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Installation
HTMD
Moleculekit
ACEMD
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PlayMolecule Viewer
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Installation
HTMD
Moleculekit
ACEMD
PlayMolecule
More
PlayMolecule Viewer
JobQueues
Help
Internal Docs
Twitter
GitHub
LinkedIn
Youtube
Medium
Section Navigation
Installation
The Molecule class
The SmallMol class
Molecule tools
Protein segmentation: Automatically detects and assigns segments in proteins
Protein preparation: Protonates proteins and optimizes hbond networks
Sequence profile: Calculates a protein sequence profile using HHBlits
Sequence-based structure alignment: Aligns two protein structures by their sequence alignment
Voxel Descriptors: Calculates 3D voxels channels containing features of a Molecule or SmallMol
Maximal substructure alignment: Aligns two small molecules by their maximal substructure
Projections
MetricCoordinate: xyz coordinate projection
MetricDihedral: dihedral angles projection
MetricDistance: atom distances/contacts projection
MetricFluctuation: atom position fluctuations
MetricPlumed2: support for Plumed2 projections
MetricRmsd: root mean square deviation of structures to a reference
MetricSasa: solvent accessible surface area projection
MetricSecondaryStructure: protein secondary structure projection
MetricShell: density of atoms in shells around other atoms
MetricSphericalCoordinate: spherical coordinates of two COMs
MetricTMscore: TMscore projection
Tutorials
Voxelization
API
moleculekit.atomselect package
moleculekit.atomselect.analyze module
moleculekit.atomselect.atomselect module
moleculekit.atomselect.languageparser module
moleculekit.fileformats package
moleculekit.fileformats.netcdf module
moleculekit.fileformats.utils module
moleculekit.interactions package
moleculekit.interactions.interactions module
moleculekit.pdbx package
moleculekit.pdbx.reader package
moleculekit.pdbx.reader.BinaryCifReader module
moleculekit.pdbx.reader.PdbxContainers module
moleculekit.pdbx.reader.PdbxParser module
moleculekit.pdbx.reader.PdbxReader module
moleculekit.pdbx.tests package
moleculekit.pdbx.tests.PdbxReadWriteTests module
moleculekit.pdbx.tests.PdbxReaderTests module
moleculekit.pdbx.tests.PdbxWriterTests module
moleculekit.pdbx.writer package
moleculekit.pdbx.writer.PdbxWriter module
moleculekit.ply package
moleculekit.ply.lex module
moleculekit.ply.yacc module
moleculekit.projections package
moleculekit.projections.metriccoordinate module
moleculekit.projections.metricdihedral module
moleculekit.projections.metricdistance module
moleculekit.projections.metricfluctuation module
moleculekit.projections.metricgyration module
moleculekit.projections.metricplumed2 module
moleculekit.projections.metricrmsd module
moleculekit.projections.metricsasa module
moleculekit.projections.metricsecondarystructure module
moleculekit.projections.metricshell module
moleculekit.projections.metricsphericalcoordinate module
moleculekit.projections.metrictmscore module
moleculekit.projections.projection module
moleculekit.projections.util module
moleculekit.smallmol package
moleculekit.smallmol.tools package
moleculekit.smallmol.tools.clustering module
moleculekit.smallmol.tools.restrainedembed module
moleculekit.smallmol.tools.test_tools module
moleculekit.smallmol.smallmol module
moleculekit.smallmol.smallmolcdp module
moleculekit.smallmol.smallmollib module
moleculekit.smallmol.test_smallmol module
moleculekit.smallmol.test_smallmollib module
moleculekit.smallmol.util module
moleculekit.tools package
moleculekit.tools.obabel_tools package
moleculekit.tools.obabel_tools.obabel_cli module
moleculekit.tools.atomtyper module
moleculekit.tools.autosegment module
moleculekit.tools.crystalpacking module
moleculekit.tools.detect module
moleculekit.tools.docking module
moleculekit.tools.graphalignment module
moleculekit.tools.hhblitsprofile module
moleculekit.tools.modelling module
moleculekit.tools.moleculechecks module
moleculekit.tools.preparation module
moleculekit.tools.preparation_customres module
moleculekit.tools.sequencestructuralalignment module
moleculekit.tools.voxeldescriptors module
moleculekit.align module
moleculekit.bondguesser module
moleculekit.config module
moleculekit.dihedral module
moleculekit.distance module
moleculekit.home module
moleculekit.molecule module
moleculekit.opm module
moleculekit.periodictable module
moleculekit.pymolgraphics module
moleculekit.rcsb module
moleculekit.rdkitintegration module
moleculekit.readers module
moleculekit.util module
moleculekit.version module
moleculekit.viewer module
moleculekit.vmdgraphics module
moleculekit.vmdviewer module
moleculekit.writers module
Moleculekit
Tutorials
Tutorials
#
Some tutorials to help you get started with moleculekit.
Contents
#
Voxelization
On this page
Contents
