/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/pdb2pqr/propka30/Source/ |
H A D | output.py | 55 def writePDB(protein, file=None, filename=None, hydrogens=False, options=None): argument 89 def writePQR(protein, label=None, hydrogens=False, options=None): argument 150 def writePKA(protein, filename=None, reference="neutral", direction="folding", options=None): argument 186 def printTmProfile(protein, reference="neutral", window=[0., 14., 1.], Tm=[0.,0.], Tms=None, ref=No… argument 202 def printResult(protein, verbose=False): argument 209 def printPKASection(protein, verbose=False): argument 223 def getDeterminantSection(protein, verbose=False): argument 248 def getSummarySection(protein, verbose=False): argument 265 def getFoldingProfileSection(protein, direction="folding", reference="neutral", window=[0., 14., 1.… argument 308 def getChargeProfileSection(protein, verbose=False, options=None): argument
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H A D | mutate.py | 48 def optimizeMutationDeterminants(protein, mutation=None, atoms=None, alignment=None, version=None, … argument 89 def optimizeMultipleMutations(protein, mutations=None, atoms=None, alignment=None, version=None, op… argument 140 def generateChainList(mutation, protein, atoms=None): argument 162 def makeMutatedProtein(protein, mutation=None, atoms=None, alignment=None, options=None): argument 396 def mutateAtomsDictionaryUsingAlignment(protein, atoms=None, mutation=None, options=None): argument 465 def mutateAtomsDictionary_old(protein, atoms=None, mutation=None, options=None): argument 733 def recastIntoDictionary(input_mutation=None, alignment=None, protein=None, chains=None): argument 1009 def mutateAtomsDictionaryUsingOverlap(protein=None, atoms=None, mutation=None, options=None): argument 1156 def makeCompositeAtomsDictionary(protein=None, pdbfiles=None, options=None): argument
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H A D | calculator.py | 356 def BackBoneReorganization(protein): argument 378 def TmProfile(protein, reference="neutral", grid=[0., 14., 0.1], Tm=None, Tms=None, ref=None, optio… argument 421 def ChargeProfile(protein, options=None): argument 434 def pI(protein, pI=7.0, options=None): argument 476 def bracketingPI(protein, bracket=[0.0, 14.0]): argument
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H A D | protonator.py | 77 def protonate(self, protein=None): argument 336 def protonate(self, protein=None): argument 345 def protonate_protein(self, protein): argument 404 def remove_all_hydrogen_atoms_from_protein(self, protein): argument 432 def set_charges(self, protein, standard_protonation_states = 1): argument
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H A D | protonate.py | 102 def protonate_protein(self, protein): argument 168 def remove_all_hydrogen_atoms_from_protein(self, protein): argument 195 def set_charges(self, protein, standard_protonation_states = 1): argument
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/dports/science/py-oddt/oddt-0.7/oddt/scoring/descriptors/ |
H A D | __init__.py | 87 protein=None, argument 149 def build(self, ligands, protein=None): argument 217 protein=None, argument 246 def build(self, ligands, protein=None): argument 319 def __init__(self, protein=None, vina_scores=None): argument 330 def set_protein(self, protein): argument 334 def build(self, ligands, protein=None): argument 364 def __init__(self, protein=None, vina_scores=None): argument 384 def set_protein(self, protein): argument 388 def build(self, ligands, protein=None): argument
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H A D | binana.py | 15 def __init__(self, protein=None): argument 182 def set_protein(self, protein): argument 196 def build(self, ligands, protein=None): argument
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/dports/biology/jalview/jalview/test/jalview/util/ |
H A D | MapListTest.java | 265 int[] protein = new int[] { 1, 4 }; in testLocateInFrom_noIntrons() local 296 int[] protein = { 1, 4 }; in testLocateInFrom_withIntrons() local 317 int[] protein = { 11, 14 }; in testGetOverlapsInFrom_withIntrons() local 352 int[] protein = { 1, 1, 3, 4, 6, 6 }; in testGetOverlapsInTo_withIntrons() local 395 int[] protein = new int[] { 1, 4 }; in testLocateInTo_noIntrons() local 437 int[] protein = { 1, 1, 3, 4, 6, 6 }; in testLocateInTo_withIntrons() local 471 int[] protein = new int[] { 1, 4 }; in testEquals() local 533 int[] protein = { 1, 1, 3, 4, 6, 6 }; in testConstructor() local 578 int[] protein = { 1, 1, 2, 3, 6, 6 }; in testConstructor_mergeRanges() local 621 int[] protein = { 1, 1, 3, 4, 6, 6 }; in testGetInverse() local [all …]
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H A D | MappingUtilsTest.java | 229 AlignmentI protein = loadAlignment(">Seq1\nK\n>Seq2\nL\n>Seq3\nQ\n", in testMapSequenceGroup_sequences() local 396 AlignmentI protein = loadAlignment( in setupMappedAlignments() local 520 AlignmentI protein = loadAlignment(">Seq1\nKA\n>Seq2\nLQ\n>Seq3\nQV\n", in testMapSequenceGroup_columns() local 604 AlignmentI protein = loadAlignment( in testMapSequenceGroup_region() local 838 SequenceI protein = new Sequence("Seq2", "-T-AS", 5, 7); in testMapEditCommand() local 1412 AlignmentI protein = new Alignment( in testMapSequenceGroup_sharedDataset() local
