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Recent Releases of pycofbuilder

pycofbuilder - v0.0.8

This version introduces the implementation of automatic bond detection for the creation of Covalent Organic Frameworks (COFs).

  • Key Features:
    • Introduces an algorithm to automatically detect bonds between atoms in COF based on their interatomic distances and covalent radii of the atoms
    • Utilizes a threshold of 1.3 times the sum of the covalent radii to consider a bond. This parameter can be changed by the variable bond_threshold when creating the Framework object.
    • The save_bonds variable on the save method control if bonds will be saved on the file.
    • The bonding information can be save in files of the format:
    • cif
    • cjson
    • pdb
    • pqr (pdb with partial charges)

Usage example:

```python a = COF.Framework( 'T3BENZCHO-L2BENZNH2H-HCBA-AA', savebb=False, loglevel='info', logformat='simple', distthreshold=0.1, symmtol=0.2, angletol=5, bond_threshold=1.3)

a.save(fmt='cif', supercell=[1, 1, 1], primitive=False, save_bonds=True) ```

This will generate the cif file below: ```cif dataT3BENZCHOH-L2BENZNH2HH-HCB_A-AA

auditcreationdate 2024-08-03 _auditcreationmethod pyCOFBuilder _auditauthor_name 'Felipe Lopes de Oliveira'

chemicalnamecommon 'T3BENZCHOH-L2BENZNH2HH-HCBA-AA' _celllengtha 22.214808 _celllengthb 22.214808 _celllengthc 3.600000 _cellanglealpha 90.00 _cellanglebeta 90.00 _cellanglegamma 120.00 _spacegroupnameH-Malt 'P 1' _spacegroupITnumber 1

loop_ symmetryequivposas_xyz 'x, y, z'

loop_ atomsitelabel _atomsitetypesymbol atomsitefractx atomsitefracty atomsitefractz H1H1Q H 0.837213986 0.837445546 0.500000000 H2H2Q H 0.162554454 0.999768440 0.500000000 H3H3Q H 0.000231560 0.162786015 0.500000000 H4H4R H 0.125277029 0.092675490 0.500000000 H5H5R H 0.907324511 0.032601540 0.500000000 H6H6R H 0.967398461 0.874722971 0.500000000 H7H7Q H 0.496119347 0.829221121 0.500000000 H8H8Q H 0.170778879 0.666898227 0.500000000 H9H9Q H 0.333101773 0.503880652 0.500000000 H10H10R H 0.208056304 0.573991177 0.500000000 H11H11R H 0.426008823 0.634065127 0.500000000 H12H12R H 0.365934873 0.791943696 0.500000000 H13H13R H 0.296656258 0.398328129 0.500000000 H14H14R H 0.036677075 0.268338538 0.500000000 H15H15R H 0.231661462 0.268338538 0.500000000 H16H16R H 0.101671871 0.398328129 0.500000000 H17H17R H 0.101671871 0.703343742 0.500000000 H18H18R H 0.231661462 0.963322925 0.500000000 H19H19R H 0.036677075 0.768338538 0.500000000 H20H20R H 0.296656258 0.898328129 0.500000000 H21H21R H 0.601671871 0.898328129 0.500000000 H22H22R H 0.731661462 0.768338538 0.500000000 H23H23R H 0.731661462 0.963322925 0.500000000 H24H24R H 0.601671871 0.703343742 0.500000000 C25C25C1 C 0.070213203 0.051941230 0.500000000 C26C26C1 C 0.018271973 0.070213203 0.500000000 C27C27C1 C 0.948058770 0.018271973 0.500000000 C28C28C1 C 0.929786797 0.948058770 0.500000000 C29C29C1 