Date: Fri, 3 May 2019 06:14:57 +0000 (UTC) From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r500698 - in head/science: . apbs Message-ID: <201905030614.x436Ev2v008141@repo.freebsd.org>
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Author: yuri Date: Fri May 3 06:14:57 2019 New Revision: 500698 URL: https://svnweb.freebsd.org/changeset/ports/500698 Log: New port: science/apbs: Electrostatic and solvation properties for complex molecules Added: head/science/apbs/ head/science/apbs/Makefile (contents, props changed) head/science/apbs/distinfo (contents, props changed) head/science/apbs/pkg-descr (contents, props changed) head/science/apbs/pkg-plist (contents, props changed) Modified: head/science/Makefile Modified: head/science/Makefile ============================================================================== --- head/science/Makefile Fri May 3 05:13:29 2019 (r500697) +++ head/science/Makefile Fri May 3 06:14:57 2019 (r500698) @@ -26,6 +26,7 @@ SUBDIR += agrum SUBDIR += aircraft-datcom SUBDIR += antioch + SUBDIR += apbs SUBDIR += atom SUBDIR += atompaw SUBDIR += avogadro2 Added: head/science/apbs/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/apbs/Makefile Fri May 3 06:14:57 2019 (r500698) @@ -0,0 +1,34 @@ +# $FreeBSD$ + +PORTNAME= apbs +DISTVERSIONPREFIX= ${PORTNAME}- +DISTVERSION= 1.5-102 +DISTVERSIONSUFFIX= -g500c1473 +CATEGORIES= science + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Electrostatic and solvation properties for complex molecules + +LICENSE= LGPL21 +xLICENSE_FILE= ${WRKSRC}/COPYING + +USES= cmake shebangfix +SHEBANG_FILES= tools/github/getReleases.sh +USE_GITHUB= yes +GH_ACCOUNT= Electrostatics +GH_PROJECT= apbs-pdb2pqr +GH_TUPLE= Electrostatics:FETK:0c6fdea:fetk/externals/fetk \ + Electrostatics:geoflow_c:e8ce510:geoflow_c/externals/geoflow_c \ + lwwilson1:TABIPB:7e3a407:bem/externals/bem \ + lwwilson1:mesh_routines:ddb75cb:mr/externals/mesh_routines \ + davas301:pb_solvers:4858465:ps/externals/pb_s_am +USE_LDCONFIG= yes + +CMAKE_ON= BUILD_SHARED_LIBS + +WRKSRC_SUBDIR= ${PORTNAME} + +post-stage: # https://github.com/Electrostatics/apbs-pdb2pqr/issues/522 + @${STRIP_CMD} ${STAGEDIR}${PREFIX}/share/apbs/tools/bin/* + +.include <bsd.port.mk> Added: head/science/apbs/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/apbs/distinfo Fri May 3 06:14:57 2019 (r500698) @@ -0,0 +1,13 @@ +TIMESTAMP = 1556863311 +SHA256 (Electrostatics-apbs-pdb2pqr-apbs-1.5-102-g500c1473_GH0.tar.gz) = 873dae1df4d271b2e433283544e9cadb81d0b06347c6ef387370dd570640fc6a +SIZE (Electrostatics-apbs-pdb2pqr-apbs-1.5-102-g500c1473_GH0.tar.gz) = 113071316 +SHA256 (Electrostatics-FETK-0c6fdea_GH0.tar.gz) = df98ae46b2e34e3817a6ba72fabf62db416620407d258110d85ec9ee089e0e94 +SIZE (Electrostatics-FETK-0c6fdea_GH0.tar.gz) = 32979631 +SHA256 (Electrostatics-geoflow_c-e8ce510_GH0.tar.gz) = 27e38916e141771b71a43cebf0739911905531100df59a9fb913626a35753c2f +SIZE (Electrostatics-geoflow_c-e8ce510_GH0.tar.gz) = 45609 +SHA256 (lwwilson1-TABIPB-7e3a407_GH0.tar.gz) = 7b2a8f02e06ec0f91d8cf30e15ac757d12bb776cf5a963fc41572398a6cb6c44 +SIZE (lwwilson1-TABIPB-7e3a407_GH0.tar.gz) = 75583 +SHA256 (lwwilson1-mesh_routines-ddb75cb_GH0.tar.gz) = 5e58ea8c419c229efb5a7d9a1bb88ba96e62790f27f97d835262417d6b098a17 +SIZE (lwwilson1-mesh_routines-ddb75cb_GH0.tar.gz) = 3869445 +SHA256 (davas301-pb_solvers-4858465_GH0.tar.gz) = c0a75fa213e369ad467ab910fb7536f963f777ff962210239ebfff3e4bde30b0 +SIZE (davas301-pb_solvers-4858465_GH0.tar.gz) = 11187305 Added: head/science/apbs/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/apbs/pkg-descr Fri May 3 06:14:57 2019 (r500698) @@ -0,0 +1,8 @@ +APBS and PDB2PQR: electrostatic and solvation properties for complex molecules. + +APBS solves the equations of continuum electrostatics for large biomolecular +assemblages. This software was designed "from the ground up" using modern design +principles to ensure its ability to interface with other computational packages +and evolve as methods and applications change over time. + +WWW: https://www.poissonboltzmann.org/ Added: head/science/apbs/pkg-plist ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/apbs/pkg-plist Fri May 3 06:14:57 2019 (r500698) @@ -0,0 +1,717 @@ +bin/apbs +include/apbs/apbs.h +include/apbs/generic/apolparm.h +include/apbs/generic/bemparm.h +include/apbs/generic/femparm.h +include/apbs/generic/geoflowparm.h +include/apbs/generic/mgparm.h +include/apbs/generic/nosh.h +include/apbs/generic/pbamparm.h +include/apbs/generic/pbeparm.h +include/apbs/generic/pbsamparm.h +include/apbs/generic/vacc.h +include/apbs/generic/valist.h +include/apbs/generic/vatom.h +include/apbs/generic/vcap.h +include/apbs/generic/vclist.h +include/apbs/generic/vgreen.h +include/apbs/generic/vhal.h +include/apbs/generic/vmatrix.h +include/apbs/generic/vparam.h +include/apbs/generic/vpbe.h +include/apbs/generic/vstring.h +include/apbs/generic/vunit.h +include/apbs/mg/vgrid.h +include/apbs/mg/vmgrid.h +include/apbs/mg/vopot.h +include/apbs/mg/vpmg.h +include/apbs/mg/vpmgp.h +include/apbs/pmgc/buildAd.h +include/apbs/pmgc/buildBd.h +include/apbs/pmgc/buildGd.h +include/apbs/pmgc/buildPd.h +include/apbs/pmgc/cgd.h +include/apbs/pmgc/gsd.h +include/apbs/pmgc/matvecd.h +include/apbs/pmgc/mgcsd.h +include/apbs/pmgc/mgdrvd.h +include/apbs/pmgc/mgfasd.h +include/apbs/pmgc/mgsubd.h +include/apbs/pmgc/mikpckd.h +include/apbs/pmgc/mlinpckd.h +include/apbs/pmgc/mypdec.h +include/apbs/pmgc/newdrvd.h +include/apbs/pmgc/newtond.h +include/apbs/pmgc/powerd.h +include/apbs/pmgc/smoothd.h +include/apbs/routines.h +include/maloc/maloc.h +include/maloc/maloc_base.h +include/maloc/psh.h +include/maloc/vcom.h +include/maloc/vio.h +include/maloc/vmem.h +include/maloc/vmp.h +include/maloc/vmpi.h +include/maloc/vnm.h +include/maloc/vpred.h +include/maloc/vset.h +include/maloc/vsh.h +include/maloc/vsys.h +lib/libapbs_generic.so +lib/libapbs_mg.so +lib/libapbs_pmgc.so +lib/libapbs_routines.so +lib/libmaloc.so +%%DATADIR%%/doc/ChangeLog.md +%%DATADIR%%/doc/README +%%DATADIR%%/doc/ReleaseNotes.md +%%DATADIR%%/doc/data-ontology/README.md +%%DATADIR%%/doc/data-ontology/catalog-v001.xml +%%DATADIR%%/doc/data-ontology/data-ontology.ttl +%%DATADIR%%/doc/data-ontology/protege.sh +%%DATADIR%%/doc/icons/APBS_1024.png +%%DATADIR%%/doc/icons/APBS_128.png +%%DATADIR%%/doc/icons/APBS_128_v2.png +%%DATADIR%%/doc/icons/APBS_16.png +%%DATADIR%%/doc/icons/APBS_256.png +%%DATADIR%%/doc/icons/APBS_32.png +%%DATADIR%%/doc/icons/APBS_512.png +%%DATADIR%%/doc/icons/APBS_64.png +%%DATADIR%%/doc/license/LICENSE.txt +%%DATADIR%%/doc/license/license.html +%%DATADIR%%/doc/%%CMAKE_BUILD_TYPE%%_procedure.txt +%%DATADIR%%/examples/FKBP/1d7h-dmso-complex.pqr +%%DATADIR%%/examples/FKBP/1d7h-dmso-mol.in +%%DATADIR%%/examples/FKBP/1d7h-dmso-smol.in +%%DATADIR%%/examples/FKBP/1d7h-dmso/UHBD/1d7h-min.qcd +%%DATADIR%%/examples/FKBP/1d7h-dmso/UHBD/bindf.inp +%%DATADIR%%/examples/FKBP/1d7h-dmso/UHBD/bindf.log +%%DATADIR%%/examples/FKBP/1d7h-dmso/UHBD/bindf.oldlog +%%DATADIR%%/examples/FKBP/1d7h-dmso/UHBD/dmso-min.qcd +%%DATADIR%%/examples/FKBP/1d7h-dmso/UHBD/pqr2qcd +%%DATADIR%%/examples/FKBP/1d7h-min.pqr +%%DATADIR%%/examples/FKBP/1d7i-dss-complex.pqr +%%DATADIR%%/examples/FKBP/1d7i-dss-mol.in +%%DATADIR%%/examples/FKBP/1d7i-dss-smol.in +%%DATADIR%%/examples/FKBP/1d7i-dss/UHBD/1d7i-min.qcd +%%DATADIR%%/examples/FKBP/1d7i-dss/UHBD/bindf.inp +%%DATADIR%%/examples/FKBP/1d7i-dss/UHBD/bindf.log +%%DATADIR%%/examples/FKBP/1d7i-dss/UHBD/dss-min.qcd +%%DATADIR%%/examples/FKBP/1d7i-min.pqr +%%DATADIR%%/examples/FKBP/README.md +%%DATADIR%%/examples/FKBP/dmso-min.pqr +%%DATADIR%%/examples/FKBP/dss-min.pqr +%%DATADIR%%/examples/README.md +%%DATADIR%%/examples/actin-dimer/README.md +%%DATADIR%%/examples/actin-dimer/UHBD/aheall-atom.charmm.dat +%%DATADIR%%/examples/actin-dimer/UHBD/nuc.3-4.full.log +%%DATADIR%%/examples/actin-dimer/UHBD/nuc.3-4.inp +%%DATADIR%%/examples/actin-dimer/UHBD/prot3.pdb +%%DATADIR%%/examples/actin-dimer/UHBD/prot4.pdb +%%DATADIR%%/examples/actin-dimer/UHBD/single.inp +%%DATADIR%%/examples/actin-dimer/UHBD/srsrf.dot +%%DATADIR%%/examples/actin-dimer/apbs-mol-auto.in +%%DATADIR%%/examples/actin-dimer/apbs-mol-parallel.in +%%DATADIR%%/examples/actin-dimer/apbs-smol-auto.in +%%DATADIR%%/examples/actin-dimer/apbs-smol-parallel.in +%%DATADIR%%/examples/actin-dimer/complex.pqr +%%DATADIR%%/examples/actin-dimer/mesh.m +%%DATADIR%%/examples/actin-dimer/mol1.pqr +%%DATADIR%%/examples/actin-dimer/mol2.pqr +%%DATADIR%%/examples/alkanes/2-methylbutane.pdb +%%DATADIR%%/examples/alkanes/Makefile.in +%%DATADIR%%/examples/alkanes/README.md +%%DATADIR%%/examples/alkanes/alkanes.in +%%DATADIR%%/examples/alkanes/apbs-forces.in +%%DATADIR%%/examples/alkanes/butane.pdb +%%DATADIR%%/examples/alkanes/cyclohexane.pdb +%%DATADIR%%/examples/alkanes/cyclopentane.pdb +%%DATADIR%%/examples/alkanes/ethane.pdb +%%DATADIR%%/examples/alkanes/force.result +%%DATADIR%%/examples/alkanes/hexane.pdb +%%DATADIR%%/examples/alkanes/isobutane.pdb +%%DATADIR%%/examples/alkanes/methane.pdb +%%DATADIR%%/examples/alkanes/mol.pdb +%%DATADIR%%/examples/alkanes/neopentane.pdb +%%DATADIR%%/examples/alkanes/parm.dat +%%DATADIR%%/examples/alkanes/pentane.pdb +%%DATADIR%%/examples/alkanes/propane.pdb +%%DATADIR%%/examples/bem-binding-energy/1d30.in +%%DATADIR%%/examples/bem-binding-energy/1d30_monomer1.in +%%DATADIR%%/examples/bem-binding-energy/1d30_monomer2.in +%%DATADIR%%/examples/bem-binding-energy/README.md +%%DATADIR%%/examples/bem-binding-energy/test_proteins/1d30.pqr +%%DATADIR%%/examples/bem-binding-energy/test_proteins/1d30_monomer1.pqr +%%DATADIR%%/examples/bem-binding-energy/test_proteins/1d30_monomer2.pqr +%%DATADIR%%/examples/bem-pKa/2LZT-ASH66.in +%%DATADIR%%/examples/bem-pKa/2LZT-ASP66.in +%%DATADIR%%/examples/bem-pKa/2LZT-noASH66.in +%%DATADIR%%/examples/bem-pKa/2LZT-noASP66.in +%%DATADIR%%/examples/bem-pKa/ASH66.in +%%DATADIR%%/examples/bem-pKa/ASP66.in +%%DATADIR%%/examples/bem-pKa/README.md +%%DATADIR%%/examples/bem-pKa/test_proteins/2LZT-ASH66.pqr +%%DATADIR%%/examples/bem-pKa/test_proteins/2LZT-ASP66.pqr +%%DATADIR%%/examples/bem-pKa/test_proteins/2LZT-noASH66.pqr +%%DATADIR%%/examples/bem-pKa/test_proteins/2LZT-noASP66.pqr +%%DATADIR%%/examples/bem-pKa/test_proteins/ASH66.pqr +%%DATADIR%%/examples/bem-pKa/test_proteins/ASP66.pqr +%%DATADIR%%/examples/bem/1a63_NanoShaper_SES.in +%%DATADIR%%/examples/bem/1a63_NanoShaper_Skin.in +%%DATADIR%%/examples/bem/1a63_msms.in +%%DATADIR%%/examples/bem/451c_order1.in +%%DATADIR%%/examples/bem/451c_order5.in +%%DATADIR%%/examples/bem/README.md +%%DATADIR%%/examples/bem/test_proteins/1a63.pqr +%%DATADIR%%/examples/bem/test_proteins/1ajj.pqr +%%DATADIR%%/examples/bem/test_proteins/1bbl.pqr +%%DATADIR%%/examples/bem/test_proteins/451c.pqr +%%DATADIR%%/examples/bem/test_proteins/oneb.pqr +%%DATADIR%%/examples/bem/test_proteins/twob.pqr +%%DATADIR%%/examples/bem/test_proteins/twob2.pqr +%%DATADIR%%/examples/born/README.md +%%DATADIR%%/examples/born/apbs-apolar.in +%%DATADIR%%/examples/born/apbs-forces.in +%%DATADIR%%/examples/born/apbs-mol-auto.in +%%DATADIR%%/examples/born/apbs-mol-fem-extmesh.in +%%DATADIR%%/examples/born/apbs-mol-fem.in +%%DATADIR%%/examples/born/apbs-mol-parallel.in +%%DATADIR%%/examples/born/apbs-smol-auto.in +%%DATADIR%%/examples/born/apbs-smol-fem.in +%%DATADIR%%/examples/born/apbs-smol-parallel.in +%%DATADIR%%/examples/born/apolarforces +%%DATADIR%%/examples/born/ion.pqr +%%DATADIR%%/examples/born/ion.xml +%%DATADIR%%/examples/born/mesh.m +%%DATADIR%%/examples/born/parm.dat +%%DATADIR%%/examples/born/pmf.dat +%%DATADIR%%/examples/born/polarforces +%%DATADIR%%/examples/geoflow/1a63.in +%%DATADIR%%/examples/geoflow/1a63.pqr +%%DATADIR%%/examples/geoflow/README.md +%%DATADIR%%/examples/geoflow/gly.pdb +%%DATADIR%%/examples/geoflow/gly.pqr +%%DATADIR%%/examples/geoflow/glycerol.in +%%DATADIR%%/examples/geoflow/imidazole.in +%%DATADIR%%/examples/geoflow/imidazole_zap.pqr +%%DATADIR%%/examples/hca-bind/README.md +%%DATADIR%%/examples/hca-bind/UHBD/bindf-nmap.err +%%DATADIR%%/examples/hca-bind/UHBD/bindf-nmap.inp +%%DATADIR%%/examples/hca-bind/UHBD/bindf-nmap.out +%%DATADIR%%/examples/hca-bind/UHBD/bindf.inp +%%DATADIR%%/examples/hca-bind/UHBD/bindf.log +%%DATADIR%%/examples/hca-bind/UHBD/bindf.out.orig +%%DATADIR%%/examples/hca-bind/UHBD/bindf1.qcd +%%DATADIR%%/examples/hca-bind/UHBD/bindf2.err +%%DATADIR%%/examples/hca-bind/UHBD/bindf2.qcd +%%DATADIR%%/examples/hca-bind/UHBD/srsrf.dot +%%DATADIR%%/examples/hca-bind/acet.pqr +%%DATADIR%%/examples/hca-bind/apbs-mol.in +%%DATADIR%%/examples/hca-bind/apbs-smol.in +%%DATADIR%%/examples/hca-bind/complex.pqr +%%DATADIR%%/examples/hca-bind/hca.pqr +%%DATADIR%%/examples/hca-bind/mesh.m +%%DATADIR%%/examples/helix/Apbs_dummy-TEMPLATE.in +%%DATADIR%%/examples/helix/Apbs_dummy.in +%%DATADIR%%/examples/helix/Apbs_solv-TEMPLATE.in +%%DATADIR%%/examples/helix/Membrane-helix-0.pqr +%%DATADIR%%/examples/helix/Membrane-helix-12.pqr +%%DATADIR%%/examples/helix/Membrane-helix-16.pqr +%%DATADIR%%/examples/helix/Membrane-helix-4.pqr +%%DATADIR%%/examples/helix/Membrane-helix-8.pqr +%%DATADIR%%/examples/helix/Run_membrane-helix.sh +%%DATADIR%%/examples/helix/draw_membrane2.c +%%DATADIR%%/examples/ion-pmf/README.md +%%DATADIR%%/examples/ion-pmf/apolarforces +%%DATADIR%%/examples/ion-pmf/complex.in +%%DATADIR%%/examples/ion-pmf/ion-pmf.in +%%DATADIR%%/examples/ion-pmf/ion-pmf.pdb +%%DATADIR%%/examples/ion-pmf/parm.dat +%%DATADIR%%/examples/ion-pmf/polarforces +%%DATADIR%%/examples/ion-pmf/runme.sh +%%DATADIR%%/examples/ion-protein/491.pqr +%%DATADIR%%/examples/ion-protein/README.md +%%DATADIR%%/examples/ion-protein/UHBD/491.pdb +%%DATADIR%%/examples/ion-protein/UHBD/small491.e2.log +%%DATADIR%%/examples/ion-protein/UHBD/small491.inp +%%DATADIR%%/examples/ion-protein/UHBD/small491.log +%%DATADIR%%/examples/ion-protein/UHBD/small491.pdb +%%DATADIR%%/examples/ion-protein/apbs-mol-pdiel12.in +%%DATADIR%%/examples/ion-protein/apbs-mol-pdiel2.in +%%DATADIR%%/examples/ion-protein/apbs-smol-pdiel12.in +%%DATADIR%%/examples/ion-protein/apbs-smol-pdiel2.in +%%DATADIR%%/examples/ion-protein/complex.pqr +%%DATADIR%%/examples/ion-protein/small491.pqr +%%DATADIR%%/examples/ionize/README.md +%%DATADIR%%/examples/ionize/UHBD/elec.dat.exam +%%DATADIR%%/examples/ionize/UHBD/elec.inp.exam +%%DATADIR%%/examples/ionize/UHBD/elec.out.orig.exam +%%DATADIR%%/examples/ionize/UHBD/elec.pdb.exam +%%DATADIR%%/examples/ionize/acetate.pqr +%%DATADIR%%/examples/ionize/acetate.xml +%%DATADIR%%/examples/ionize/acetic-acid.pqr +%%DATADIR%%/examples/ionize/acetic-acid.xml +%%DATADIR%%/examples/ionize/apbs-mol.in +%%DATADIR%%/examples/ionize/apbs-smol.in +%%DATADIR%%/examples/ionize/proton.pqr +%%DATADIR%%/examples/ionize/proton.xml +%%DATADIR%%/examples/membrane/memv.in +%%DATADIR%%/examples/membrane/pot.pqr +%%DATADIR%%/examples/membrane/readme.md +%%DATADIR%%/examples/misc/README.md +%%DATADIR%%/examples/misc/achbp.pqr +%%DATADIR%%/examples/misc/apbs-PDB.in +%%DATADIR%%/examples/misc/apbs.in +%%DATADIR%%/examples/misc/fas2.pqr +%%DATADIR%%/examples/misc/mache.pqr +%%DATADIR%%/examples/misc/param.dat +%%DATADIR%%/examples/opal/README.md +%%DATADIR%%/examples/opal/actin-complex.pqr +%%DATADIR%%/examples/opal/actin-dimer-para.in +%%DATADIR%%/examples/opal/actin-dimer.in +%%DATADIR%%/examples/opal/actin-mol1.pqr +%%DATADIR%%/examples/opal/actin-mol2.pqr +%%DATADIR%%/examples/opal/born.xml +%%DATADIR%%/examples/pbam/1a63.in 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