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Link any residues #29

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ee67c5d
first commit. The linking of residues is not fully implemented.
js1710 Dec 19, 2018
655c6d7
first commit. The linking of residues is not fully implemented.
js1710 Dec 19, 2018
26ce80d
Now can connect residues using the [ global ] section. Will only work…
js1710 Dec 22, 2018
a9d67ad
Updated documentation
js1710 Dec 22, 2018
a67d29e
Fixed multiple bugs in the output of multi-residue information. At th…
js1710 Jan 18, 2019
2dfa5cd
updated tests
js1710 Jan 18, 2019
e51667c
Global section removed. Now can enter inter residue connections under…
js1710 Jan 21, 2019
4ad9e90
updated inter residue test files
js1710 Jan 21, 2019
87820c3
updated all bonset workflow to go via Molecule objects. Added test fo…
js1710 Feb 22, 2019
0ff2ca4
fixed bug in previous commit
js1710 Feb 22, 2019
bec6af4
refactored output to make more streamlined for molecules with any num…
js1710 Feb 22, 2019
46ab34e
removed any overlap between Molecule instances and Bead instances
js1710 Feb 23, 2019
dfadc0a
updated documentation
js1710 Feb 25, 2019
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1 change: 1 addition & 0 deletions README.md
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Expand Up @@ -2,6 +2,7 @@


# PyCGTOOL
WARNING THIS IS A VERY EXPERIMENTAL BRANCH - EXERCISE CAUTION!
Please see http://pycgtool.readthedocs.io/en/master/ for full documentation.


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9 changes: 9 additions & 0 deletions doc/source/index.rst
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Expand Up @@ -191,6 +191,15 @@ generate_angles Generate angles from bonds **True**, Fals
generate_dihedrals Generate dihedrals from bonds **False**, True
================== ========================================== =======================

Connect Residues
~~~~~~~~~~~~~~~~
In the .bnd file the [< mol >] section can be used to form bonds, angles or dihedrals between any residue in a system.
The syntax for an inter residue bond is::
[atom_name1]_[resid1]_[resname1] [atom_name2]_[resid2]_[resname2]
or angle::
[atom_name1]_[resid1]_[resname1] [atom_name2]_[resid2]_[resname2] [atom_name3]_[resid3]_[resname3]
Currently this feature only works for a single molecule. Note that itp reading is not currently supported for multi-residue itps

Indexes
=======

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