C 0.981728027 0.929786797 0.500000000 C30C30C1 C 0.051941230 0.981728027 0.500000000 C31C31Q C 0.857149836 0.894324530 0.500000000 C32C32Q C 0.105675470 0.962825306 0.500000000 C33C33Q C 0.037174695 0.142850165 0.500000000 C34C34C1 C 0.263120130 0.614725437 0.500000000 C35C35C1 C 0.315061360 0.596453463 0.500000000 C36C36C1 C 0.385274563 0.648394693 0.500000000 C37C37C1 C 0.403546536 0.718607897 0.500000000 C38C38C1 C 0.351605306 0.736879870 0.500000000 C39C39C1 C 0.281392103 0.684938640 0.500000000 C40C40Q C 0.476183498 0.772342137 0.500000000 C41C41Q C 0.227657863 0.703841361 0.500000000 C42C42Q C 0.296158639 0.523816502 0.500000000 C43C43C2 C 0.239521089 0.369760544 0.500000000 C44C44C2 C 0.203093878 0.406187756 0.500000000 C45C45C2 C 0.130239456 0.369760544 0.500000000 C46C46C2 C 0.093812244 0.296906122 0.500000000 C47C47C2 C 0.130239456 0.260478911 0.500000000 C48C48C2 C 0.203093878 0.296906122 0.500000000 C49C49C2 C 0.130239456 0.760478911 0.500000000 C50C50C2 C 0.203093878 0.796906122 0.500000000 C51C51C2 C 0.239521089 0.869760544 0.500000000 C52C52C2 C 0.203093878 0.906187756 0.500000000 C53C53C2 C 0.130239456 0.869760544 0.500000000 C54C54C2 C 0.093812244 0.796906122 0.500000000 C55C55C2 C 0.630239456 0.869760544 0.500000000 C56C56C2 C 0.593812244 0.796906122 0.500000000 C57C57C2 C 0.630239456 0.760478911 0.500000000 C58C58C2 C 0.703093878 0.796906122 0.500000000 C59C59C2 C 0.739521089 0.869760544 0.500000000 C60C60C2 C 0.703093878 0.906187756 0.500000000 N61N61Q N 0.236880141 0.473760281 0.500000000 N62N62Q N 0.096453193 0.192906386 0.500000000 N63N63Q N 0.236880141 0.763119859 0.500000000 N64N64Q N 0.096453193 0.903546807 0.500000000 N65N65Q N 0.526239719 0.763119859 0.500000000 N66N66Q N 0.807093614 0.903546807 0.500000000

loop_ geombondatomsitelabel1 geombondatomsitelabel2 geombonddistance H1Q C31Q 1.11046 H2Q C32Q 1.11046 H3Q C33Q 1.11046 H4R C25C1 1.09920 H5R C27C1 1.09920 H6R C29C1 1.09920 H7Q C40Q 1.11046 H8Q C41Q 1.11046 H9Q C42Q 1.11046 H10R C34C1 1.09920 H11R C36C1 1.09920 H12R C38C1 1.09920 H13R C43C2 1.09920 H14R C46C2 1.09920 H15R C48C2 1.09920 H16R C45C2 1.09920 H17R C49C2 1.09920 H18R C52C2 1.09920 H19R C54C2 1.09920 H20R C51C2 1.09920 H21R C55C2 1.09920 H22R C58C2 1.09920 H23R C60C2 1.09920 H24R C57C2 1.09920 C25C1 C26C1 1.40162 C25C1 C30C1 1.40162 C25C1 H4R 1.09920 C26C1 C33Q 1.45000 C26C1 C27C1 1.40162 C26C1 C25C1 1.40162 C27C1 H5R 1.09920 C27C1 C28C1 1.40162 C27C1 C26C1 1.40162 C28C1 C27C1 1.40162 C28C1 C31Q 1.45000 C28C1 C29C1 1.40162 C29C1 C28C1 1.40162 C29C1 C30C1 1.40162 C29C1 H6R 1.09920 C30C1 C25C1 1.40162 C30C1 C29C1 1.40162 C30C1 C32Q 1.45000 C31Q N66Q 1.22732 C31Q C28C1 1.45000 C31Q H1Q 1.11046 C32Q N64Q 1.22732 C32Q C30C1 1.45000 C32Q H2Q 1.11046 C33Q N62Q 1.22732 C33Q C26C1 1.45000 C33Q H3Q 1.11046 C34C1 C39C1 1.40162 C34C1 H10R 1.09920 C34C1 C35C1 1.40162 C35C1 C34C1 1.40162 C35C1 C42Q 1.45000 C35C1 C36C1 1.40162 C36C1 C37C1 1.40162 