In process

uibcdf · Jul 3, 2023 · 7b9999f · 7b9999f
1 parent 2c54148
commit 7b9999f
Show file tree

Hide file tree

Showing 172 changed files with 2,605 additions and 241 deletions.
diff --git a/docs/api/element/group/api_group.md b/docs/api/element/group/api_group.md
@@ -71,12 +71,12 @@ API of the set of functions to examine waters.
 
    amino_acid/api_amino_acid.rst
    ion/api_ion.rst
-   lipid/lipid.rst
-   nucleotide/nucleotide.rst
-   saccharide/saccharide.rst
-   small_molecule/small_molecule.rst
-   terminal_capping/terminal_capping.rst
-   water/water.rst
+   lipid/api_lipid.rst
+   nucleotide/api_nucleotide.rst
+   saccharide/api_saccharide.rst
+   small_molecule/api_small_molecule.rst
+   terminal_capping/api_terminal_capping.rst
+   water/api_water.rst
 ```
 
 

diff --git a/docs/api/element/group/saccharide/api_saccharide.rst b/docs/api/element/group/saccharide/api_saccharide.rst
@@ -0,0 +1,10 @@
+API Saccharide
+==============
+
+.. currentmodule:: molsysmt.element.group.saccharide
+
+.. autosummary::
+   :toctree: autosummary
+
+   is_saccharide
+
diff --git a/...roup/saccharide/autosummary/molsysmt.element.group.saccharide.is_saccharide.rst b/...roup/saccharide/autosummary/molsysmt.element.group.saccharide.is_saccharide.rst
@@ -0,0 +1,6 @@
+molsysmt.element.group.saccharide.is\_saccharide
+================================================
+
+.. currentmodule:: molsysmt.element.group.saccharide
+
+.. autofunction:: is_saccharide
diff --git a/docs/api/form/MDAnalysis_Topology/api_MDAnalysis_Topology.rst b/docs/api/form/MDAnalysis_Topology/api_MDAnalysis_Topology.rst
@@ -13,8 +13,7 @@ MDAnalysis.Topology
    get
    has_attribute
    is_form
-   StructuresIterator
-   TopologicalIterator
+   TopologyIterator
    merge
    set
 
diff --git a/...sis_Topology/autosummary/molsysmt.form.MDAnalysis_Topology.TopologyIterator.rst b/...sis_Topology/autosummary/molsysmt.form.MDAnalysis_Topology.TopologyIterator.rst
@@ -0,0 +1,22 @@
+molsysmt.form.MDAnalysis\_Topology.TopologyIterator
+===================================================
+
+.. currentmodule:: molsysmt.form.MDAnalysis_Topology
+
+.. autoclass:: TopologyIterator
+
+
+   .. automethod:: __init__
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~TopologyIterator.__init__
+
+
+
+
+
+
diff --git a/docs/api/form/MDAnalysis_Universe/api_MDAnalysis_Universe.rst b/docs/api/form/MDAnalysis_Universe/api_MDAnalysis_Universe.rst
@@ -14,7 +14,7 @@ MDAnalysis.Universe
    has_attribute
    is_form
    StructuresIterator
-   TopologicalIterator
+   TopologyIterator
    merge
    set
    to_file_pdb

diff --git a/...sis_Universe/autosummary/molsysmt.form.MDAnalysis_Universe.TopologyIterator.rst b/...sis_Universe/autosummary/molsysmt.form.MDAnalysis_Universe.TopologyIterator.rst
@@ -0,0 +1,22 @@
+molsysmt.form.MDAnalysis\_Universe.TopologyIterator
+===================================================
+
+.. currentmodule:: molsysmt.form.MDAnalysis_Universe
+
+.. autoclass:: TopologyIterator
+
+
+   .. automethod:: __init__
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~TopologyIterator.__init__
+
+
+
+
+
+
diff --git a/docs/api/form/XYZ/api_XYZ_text.rst → docs/api/form/XYZ/api_XYZ.rst b/docs/api/form/XYZ/api_XYZ_text.rst → docs/api/form/XYZ/api_XYZ.rst
@@ -14,7 +14,7 @@ XYZ
    has_attribute
    is_form
    StructuresIterator
-   TopologicalIterator
+   TopologyIterator
    merge
    set
    to_file_xyznpy

diff --git a/docs/api/form/XYZ/autosummary/molsysmt.form.XYZ.TopologyIterator.rst b/docs/api/form/XYZ/autosummary/molsysmt.form.XYZ.TopologyIterator.rst
@@ -0,0 +1,22 @@
+molsysmt.form.XYZ.TopologyIterator
+==================================
+
+.. currentmodule:: molsysmt.form.XYZ
+
+.. autoclass:: TopologyIterator
