Package structutils

A package containing Schrodinger structure utility modules.

Submodules

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schrodinger.structutils.analyze: Functions for analyzing Structure objects.
schrodinger.structutils.assignbondorders: A module to assign bond orders based on molecular geometry.
schrodinger.structutils.build: Functions for modifying chemical structures.
schrodinger.structutils.color: An interface to the Maestro color palette and color schemes.
schrodinger.structutils.createfragments: This script will break up a set of input molecules into fragments based on some simple rules, similar to those described in the original RECAP paper.
schrodinger.structutils.interactionfp: Calculate structural interaction fingerprints.
schrodinger.structutils.interactions: A module for detecting interactions between structures.
- schrodinger.structutils.interactions.hbond: Module for identifying hydrogen and halogen bond interactions.
- schrodinger.structutils.interactions.pi: A module for detecting pi-pi and pi-cation interactions.
- schrodinger.structutils.interactions.salt_bridge: Find salt-bridge interactions.
- schrodinger.structutils.interactions.steric_clash
schrodinger.structutils.io: This module is deprecated.
schrodinger.structutils.measure: Functions for measuring distances and angles in structures.
schrodinger.structutils.minimize: A module for force field energy evaluation and minimization.
schrodinger.structutils.ringspear: Functions and classes useful for finding ring spears.
schrodinger.structutils.rmsd: Functionality for calculating conformer RMSDs.
schrodinger.structutils.sitealign: Perform a pairwise superposition of multiple structures using the C-alpha atoms of selected residues.
schrodinger.structutils.smiles: A module for generating SMILES and unique SMILES strings.
schrodinger.structutils.smilesfilter: A group of functions and classes to help filtering structure files on unique SMILES strings.
schrodinger.structutils.sort: A module for sorting structure files by Structure-level property values.
schrodinger.structutils.structalign: A module for performing protein structure alignment.
schrodinger.structutils.transform: A module for manipulating atom coordinates with matrix operations.

Variables

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_version = '$Revision: 1.14 $'

POLAR_NOT_CHARGED_RESIDUES = ['ASN', 'GLN', 'SER', 'THR']

POLAR_RESIDUES = ['ARG', 'ASP', 'GLU', 'HIS', 'ASN', 'GLN', 'L...

NON_POLAR_RESIDUES = ['PHE', 'LEU', 'ILE', 'TYR', 'TRP', 'VAL'...

BASIC_RESIDUES = ['ARG', 'LYS', 'HIS']

ACIDIC_RESIDUES = ['ASP', 'GLU']

ALIPHATIC_RESIDUES = ['ALA', 'VAL', 'ILE', 'LEU']

AROMATIC_RESIDUES = ['PHE', 'TYR', 'TRP']

SMALL_RESIDUES = ['ALA', 'VAL', 'CYS', 'PRO', 'ASP', 'ASN', 'S...

TINY_RESIDUES = ['ALA', 'GLY', 'SER']

CHARGED_RESIDUES = ['ARG', 'LYS', 'HIS', 'ASP', 'GLU']

NEUTRAL_RESIDUES = ['ALA', 'ASN', 'CYS', 'GLN', 'GLY', 'ILE', ...

__package__ = None
hash(x)

Variables Details

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POLAR_RESIDUES

Value:

['ARG', 'ASP', 'GLU', 'HIS', 'ASN', 'GLN', 'LYS', 'SER', 'THR']

NON_POLAR_RESIDUES

Value:

['PHE', 'LEU', 'ILE', 'TYR', 'TRP', 'VAL', 'MET', 'PRO', 'CYS', 'ALA']

SMALL_RESIDUES

Value:

['ALA', 'VAL', 'CYS', 'PRO', 'ASP', 'ASN', 'SER', 'THR', 'GLY']

NEUTRAL_RESIDUES

Value:

['ALA',
 'ASN',
 'CYS',
 'GLN',
 'GLY',
 'ILE',
 'LEU',
 'MET',
...