Digichem Convert

digichem convert is used to convert different coordinate file types.

$ digichem convert INPUT_FILE -O OUTPUT_FILE

By default, the format of both the input and output files is determined by their extension. For example:

$ digichem convert Benzene.com -O Benzene.xyz

Would convert a Gaussian input file (.com) to a platform independent XYZ (.xyz) file.

The file formats can also be explicitly specified using the --input (or -i) and --output (or -o) options:

$ digichem convert Benzene.in -O Benzene.out -i com -o xyz
$ cat Benzene.out
12

C          1.38314       -0.22144        0.00537
C          0.50694       -1.30651       -0.00792
C         -0.87093       -1.09053       -0.01470
C         -1.37290        0.21095       -0.00441
C         -0.49670        1.29607        0.01060
C          0.88118        1.07996        0.01366
H          2.45680       -0.38978        0.00923
H          0.89795       -2.32061       -0.01321
H         -1.55354       -1.93593       -0.02737
H         -2.44648        0.37928       -0.00825
H         -0.88777        2.31003        0.01974
H          1.56378        1.92549        0.02297

See below for a full list of supported input and output formats.

Certain coordinate formats, including the Digichem native format (.si) and Gaussian input format (.com), natively support molecular charge and multiplicity. These can be set using the --charge (or -C) and --multiplicity (or -M) options respectively:

$ digichem convert Benzene.xyz -O Benzene_rad_cation.si -C 1 -M 2
$ digichem convert Benzene.xyz -O Benzene_rad_anion.si -C -1 -M 2

Warning

Most coordinate formats do not retain electron information (charge or multiplicity). In these cases, any values set with the -C or -M options will be silently ignored. When working with radicals and/or charged species, make sure to use a format that supports lossless conversion of charge and multiplicity (see C&M column below), or set the charge and multiplicity appropriately with the digichem submit command.

Some formats only store coordinates in two dimensions. This is common in formats used by 2D drawing programs, such as ChemDraw (.cdx, .cdxml, etc.) and Marvin Sketch (.cml, .mrv, .etc). Other formats may contain coordinates in either two or three dimensions, depending on how the structure was drawn (.cml, etc.), while yet others do not use coordinates to represent the molecule at all (SMILES, etc.).

When converting between formats, digichem convert will automatically detect whether the input file contains 3D coordinates. If it does not, then a rapid force-field optimisation (using the obabel --gen3D command) will be performed to generate 3D coordinates. In most cases, this is beneficial because the resulting 3D coordinates will be a better starting point for the full optimisation using your chosen calculation engine and method. However, the preoptimisation will change the geometry between the input and output files. This may be unexpected, and in some cases undesirable, in which case the preoptimisation can be disabled by using the -gen3D False option:

$ digichem convert Benzene.cdx -O Benzene.xyz --gen3D False

Warning

The --gen3D option should not be considered a substitute for a true optimisation with a computational chemistry method. When drawing molecules from scratch, whether in two dimensions or three, always perform a geometry optimisation before calculating other properties.

