bundle_info.xml

<BundleInfo name="SEQCROW" 
            customInit="true"
            minSessionVersion="3"
            maxSessionVersion="3"
            package="SEQCROW"
            purePython="true"
            version="1.8.3">
            
            <Author>QChASM</Author>
            <Email>catalysttrends@uga.edu</Email>
            <URL>http://qchasm.wheelergroupresearch.com/</URL>
            <License>license.txt</License>
            <Synopsis>Structure Editing and Quantum Chemical Representation and Organization for Workflows</Synopsis>
            <Description>SEQCROW is an AaronTools-based bundle for ChimeraX. 

            ## File Types
            * Open XYZ, Gaussian input and output, ORCA output, and Psi4 output files
            * Save atomic models to XYZ files
            * A tool is also available to save Gaussian, ORCA, or Psi4 input files
            
            ## Tools
            ### AaronTools
            * <b>Add to Personal Library</b> - add substituents, ligands, or rings to your personal AaronTools library
            * <b>Browse AaronTools</b> - browse substituents, ligands, and rings in the AaronTools library
            * <b>Build QM Input</b> - build Gaussian, ORCA, Psi4, or SQM input files
            * <b>Process QM Thermochemistry</b> - compute thermal corrections for models with vibrational mode information
            * <b>Structure Modification</b> - modify your structure using components from the AaronTools libraries (substituents, ligands, ring fragments)
            * <b>Visualize Normal Modes</b> - display normal modes for models with vibrational mode information as vectors or an animation
            * <b>File Info</b> - list most of the info AaronTools parses from output files
            
            ### SEQCROW
            * <b>Job Queue</b> - manage QM jobs that are run with SEQCROW
            * <b>Managed Models</b> - restore models opened through SEQCROW to their original state
            
            ### Structure Editing
            * <b>Bond Editor</b> - draw or erase bonds and TS bonds, and change bond lengths
            * <b>Coordination Complex Generator</b> - Generate coordination complexes
            
            ### Structure Analysis
            * <b>Sterimol</b> - determine the L, B<sub>1</sub>-B<sub>5</sub> Sterimol parameters for a selected substituent 
            * <b>Cone Angle</b> - determine the cone angle for ligands 
            * <b>Buried Volume</b> - calculate buried volume around a reaction center
            
            ### Selectors
            * <b>tm</b> - select all transition metals
            * several substituent selectors, including <b>Me</b>, <b>Ph</b>, and <b>iPr</b>
            
            ## Graphical Presets
            * <b>ball-stick-endcap</b> - all non-H atoms are represented as balls and sticks; H atoms are represented as sticks/endcaps
            * <b>index labels</b> - label each atom with its index (1-indexed)
            * <b>sticks</b> - all atoms are represented as sticks/endcaps
            * <b>vdw</b> - space filling representation
            
            ## Commands
            * <b>rmsdAlign</b> - calculate RMSD and align molecular structures, similar to ChimeraX's built-in `align` command
            * <b>substitute</b> - add or change substituents
            * <b>fuseRing</b> - attach a ring to a structure
            * <b>angle</b> - print the angle defined by three atoms to the log
            * <b>dihedral</b> - print the torsional angle defined by four atoms to the log
            * <b>tsbond</b> - display forming/breaking bond as semi-transparent
            * <b>highlight</b> - outline atoms or bonds
            * <b>lookDown</b> - align the vector between two atoms along the x, y, or z axis
            * <b>percentBuriedVolume</b> - calculate percent buried volume around a reaction center
            * <b>pointGroup</b> - determine point group of an atomic structure
            * <b>sterimol</b> - calculate sterimol parameters for substituents
            </Description>
            
            <Dependencies>
                <Dependency name="ChimeraX-Core" version="&gt;=1.3, &lt;=1.7"/>
                <Dependency name="scipy"/>
                <Dependency name="Send2Trash"/>
                <Dependency name="psutil"/>
                <Dependency name="jinja2"/>
                <!--
                bse is large and may fail to install with bad internet
                <Dependency name="basis-set-exchange"/>
                -->
                <!-- wait for numpy to fix fortran stuff in python 3.8
                I've tried installing this with just gfortran on windows, but no luck
                <Dependency name="stripy"/>
                -->
            </Dependencies>

