOL OW71676 9.153 8.935 8.552\n+23573SOL HW171677 9.060 8.910 8.525\n+23573SOL HW271678 9.179 8.885 8.634\n+23574SOL OW71679 7.765 7.995 8.728\n+23574SOL HW171680 7.803 7.936 8.800\n+23574SOL HW271681 7.805 7.969 8.640\n+23575SOL OW71682 8.872 7.662 8.560\n+23575SOL HW171683 8.924 7.597 8.615\n+23575SOL HW271684 8.823 7.725 8.621\n+23576SOL OW71685 8.449 7.482 8.602\n+23576SOL HW171686 8.386 7.410 8.571\n+23576SOL HW271687 8.542 7.446 8.602\n+23577SOL OW71688 8.218 8.778 7.749\n+23577SOL HW171689 8.172 8.691 7.766\n+23577SOL HW271690 8.309 8.775 7.790\n+23578SOL OW71691 8.066 9.015 8.732\n+23578SOL HW171692 8.061 9.097 8.789\n+23578SOL HW271693 8.155 9.012 8.687\n+23579SOL OW71694 8.800 7.500 7.616\n+23579SOL HW171695 8.835 7.459 7.532\n+23579SOL HW271696 8.710 7.462 7.636\n+23580SOL OW71697 8.748 7.901 8.139\n+23580SOL HW171698 8.689 7.981 8.143\n+23580SOL HW271699 8.763 7.866 8.232\n+23581SOL OW71700 7.487 8.525 7.748\n+23581SOL HW171701 7.586 8.514 7.739\n+23581SOL HW271702 7.447 8.439 7.780\n+ 9.00078 9.00078 9.00078\n' |
| b |
| diff -r 21a0f28aea68 -r 4c626e984fde test-data/biobb_solvate_solvate.zip |
| b |
| Binary file test-data/biobb_solvate_solvate.zip has changed |