Previous changeset 3:3549852f413f (2020-02-12) Next changeset 5:96b872138d3b (2020-04-07) |
Commit message:
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit a68f9fb01e0cfff122aef8ddce5c866c687a4f9a" |
modified:
macros.xml |
added:
template_mmpbsa_mmgbsa.j2 test-data/1err_desolvated_mini.nc test-data/complex.prmtop test-data/ligand.prmtop test-data/receptor.prmtop |
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diff -r 3549852f413f -r dbfb86927de6 macros.xml --- a/macros.xml Wed Feb 12 06:28:05 2020 -0500 +++ b/macros.xml Fri Feb 28 03:47:10 2020 -0500 |
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@@ -17,4 +17,7 @@ <yield/> </citations> </xml> + <xml name="mmpbsa_citation"> + <citation type="doi">10.1021/ct300418h</citation> + </xml> </macros> |
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diff -r 3549852f413f -r dbfb86927de6 template_mmpbsa_mmgbsa.j2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/template_mmpbsa_mmgbsa.j2 Fri Feb 28 03:47:10 2020 -0500 |
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@@ -0,0 +1,22 @@ +# Template for mmpbsa in Galaxy +# +&general +startframe={{ allparams.startframe }}, endframe={{ allparams.endframe }}, interval={{ allparams.interval }}, +verbose={{ allparams.verbose }}, keep_files={{ allparams.keep_files | int }}, strip_mask={{ allparams.strip_mask }}, use_sander={{ allparams.use_sander | int }}, entropy={{ allparams.entropy | int }} +/ +{% if calcdetails.gbcalc.calctype == 'yes' %} +&gb +igb={{ calcdetails.gbcalc.igb }}, saltcon={{ calcdetails.gbcalc.saltcon }} +/ +{% endif %} +{% if calcdetails.pbcalc.calctype == 'yes' %} +&pb +istrng={{ calcdetails.pbcalc.istrng }}, fillratio={{ calcdetails.pbcalc.fillratio }}, inp={{ calcdetails.pbcalc.inp }},radiopt={{ calcdetails.pbcalc.radiopt }} +/ +{% endif %} +{% if calcdetails.decomposition.decomposition == 'yes' %} +&decomp +csv_format={{ calcdetails.decomposition.csv_format | int }}, dec_verbose={{ calcdetails.decomposition.dec_verbose }}, idecomp={{ calcdetails.decomposition.idecomp }}, +/ +{% endif %} + |
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diff -r 3549852f413f -r dbfb86927de6 test-data/1err_desolvated_mini.nc |
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Binary file test-data/1err_desolvated_mini.nc has changed |
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diff -r 3549852f413f -r dbfb86927de6 test-data/complex.prmtop --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/complex.prmtop Fri Feb 28 03:47:10 2020 -0500 |