            <Initializations>
                <InitAfter type="custom" bundle="ChimeraX-MouseModes"/>
            </Initializations>

            <Categories>
                <Category name="General"/>
                <Category name="Input/Output"/>
                <Category name="Structre Editing"/>
                <Category name="Structre Analysis"/>
                <Category name="External Program"/>
            </Categories>
            
            <Managers>
                <Manager name="filereader_manager" uiOnly="false"/>
                <Manager name="seqcrow_job_manager" uiOnly="false"/>
                <Manager name="seqcrow_qm_input_manager" uiOnly="true"/>
                <Manager name="seqcrow_cluster_scheduling_software_manager" uiOnly="true"/>
                <Manager name="Slurm" uiOnly="true"/>
                <Manager name="SGE" uiOnly="true"/>
                <Manager name="PBS" uiOnly="true"/>
                <Manager name="LSF" uiOnly="true"/>
				<Manager name="tss_finder_manager" uiOnly="true"/>
				<Manager name="conformer_search_manager" uiOnly="true"/>
            </Managers>
            
            <Providers manager="data formats">
                <Provider name="Gaussian input file" 
                          category="Molecular structure" 
                          suffixes=".com,.gjf" 
                          encoding="utf-8" 
                          nicknames="com" 
                          reference_url="http://gaussian.com/input/"
                          synopsis="Gaussian input file"
                />

                <Provider name="Gaussian output file" 
                          category="Molecular structure" 
                          suffixes=".log" 
                          encoding="utf-8" 
                          nicknames="log" 
                          synopsis="Gaussian output file"
                />

                <Provider name="ORCA output file" 
                          category="Molecular structure" 
                          suffixes=".out" 
                          encoding="utf-8" 
                          nicknames="out" 
                          synopsis="ORCA output file"
                />

                <Provider name="Psi4 output file" 
                          category="Molecular structure" 
                          suffixes=".dat,.out" 
                          encoding="utf-8" 
                          nicknames="dat" 
                          synopsis="Psi4 output file"
                />

                <Provider name="Q-Chem output file" 
                          category="Molecular structure" 
                          suffixes=".qout,.out,.dat" 
                          encoding="utf-8" 
                          nicknames="qout" 
                          synopsis="Q-Chem output file"
                />
                
                <Provider name="XYZ file" 
                          category="Molecular structure" 
                          suffixes=".xyz" 
                          encoding="utf-8" 
                          nicknames="xyz" 
                          reference_url="https://en.wikipedia.org/wiki/XYZ_file_format" 
                          synopsis="XYZ coordinate file"
                />                

				<Provider name="XYZ trajectory file" 
                          category="Molecular trajectory" 
                          suffixes=".allxyz" 
                          encoding="utf-8" 
                          nicknames="allxyz" 
                          reference_url="https://en.wikipedia.org/wiki/XYZ_file_format" 
                          synopsis="XYZ trajectory file"
                />                
                
                <Provider name="FCHK file" 
                          category="Molecular structure" 
                          suffixes=".fchk" 
                          encoding="utf-8" 
                          nicknames="fchk" 
                          reference_url="http://theochem.mercer.edu/chm295/g09ur/f_formchk.htm" 
                          synopsis="Formatted Checkpoint file"
                />

                <Provider name="sqm output file" 
                          category="Molecular structure" 
                          suffixes=".sqmout" 
                          encoding="utf-8" 
                          nicknames="sqmout" 
                          synopsis="Amber SQM output file"
                />

                <Provider name="NBO input file" 
                          category="Molecular structure" 
                          suffixes=".47" 
                          encoding="utf-8" 
                          nicknames="nbo47" 
                          synopsis="NBO input file"
                />

                <Provider name="NBO output file" 
                          category="Molecular structure" 
                          suffixes=".31" 
                          encoding="utf-8" 
                          nicknames="nbo31" 
                          synopsis="NBO output file"
                />
            </Providers>
            
