diff options
Diffstat (limited to 'sci-chemistry/aria')
| -rw-r--r-- | sci-chemistry/aria/ChangeLog | 11 | ||||
| -rw-r--r-- | sci-chemistry/aria/aria-2.3.2-r3.ebuild | 94 | ||||
| -rw-r--r-- | sci-chemistry/aria/files/aria-2.3.2-through-space-2.patch | 139 |
3 files changed, 242 insertions, 2 deletions
diff --git a/sci-chemistry/aria/ChangeLog b/sci-chemistry/aria/ChangeLog index 040317c19665..da77675600b7 100644 --- a/sci-chemistry/aria/ChangeLog +++ b/sci-chemistry/aria/ChangeLog @@ -1,6 +1,13 @@ # ChangeLog for sci-chemistry/aria -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/aria/ChangeLog,v 1.11 2011/10/11 14:24:22 jlec Exp $ +# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/aria/ChangeLog,v 1.12 2012/03/21 11:48:20 jlec Exp $ + +*aria-2.3.2-r3 (21 Mar 2012) + + 21 Mar 2012; Justin Lecher <jlec@gentoo.org> +aria-2.3.2-r3.ebuild, + +files/aria-2.3.2-through-space-2.patch: + Added latest correction to through-space patch needed for global name + 'excludeSimulated' is not defined *aria-2.3.2-r2 (11 Oct 2011) diff --git a/sci-chemistry/aria/aria-2.3.2-r3.ebuild b/sci-chemistry/aria/aria-2.3.2-r3.ebuild new file mode 100644 index 000000000000..0d417c1cdad7 --- /dev/null +++ b/sci-chemistry/aria/aria-2.3.2-r3.ebuild @@ -0,0 +1,94 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/aria/aria-2.3.2-r3.ebuild,v 1.1 2012/03/21 11:48:20 jlec Exp $ + +EAPI=3 + +PYTHON_DEPEND="2" +PYTHON_USE_WITH="tk" + +inherit base eutils python versionator + +MY_P="${PN}$(get_version_component_range 1-2 ${PV})" + +DESCRIPTION="Automated NOE assignment and NMR structure calculation" +HOMEPAGE="http://aria.pasteur.fr/" +SRC_URI="http://aria.pasteur.fr/archives/${MY_P}.2.tar.gz" + +SLOT="0" +LICENSE="cns" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="examples" + +RDEPEND=" + sci-chemistry/clashlist + sci-chemistry/procheck + sci-libs/clashscore-db + dev-python/numpy + dev-python/matplotlib[tk] + >=sci-chemistry/cns-1.2.1-r7[aria,openmp] + >=dev-lang/tk-8.3 + >=sci-chemistry/ccpn-2.0.5 + >=dev-tcltk/tix-8.1.4" +DEPEND="${RDEPEND}" + +RESTRICT="fetch" + +S="${WORKDIR}/${MY_P}" + +pkg_nofetch(){ + einfo "Go to ${HOMEPAGE}, download ${A}" + einfo "and place it in ${DISTDIR}" +} + +src_prepare() { + epatch \ + "${FILESDIR}"/${P}-python.patch \ + "${FILESDIR}"/${P}-through-space-2.patch +} + +src_test(){ + export CCPNMR_TOP_DIR="${EPREFIX}"/$(python_get_sitedir) + export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python + $(PYTHON) check.py || die +} + +src_install(){ + insinto "$(python_get_sitedir)/${PN}" + doins -r src aria2.py || die "failed to install ${PN}" + insinto "$(python_get_sitedir)/${PN}"/cns + doins -r cns/{protocols,toppar,src/helplib} || die "failed to install cns part" + + if use examples; then + insinto /usr/share/${P}/ + doins -r examples || die + fi + + # ENV + cat >> "${T}"/20aria <<- EOF + ARIA2="${EPREFIX}/$(python_get_sitedir)/${PN}" + EOF + + doenvd "${T}"/20aria + + # Launch Wrapper + cat >> "${T}"/aria <<- EOF + #!/bin/sh + export CCPNMR_TOP_DIR="${EPREFIX}/$(python_get_sitedir)" + export PYTHONPATH="${EPREFIX}/$(python_get_sitedir)/ccpn/python" + exec "$(PYTHON)" -O "\${ARIA2}"/aria2.py \$@ + EOF + + dobin "${T}"/aria || die "failed to install wrapper" + dosym aria /usr/bin/aria2 + + dodoc README || die +} + +pkg_postinst() { + python_mod_optimize ${PN} +} + +pkg_postrm() { + python_mod_cleanup ${PN} +} diff --git a/sci-chemistry/aria/files/aria-2.3.2-through-space-2.patch b/sci-chemistry/aria/files/aria-2.3.2-through-space-2.patch new file mode 100644 index 000000000000..6a363d098632 --- /dev/null +++ b/sci-chemistry/aria/files/aria-2.3.2-through-space-2.patch @@ -0,0 +1,139 @@ + src/py/aria/exportToCcpn.py | 24 +++++++++++------------- + src/py/aria/importFromCcpn.py | 32 ++++++++++++-------------------- + 2 files changed, 23 insertions(+), 33 deletions(-) + +diff --git a/src/py/aria/exportToCcpn.py b/src/py/aria/exportToCcpn.py +index c742a88..aae7b7d 100644 +--- a/src/py/aria/exportToCcpn.py ++++ b/src/py/aria/exportToCcpn.py +@@ -1,5 +1,5 @@ + from ccpnmr.analysis.core.ConstraintBasic import makeNmrConstraintStore, makeStructureGeneration, getFixedResonance +-from ccpnmr.analysis.core.ExperimentBasic import getOnebondDataDims ++from ccpnmr.analysis.core.ExperimentBasic import getOnebondDataDims, getThroughSpaceDataDims + from ccpnmr.analysis.core.AssignmentBasic import assignAtomsToRes, assignResToDim + from ccpnmr.analysis.core.PeakBasic import