Search results for "distribution:HackaMol Atom"
HackaMol::Atom - HackaMol Atom Class
Central to HackaMol, the Atom class provides methods and attributes for a given atom. The Atom class consumes HackaMol::PhysVecMVRRole, HackaMol::PdbRole, and HackaMol::QmAtomRole. See the documentation of those roles for details. The Atom class adds...
DEMIAN/HackaMol-0.053 - 23 Feb 2022 00:55:44 UTC
HackaMol::AtomGroup - HackaMol AtomGroup class
The HackaMol AtomGroup class provides methods and attributes for groups of atoms. Atom groupings can be defined to mimic conventional forcefields or manipulated to generate novel analytical tools. For example, with a trajectory loaded, a dynamic clus...
DEMIAN/HackaMol-0.053 - 23 Feb 2022 00:55:44 UTC
HackaMol::Roles::QmAtomRole - simple role that provides attributes needed for setting up quantum chemistry calculations
QmAtomRole provides attributes that will be useful for setting up interfaces to quantum chemistry packages. All attributes are 'rw' and lazy, so they will not contaminate the namespace unless called upon. The functionality for QM calculations is exte...
DEMIAN/HackaMol-0.053 - 23 Feb 2022 00:55:44 UTC
HackaMol::Roles::AtomGroupRole - Role for a group of atoms
The HackaMol AtomGroupRole class provides core methods and attributes for consuming classes that use groups of atoms. The original implementation of this role relied heavily on attributes, builders, and clearers. Such an approach naturally gives fast...
DEMIAN/HackaMol-0.053 - 23 Feb 2022 00:55:44 UTC
HackaMol - HackaMol: Object-Oriented Library for Molecular Hacking
The HackaMol publication <http://pubs.acs.org/doi/abs/10.1021/ci500359e> has a more complete description of the library (pdf available from researchgate <http://www.researchgate.net/profile/Demian_Riccardi/publication/2737781 91_HackaMol_an_object-or...
DEMIAN/HackaMol-0.053 - 23 Feb 2022 00:55:44 UTC
HackaMol::Bond - HackaMol Bond class
The HackaMol Bond class provides a set of methods and attributes for working with connections between two atoms. The Bond class consumes the AtomGroupRole providing Bond objects with methods to determine the center of mass, total charge, etc (see Hac...
DEMIAN/HackaMol-0.053 - 23 Feb 2022 00:55:44 UTC
HackaMol::Angle - Angle class for HackaMol
The HackaMol Angle class provides a set of methods and attributes for working with two connections between three atoms. Like the Bond, the Angle class consumes the AtomGroupRole providing methods to determine the center of mass, total charge, etc (se...
DEMIAN/HackaMol-0.053 - 23 Feb 2022 00:55:44 UTC
HackaMol::Roles::SelectionRole - Atom selections in molecules
The goal of HackaMol::Roles::SelectionRole is to simplify atom selections. This role is not loaded with the core; it must be applied as done in the synopsis. The method commonly used is select_group, which uses regular expressions to convert a string...
DEMIAN/HackaMol-0.053 - 23 Feb 2022 00:55:44 UTC
HackaMol::Dihedral - Dihedral Angle class for HackaMol
The HackaMol Dihedral class provides a set of methods and attributes for working with three connections between four atoms. Like the HackaMol::Bond and HackaMol::Angle classes, the Dihedral class consumes the HackaMol::AtomGroupRole providing methods...
DEMIAN/HackaMol-0.053 - 23 Feb 2022 00:55:44 UTC
HackaMol::Molecule - Molecule class for HackaMol
The Molecule class provides methods and attributes for collections of atoms that may be divided into groups, placed into bonds, angles, and dihedrals. The Molecule class extends the AtomGroup parent class, which consumes the AtomGroupRole, and consum...
DEMIAN/HackaMol-0.053 - 23 Feb 2022 00:55:44 UTC
HackaMol::Roles::PdbRole - PdbRole of lazy attributes for HackaMol atoms
PdbRole provides atom attributes for PDB parsing. All attributes are 'rw' and lazy, so they will not contaminate the namespace unless called upon. The functionality of the PdbRole may be extended in the future. An extension (HackaMolX::PDB or HackaMo...
DEMIAN/HackaMol-0.053 - 23 Feb 2022 00:55:44 UTC
HackaMol::Roles::PhysVecMVRRole - Provides the core of HackaMol Atom and Molecule classes.
PhysVecMVR provides the core attributes and methods shared between Atom and Molecule classes. Consuming this role gives Classes a place to store coordinates, forces, and charges, perhaps, over the course of a simulation or for a collection of configu...
DEMIAN/HackaMol-0.053 - 23 Feb 2022 00:55:44 UTC
HackaMol::Roles::QmMolRole - provides attributes needed for quantum chemistry calculations
QmMolRole provides attributes that will be useful for setting up interfaces to quantum chemistry packages. This role consumes the QmAtomRole so there is some overlap for basis_geom, basis, and ecp. For interfaces, the Molecule should take precedence ...
DEMIAN/HackaMol-0.053 - 23 Feb 2022 00:55:44 UTC
HackaMol::Roles::ReadXyzRole - Read files with molecular information
The HackaMol::Roles::ReadXyzRole provides read_xyz_atoms reading xyz files....
DEMIAN/HackaMol-0.053 - 23 Feb 2022 00:55:44 UTC
HackaMol::Roles::ReadPdbRole - Read files with molecular information
The HackaMol::Roles::ReadPdbRole provides read_pdb_atoms reading protein database files....
DEMIAN/HackaMol-0.053 - 23 Feb 2022 00:55:44 UTC
HackaMol::Roles::MolReadRole - Read files with molecular information
The HackaMol::Role::MolReadRole role provides methods for reading common structural files. Currently, pdb, pdbqt, Z-matrix, and xyz are provided. The methods are all provided in separate roles. Adding additional formats is straightforward: 1. Add a R...
DEMIAN/HackaMol-0.053 - 23 Feb 2022 00:55:44 UTC
HackaMol::Roles::ReadPdbxRole - parse PDBx/mmCIF files
The HackaMol::Roles::ReadPdbxRole provides methods (such as read_cif_atoms for building HM atoms) for pulling information from PDBx/mmcif. More info available in cif and more attributes are populated than via ReadPdbRole....
DEMIAN/HackaMol-0.053 - 23 Feb 2022 00:55:44 UTC
HackaMol::Roles::ReadYAMLRole - Read files with molecular information
The HackaMol::Roles::ReadZmatRole provides read_zmat_atoms for the flexible reading of Z-matrix files. It supports inline cartesian coordinates and variables as in the following example: N 0 -12.781 3.620 15.274 C 0 -11.976 4.652 15.944 C 0 -12.722 6...
DEMIAN/HackaMol-0.053 - 23 Feb 2022 00:55:44 UTC
HackaMol::Roles::ReadZmatRole - Read files with molecular information
The HackaMol::Roles::ReadZmatRole provides read_zmat_atoms for the flexible reading of Z-matrix files. It supports inline cartesian coordinates and variables as in the following example: N 0 -12.781 3.620 15.274 C 0 -11.976 4.652 15.944 C 0 -12.722 6...
DEMIAN/HackaMol-0.053 - 23 Feb 2022 00:55:44 UTC
HackaMol::Roles::ReadPdbqtRole - Read files with molecular information
The HackaMol::Roles::ReadPdbqtRole provides read_pdbqt_atoms for reading docking files....
DEMIAN/HackaMol-0.053 - 23 Feb 2022 00:55:44 UTC