Mercurial > repos > chemteam > ambertools_acpype

comparison template_mmpbsa_mmgbsa.j2 @ 5:27ee142314a9 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 4a3f58846bcad26240ccdc6b76e8f4d2cbe63631"
author chemteam
date Mon, 25 Jan 2021 11:15:57 +0000
parents c6afbb28f547
children
comparison
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4:f4230f116196 5:27ee142314a9
1 # Template for mmpbsa in Galaxy 1 # Template for mmpbsa in Galaxy
2 # 2 #
3 &general 3 &general
4 startframe={{ allparams.startframe }}, endframe={{ allparams.endframe }}, interval={{ allparams.interval }}, 4 startframe={{ allparams.startframe }}, endframe={{ allparams.endframe }}, interval={{ allparams.interval }},
5 verbose={{ allparams.verbose }}, keep_files={{ allparams.keep_files | int }}, strip_mask={{ allparams.strip_mask }}, use_sander={{ allparams.use_sander | int }}, entropy={{ allparams.entropy | int }} 5 verbose=2, keep_files={{ allparams.keep_files | int }}, strip_mask={{ allparams.strip_mask }}, use_sander={{ allparams.use_sander | int }}, entropy={{ allparams.entropy | int }}, netcdf=1
6 / 6 /
7 {% if calcdetails.gbcalc.calctype == 'yes' %} 7 {% if calcdetails.gb_pb_calc.calctype == 'gb' %}
8 &gb 8 &gb
9 igb={{ calcdetails.gbcalc.igb }}, saltcon={{ calcdetails.gbcalc.saltcon }} 9 igb={{ calcdetails.gb_pb_calc.igb }}, saltcon={{ calcdetails.gb_pb_calc.saltcon }}, surfoff={{ calcdetails.gb_pb_calc.surfoff }}, molsurf={{ calcdetails.gb_pb_calc.molsurf | int}}, probe={{ calcdetails.gb_pb_calc.probe }}, msoffset={{ calcdetails.gb_pb_calc.msoffset }}
10 / 10 /
11 {% endif %} 11 {% elif calcdetails.gb_pb_calc.calctype == 'pb' %}
12 {% if calcdetails.pbcalc.calctype == 'yes' %}
13 &pb 12 &pb
14 istrng={{ calcdetails.pbcalc.istrng }}, fillratio={{ calcdetails.pbcalc.fillratio }}, inp={{ calcdetails.pbcalc.inp }},radiopt={{ calcdetails.pbcalc.radiopt }} 13 istrng={{ calcdetails.gb_pb_calc.istrng }}, fillratio={{ calcdetails.gb_pb_calc.fillratio }}, inp={{ calcdetails.gb_pb_calc.inp }}, radiopt={{ calcdetails.gb_pb_calc.radiopt }}, cavity_offset={{ calcdetails.gb_pb_calc.cavity_offset }}, scale={{ calcdetails.gb_pb_calc.scale }}, linit={{ calcdetails.gb_pb_calc.linit }}, prbrad={{ calcdetails.gb_pb_calc.prbrad }}
15 / 14 /
16 {% endif %} 15 {% endif %}
17 {% if calcdetails.decomposition.decomposition == 'yes' %} 16 {% if calcdetails.decomposition.decomposition == 'yes' %}
18 &decomp 17 &decomp
19 csv_format={{ calcdetails.decomposition.csv_format | int }}, dec_verbose={{ calcdetails.decomposition.dec_verbose }}, idecomp={{ calcdetails.decomposition.idecomp }}, 18 csv_format={{ calcdetails.decomposition.csv_format | int }}, dec_verbose={{ calcdetails.decomposition.dec_verbose }}, idecomp={{ calcdetails.decomposition.idecomp }},