C36C1 C35C1 1.40162 C36C1 H11R 1.09920 C37C1 C38C1 1.40162 C37C1 C40Q 1.45000 C37C1 C36C1 1.40162 C38C1 C39C1 1.40162 C38C1 H12R 1.09920 C38C1 C37C1 1.40162 C39C1 C41Q 1.45000 C39C1 C38C1 1.40162 C39C1 C34C1 1.40162 C40Q N65Q 1.22732 C40Q C37C1 1.45000 C40Q H7Q 1.11046 C41Q N63Q 1.22732 C41Q C39C1 1.45000 C41Q H8Q 1.11046 C42Q N61Q 1.22732 C42Q H9Q 1.11046 C42Q C35C1 1.45000 C43C2 C44C2 1.40162 C43C2 C48C2 1.40162 C43C2 H13R 1.09920 C44C2 N61Q 1.30000 C44C2 C45C2 1.40162 C44C2 C43C2 1.40162 C45C2 C46C2 1.40162 C45C2 C44C2 1.40162 C45C2 H16R 1.09920 C46C2 C47C2 1.40162 C46C2 H14R 1.09920 C46C2 C45C2 1.40162 C47C2 N62Q 1.30000 C47C2 C46C2 1.40162 C47C2 C48C2 1.40162 C48C2 C47C2 1.40162 C48C2 H15R 1.09920 C48C2 C43C2 1.40162 C49C2 C54C2 1.40162 C49C2 H17R 1.09920 C49C2 C50C2 1.40162 C50C2 C49C2 1.40162 C50C2 N63Q 1.30000 C50C2 C51C2 1.40162 C51C2 C52C2 1.40162 C51C2 C50C2 1.40162 C51C2 H20R 1.09920 C52C2 C53C2 1.40162 C52C2 H18R 1.09920 C52C2 C51C2 1.40162 C53C2 C54C2 1.40162 C53C2 N64Q 1.30000 C53C2 C52C2 1.40162 C54C2 C49C2 1.40162 C54C2 H19R 1.09920 C54C2 C53C2 1.40162 C55C2 C56C2 1.40162 C55C2 H21R 1.09920 C55C2 C60C2 1.40162 C56C2 N65Q 1.30000 C56C2 C55C2 1.40162 C56C2 C57C2 1.40162 C57C2 C56C2 1.40162 C57C2 C58C2 1.40162 C57C2 H24R 1.09920 C58C2 C57C2 1.40162 C58C2 H22R 1.09920 C58C2 C59C2 1.40162 C59C2 C58C2 1.40162 C59C2 N66Q 1.30000 C59C2 C60C2 1.40162 C60C2 C55C2 1.40162 C60C2 C59C2 1.40162 C60C2 H23R 1.09920 N61Q C44C2 1.30000 N61Q C42Q 1.22732 N62Q C47C2 1.30000 N62Q C33Q 1.22732 N63Q C50C2 1.30000 N63Q C41Q 1.22732 N64Q C53C2 1.30000 N64Q C32Q 1.22732 N65Q C56C2 1.30000 N65Q C40Q 1.22732 N66Q C59C2 1.30000 N66Q C31_Q 1.22732 ```

- Python
Published by lipelopesoliveira over 2 years ago

pycofbuilder - v0.0.7

What's Changed

  • Uptade beta by @lipelopesoliveira in https://github.com/lipelopesoliveira/pyCOFBuilder/pull/46
  • Update README.md by @lipelopesoliveira in https://github.com/lipelopesoliveira/pyCOFBuilder/pull/47
  • Update README.md by @lipelopesoliveira in https://github.com/lipelopesoliveira/pyCOFBuilder/pull/49
  • Update README.md by @lipelopesoliveira in https://github.com/lipelopesoliveira/pyCOFBuilder/pull/50
  • Add Sphynx-based documentation by @lipelopesoliveira in https://github.com/lipelopesoliveira/pyCOFBuilder/pull/52
  • Update README.md by @lipelopesoliveira in https://github.com/lipelopesoliveira/pyCOFBuilder/pull/55
  • Update to version 0.0.6 by @lipelopesoliveira in https://github.com/lipelopesoliveira/pyCOFBuilder/pull/53

Full Changelog: https://github.com/lipelopesoliveira/pyCOFBuilder/compare/v0.0.4...v0.0.7

- Python
Published by lipelopesoliveira over 2 years ago

pycofbuilder - v0.0.4-beta

v0.0.4 beta released with the preprint of the pyCOFBuilder paper: https://arxiv.org/abs/2310.14822

- Python
Published by lipelopesoliveira over 2 years ago

pycofbuilder - v0.0.3-beta

This PR adds some updates and improvements into the code.