            <Providers manager="open command">
                <Provider name="Gaussian input file" want_path="false"/>
                <Provider name="Gaussian output file" want_path="false"/>
                <Provider name="ORCA output file" want_path="false"/>
                <Provider name="Psi4 output file" want_path="false"/>
                <Provider name="XYZ file" want_path="false"/>
                <Provider name="XYZ trajectory file" want_path="false"/>
                <Provider name="FCHK file" want_path="false"/>
                <Provider name="sqm output file" want_path="false"/>
                <Provider name="NBO input file" want_path="true"/>
                <Provider name="NBO output file" want_path="true"/>
                <Provider name="Q-Chem output file" want_path="false"/>
            </Providers>
            
            <!--we can save Gaussian input files, but not with the save command-->
            <Providers manager="save command">
                <Provider name="XYZ file"/>
            </Providers>
            
            <Providers manager="seqcrow_job_manager">
                <Provider name="Gaussian"/>
                <Provider name="ORCA"/>
                <Provider name="Psi4"/>
                <Provider name="SQM"/>
                <Provider name="xTB"/>
                <Provider name="CREST"/>
                <!--
                <Provider name="Raven"/>
                -->
                <Provider name="ParallelRaven"/>
                <Provider name="Gaussian STQN"/>
                <Provider name="ORCA NEB"/>
                <!--
                I have not gotten Q-Chem jobs to work
                maybe something in ChimeraX's environment conflicts with Q-Chem
                -->
                <Provider name="Q-Chem FSM"/>
                <Provider name="Q-Chem"/>
            </Providers>
            
            <Providers manager="seqcrow_qm_input_manager">
                <Provider name="Gaussian"/>
                <Provider name="ORCA"/>
                <Provider name="Psi4"/>
                <Provider name="SQM"/>
                <Provider name="Q-Chem"/>
                <Provider name="xTB"/>
            </Providers>
            
            <Providers manager="test_manager">
                <Provider name="fuseRing_command"/>
                <Provider name="input_builder"/>
                <Provider name="normal_modes"/>
                <Provider name="substitute_command"/>
                <Provider name="buried_volume"/>
                <Provider name="lookDown_command"/>
                <Provider name="cone_angle"/>
                <Provider name="substituent_sterimol"/>
            </Providers>
  
            <Providers manager="seqcrow_cluster_scheduling_software_manager">
                <Provider name="Slurm"/>
                <Provider name="SGE"/>
                <Provider name="PBS"/>
                <Provider name="LSF"/>
            </Providers>
  
            <Providers manager="Slurm">
                <Provider name="Gaussian"/>
                <Provider name="ORCA"/>
                <Provider name="Psi4"/>
                <Provider name="Q-Chem"/>
                <Provider name="SQM"/>
                <Provider name="xTB"/>
                <Provider name="CREST"/>
            </Providers>
    
            <Providers manager="SGE">
                <Provider name="Gaussian"/>
                <Provider name="ORCA"/>
                <Provider name="Psi4"/>
                <Provider name="Q-Chem"/>
                <Provider name="SQM"/>
                <Provider name="xTB"/>
                <Provider name="CREST"/>
            </Providers>
      
            <Providers manager="PBS">
                <Provider name="Gaussian"/>
                <Provider name="ORCA"/>
                <Provider name="Psi4"/>
                <Provider name="Q-Chem"/>
                <Provider name="SQM"/>
                <Provider name="xTB"/>
                <Provider name="CREST"/>
            </Providers>
        
            <Providers manager="LSF">
                <Provider name="Gaussian"/>
                <Provider name="ORCA"/>
                <Provider name="Psi4"/>
                <Provider name="Q-Chem"/>
                <Provider name="SQM"/>
                <Provider name="xTB"/>
                <Provider name="CREST"/>
            </Providers>
  