Supported File Formats

Code	Description	Read	Write	C&M
abinit	ABINIT Output Format	✅	❌	❌
acesin	ACES input format	❌	✅	❌
acesout	ACES output format	✅	❌	❌
acr	ACR format	✅	❌	❌
adf	ADF cartesian input format	❌	✅	❌
adfband	ADF Band output format	✅	❌	❌
adfdftb	ADF DFTB output format	✅	❌	❌
adfout	ADF output format	✅	❌	❌
alc	Alchemy format	✅	✅	❌
aoforce	Turbomole AOFORCE output format	✅	❌	❌
arc	Accelrys/MSI Biosym/Insight II CAR format	✅	❌	❌
ascii	ASCII format	❌	✅	❌
axsf	XCrySDen Structure Format	✅	❌	❌
bgf	MSI BGF format	✅	✅	❌
box	Dock 3.5 Box format	✅	✅	❌
bs	Ball and Stick format	✅	✅	❌
c09out	Crystal 09 output format	✅	❌	❌
c3d1	Chem3D Cartesian 1 format	✅	✅	❌
c3d2	Chem3D Cartesian 2 format	✅	✅	❌
cac	CAChe MolStruct format	❌	✅	❌
caccrt	Cacao Cartesian format	✅	✅	❌
cache	CAChe MolStruct format	❌	✅	❌
cacint	Cacao Internal format	❌	✅	❌
can	Canonical SMILES format	✅	✅	❌
car	Accelrys/MSI Biosym/Insight II CAR format	✅	❌	❌
castep	CASTEP format	✅	❌	❌
ccc	CCC format	✅	❌	❌
cdjson	ChemDoodle JSON	✅	✅	❌
cdx	ChemDraw binary format	✅	❌	❌
cdxml	ChemDraw CDXML format	✅	✅	❌
cht	Chemtool format	❌	✅	❌
cif	Crystallographic Information File	✅	✅	❌
ck	ChemKin format	✅	✅	❌
cml	Chemical Markup Language	✅	✅	❌
cmlr	CML Reaction format	✅	✅	❌
cof	Culgi object file format	✅	✅	❌
com	Gaussian Input	✅	✅	✅
confabreport	Confab report format	❌	✅	❌
CONFIG	DL-POLY CONFIG	✅	✅	❌
CONTCAR	VASP format	✅	✅	❌
CONTFF	MDFF format	✅	✅	❌
crk2d	Chemical Resource Kit diagram(2D)	✅	✅	❌
crk3d	Chemical Resource Kit 3D format	✅	✅	❌
csr	Accelrys/MSI Quanta CSR format	❌	✅	❌
cssr	CSD CSSR format	❌	✅	❌
ct	ChemDraw Connection Table format	✅	✅	❌
cub	Gaussian cube format	✅	✅	❌
cube	Gaussian cube format	✅	✅	❌
dallog	DALTON output format	✅	❌	❌
dalmol	DALTON input format	✅	✅	✅
dat	Generic Output file format	✅	❌	❌
dmol	DMol3 coordinates format	✅	✅	❌
dx	OpenDX cube format for APBS	✅	✅	❌
ent	Protein Data Bank format	✅	✅	❌
exyz	Extended XYZ cartesian coordinates format	✅	✅	❌
fa	FASTA format	✅	✅	❌
fasta	FASTA format	✅	✅	❌
fch	Gaussian formatted checkpoint file format	✅	❌	❌
fchk	Gaussian formatted checkpoint file format	✅	❌	❌
fck	Gaussian formatted checkpoint file format	✅	❌	❌
feat	Feature format	✅	✅	❌
fh	Fenske-Hall Z-Matrix format	❌	✅	❌
fhiaims	FHIaims XYZ format	✅	✅	❌
fix	SMILES FIX format	❌	✅	❌
fps	FPS text fingerprint format (Dalke)	❌	✅	❌
fpt	Fingerprint format	❌	✅	❌
fract	Free Form Fractional format	✅	✅	❌
fs	Fastsearch format	✅	✅	❌
fsa	FASTA format	✅	✅	❌
g03	Gaussian Output	✅	❌	❌
g09	Gaussian Output	✅	❌	❌
g16	Gaussian Output	✅	❌	❌
g92	Gaussian Output	✅	❌	❌
g94	Gaussian Output	✅	❌	❌
g98	Gaussian Output	✅	❌	❌
gal	Gaussian Output	✅	❌	❌
gam	GAMESS Output	✅	❌	❌
gamess	GAMESS Output	✅	❌	❌
gamin	GAMESS Input	✅	✅	❌
gamout	GAMESS Output	✅	❌	❌
gau	Gaussian Input	✅	✅	✅
gjc	Gaussian Input	✅	✅	✅
gjf	Gaussian Input	✅	✅	✅
got	GULP format	✅	❌	❌
gpr	Ghemical format	✅	✅	❌
gr96	GROMOS96 format	❌	✅	❌
gro	GRO format	✅	✅	❌
gukin	GAMESS-UK Input	✅	✅	❌
gukout	GAMESS-UK Output	✅	✅	❌
gzmat	Gaussian Z-Matrix Input	✅	✅	✅
hin	HyperChem HIN format	✅	✅	❌
