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* fix website links

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rasbt authored Dec 10, 2019
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190 changes: 190 additions & 0 deletions docs/api_modules/biopandas.mol2/PandasMol2.md
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## PandasMol2

*PandasMol2()*

Object for working with Tripos Mol2 structure files.

**Attributes**

- `df` : pandas.DataFrame

DataFrame of a Mol2's ATOM section


- `mol2_text` : str

Mol2 file contents in string format


- `code` : str

ID, code, or name of the molecule stored


- `pdb_path` : str

Location of the MOL2 file that was read in via `read_mol2`

### Methods

<hr>

*distance(xyz=(0.0, 0.0, 0.0))*

Computes Euclidean distance between atoms in
self.df and a 3D point.

**Parameters**

- `xyz` : tuple (0.00, 0.00, 0.00)

X, Y, and Z coordinate of the reference center for the distance
computation

**Returns**

- `pandas.Series` : Pandas Series object containing the Euclidean

distance between the atoms in the atom section and `xyz`.

<hr>

*distance_df(df, xyz=(0.0, 0.0, 0.0))*

Computes Euclidean distance between atoms and a 3D point.

**Parameters**

- `df` : DataFrame

DataFrame containing entries similar to the PandasMol2.df
format for the
the distance computation to the `xyz` reference coordinates.

- `xyz` : tuple (0.00, 0.00, 0.00)

X, Y, and Z coordinate of the reference center for the distance
computation

**Returns**

- `pandas.Series` : Pandas Series object containing the Euclidean

distance between the atoms in the atom section and `xyz`.

<hr>

*read_mol2(path, columns=None)*

Reads Mol2 files (unzipped or gzipped) from local drive

Note that if your mol2 file contains more than one molecule,
only the first molecule is loaded into the DataFrame

**Attributes**

- `path` : str

Path to the Mol2 file in .mol2 format or gzipped format (.mol2.gz)


- `columns` : dict or None (default: None)

If None, this methods expects a 9-column ATOM section that contains
the following columns:

{0:('atom_id', int), 1:('atom_name', str),
2:('x', float), 3:('y', float), 4:('z', float),
5:('atom_type', str), 6:('subst_id', int),
7:('subst_name', str), 8:('charge', float)}

If your Mol2 files are formatted differently, you can provide your
own column_mapping dictionary in a format similar to the one above.
However, note that not all assert_raise_message methods
may be supported then.

**Returns**

self

<hr>

*read_mol2_from_list(mol2_lines, mol2_code, columns=None)*

Reads Mol2 file from a list into DataFrames

**Attributes**

- `mol2_lines` : list

A list of lines containing the mol2 file contents. For example,
['@<TRIPOS>MOLECULE\n',
'ZINC38611810\n',
' 65 68 0 0 0\n',
'SMALL\n',
'NO_CHARGES\n',
'\n',
'@<TRIPOS>ATOM\n',
' 1 C1 -1.1786 2.7011 -4.0323 C.3 1 <0> -0.1537\n',
' 2 C2 -1.2950 1.2442 -3.5798 C.3 1 <0> -0.1156\n',
...]


- `mol2_code` : str or None

Name or ID of the molecule.


- `columns` : dict or None (default: None)

If None, this methods expects a 9-column ATOM section that contains
the following columns:
{0:('atom_id', int), 1:('atom_name', str),
2:('x', float), 3:('y', float), 4:('z', float),
5:('atom_type', str), 6:('subst_id', int),
7:('subst_name', str), 8:('charge', float)}
If your Mol2 files are formatted differently, you can provide your
own column_mapping dictionary in a format similar to the one above.
However, note that not all assert_raise_message methods may be
supported then.

**Returns**

self

<hr>

*rmsd(df1, df2, heavy_only=True)*

Compute the Root Mean Square Deviation between molecules

**Parameters**

- `df1` : pandas.DataFrame

DataFrame with HETATM, ATOM, and/or ANISOU entries

- `df2` : pandas.DataFrame

Second DataFrame for RMSD computation against df1. Must have the
same number of entries as df1

- `heavy_only` : bool (default: True)

Which atoms to compare to compute the RMSD. If `True` (default),
computes the RMSD between non-hydrogen atoms only.

**Returns**

- `rmsd` : float

Root Mean Square Deviation between df1 and df2

### Properties

<hr>

*df*

Acccesses the pandas DataFrame

21 changes: 21 additions & 0 deletions docs/api_modules/biopandas.mol2/split_multimol2.md
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## split_multimol2

*split_multimol2(mol2_path)*

Splits a multi-mol2 file into individual Mol2 file contents.

**Parameters**

- `mol2_path` : str

Path to the multi-mol2 file. Parses gzip files if the filepath
ends on .gz.

**Returns**

A generator object for lists for every extracted mol2-file. Lists contain
the molecule ID and the mol2 file contents.
e.g., ['ID1234', ['@<TRIPOS>MOLECULE\n', '...']]. Note that bytestrings
are returned (for reasons of efficieny) if the Mol2 content is read
from a gzip (.gz) file.

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