            <!--
            mouse modes don't fit well if you have a smaller
            screen (laptop)
            add a new tab for SEQCROW mouse modes
            -->
            <Providers manager="toolbar">
                <!--
                <Provider tab="More Right Mouse"
                          section="Select"
                          name="mm1"
                          mouse_mode="select"
                          display_name="Select" 
                          description="Select items"
                          icon="select.png"
                />
                -->
                <Provider tab="More Right Mouse"
                          section="Select"
                          name="select_fragment"
                          mouse_mode="select fragment"
                          display_name="Select Fragment" 
                          description="Select molecular fragment"
                          icon="connected.png"
                />
                <Provider tab="More Right Mouse"
                          section="Select"
                          name="select_same"
                          mouse_mode="select similar fragments"
                          display_name="Select Same Types" 
                          description="Select molecular fragment of the clicked type"
                          icon="sel_group_icon.png"
                />
                <Provider tab="More Right Mouse"
                          section="Structure Modification"
                          name="bond"
                          mouse_mode="bond"
                          display_name="Bond" 
                          description="Draw a new bond"
                          icon="bond.png"
                />
                <Provider tab="More Right Mouse"
                          section="Structure Modification"
                          name="tsbond"
                          mouse_mode="tsbond"
                          display_name="TS Bond" 
                          description="Draw a forming/breaking bond"
                          icon="tsbond.png"
                />
                <Provider tab="More Right Mouse"
                          section="Structure Modification"
                          name="coordinationbond"
                          mouse_mode="coordinationbond"
                          display_name="Coordination Bond" 
                          description="Draw a metal coordination bond"
                          icon="coordinationbond.png"
                />
                <Provider tab="More Right Mouse"
                          section="Structure Modification"
                          name="hbonds"
                          mouse_mode="hbonds"
                          display_name="Hydrogen Bond" 
                          description="Draw a hydrogen bond"
                          icon="hbonds_icon.png"
                />
                <Provider tab="More Right Mouse"
                          section="Structure Modification"
                          name="change_element"
                          mouse_mode="change element"
                          display_name="Change Element" 
                          description="Change the element of picked atoms"
                          icon="element.png"
                />
                <Provider tab="More Right Mouse"
                          section="Structure Modification"
                          name="structure_eraser"
                          mouse_mode="structure eraser"
                          display_name="Erase Structure" 
                          description="Erase atomic structures"
                          icon="eraser.png"
                />
                <Provider tab="More Right Mouse"
                          section="Structure Modification"
                          name="substitute"
                          mouse_mode="substitute"
                          display_name="Substitute" 
                          description="Add or change substituents"
                          icon="substitute.png"
                />
            </Providers>
            
			<Providers manager="tss_finder_manager">
                <!--
				<Provider name="GPR growing string method"/>
                -->
				<Provider name="synchornous transit-guided quasi-Newton"/>
				<Provider name="nudged elastic band"/>
				<Provider name="freezing string method"/>
				<Provider name="metadynamics pathfinding"/>
			</Providers>
			
			<Providers manager="conformer_search_manager">
				<Provider name="CREST"/>
				<Provider name="CREST QCG"/>
			</Providers>
			
            <Classifiers>
                <PythonClassifier>Development Status :: 4 - Beta</PythonClassifier>
                <PythonClassifier>License :: OSI Approved :: GNU General Public License v3 (GPLv3)</PythonClassifier>
                <PythonClassifier>Framework :: ChimeraX</PythonClassifier>
                <PythonClassifier>Intended Audience :: Science/Research</PythonClassifier>
                <PythonClassifier>Natural Language :: English</PythonClassifier>
                <PythonClassifier>Programming Language :: Python :: 3</PythonClassifier>
                <PythonClassifier>Topic :: Scientific/Engineering :: Chemistry</PythonClassifier>
                <PythonClassifier>Topic :: Scientific/Engineering :: Visualization</PythonClassifier>
                