HISTORY	DL-POLY HISTORY	✅	❌	❌
inchi	InChI format	✅	✅	❌
inchikey	InChIKey	❌	✅	❌
inp	GAMESS Input	✅	✅	❌
ins	ShelX format	✅	❌	❌
jin	Jaguar input format	✅	✅	❌
jout	Jaguar output format	✅	❌	❌
k	Compare molecules using InChI	❌	✅	❌
lmpdat	The LAMMPS data format	❌	✅	❌
log	Generic Output file format	✅	❌	❌
lpmd	LPMD format	✅	✅	❌
mcdl	MCDL format	✅	✅	❌
mcif	Macromolecular Crystallographic Info	✅	✅	❌
MDFF	MDFF format	✅	✅	❌
mdl	MDL MOL format	✅	✅	❌
ml2	Sybyl Mol2 format	✅	✅	❌
mmcif	Macromolecular Crystallographic Info	✅	✅	❌
mmd	MacroModel format	✅	✅	❌
mmod	MacroModel format	✅	✅	❌
mna	Multilevel Neighborhoods of Atoms (MNA)	❌	✅	❌
mol	MDL MOL format	✅	✅	❌
mol2	Sybyl Mol2 format	✅	✅	❌
mold	Molden format	✅	✅	❌
molden	Molden format	✅	✅	❌
molf	Molden format	✅	✅	❌
molreport	Open Babel molecule report	❌	✅	❌
moo	MOPAC Output format	✅	❌	❌
mop	MOPAC Cartesian format	✅	✅	❌
mopcrt	MOPAC Cartesian format	✅	✅	❌
mopin	MOPAC Internal	✅	✅	❌
mopout	MOPAC Output format	✅	❌	❌
mp	Molpro input format	❌	✅	❌
mpc	MOPAC Cartesian format	✅	✅	❌
mpd	MolPrint2D format	❌	✅	❌
mpo	Molpro output format	✅	❌	❌
mpqc	MPQC output format	✅	❌	❌
mpqcin	MPQC simplified input format	❌	✅	❌
mrv	Chemical Markup Language	✅	✅	❌
msi	Accelrys/MSI Cerius II MSI format	✅	❌	❌
msms	M.F. Sanner’s MSMS input format	❌	✅	❌
nul	Outputs nothing	❌	✅	❌
nw	NWChem input format	❌	✅	❌
nwo	NWChem output format	✅	❌	❌
orca	ORCA output format	✅	❌	❌
orcainp	ORCA input format	❌	✅	❌
out	Generic Output file format	✅	❌	❌
outmol	DMol3 coordinates format	✅	✅	❌
output	Generic Output file format	✅	❌	❌
paint	Painter format	❌	✅	❌
pc	PubChem format	✅	❌	❌
pcjson	PubChem JSON	✅	✅	❌
pcm	PCModel Format	✅	✅	❌
pdb	Protein Data Bank format	✅	✅	❌
pdbqt	AutoDock PDBQT format	✅	✅	❌
png	PNG 2D depiction	✅	✅	❌
pointcloud	Point cloud on VDW surface	❌	✅	❌
pos	POS cartesian coordinates format	✅	❌	❌
POSCAR	VASP format	✅	✅	❌
POSFF	MDFF format	✅	✅	❌
pov	POV-Ray input format	❌	✅	❌
pqr	PQR format	✅	✅	❌
pqs	Parallel Quantum Solutions format	✅	✅	❌
prep	Amber Prep format	✅	❌	❌
pwscf	PWscf format	✅	❌	❌
qcin	Q-Chem input format	❌	✅	❌
qcout	Q-Chem output format	✅	❌	❌
report	Open Babel report format	❌	✅	❌
res	ShelX format	✅	❌	❌
rinchi	RInChI	❌	✅	❌
rsmi	Reaction SMILES format	✅	✅	❌
rxn	MDL RXN format	✅	✅	❌
sd	MDL MOL format	✅	✅	❌
sdf	MDL MOL format	✅	✅	❌
si	Silico Input Format	✅	✅	✅
siesta	SIESTA format	✅	❌	❌
smi	SMILES format	✅	✅	❌
smiles	SMILES format	✅	✅	❌
smy	SMILES format using Smiley parser	✅	❌	❌
stl	STL 3D-printing format	❌	✅	❌
svg	SVG 2D depiction	❌	✅	❌
sy2	Sybyl Mol2 format	✅	✅	❌
t41	ADF TAPE41 format	✅	❌	❌
tdd	Thermo format	✅	✅	❌
therm	Thermo format	✅	✅	❌
tmol	TurboMole Coordinate format	✅	✅	❌
txyz	Tinker XYZ format	✅	✅	❌
unixyz	UniChem XYZ format	✅	✅	❌
VASP	VASP format	✅	✅	❌
vmol	ViewMol format	✅	✅	❌
wln	Wiswesser Line Notation	✅	❌	❌
xed	XED format	❌	✅	❌
xml	General XML format	✅	❌	❌
xsf	XCrySDen Structure Format	✅	❌	❌
xtc	XTC format	✅	❌	❌
xyz	XYZ cartesian coordinates format	✅	✅	❌
yob	YASARA.org YOB format	✅	✅	❌
zin	ZINDO input format	❌	✅	❌