List of changes:

  • Now the building block file structures are saved in the save_dir folder;
  • The Tools.elements_dict module has new features:
    • full_name
    • atomic_number
    • atomic_mass
    • polarizability
    • pauling_electronegativity
    • thermo_electronegativity
    • mulliken_electronegativity
    • sanderson_electronegativity
    • allen_electronegativity
    • ghosh_electronegativity
    • martynov_batsanov_electronegativity
    • atomic_radius
    • covalent_radius
    • vdw_radius
  • The Tools now has the capability to save in the qe format
  • Tools.get_kgrid now returns integers
  • The gjf now are json files, as a result of #4, #33, #28
  • print and repr methods are implemented
  • SMILES codes are available on BuildingBlock.smiles
  • Save functios were remodeled. Now it is possible to use BuildingBlock.save() and Reticulum.save() to save the structures;
  • New linear building blocks were added as a result of #29
  • Add new building blocks with carbenes as result of #34
  • Change the Building Blocks symbols as result of #36

- Python
Published by lipelopesoliveira about 3 years ago

pycofbuilder - v0.0.2-beta

This is the release of the v0.0.2 Beta (17/06/2022)

Added

  • Add AA, AB1, AB2, AAl, AAt, ABC1 e ABC2 stakings for KDG net https://github.com/lipelopesoliveira/pyCOFBuilder/pull/23
  • Add a new C6 HEXB buinding block derived from hexaphenilbenzene https://github.com/lipelopesoliveira/pyCOFBuilder/pull/23
  • Code for creation of C6 building block https://github.com/lipelopesoliveira/pyCOFBuilder/pull/23
  • AA, AB1, AB2, AAl, AAt, ABC1 e ABC2 stakings for HXL-A net https://github.com/lipelopesoliveira/pyCOFBuilder/pull/24
  • Add a new C4 Buiding Block derived from 4,4',4'',4'''-(pyrene-1,3,6,8-tetrayl)tetrabenzene. https://github.com/lipelopesoliveira/pyCOFBuilder/pull/25
  • Add AA, AB1x, AB1y, AB1xy, AB2, AAl, AAt, stakings for KGM and KGM-A net https://github.com/lipelopesoliveira/pyCOFBuilder/issues/18
  • Add proper documentaion of the net methods
  • Add the class methods documentations

Know bugs

  • KGM and KGM-A nets do not generate the proper structure
  • HXL-A and KDG stakings are not tested

- Python
Published by lipelopesoliveira about 4 years ago

pycofbuilder - v0.0.1-alpha

This is the first release of the version 0.0.1 Alpha.

Added

  • General structure of the code

  • COF generation with HCB and HCB-A nets

  • AA, AB1, AB2, AAl, AAt, ABC1 e ABC2 stakings for HCB and HCB-A nets

  • Several types of organic cores, functional groups and conectors

Changed

  • None

Fixed

  • None

- Python
Published by lipelopesoliveira about 4 years ago