                <!-- TODO: move tools to appropriate menus -->
                <!--NOTE:
                including my own Bundle line will prevent anything after it from being loaded
                ChimeraX's devel build
                ChimeraXClassifier>ChimeraX :: Bundle :: General,Input/Output,Structure Editing,External Program :: 1,1 :: SEQCROW :: ChimAARON,SEQCRO,SEQCROW :: true</ChimeraXClassifier
                -->
                <ChimeraXClassifier>ChimeraX :: Tool :: Build QM Input                 :: Quantum Chemistry    :: Create Gaussian, ORCA, Psi4, Q-Chem, xTB, or SQM input file</ChimeraXClassifier>
                <!--
                <ChimeraXClassifier>ChimeraX :: Tool :: Structure Modification         :: AaronTools           :: Modify substituents, swap ligands, and fuse rings</ChimeraXClassifier>
                -->
                <ChimeraXClassifier>ChimeraX :: Tool :: Change Substituents            :: Structure Editing    :: Modify substituents, swap ligands, and fuse rings</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Tool :: Swap Transition Metal Ligands  :: Structure Editing    :: Modify substituents, swap ligands, and fuse rings</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Tool :: Fuse Ring                      :: Structure Editing    :: Modify substituents, swap ligands, and fuse rings</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Tool :: AaronTools Fragment Library    :: SEQCROW              :: Browse the AaronTools ligand, substituent, and ring libraries</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Tool :: Thermochemistry                :: Quantum Chemistry    :: Compute the free energy of a molecule with frequency data</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Tool :: Managed Models                 :: SEQCROW              :: see models managed by SEQCROW</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Tool :: Add to Personal Library        :: SEQCROW              :: Add to your personal ligand, substituent, and ring libraries</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Tool :: Visualize Normal Modes         :: Quantum Chemistry    :: Visualize normal modes from a frequency output file as displacement vectors or as an animation</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Tool :: Job Queue                      :: SEQCROW              :: View status of jobs</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Tool :: Substituent Sterimol           :: Structure Analysis   :: Calculate L, and B1-B5 Sterimol parameters for a substituent</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Tool :: Bond Editor                    :: Structure Editing    :: Draw or erase bonds</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Tool :: Change Element                 :: Structure Editing    :: Modify substituents, swap ligands, and fuse rings</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Tool :: Rotate Atoms                   :: Structure Editing    :: Rotate all or part of a molecular structure</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Tool :: Buried Volume                  :: Structure Analysis   :: Calculate percent buried volume</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Tool :: File Info                      :: SEQCROW              :: Miscellaneous file data</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Tool :: Cone Angle                     :: Structure Analysis   :: Calculate ligand cone angles</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Tool :: Coordination Complex Generator :: Structure Editing    :: Create coordination complexes with mono- or bidentate ligands</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Tool :: Orbital Viewer                 :: Quantum Chemistry    :: View molecular orbitals</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Tool :: Ligand Sterimol                :: Structure Analysis   :: Calculate Sterimol parameters for ligands on organo- or organometallic catalysts</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Tool :: IR Spectrum                    :: Quantum Chemistry    :: plot simulated IR spectra</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Tool :: UV/Vis Spectrum                :: Quantum Chemistry    :: plot simulated UV/vis spectra</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Tool :: 2D Builder                     :: Structure Editing    :: molecule using ChemDoodle Web Components</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Tool :: Transition State Structures    :: Structure Prediction :: locate transition state structures using the growing string method</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Tool :: Ligand Solid Angle             :: Structure Analysis   :: Calculate ligand solid angles</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Tool :: Conformer Search               :: Structure Prediction :: automated conformer search</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Tool :: Z-Matrix Builder               :: Structure Editing    :: build structure using internal coordinates</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Tool :: NMR Spectrum                   :: Quantum Chemistry    :: plot simulated NMR spectra from DFT computations</ChimeraXClassifier>
                <!--<ChimeraXClassifier>ChimeraX :: Tool :: AaronJr Input Builder          :: AaronJr            :: Create input files for AaronJr</ChimeraXClassifier>-->
                <!--ChimeraXClassifier>ChimeraX :: Tool :: AARON Input Builder :: AARON :: Build AARON input file</ChimeraXClassifier-->
                