+
+
+   .. automethod:: __init__
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~TopologyIterator.__init__
+
+
+
+
+
+
diff --git a/docs/api/form/api_form.rst b/docs/api/form/api_form.rst
@@ -22,8 +22,8 @@ Form
    file_trjpk/api_file_trjpk.rst
    file_xtc/api_file_xtc.rst
    file_xyznpy/api_file_xyznpy.rst
-   mdanalysis_Topology/api_mdanalysis_Topology.rst
-   mdanalysis_Universe/api_mdanalysis_Universe.rst
+   MDAnalysis_Topology/api_MDAnalysis_Topology.rst
+   MDAnalysis_Universe/api_MDAnalysis_Universe.rst
    mdtraj_DCDTrajectoryFile/api_mdtraj_DCDTrajectoryFile.rst
    mdtraj_HDF5TrajectoryFile/api_mdtraj_HDF5TrajectoryFile.rst
    mdtraj_Topology/api_mdtraj_Topology.rst

diff --git a/docs/api/form/biopython_Seq/api_biopython_Seq.rst b/docs/api/form/biopython_Seq/api_biopython_Seq.rst
@@ -12,7 +12,7 @@ biopython.Seq
    get
    has_attribute
    is_form
-   TopologicalIterator
+   TopologyIterator
    merge
    set
    to_biopython_SeqRecord

diff --git a/...form/biopython_Seq/autosummary/molsysmt.form.biopython_Seq.TopologyIterator.rst b/...form/biopython_Seq/autosummary/molsysmt.form.biopython_Seq.TopologyIterator.rst
@@ -0,0 +1,22 @@
+molsysmt.form.biopython\_Seq.TopologyIterator
+=============================================
+
+.. currentmodule:: molsysmt.form.biopython_Seq
+
+.. autoclass:: TopologyIterator
+
+
+   .. automethod:: __init__
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~TopologyIterator.__init__
+
+
+
+
+
+
diff --git a/docs/api/form/biopython_SeqRecord/api_biopython_SeqRecord.rst b/docs/api/form/biopython_SeqRecord/api_biopython_SeqRecord.rst
@@ -7,12 +7,11 @@ biopython.SeqRecord
    :toctree: autosummary
 
    add
-   copy
    extract
    get
    has_attribute
    is_form
-   TopologicalIterator
+   TopologyIterator
    merge
    set
 
diff --git a/...on_SeqRecord/autosummary/molsysmt.form.biopython_SeqRecord.TopologyIterator.rst b/...on_SeqRecord/autosummary/molsysmt.form.biopython_SeqRecord.TopologyIterator.rst
@@ -0,0 +1,22 @@
+molsysmt.form.biopython\_SeqRecord.TopologyIterator
+===================================================
+
+.. currentmodule:: molsysmt.form.biopython_SeqRecord
+
+.. autoclass:: TopologyIterator
+
+
+   .. automethod:: __init__
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~TopologyIterator.__init__
+
+
+
+
+
+
diff --git a/docs/api/form/file_crd/api_file_crd.rst b/docs/api/form/file_crd/api_file_crd.rst
@@ -14,7 +14,7 @@ file:crd
    has_attribute
    is_form
    StructuresIterator
-   TopologicalIterator
+   TopologyIterator
    merge
    set
    to_molsysmt_MolSys

diff --git a/docs/api/form/file_crd/autosummary/molsysmt.form.file_crd.TopologyIterator.rst b/docs/api/form/file_crd/autosummary/molsysmt.form.file_crd.TopologyIterator.rst
@@ -0,0 +1,22 @@
+molsysmt.form.file\_crd.TopologyIterator
+========================================
+
+.. currentmodule:: molsysmt.form.file_crd
+
+.. autoclass:: TopologyIterator
+
+
+   .. automethod:: __init__
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~TopologyIterator.__init__
+
+
+
+
+
+
diff --git a/docs/api/form/file_dcd/api_file_dcd.rst b/docs/api/form/file_dcd/api_file_dcd.rst
@@ -14,7 +14,6 @@ file:dcd
    has_attribute
    is_form
    StructuresIterator
-   TopologicalIterator
    merge
    set
    to_mdtraj_DCDTrajectoryFile

diff --git a/docs/api/form/file_gro/api_file_gro.rst b/docs/api/form/file_gro/api_file_gro.rst
@@ -14,7 +14,7 @@ file:gro
    has_attribute
    is_form
    StructuresIterator
-   TopologicalIterator
+   TopologyIterator
    merge
    set
    to_mdtraj_GroTrajectoryFile

diff --git a/docs/api/form/file_gro/autosummary/molsysmt.form.file_gro.TopologyIterator.rst b/docs/api/form/file_gro/autosummary/molsysmt.form.file_gro.TopologyIterator.rst