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/dports/science/cdk/cdk-cdk-2.3/storage/pdb/src/main/java/org/openscience/cdk/tools/ |
H A D | ProteinBuilderTool.java | 60 …public static IBioPolymer addAminoAcidAtNTerminus(IBioPolymer protein, IAminoAcid aaToAdd, IStrand… in addAminoAcidAtNTerminus() 84 …public static IBioPolymer addAminoAcidAtCTerminus(IBioPolymer protein, IAminoAcid aaToAdd, IStrand… in addAminoAcidAtCTerminus() 130 IBioPolymer protein = builder.newInstance(IBioPolymer.class); in createProtein() local 167 … private static IBioPolymer addAminoAcid(IBioPolymer protein, IAminoAcid aaToAdd, IStrand strand) { in addAminoAcid()
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/dports/science/cdk/cdk-cdk-2.3/descriptor/qsarprotein/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/ |
H A D | AminoAcidCountDescriptorTest.java | 48 IBioPolymer protein = ProteinBuilderTool.createProtein("ARNDCFQEGHIPLKMSTYVW", in testAACount() local 61 …IBioPolymer protein = ProteinBuilderTool.createProtein("FF", SilentChemObjectBuilder.getInstance()… in testFCount() local 71 …IBioPolymer protein = ProteinBuilderTool.createProtein("TT", SilentChemObjectBuilder.getInstance()… in testTCount() local
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/dports/biology/wise/wise2.4.1/src/dynlibsrc/ |
H A D | protein.tex | 1 \section{protein} section in \\numhead0{#1} 9 \subsection{Object Protein}
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/dports/science/py-oddt/oddt-0.7/oddt/docking/ |
H A D | AutodockVina.py | 21 protein=None, argument 144 def set_protein(self, protein): argument 172 def score(self, ligands, protein=None): argument 218 def dock(self, ligands, protein=None): argument
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/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/pdb2pqr/propka30/ |
H A D | compare.py | 45 def compareWithExperiment(protein, file=None, list=None, set=None, label="ALL", **argv): argument 144 def printDesolvationDistances(protein): argument
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/dports/science/py-oddt/oddt-0.7/oddt/ |
H A D | fingerprints.py | 32 def InteractionFingerprint(ligand, protein, strict=True): argument 110 def SimpleInteractionFingerprint(ligand, protein, strict=True): argument 578 def SPLIF(ligand, protein, depth=1, size=4096, distance_cutoff=4.5): argument 708 def PLEC(ligand, protein, depth_ligand=2, depth_protein=4, distance_cutoff=4.5, argument
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H A D | virtualscreening.py | 170 def similarity(self, method, query, cutoff=0.9, protein=None): argument 230 def dock(self, engine, protein, *args, **kwargs): argument 254 def score(self, function, protein=None, *args, **kwargs): argument
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H A D | datasets.py | 124 def protein(self): member in _pdbbind_id 230 def protein(self): member in _dude_target 430 def protein(self): member in _CASFTarget
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/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/pdb2pqr/pdb2pka/ |
H A D | apbs.py | 75 def runAPBS(self,protein, inputpath, routines, CM=None): argument 307 def get_potentials(self,protein): argument
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/blast/seqdb_writer/ |
H A D | writedb_files.cpp | 268 bool protein, in CWriteDB_IndexFile() 412 bool protein, in CWriteDB_HeaderFile() 425 bool protein, in CWriteDB_SequenceFile()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/blast/seqdb_writer/ |
H A D | writedb_files.cpp | 268 bool protein, in CWriteDB_IndexFile() 412 bool protein, in CWriteDB_HeaderFile() 425 bool protein, in CWriteDB_SequenceFile()
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/dports/science/cdk/cdk-cdk-2.3/storage/pdb/src/test/java/org/openscience/cdk/tools/ |
H A D | ProteinBuilderToolTest.java | 35 …IBioPolymer protein = ProteinBuilderTool.createProtein("GAGA", SilentChemObjectBuilder.getInstance… in testCreateProtein() local
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/dports/biology/exonerate/exonerate-2.4.0/test/data/ |
H A D | Makefile.am | 2 SUBDIRS = cdna protein subdir
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/dports/science/py-oddt/oddt-0.7/tests/ |
H A D | test_surface.py | 14 protein = next(oddt.toolkit.readfile('pdb', os.path.join( variable
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/dports/biology/jalview/jalview/src/jalview/appletgui/ |
H A D | SplitFrame.java | 76 AlignmentViewport protein = !topAlignment.isNucleotide() ? topViewport in init() local 122 AlignmentViewport protein = cdna == topFrame.viewport in adjustLayout() local
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/dports/misc/nut/nut-20.1/fltk/ |
H A D | NutCharts.h | 34 float protein[1001]; variable
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