pickPeak, setManualPeakIntensity + from ccpnmr.analysis.core.MoleculeBasic import DEFAULT_ISOTOPES +@@ -791,12 +791,13 @@ def getPeakAssignmentsFromAria2(project, ariaRestraints, namesDict=None, + ariaDims = ariaDimDict.get(spectrum) + if not ariaDims: + ariaDims = [] #[0,1,2] ++ throughSpaceDataDims = getThroughSpaceDataDims(spectrum) + + dataDims = spectrum.sortedDataDims() + if len(dataDims) == 3: + for dataDim in dataDims: + expDimRef = dataDim.findFirstDataDimRef().expDimRef +- if '1H' in expDimRef.isotopeCodes: # 0 or 2 ++ if dataDim in throughSpaceDataDims: # 0 or 2 + if onebondDims.get(dataDim.dim): + if ppmX1 is None: + ariaDims.append(2) +@@ -816,21 +817,18 @@ def getPeakAssignmentsFromAria2(project, ariaRestraints, namesDict=None, + ariaDims.append(1) + + else: +- transfer = spectrum.experiment.findFirstExpTransfer(transferType='through-space') or \ +- spectrum.experiment.findFirstExpTransfer(transferType='NOESY') + ++ i = 0 + for dataDim in dataDims: +- expDimRefs = [dataDimRef.expDimRef for dataDimRef in dataDim.dataDimRefs] +- i = 0 +- for expDimRef in transfer.sortedExpDimRefs(): +- if expDimRef in expDimRefs: +- ariaDims.append(i) +- boundDim = onebondDims.get(dataDim.dim) +- if boundDim: +- ariaDims.append(i+1) +- ++ if dataDim in throughSpaceDataDims: ++ ariaDims.append(i) ++ boundDim = onebondDims.get(dataDim.dim) ++ if boundDim: ++ ariaDims.append(i+1) ++ + i += 2 + ++ + ariaDimDict[spectrum] = ariaDims + + if namesDict: +diff --git a/src/py/aria/importFromCcpn.py b/src/py/aria/importFromCcpn.py +index a65ae3e..f63ba16 100644 +--- a/src/py/aria/importFromCcpn.py ++++ b/src/py/aria/importFromCcpn.py +@@ -165,7 +165,7 @@ def getStructureEnsembles(project, ccpChains): + + return ensembles + +-def getNoesyPeakLists(project, molSystem=None): ++def getNoesyPeakLists(project, molSystem=None, excludeSimulated=True): + """Descrn: Get the NOE peak lists from a CCPN project. Can filter if appropriate to a given + molecular system if passed in. + Inputs: Implementation.Project, ccp.molecule.MolSystem.MolSystem +@@ -196,19 +196,10 @@ def getNoesyPeakLists(project, molSystem=None): + + for spectrum in experiment.dataSources: + if (spectrum.dataType == 'processed') and (spectrum.numDim > 1): +- +- isotopes = [] +- for dataDim in spectrum.dataDims: +- for expDimRef in dataDim.expDim.expDimRefs: +- if expDimRef.measurementType in ('shift','Shift'): +- isotope = ','.join(expDimRef.isotopeCodes) +- isotopes.append(isotope) +- break +- +- if isotopes.count('1H') > 1: +- for peakList in spectrum.peakLists: +- if peakList.findFirstPeak(): +- peakLists.append(peakList) ++ for peakList in spectrum.sortedPeakLists(): ++ if excludeSimulated and peakList.isSimulated: ++ continue ++ peakLists.append(peakList) + + + return peakLists +@@ -490,7 +481,10 @@ def makeAriaChain(ccpChain): + # Does below work for DNA/RNA? + + aria_settings = ChainSettings() +- aria_settings['type'] = chainTypeMapping[ccpChain.molecule.molType] ++ # wb104: below changed 31 Oct 2011 to try and get around case when molType is None ++ #aria_settings['type'] = chainTypeMapping[ccpChain.molecule.molType] ++ molType = ccpChain.molecule.molType or 'protein' ++ aria_settings['type'] = chainTypeMapping[molType] + + aria_chain = Chain(settings=aria_settings, segid=string_to_segid(ccpChain.code)) + +@@ -952,8 +946,6 @@ def makeAriaSpectrum(peakList, ariaMolecule, filterRejected=True): + expDimRefDict = {} + + for expDimRef in transfer.sortedExpDimRefs(): +- if expDimRef.isotopeCodes != ('1H',): +- raise Exception('Not an H-H experiment') + + onebondTransfer = expDimRef.findFirstExpTransfer(transferType='onebond') + +@@ -1095,7 +1087,7 @@ def getAriaAtomsFromResonance(resonance, ariaMolecule, cache={}): + + # TJS modify to return just a list of atoms, rather than a list of list + ariaAtoms = [] +- for atom in atomSet.sortedAtoms(): ++ for atom in atomSet.atoms: + ariaAtom = ariaResidue.atoms.get(atom.name) + if not ariaAtom: + messager.warning('Could not find ARIA Atom for CCPN atom %d%s %s' % (residue.seqCode,residue.ccpCode, atom.name)) +@@ -1256,9 +1248,9 @@ def getAriaDistanceRestraintsList(constraint_list, constraint_type, aria_mol): + restraint.setWeight(weight) + + +- for constrItem in distConstr.sortedItems(): ++ for constrItem in distConstr.items: + +- reso1, reso2 = constrItem.sortedResonances() ++ reso1, reso2 = constrItem.resonances + + # TJS fix for mapping prochirals + # always use real resonnances where possible |