Mercurial > repos > chemteam > qiskit_xyz2pdb
changeset 0:7372df4e8513 draft default tip
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 02ff1748664d6b2729209b6bf1ef17ff81f6b290
| author | chemteam |
|---|---|
| date | Wed, 05 Jun 2024 20:06:27 +0000 |
| parents | |
| children | |
| files | qiskit_xyz2pdb.xml test-data/RHYYKFNSTGRHYHYY_hetatm.pdb test-data/RHYYKFNSTGRHYHYY_trace.pdb test-data/structure_input.xyz |
| diffstat | 4 files changed, 165 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiskit_xyz2pdb.xml Wed Jun 05 20:06:27 2024 +0000 @@ -0,0 +1,93 @@ +<tool id="qiskit_xyz2pdb" name="Convert Qiskit's XYZ files to" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> + <description>alpha carbon PDB files</description> + <macros> + <token name="@TOOL_VERSION@">0.1.2</token> + <token name="@GALAXY_VERSION@">0</token> + </macros> + <requirements> + <requirement type="package" version="0.1.2">qiskit-xyz2pdb</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + + ln -s '$structure_input' ./structure_input.${structure_input.ext} && + #if $output_format == "hetatm": + qiskit-xyz2pdb --in-xyz ./structure_input.${structure_input.ext} --hetero-atoms + #end if + + #if $output_format == "alpha_carbon_trace": + qiskit-xyz2pdb --in-xyz ./structure_input.${structure_input.ext} --alpha-c-traces + #end if + + ]]></command> + <inputs> + <param name="structure_input" type="data" format="xyz" label="XYZ Structure file" help="In XYZ format. This file should be the initial output from the quantum algorithm, containing the coarse grain coordinates in XYZ format."/> + <param name="output_format" type="select" label="Output format"> + <option value="alpha_carbon_trace">Alpha carbon trace file (generic alpha carbon trace format with no CONNECT lines)</option> + <option value="hetatm">HETATM (generic heterogenous atom format with CONNECT lines representing bonds)</option> + </param> + </inputs> + <outputs> + <data name="output1" format="pdb" from_work_dir="*.pdb" label="Converted PDB file on ${on_string}"/> + </outputs> + <tests> + <test> + <param name="structure_input" value="structure_input.xyz"/> + <param name="output_format" value="hetatm" /> + <output name="output1" ftype="pdb"> + <assert_contents> + <has_text text="HETATM 1 R PEP 1 0.000 0.000 0.000 1.00 0.00 R"/> + <has_text text="HETATM 2 H PEP 2 2.194 2.194 -2.194 1.00 0.00 H"/> + <has_text text="HETATM 3 Y PEP 3 4.388 0.000 -4.388 1.00 0.00 Y"/> + </assert_contents> + </output> + </test> + <test> + <param name="structure_input" value="structure_input.xyz"/> + <param name="output_format" value="alpha_carbon_trace" /> + <output name="output1" ftype="pdb"> + <assert_contents> + <has_text text="ATOM 1 CA ARG 1 0.000 0.000 0.000 1.00 0.00 R"/> + <has_text text="ATOM 2 CA HIS 2 2.194 2.194 -2.194 1.00 0.00 H"/> + <has_text text="ATOM 3 CA TYR 3 4.388 0.000 -4.388 1.00 0.00 Y"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + + .. class:: infomark + + **What it does** + + This tool takes the XYZ files from Qiskit's protein folding algorithm and converts them to a proper alpha carbon PDB file. + +_____ + + .. class:: infomark + + **Input** + + - XYZ file of coarse grain model coordinates + + +_____ + + + .. class:: infomark + + **Output** + + - Alpha carbon PDB file in either trace or HETATM format + + ]]></help> + <citations> + <citation type="bibtex">@misc{pypiQiskitxyz2pdb, + author = {}, + title = {qiskit-xyz2pdb --- pypi.org}, + howpublished = {\url{https://pypi.org/project/qiskit-xyz2pdb/#history}}, + year = {}, + note = {[Accessed 22-05-2024]}, + }</citation> + </citations> +</tool> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/RHYYKFNSTGRHYHYY_hetatm.pdb Wed Jun 05 20:06:27 2024 +0000 @@ -0,0 +1,35 @@ +COMPND My Protein Sequence +AUTHOR Galaxy User +HETATM 1 R PEP 1 0.000 0.000 0.000 1.00 0.00 R +HETATM 2 H PEP 2 2.194 2.194 -2.194 1.00 0.00 H +HETATM 3 Y PEP 3 4.388 0.000 -4.388 1.00 0.00 Y +HETATM 4 Y PEP 4 2.194 -2.194 -6.582 1.00 0.00 Y +HETATM 5 K PEP 5 0.000 -4.388 -4.388 1.00 0.00 K +HETATM 6 F PEP 6 2.194 -2.194 -6.582 1.00 0.00 F +HETATM 7 N PEP 7 4.388 0.000 -4.388 1.00 0.00 N +HETATM 8 S PEP 8 2.194 2.194 -2.194 1.00 0.00 S +HETATM 9 T PEP 9 0.000 4.388 -4.388 1.00 0.00 T +HETATM 10 G PEP 10 -2.194 6.582 -2.194 1.00 0.00 G +HETATM 11 R PEP 11 -4.388 4.388 -0.000 1.00 0.00 R +HETATM 12 H PEP 12 -2.194 2.194 2.194 1.00 0.00 H +HETATM 13 Y PEP 13 0.000 0.000 -0.000 1.00 0.00 Y +HETATM 14 H PEP 14 2.194 2.194 -2.194 1.00 0.00 H +HETATM 15 Y PEP 15 4.388 0.000 -4.388 1.00 0.00 Y +HETATM 16 Y PEP 16 2.194 2.194 -2.194 1.00 0.00 Y +CONECT 1 2 0 0 0 +CONECT 2 3 0 0 0 +CONECT 3 4 0 0 0 +CONECT 4 5 0 0 0 +CONECT 5 6 0 0 0 +CONECT 6 7 0 0 0 +CONECT 7 8 0 0 0 +CONECT 8 9 0 0 0 +CONECT 9 10 0 0 0 +CONECT 10 11 0 0 0 +CONECT 11 12 0 0 0 +CONECT 12 13 0 0 0 +CONECT 13 14 0 0 0 +CONECT 14 15 0 0 0 +CONECT 15 16 0 0 0 +MASTER 0 0 0 0 0 0 0 0 16 0 16 0 +END \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/RHYYKFNSTGRHYHYY_trace.pdb Wed Jun 05 20:06:27 2024 +0000 @@ -0,0 +1,19 @@ +COMPND My Protein Sequence +AUTHOR Galaxy User +ATOM 1 CA ARG 1 0.000 0.000 0.000 1.00 0.00 R +ATOM 2 CA HIS 2 2.194 2.194 -2.194 1.00 0.00 H +ATOM 3 CA TYR 3 4.388 0.000 -4.388 1.00 0.00 Y +ATOM 4 CA TYR 4 2.194 -2.194 -6.582 1.00 0.00 Y +ATOM 5 CA LYS 5 0.000 -4.388 -4.388 1.00 0.00 K +ATOM 6 CA PHE 6 2.194 -2.194 -6.582 1.00 0.00 F +ATOM 7 CA ASN 7 4.388 0.000 -4.388 1.00 0.00 N +ATOM 8 CA SER 8 2.194 2.194 -2.194 1.00 0.00 S +ATOM 9 CA THR 9 0.000 4.388 -4.388 1.00 0.00 T +ATOM 10 CA GLY 10 -2.194 6.582 -2.194 1.00 0.00 G +ATOM 11 CA ARG 11 -4.388 4.388 -0.000 1.00 0.00 R +ATOM 12 CA HIS 12 -2.194 2.194 2.194 1.00 0.00 H +ATOM 13 CA TYR 13 0.000 0.000 -0.000 1.00 0.00 Y +ATOM 14 CA HIS 14 2.194 2.194 -2.194 1.00 0.00 H +ATOM 15 CA TYR 15 4.388 0.000 -4.388 1.00 0.00 Y +ATOM 16 CA TYR 16 2.194 2.194 -2.194 1.00 0.00 Y +END \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/structure_input.xyz Wed Jun 05 20:06:27 2024 +0000 @@ -0,0 +1,18 @@ +16 + +R 0.0 0.0 0.0 +H 2.193931 2.193931 -2.193931 +Y 4.387862 0.0 -4.387862 +Y 2.193931 -2.193931 -6.581793 +K 0.0 -4.387862 -4.387862 +F 2.193931 -2.193931 -6.581793 +N 4.387862 0.0 -4.387862 +S 2.193931 2.193931 -2.193931 +T 0.0 4.387862 -4.387862 +G -2.193931 6.581793 -2.193931 +R -4.387862 4.387862 -0.0 +H -2.193931 2.193931 2.193931 +Y 0.0 0.0 -0.0 +H 2.193931 2.193931 -2.193931 +Y 4.387862 0.0 -4.387862 +Y 2.193931 2.193931 -2.193931