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b'@@ -0,0 +1,19476 @@\n+%VERSION VERSION_STAMP = V0001.000 DATE = 10/09/09 16:22:47 \n+%FLAG TITLE \n+%FORMAT(20a4) \n+ \n+%FLAG POINTERS \n+%FORMAT(10I8) \n+ 3941 15 1991 1991 4536 2694 8432 6711 0 0\n+ 21774 241 1991 2694 6711 59 119 51 42 0\n+ 0 0 0 0 0 0 0 0 61 0\n+ 0\n+%FLAG ATOM_NAME \n+%FORMAT(20a4) \n+N H1 H2 H3 CA HA CB HB1 HB2 HB3 C O N H CA HA CB HB2 HB3 CG \n+HG CD1 HD11HD12HD13CD2 HD21HD22HD23C O N H CA HA CB HB2 HB3 OG HG \n+C O N H CA HA CB HB2 HB3 CG HG CD1 HD11HD12HD13CD2 HD21HD22HD23C \n+O N H CA HA CB HB CG2 HG21HG22HG23OG1 HG1 C O N H CA HA CB \n+HB1 HB2 HB3 C O N H CA HA CB HB2 HB3 CG OD1 OD2 C O N H CA \n+HA CB HB2 HB3 CG HG2 HG3 CD OE1 NE2 HE21HE22C O N H CA HA CB HB2 \n+HB3 CG HG2 HG3 SD CE HE1 HE2 HE3 C O N H CA HA CB HB CG1 HG11HG12\n+HG13CG2 HG21HG22HG23C O N H CA HA CB HB2 HB3 OG HG C O N H \n+CA HA CB HB1 HB2 HB3 C O N H CA HA CB HB2 HB3 CG HG CD1 HD11HD12\n+HD13CD2 HD21HD22HD23C O N H CA HA CB HB2 HB3 CG HG CD1 HD11HD12HD13\n+CD2 HD21HD22HD23C O N H CA HA 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7.20000000E-01 8.50000000E-01 7.20000000E-01\n+ 7.20000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01 7.20000000E-01\n+ 7.20000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01\n+ 7.20000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01\n+ 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01\n+ 7.90000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01\n+ 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01\n+ 7.20000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01\n+ 8.50000000E-01\n' |
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diff -r 3549852f413f -r dbfb86927de6 test-data/ligand.prmtop --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ligand.prmtop Fri Feb 28 03:47:10 2020 -0500 |
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b'@@ -0,0 +1,454 @@\n+%VERSION VERSION_STAMP = V0001.000 DATE = 10/09/09 16:30:00 \n+%FLAG TITLE \n+%FORMAT(20a4) \n+ \n+%FLAG POINTERS \n+%FORMAT(10I8) \n+ 61 11 27 38 59 53 108 91 0 0\n+ 329 1 38 53 91 18 30 19 14 0\n+ 0 0 0 0 0 0 0 0 61 0\n+ 0\n+%FLAG ATOM_NAME \n+%FORMAT(20a4) \n+O11 H7 C11 C12 C13 H9 H8 C10 H6 C9 H5 C8 C7 S6 C5 C4 H4 C3 O3 H3 \n+C2 H2 C1 H1 C14 C15 C16 O16 C17 C22 C21 H12 H13 C18 H10 C19 H11 C20 O23 C24 \n+H14 H15 C25 H16 H17 N26 C27 H18 H19 C28 H20 H21 C29 H22 H23 C30 H24 H25 C31 H26 \n+H27 \n+%FLAG CHARGE \n+%FORMAT(5E16.8) \n+ -9.01274958E+00 7.67158830E+00 2.44725489E+00 -3.86312760E+00 -1.24093863E+00\n+ 2.64405573E+00 2.50374402E+00 -2.84450103E+00 2.80076751E+00 -1.48329522E+00\n+ 2.58938883E+00 -1.16622720E+00 -4.42619667E+00 5.00931027E+00 -7.96314510E-01\n+ -3.48957045E+00 2.56023315E+00 2.52561078E+00 -9.00728289E+00 7.66247715E+00\n+ -2.73881169E+00 2.81716758E+00 -1.05142671E+00 2.68414479E+00 -1.46142846E+00\n+ -2.43996597E+00 1.08240462E+01 -9.42639579E+00 -4.00708377E+00 -9.62137440E-01\n+ -3.25632501E+00 2.79894528E+00 2.72423385E+00 -6.70580640E-01 2.86090110E+00\n+ -4.11459534E+00 2.62218897E+00 2.91556800E+00 -6.04798137E+00 2.25227628E+00\n+ 7.61692140E-01 1.15347159E+00 3.11419107E+00 6.65113950E-01 1.03867110E+00\n+ -1.33769904E+01 3.13970229E+00 2.05911990E-01 8.18181270E-01 -1.39400595E+00\n+ 7.61692140E-01 9.38448450E-01 -1.42862832E+00 6.86980710E-01 7.67158830E-01\n+ -1.40676156E+00 7.92670050E-01 9.25692840E-01 3.03947964E+00 1.12249368E+00\n+ 2.75156730E-01\n+%FLAG MASS \n+%FORMAT(5E16.8) \n+ 1.60000000E+01 1.00800000E+00 1.20100000E+01 1.20100000E+01 1.20100000E+01\n+ 1.00800000E+00 1.00800000E+00 1.20100000E+01 1.00800000E+00 1.20100000E+01\n+ 1.00800000E+00 1.20100000E+01 1.20100000E+01 3.20600000E+01 1.20100000E+01\n+ 1.20100000E+01 1.00800000E+00 1.20100000E+01 1.60000000E+01 1.00800000E+00\n+ 1.20100000E+01 1.00800000E+00 1.20100000E+01 1.00800000E+00 1.20100000E+01\n+ 1.20100000E+01 1.20100000E+01 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0\n+ 0 0 0 0 0 0 0 0 0 0\n+ 0 0 0 0 0 0 0 0 0 0\n+ 0 0 0 0 0 0 0 0 0 0\n+ 0\n+%FLAG RADIUS_SET \n+%FORMAT(1a80) \n+H(N)-modified Bondi radii (mbondi2) \n+%FLAG RADII \n+%FORMAT(5E16.8) \n+ 1.50000000E+00 1.20000000E+00 1.70000000E+00 1.70000000E+00 1.70000000E+00\n+ 1.20000000E+00 1.20000000E+00 1.70000000E+00 1.20000000E+00 1.70000000E+00\n+ 1.20000000E+00 1.70000000E+00 1.70000000E+00 1.80000000E+00 1.70000000E+00\n+ 1.70000000E+00 1.20000000E+00 1.70000000E+00 1.50000000E+00 1.20000000E+00\n+ 1.70000000E+00 1.20000000E+00 1.70000000E+00 1.20000000E+00 1.70000000E+00\n+ 1.70000000E+00 1.70000000E+00 1.50000000E+00 1.70000000E+00 1.70000000E+00\n+ 1.70000000E+00 1.20000000E+00 1.20000000E+00 1.70000000E+00 1.20000000E+00\n+ 1.70000000E+00 1.20000000E+00 1.70000000E+00 1.50000000E+00 1.70000000E+00\n+ 1.20000000E+00 1.20000000E+00 1.70000000E+00 1.20000000E+00 1.20000000E+00\n+ 1.55000000E+00 1.70000000E+00 1.20000000E+00 1.20000000E+00 1.70000000E+00\n+ 1.20000000E+00 1.20000000E+00 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diff -r 3549852f413f -r dbfb86927de6 test-data/receptor.prmtop --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/receptor.prmtop Fri Feb 28 03:47:10 2020 -0500 |
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b'@@ -0,0 +1,19148 @@\n+%VERSION VERSION_STAMP = V0001.000 DATE = 10/09/09 16:29:33 \n+%FLAG TITLE \n+%FORMAT(20a4) \n+ \n+%FLAG POINTERS \n+%FORMAT(10I8) \n+ 3880 14 1964 1953 4477 2641 8324 6620 0 0\n+ 21445 240 1953 2641 6620 41 89 42 28 0\n+ 0 0 0 0 0 0 0 0 24 0\n+ 0\n+%FLAG ATOM_NAME \n+%FORMAT(20a4) \n+N H1 H2 H3 CA HA CB HB1 HB2 HB3 C O N H CA HA CB HB2 HB3 CG \n+HG CD1 HD11HD12HD13CD2 HD21HD22HD23C O N H CA HA CB HB2 HB3 OG HG \n+C O N H CA HA CB HB2 HB3 CG HG CD1 HD11HD12HD13CD2 HD21HD22HD23C \n+O N H CA HA CB HB CG2 HG21HG22HG23OG1 HG1 C O N H CA HA CB \n+HB1 HB2 HB3 C O N H CA HA CB HB2 HB3 CG OD1 OD2 C O N H CA \n+HA CB HB2 HB3 CG HG2 HG3 CD OE1 NE2 HE21HE22C O N H CA HA CB HB2 \n+HB3 CG HG2 HG3 SD CE HE1 HE2 HE3 C O N H CA HA CB HB CG1 HG11HG12\n+HG13CG2 HG21HG22HG23C O N H CA HA CB HB2 HB3 OG HG C O N H \n+CA HA CB HB1 HB2 HB3 C O N H CA HA CB HB2 HB3 CG HG CD1 HD11HD12\n+HD13CD2 HD21HD22HD23C O N H CA HA CB HB2 HB3 CG HG CD1 HD11HD12HD13\n+CD2 HD21HD22HD23C O N H CA HA 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