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Link any residues #29

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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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