moleculekit.tools package

Subpackages

• moleculekit.tools.obabel_tools package
  • Submodules
    • moleculekit.tools.obabel_tools.obabel_cli module
      • getOpenBabelProperties()
  • Module contents
    • getOpenBabelProperties()
    • openbabelConvert()

Submodules

• moleculekit.tools.atomnames module
  • canonicalizeAtomNames()
• moleculekit.tools.atomtyper module
  • atomtypingValidityChecks()
  • getFeatures()
  • getPDBQTAtomType()
  • getPDBQTAtomTypesAndCharges()
  • parallel()
  • prepareProteinForAtomtyping()
• moleculekit.tools.autosegment module
  • autoSegment()
  • autoSegment2()
• moleculekit.tools.backbone module
  • MissingBackboneError
  • check_backbone()
• moleculekit.tools.crystalpacking module
  • generateCrystalPacking()
• moleculekit.tools.detect module
  • connected_component_subgraphs()
  • detectEquivalentAtoms()
  • detectParameterizableCores()
  • detectParameterizableDihedrals()
  • rooted_tree_isomorphism()
• moleculekit.tools.docking module
  • dock()
• moleculekit.tools.glycans module
  • GlycanResidueInfo
    • GlycanResidueInfo.linked_positions
    • GlycanResidueInfo.anchor_res
    • GlycanResidueInfo.anchor_atom
    • GlycanResidueInfo.free_reducing_end
    • GlycanResidueInfo.anchor_atom
    • GlycanResidueInfo.anchor_res
    • GlycanResidueInfo.free_reducing_end
    • GlycanResidueInfo.linked_positions
  • SugarTemplate
    • SugarTemplate.letter
    • SugarTemplate.anomer
    • SugarTemplate.anomeric_carbon
    • SugarTemplate.anomeric_oxygen
    • SugarTemplate.atom_renames
    • SugarTemplate.anomer
    • SugarTemplate.anomeric_carbon
    • SugarTemplate.anomeric_oxygen
    • SugarTemplate.atom_renames
    • SugarTemplate.letter
  • analyzeGlycanResidues()
  • glycamResname()
  • glycamUnitMask()
  • glycanBondsFromNames()
  • linkedPositionsFromGlycamResname()
  • pdbSugarMask()
• moleculekit.tools.graphalignment module
  • compareGraphs()
  • createProductGraph()
  • makeMolGraph()
  • maximalSubstructureAlignment()
  • mcsAtomMatching()
• moleculekit.tools.hhblitsprofile module
  • getSequenceProfile()
• moleculekit.tools.modelling module
  • detectBackboneBreaks()
  • detectSequenceGaps()
  • detectSplicedClashes()
  • model_gaps()
  • prepareGapModellingInput()
  • spliceMissingResidues()
• moleculekit.tools.moleculechecks module
  • areLigandsDocked()
  • areLigandsOptimized()
  • closestDistance()
  • isLigandDocked()
  • isLigandOptimized()
  • isProteinProtonated()
  • proteinHasBonds()
• moleculekit.tools.mutate module
  • mutate_residue()
• moleculekit.tools.nonstandard_residues module
  • ChainResidueSpec
    • ChainResidueSpec.anchor_atom
    • ChainResidueSpec.is_c_term
    • ChainResidueSpec.is_n_term
    • ChainResidueSpec.new_resname
    • ChainResidueSpec.residue
    • ChainResidueSpec.resname
  • CovalentLigandSpec
    • CovalentLigandSpec.residue
    • CovalentLigandSpec.resname
  • GlycanSpec
    • GlycanSpec.anchor_atom
    • GlycanSpec.anchor_new_resname
    • GlycanSpec.anchor_residue
    • GlycanSpec.atom_renames
    • GlycanSpec.free_reducing_end
    • GlycanSpec.new_resname
    • GlycanSpec.residue
    • GlycanSpec.resname
  • LigandSpec
    • LigandSpec.residue
    • LigandSpec.resname
  • ScaffoldSpec
    • ScaffoldSpec.residue
    • ScaffoldSpec.resname
  • TemplateMismatchReport
    • TemplateMismatchReport.copies
    • TemplateMismatchReport.formula
    • TemplateMismatchReport.heavy_atoms_structure
    • TemplateMismatchReport.heavy_atoms_template
    • TemplateMismatchReport.name
    • TemplateMismatchReport.resname
  • applyResidueTemplates()
  • detectNonStandardResidues()
  • diagnoseTemplateMismatch()
  • geometric_interresidue_links()
  • getResidueMask()
  • infer_nonstandard_junction_bonds()
  • requiresTemplate()
  • residuesRequiringTemplate()
• moleculekit.tools.preparation module
  • MissingTopologyError
  • systemPrepare()
• moleculekit.tools.preparation_customres module
  • CustomNucleicResidue
    • CustomNucleicResidue.letter_code()
    • CustomNucleicResidue.set_state()
  • CustomResidue
    • CustomResidue.letter_code()
  • CustomSugarResidue
    • CustomSugarResidue.letter_code()
    • CustomSugarResidue.set_state()
• moleculekit.tools.residue_titration module
  • capNonstandardResiduesForTitration()
  • templatesFromTitration()
• moleculekit.tools.sequencestructuralalignment module
  • sequenceStructureAlignment()
• moleculekit.tools.survey module
  • SurveyReport
    • SurveyReport.candidate_pdbid
    • SurveyReport.chains
    • SurveyReport.gaps
    • SurveyReport.membrane
    • SurveyReport.mismatches
    • SurveyReport.nonstandard
    • SurveyReport.outdir
    • SurveyReport.pdbid
    • SurveyReport.skipped_ncaa_chains
    • SurveyReport.structure
    • SurveyReport.termini
    • SurveyReport.unresolved
  • VerifyReport
    • VerifyReport.breaks
    • VerifyReport.caps
    • VerifyReport.caps_extra
    • VerifyReport.caps_missing
    • VerifyReport.clean
    • VerifyReport.reference
    • VerifyReport.residues_in
    • VerifyReport.residues_out
    • VerifyReport.result
  • surveyStructure()
  • verifyBuildResult()
• moleculekit.tools.termini module
  • CAP_VOCABULARY
  • detectTermini()
• moleculekit.tools.voxeldescriptors module
  • getCenters()
  • getChannels()
  • getVoxelDescriptors()
  • rotateCoordinates()
  • viewVoxelFeatures()

Module contents