franciscoadasme chem.cr issues

franciscoadasme / chem.cr

Library for dealing with computational chemistry files

https://franciscoadasme.github.io/chem.cr/

MIT License

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issues

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Add a convenience method to delete a bond

#224 franciscoadasme opened 1 week ago
0
Atom name setter does not update residue's atom table

#223 franciscoadasme opened 1 week ago
0
Chem::ParseException reading a PDB with empty REMARK field

#222 maurobedoya closed 6 days ago
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Incorrect unit for structure coordinates from Cube

#221 franciscoadasme opened 1 month ago
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Cache the residue templates

#220 franciscoadasme opened 1 month ago
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Add residue templates from PDB/CCD as default

#219 franciscoadasme opened 1 month ago
0
Fetch template from PDB/CCD

#218 franciscoadasme opened 1 month ago
1
Add a type to model coordinates files

#217 franciscoadasme opened 1 month ago
0
Add support for pattern matching for chains, residues and atoms

#216 franciscoadasme opened 2 months ago
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Avoid adding ficticious topology for isolated atoms

#215 franciscoadasme opened 2 months ago
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Refactor #guess_bonds implementation

#214 franciscoadasme opened 2 months ago
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Implement base unit support

#213 franciscoadasme opened 2 months ago
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Simplify the file format support implementation

#212 franciscoadasme opened 2 months ago
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Missing Spatial.distance method to support for Chem::Spatial::Vec3 objects

#211 maurobedoya closed 2 weeks ago
1
Compilation issue due to undefined constant definition in dcd format

#210 maurobedoya closed 2 weeks ago
1
Topology guessing fails on molecule with a symmetric group

#209 franciscoadasme opened 7 months ago
0
Add root mean square (rms) method

#208 franciscoadasme opened 11 months ago
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Radius of gyration method

#207 maurobedoya closed 11 months ago
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Do not include bonds with external atoms

#206 franciscoadasme opened 12 months ago
0
Incorrect bond guessing on a Structure with connectivity

#205 maurobedoya closed 1 year ago
1
Add shorthand methods to get and query axis vectors

#204 franciscoadasme closed 1 year ago
0
Implement VMD client/server

#203 franciscoadasme opened 1 year ago
0
Add PARCHG and others when registering CHGCAR format

#202 franciscoadasme opened 1 year ago
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Add convenience method to reset Parallelepiped's origin

#201 franciscoadasme opened 1 year ago
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Add convenience methods to get plane components of Vec3

#200 franciscoadasme closed 1 year ago
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Add Spatial::Point type

#199 franciscoadasme opened 1 year ago
1
Add measurement methods to Vec3 to allow method chaining

#198 franciscoadasme opened 1 year ago
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Move Angle, Dihedral, and Improper to Topology namespace

#197 franciscoadasme opened 1 year ago
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Move renumber_residues methods to ResidueView

#196 franciscoadasme opened 1 year ago
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Add convenience method to easily resize a parallelepiped

#195 franciscoadasme closed 1 year ago
0
Add structure's cell raising method

#194 franciscoadasme closed 1 year ago
0
Replicate periodic structure

#193 franciscoadasme opened 1 year ago
0
Chem::Structure.from_pdb is not working

#192 maurobedoya closed 1 year ago
0
Improve parallelepiped resizing

#191 franciscoadasme closed 1 year ago
0
Issue reading psf file generated with ParmEd

#190 maurobedoya closed 1 year ago
1
Issue reading PDB file for non-X-ray PDB (CRYST1 header)

#189 maurobedoya closed 1 year ago
0
Add custom select/reject methods to atom/residue/chain views

#188 franciscoadasme opened 2 years ago
0
Add to_cart/fract methods to Vec3 for method chaining

#187 franciscoadasme opened 2 years ago
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Standardize transformation methods among spatial objects

#186 franciscoadasme closed 1 year ago
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Rename AffineTransform.euler to rotation

#185 franciscoadasme closed 1 year ago
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Add rotation and other transformation methods to CoordinatesProxy

#184 franciscoadasme closed 1 year ago
0
Alignment by a subset of atoms produces incorrect coordinates

#183 franciscoadasme closed 1 year ago
2
Building a structure with elements only takes too long

#182 franciscoadasme closed 2 years ago
2
Structure generation using Grid objects takes a long time

#181 maurobedoya closed 2 years ago
1
PDB writing takes a long time

#180 maurobedoya opened 2 years ago
0
Reading PDB fails if occupancy is missing

#179 maurobedoya closed 2 years ago
0
Reading PSF block with non-multiple number of records fails

#178 maurobedoya closed 2 years ago
0
Add Residue#pred and succ question methods

#177 franciscoadasme closed 2 years ago
0
Add common termination templates

#176 franciscoadasme opened 2 years ago
0
Disable auto-detection of bonds

#175 franciscoadasme closed 2 years ago
0