Make _nonstd_charge() public

[Tristan Croll]

The following bug report has been submitted:
Platform:        Linux-3.10.0-1160.25.1.el7.x86_64-x86_64-with-glibc2.17
ChimeraX Version: 1.3rc202110301701 (2021-10-30 17:01:03 UTC)
Description
TL/DR: `add_charge.charge._nonstd_charge()` does almost everything that `phenix.elbow --amber` does for generating OpenMM AMBER parameters, but eats the output I need. Basically I just need to take the .mol2 it generates, run it through `parmchk2` to make a .frcmod file, then use the .mol2 and .frcmod in `parmed` to make an OpenMM ffXML. Would you consider making this a public method with the option to keep the .mol2 file (or, alternatively, would you be averse to me copying it more-or-less wholesale and making the few adjustments I need within ISOLDE)?

Longer rant: I've tried to persevere with phenix.elbow, but it's just hopeless and never seems to get any better. It insists on "optimising" the input geometry before passing it to antechamber (typically forcing most nitrogens and double-bonded carbons to tetrahedral geometry ... antechamber will generally fix that, at least), and doesn't seem to even attempt to determine the overall charge (there is a `mol.charge` variable in its antechamber input code, but I've never seen its value to be anything other than zero). Finally, whenever it fails to run it eats all of antechamber's error messages making it awful to debug. I reported almost all of this to Nigel almost two years ago, and nothing has changed since. Would be great to see the back of it. 

Log:
> alias preview_toolshed toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu; toolshed reload available

> alias production_toolshed toolshed url https://cxtoolshed.rbvi.ucsf.edu;
> toolshed reload available

> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  
UCSF ChimeraX version: 1.3rc202110301701 (2021-10-30)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open jwx.pdb

Summary of feedback from opening jwx.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 26
GLY A 32 1 7  
Start residue of secondary structure not found: HELIX 2 2 HIS A 47 GLU A 51 1
5  
Start residue of secondary structure not found: HELIX 3 3 ASP A 61 HIS A 73 1
13  
Start residue of secondary structure not found: HELIX 4 4 SER A 78 LYS A 91 1
14  
Start residue of secondary structure not found: HELIX 5 5 ASN A 110 GLN A 121
1 12  
83 messages similar to the above omitted  
Cannot find LINK/SSBOND residue CYS (189 )  
Cannot find LINK/SSBOND residue CYS (192 )  
Cannot find LINK/SSBOND residue CYS (224 )  
Cannot find LINK/SSBOND residue CYS (226 )  
Cannot find LINK/SSBOND residue CYS (189 )  
7 messages similar to the above omitted  
  

> al JWX

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

place_ligand() was called with use_md_template=True, but no suitable template
was found. This command has been ignored.  

Done loading forcefield  

> select up

47 atoms, 50 bonds, 1 residue, 1 model selected  

> ui mousemode right "translate selected atoms"

> show

> select clear

> select up

47 atoms, 50 bonds, 1 residue, 1 model selected  

> delete sel

> select up

46 atoms, 49 bonds, 1 residue, 1 model selected  

> addh

Summary of feedback from adding hydrogens to jwx.pdb #1.2  
---  
notes | Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
1 hydrogens added  
  

> ui tool show Shell




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OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Cache Size: 20480 KB
Memory:
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	Mem:            62G         17G         10G        544M         35G         44G
	Swap:          4.9G         69M        4.9G

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:11df]	
	Kernel driver in use: nvidia
Locale: ('en_GB', 'UTF-8')
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[pett]

I could probably refactor it to make it public and have it optionally accept a directory name to use for its files. If you supply the directory name it leaves it untouched afterwards, and if you don't supply it then it does what it does now -- uses a temporary directory that gets removed afterward.

Would you need this in the 1.3 release?

[Tristan Croll]

It would be nice to have it in 1.3 - ISOLDE’s nearly ready to go, but while trying to improve its existing interface to phenix.elbow I’ve been forced to conclude it’s unusable for all but the simplest cases. If I can use this instead it would be a big enhancement.

[pett]

Okay, _nonstd_charge() has become nonstd_charge(), its "status" argument is now optional, and it has a "temp_dir" argument for specifying the Antechamber input/output directory path, which is not deleted afterward if specified. Let me know if there's further changes you need.

[Tristan Croll]

That sounds perfect! Will give it a spin tomorrow.

[Tristan Croll]

Beautiful! parmchk2 does require amber20/dat/leap/parm/gaff2.dat to work, but that was the only issue. I can bundle that into ISOLDE if you don't want it in the main ChimeraX distribution.

[pett]

I have no issue shipping a few additional files that will actually get used -- just don't want to ship unused parts for download size considerations. I've added gaff2.dat to the manifest.

[pett]

gaff2.dat is now included