Read: This format can be read. Write: This format can be written. C&M: This format supports lossless charge and multiplicity information (the charge and multiplicity can be both read and written).

The Digichem native format (.si), the program-independent XYZ (.xyz), and the Gaussian input format (.com, .gjf, etc.) are handled natively. Calculation log files are parsed using the cclib library [12]. All other formats are converted by calling the external obabel command, and thus require a functioning installing of Open Babel [11].

Digichem Native Format (.si)

The Digichem coordinate format is written in YAML, and contains six properties:

$ digichem convert Benzene.xyz -o si
version: 2.1.0
name: null
charge: 0
multiplicity: 1
atoms:
- {atom: C, x: 1.38314, y: -0.22144, z: 0.00537}
- {atom: C, x: 0.50694, y: -1.30651, z: -0.00792}
- {atom: C, x: -0.87093, y: -1.09053, z: -0.0147}
- {atom: C, x: -1.3729, y: 0.21095, z: -0.00441}
- {atom: C, x: -0.4967, y: 1.29607, z: 0.0106}
- {atom: C, x: 0.88118, y: 1.07996, z: 0.01366}
- {atom: H, x: 2.4568, y: -0.38978, z: 0.00923}
- {atom: H, x: 0.89795, y: -2.32061, z: -0.01321}
- {atom: H, x: -1.55354, y: -1.93593, z: -0.02737}
- {atom: H, x: -2.44648, y: 0.37928, z: -0.00825}
- {atom: H, x: -0.88777, y: 2.31003, z: 0.01974}
- {atom: H, x: 1.56378, y: 1.92549, z: 0.02297}
history: null

version

The version string of the input file, used by the digichem parser for backwards compatibility.

name

An optional string describing the name of the molecule. The name is only used for descriptive purposes, and can be omitted. If it is omitted, the name of the file itself is used as the name of the molecule.

charge

Integer charge of the molecule.

multiplicity

Integer multiplicity of the molecule.

atoms

A list of dictionaries describing the geometry of the molecule. Each dictionary contains four key:value pairs:

• atom: The atom type as its standard element symbol.

• x: The x coordinate, in angstrom.

• y: The y coordinate, in angstrom.

• z: The z coordinate, in angstrom.

history

An optional unique identifier describing the calculation that generated the geometry in this file.