                <ChimeraXClassifier>ChimeraX :: Selector :: tm             :: Transition metals</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: rings          :: any atoms in rings</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: Ad             :: Adamantyl substituent</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: BF2            :: Difluoroboro substituent</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: CCH            :: Alkynyl substituent</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: CF3            :: Trifluoromethyl substituent</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: CH2Cl          :: Chloromethyl substituent</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: CH2F           :: Fluoromethyl substituent</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: CH2OH          :: Hydroxymethyl substituent</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: CHCH2          :: Vinyl substituent</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: CHCl2          :: Dichloromethyl substituent</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: CHF2           :: Difluoromethyl substituent</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: CHO            :: Formyl substituent</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: CN             :: Cyano substituent</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: COCH3          :: Acetyl substituent</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: COOCH3         :: Methylcarboxyl substituent</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: Cy             :: Cyclohexyl substituent</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: Et             :: Ethyl substituent</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: iPr            :: iso-Propyl substituent</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: Me             :: Methyl substituent</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: Mes            :: Mesityl substituent</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: NH2            :: Amino substituent</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: NHOH           :: Hydroxylamino substituent</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: NO             :: Nitroso substituent</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: NO2            :: Nitro substituent</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: OCF3           :: Trifluoromethoxy substituent</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: OH             :: Hydroxyl substituent</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: OMe            :: Methoxy substituent</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: Ph             :: Phenyl substituent</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: SCH3           :: Methylthio substituent</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: SH             :: Thio substituent</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: SiF3           :: Trifluorosilyl substituent</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: SiH3           :: Silyl substituent</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: SuperMes       :: Super Mesityl substituent</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: tBu            :: tert-Butyl substituent</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: connected      :: fragment of current selection</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: chiral-centers :: chiral centers</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: spiro-centers  :: chiral centers</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: bridgehead     :: chiral centers</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: linear :: VSEPR </ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: bent :: VSEPR </ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: planar :: VSEPR </ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: t-shaped :: VSEPR </ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: trigonal-planar :: VSEPR </ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: tetrahedral :: VSEPR </ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: sawhorse :: VSEPR </ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: seesaw :: VSEPR </ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: square-planar :: VSEPR </ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: trigonal-pyramidal :: VSEPR </ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: trigonal-bipyramidal :: VSEPR </ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: square-pyramidal :: VSEPR </ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: pentagonal :: VSEPR </ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: octahedral :: VSEPR </ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: hexagonal :: VSEPR </ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: trigonal-prismatic :: VSEPR </ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: pentagonal-pyramidal :: VSEPR </ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: capped-octahedral :: VSEPR </ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: capped-trigonal-prismatic :: VSEPR </ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: heptagonal :: VSEPR </ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: hexagonal-pyramidal :: VSEPR </ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: pentagonal-bipyramidal :: VSEPR </ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: biaugmented-trigonal-prismatic :: VSEPR </ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: cubic :: VSEPR </ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: elongated-trigonal-bipyramidal :: VSEPR </ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: hexagonal-bipyramidal :: VSEPR </ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: heptagonal-pyramidal :: VSEPR </ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: octagonal :: VSEPR </ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: square-antiprismatic :: VSEPR </ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: trigonal-dodecahedral :: VSEPR </ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: capped-cube :: VSEPR </ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: capped-square-antiprismatic :: VSEPR </ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: enneagonal :: VSEPR </ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: hula-hoop :: VSEPR </ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: tridiminished-icosahedral :: VSEPR </ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: muffin :: VSEPR </ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: octagonal-pyramidal :: VSEPR </ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Selector :: tricapped-trigonal-prismatic :: VSEPR </ChimeraXClassifier>


                <!--NOTE: this synopsis will not appear when `help <command>` is used-->
                <ChimeraXClassifier>ChimeraX :: Command :: rmsdAlign           :: Structure Analysis :: Calculate RMSD between structures</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Command :: substitute          :: Structure Editing  :: change substiuents</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Command :: fuseRing            :: Structure Editing  :: fuse a ring</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Command :: tsbond              :: Structure Editing  :: display a forming/breaking bond as semi-transparent</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Command :: ~tsbond             :: Structure Editing  :: remove a forming/breaking bond</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Command :: sterimol            :: Structure Analysis :: calculate Sterimol parameters</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Command :: percentVolumeBuried :: Structure Analysis :: calculate percent volume buried by ligands around a metal center</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Command :: highlight           :: General            :: make some atoms or bonds stand out</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Command :: ~highlight          :: General            :: remove highlights</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Command :: lookDown            :: General            :: reorient molecule along bond</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Command :: pointGroup          :: General            :: print the point group of atomic structures to the log</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Command :: ligandSterimol      :: Structure Analysis :: calculate sterimol parameters for ligands on a metal center</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Command :: solidAngle          :: Structure Analysis :: calculate ligand solid angle</ChimeraXClassifier>
                <ChimeraXClassifier>ChimeraX :: Command :: force               :: Structure Analysis :: display computed force vector</ChimeraXClassifier>
       </Classifiers>
    
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        <!--
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