insilichem/gaudi

GaudiMM: A modular optimization platform for molecular design

gaudi's Issues

Is there some doc on how to do protein-ligand docking with gaudi?

Thanks!

v0.0.7 checklist

• Merge new objective: map fitting PR #4
• Merge improvements in objectives.energy: PR #6

Installation problem

Hi everyone or anyone,

I desperately need help.

I was trying to install in both py2 and py3 environment but both gives me an error.

UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:

Specifications:

• gaudi -> python[version='>=3.10,<3.11.0a0|>=3.11,<3.12.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.8,<3.9.0a0|>=3.9,<3.10.0a0']

Your python: python=2.7

If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Note that conda will not
change your python version to a different minor version unless you explicitly specify
that.

The following specifications were found to be incompatible with your system:

• feature:/linux-64::__glibc==2.35=0
• feature:|@/linux-64::__glibc==2.35=0

Your installed version is: 2.35

UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:

Specifications:

• gaudi -> python[version='2.7.*|>=2.7,<2.8.0a0']

Your python: python=3.10

If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Note that conda will not
change your python version to a different minor version unless you explicitly specify
that.

The following specifications were found to be incompatible with your system:

• feature:/linux-64::__glibc==2.35=0
• feature:|@/linux-64::__glibc==2.35=0

Your installed version is: 2.35

maybe interesting scoring function to support for docking

paper: https://www.ncbi.nlm.nih.gov/pubmed/21863864
software: http://pc1664.pharmazie.uni-marburg.de/drugscore/dsx_download.php

Allow Chimera selection specifications

Instead of requesting Molecule/residue_position or Molecule/atom_serial_number, allow Chimera selection commands when possible. Maybe this can be bone at the gaudi.genes.molecule.Compound level, but we first have to figure out how to implement it without breaking the existing find_* calls.

Mode 'calpha' in Normal Modes gene does not work

Using this mode in the tests result in error at prody/dynamics/sampling.py:

def sampleModes(modes, atoms=None, n_confs=1000, rmsd=1.0):

        if not isinstance(modes, (Mode, NMA, ModeSet)):
            raise TypeError('modes must be a NMA or ModeSet instance, '
                            'not {0}'.format(type(modes)))
        if not modes.is3d():
            raise ValueError('modes must be from a 3-dimensional model')
        n_confs = int(n_confs)
        n_atoms = modes.numAtoms()
        initial = None
        if atoms is not None:
            if not isinstance(atoms, (Atomic)):
                raise TypeError('{0} is not correct type for atoms'
                                .format(type(atoms)))
            if atoms.numAtoms() != n_atoms:
>               raise ValueError('number of atoms do not match')

The relevant code on our end was written long ago by somebody who is not working here anymore, so we can expect some rough edges.

Error when running gaudi for the first time

Hi! There is an error coming up when trying to run Gaudi.
This is the information you want:

On Ubuntu 18.04.02 LTS, with the followin sorted list of environments:

CHIMERADIR=/opt/UCSF/Chimera64-1.13.1
CLUTTER_IM_MODULE=xim
COLORTERM=truecolor
CONDA_DEFAULT_ENV=insilichem
CONDA_EXE=/home/gja_95/miniconda2/bin/conda
CONDA_PREFIX_1=/home/gja_95/miniconda2
CONDA_PREFIX=/home/gja_95/miniconda2/envs/insilichem
CONDA_PROMPT_MODIFIER=(insilichem)
CONDA_PYTHON_EXE=/home/gja_95/miniconda2/bin/python
CONDA_SHLVL=2
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/1000/bus
DESKTOP_AUTOSTART_ID=1016070c1866ba60b7155337562287089300000010520007
DESKTOP_SESSION=ubuntu
DISPLAY=:0
GDMSESSION=ubuntu
GNOME_DESKTOP_SESSION_ID=this-is-deprecated
GNOME_SHELL_SESSION_MODE=ubuntu
GNOME_TERMINAL_SCREEN=/org/gnome/Terminal/screen/171be68e_f490_4ac7_9647_5f843040b708
GNOME_TERMINAL_SERVICE=:1.100
GPG_AGENT_INFO=/run/user/1000/gnupg/S.gpg-agent:0:1
GTK_IM_MODULE=ibus
GTK_MODULES=gail:atk-bridge
HOME=/home/gja_95
IM_CONFIG_PHASE=2
LANG=ca_ES.UTF-8
LESSCLOSE=/usr/bin/lesspipe %s %s
LESSOPEN=| /usr/bin/lesspipe %s
LOGNAME=gja_95
LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:.tar=01;31:.tgz=01;31:.arc=01;31:.arj=01;31:.taz=01;31:.lha=01;31:.lz4=01;31:.lzh=01;31:.lzma=01;31:.tlz=01;31:.txz=01;31:.tzo=01;31:.t7z=01;31:.zip=01;31:.z=01;31:.Z=01;31:.dz=01;31:.gz=01;31:.lrz=01;31:.lz=01;31:.lzo=01;31:.xz=01;31:.zst=01;31:.tzst=01;31:.bz2=01;31:.bz=01;31:.tbz=01;31:.tbz2=01;31:.tz=01;31:.deb=01;31:.rpm=01;31:.jar=01;31:.war=01;31:.ear=01;31:.sar=01;31:.rar=01;31:.alz=01;31:.ace=01;31:.zoo=01;31:.cpio=01;31:.7z=01;31:.rz=01;31:.cab=01;31:.wim=01;31:.swm=01;31:.dwm=01;31:.esd=01;31:.jpg=01;35:.jpeg=01;35:.mjpg=01;35:.mjpeg=01;35:.gif=01;35:.bmp=01;35:.pbm=01;35:.pgm=01;35:.ppm=01;35:.tga=01;35:.xbm=01;35:.xpm=01;35:.tif=01;35:.tiff=01;35:.png=01;35:.svg=01;35:.svgz=01;35:.mng=01;35:.pcx=01;35:.mov=01;35:.mpg=01;35:.mpeg=01;35:.m2v=01;35:.mkv=01;35:.webm=01;35:.ogm=01;35:.mp4=01;35:.m4v=01;35:.mp4v=01;35:.vob=01;35:.qt=01;35:.nuv=01;35:.wmv=01;35:.asf=01;35:.rm=01;35:.rmvb=01;35:.flc=01;35:.avi=01;35:.fli=01;35:.flv=01;35:.gl=01;35:.dl=01;35:.xcf=01;35:.xwd=01;35:.yuv=01;35:.cgm=01;35:.emf=01;35:.ogv=01;35:.ogx=01;35:.aac=00;36:.au=00;36:.flac=00;36:.m4a=00;36:.mid=00;36:.midi=00;36:.mka=00;36:.mp3=00;36:.mpc=00;36:.ogg=00;36:.ra=00;36:.wav=00;36:.oga=00;36:.opus=00;36:.spx=00;36:.xspf=00;36:
OLDPWD=/home/gja_95/Baixades
PATH=/home/gja_95/miniconda2/envs/insilichem/bin:/home/gja_95/miniconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
PWD=/home/gja_95/Baixades/Prova
QT4_IM_MODULE=xim
QT_ACCESSIBILITY=1
QT_IM_MODULE=xim
SESSION_MANAGER=local/Ubuntu-Gil:@/tmp/.ICE-unix/1052,unix/Ubuntu-Gil:/tmp/.ICE-unix/1052
SHELL=/bin/bash
SHLVL=1
SSH_AGENT_PID=1167
SSH_AUTH_SOCK=/run/user/1000/keyring/ssh
TERM=xterm-256color
TEXTDOMAINDIR=/usr/share/locale/
TEXTDOMAIN=im-config
USER=gja_95
USERNAME=gja_95
_=/usr/bin/env
VTE_VERSION=5202
WINDOWPATH=1
XAUTHORITY=/run/user/1000/gdm/Xauthority
XDG_CONFIG_DIRS=/etc/xdg/xdg-ubuntu:/etc/xdg
XDG_CURRENT_DESKTOP=ubuntu:GNOME
XDG_DATA_DIRS=/usr/share/ubuntu:/usr/local/share:/usr/share:/var/lib/snapd/desktop
XDG_MENU_PREFIX=gnome-
XDG_RUNTIME_DIR=/run/user/1000
XDG_SEAT=seat0
XDG_SESSION_DESKTOP=ubuntu
XDG_SESSION_ID=1
XDG_SESSION_TYPE=x11
XDG_VTNR=1
XMODIFIERS=@im=ibus

The commands used to install were the ones found in https://gaudi.readthedocs.io/en/latest/installation.html.
When running the first calculation with command " gaudi run input.yaml " the following error comes up:

File "/home/gja_95/miniconda2/envs/insilichem/bin/gaudi", line 11, in
load_entry_point('gaudi==0.0.6', 'console_scripts', 'gaudi')()
File "/home/gja_95/miniconda2/envs/insilichem/lib/python2.7/site-packages/click/core.py", line 722, in call
return self.main(*args, **kwargs)
File "/home/gja_95/miniconda2/envs/insilichem/lib/python2.7/site-packages/click/core.py", line 697, in main
rv = self.invoke(ctx)
File "/home/gja_95/miniconda2/envs/insilichem/lib/python2.7/site-packages/click/core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/gja_95/miniconda2/envs/insilichem/lib/python2.7/site-packages/click/core.py", line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/gja_95/miniconda2/envs/insilichem/lib/python2.7/site-packages/click/core.py", line 535, in invoke
return callback(*args, **kwargs)
File "/home/gja_95/miniconda2/envs/insilichem/lib/python2.7/site-packages/gaudi/cli/gaudi_cli.py", line 114, in run
load_chimera()
File "/home/gja_95/miniconda2/envs/insilichem/lib/python2.7/site-packages/gaudi/cli/gaudi_cli.py", line 73, in load_chimera
pychimera.enable_chimera()
File "/home/gja_95/miniconda2/envs/insilichem/lib/python2.7/site-packages/pychimera/core.py", line 67, in enable_chimera
nogui=nogui, eventloop=not nogui, exitonquit=not nogui)
File "/opt/UCSF/Chimera64-1.13.1/share/chimeraInit.py", line 666, in init
import chimera
File "/opt/UCSF/Chimera64-1.13.1/share/chimera/init.py", line 16, in
from _chimera import BBox, Camera, Color, ColorGroup, DirectionalLight, LODControl, Lens, LensViewer, Light, Material, MaterialColor, Model, NoGuiViewer, OGLFont, OSLAbbreviation, OpenModels, OpenState, PathFinder, PixelMap, Plane, Point, PositionalLight, Selectable, SharedState, SpotLight, Sphere, Texture, TextureColor, TrackChanges, Vector, Viewer, X3DScene, Xform
ImportError: /opt/UCSF/Chimera64-1.13.1/lib/libgfxinfo.so: undefined symbol: _ZN7pcrecpp2RE4InitERKSsPKNS_10RE_OptionsE

Thank you!

psi4 support

Provide an objective that wraps psi4. This open-source QM software has Python bindings and conda packages, so it suits us better than NWChem.