@@ -0,0 +1,22 @@
+molsysmt.form.file\_gro.TopologyIterator
+========================================
+
+.. currentmodule:: molsysmt.form.file_gro
+
+.. autoclass:: TopologyIterator
+
+
+   .. automethod:: __init__
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~TopologyIterator.__init__
+
+
+
+
+
+
diff --git a/docs/api/form/file_h5/api_file_h5.rst b/docs/api/form/file_h5/api_file_h5.rst
@@ -14,16 +14,16 @@ file:h5
    has_attribute
    is_form
    StructuresIterator
-   TopologicalIterator
+   TopologyIterator
    merge
    set
-   to_file_pdb.py
-   to_mdtraj_HDF5TrajectoryFile.py
-   to_mdtraj_Topology.py
-   to_mdtraj_Trajectory.py
-   to_molsysmt_MolSys.py
-   to_molsysmt_Structures.py
-   to_molsysmt_Topology.py
-   to_nglview_NGLWidget.py
-   to_openmm_Topology.py
+   to_file_pdb
+   to_mdtraj_HDF5TrajectoryFile
+   to_mdtraj_Topology
+   to_mdtraj_Trajectory
+   to_molsysmt_MolSys
+   to_molsysmt_Structures
+   to_molsysmt_Topology
+   to_nglview_NGLWidget
+   to_openmm_Topology
 
diff --git a/docs/api/form/file_h5/autosummary/molsysmt.form.file_h5.TopologyIterator.rst b/docs/api/form/file_h5/autosummary/molsysmt.form.file_h5.TopologyIterator.rst
@@ -0,0 +1,22 @@
+molsysmt.form.file\_h5.TopologyIterator
+=======================================
+
+.. currentmodule:: molsysmt.form.file_h5
+
+.. autoclass:: TopologyIterator
+
+
+   .. automethod:: __init__
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~TopologyIterator.__init__
+
+
+
+
+
+
diff --git a/docs/api/form/file_h5/autosummary/molsysmt.form.file_h5.to_file_pdb.rst b/docs/api/form/file_h5/autosummary/molsysmt.form.file_h5.to_file_pdb.rst
@@ -0,0 +1,6 @@
+molsysmt.form.file\_h5.to\_file\_pdb
+====================================
+
+.. currentmodule:: molsysmt.form.file_h5
+
+.. autofunction:: to_file_pdb
diff --git a/...form/file_h5/autosummary/molsysmt.form.file_h5.to_mdtraj_HDF5TrajectoryFile.rst b/...form/file_h5/autosummary/molsysmt.form.file_h5.to_mdtraj_HDF5TrajectoryFile.rst
@@ -0,0 +1,6 @@
+molsysmt.form.file\_h5.to\_mdtraj\_HDF5TrajectoryFile
+=====================================================
+
+.. currentmodule:: molsysmt.form.file_h5
+
+.. autofunction:: to_mdtraj_HDF5TrajectoryFile
diff --git a/docs/api/form/file_h5/autosummary/molsysmt.form.file_h5.to_mdtraj_Topology.rst b/docs/api/form/file_h5/autosummary/molsysmt.form.file_h5.to_mdtraj_Topology.rst
@@ -0,0 +1,6 @@
+molsysmt.form.file\_h5.to\_mdtraj\_Topology
+===========================================
+
+.. currentmodule:: molsysmt.form.file_h5
+
+.. autofunction:: to_mdtraj_Topology
diff --git a/docs/api/form/file_h5/autosummary/molsysmt.form.file_h5.to_mdtraj_Trajectory.rst b/docs/api/form/file_h5/autosummary/molsysmt.form.file_h5.to_mdtraj_Trajectory.rst
@@ -0,0 +1,6 @@
+molsysmt.form.file\_h5.to\_mdtraj\_Trajectory
+=============================================
+
+.. currentmodule:: molsysmt.form.file_h5
+
+.. autofunction:: to_mdtraj_Trajectory
diff --git a/docs/api/form/file_h5/autosummary/molsysmt.form.file_h5.to_molsysmt_MolSys.rst b/docs/api/form/file_h5/autosummary/molsysmt.form.file_h5.to_molsysmt_MolSys.rst
@@ -0,0 +1,6 @@
+molsysmt.form.file\_h5.to\_molsysmt\_MolSys
+===========================================
+
+.. currentmodule:: molsysmt.form.file_h5
+
+.. autofunction:: to_molsysmt_MolSys
diff --git a/docs/api/form/file_h5/autosummary/molsysmt.form.file_h5.to_molsysmt_Structures.rst b/docs/api/form/file_h5/autosummary/molsysmt.form.file_h5.to_molsysmt_Structures.rst
@@ -0,0 +1,6 @@
+molsysmt.form.file\_h5.to\_molsysmt\_Structures
+===============================================
+
+.. currentmodule:: molsysmt.form.file_h5
+
+.. autofunction:: to_molsysmt_Structures