libcif

Module libcif

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Module libcif

Classes
`XMLWriter`

Function Summary
	`AbsStructEN(html, cif)` Adds some text to the English report about the absolute configuration of the molecule
	`AsymetricCellContents(cif)` tries to find the contents of the asymetric cell
	`AtomicCoord(html, table)` This function appends a table with label, y, y, z and U to the html file
tupple	`AtomPositions(cif)` Extract the atome name, position and U(eq) fropm the CIF.
dictionnary	`BondAngle(cif)` Returns a dictionnary with all the bond/valence angles between heavy atoms Datas have to be already in the CIF
dictionnary	`BondLength(cif)` Returns a dictionnary with all the bond lengths between heavy atoms.
	`CellVol(cif)` calculate the cell volume and return it as a real (in Å³)
	`ChechForCSD(cif, name)` check in the CIF data if all the data needed to generate a RST report are present.
	`ChechForRST(cif)` check in the CIF data if all the data needed to generate a RST report are present.
string	`CheckSym(cif, fix)` Checks the symetry of a CIF file based on the symmetry operations
	`cif2str(cif)` converts a cif dictionnary to a string according to the CIF syntax
	`Density(cif)` calculate the density in Mg/m³, for information : 10^30/Na/10^6=1.66054018667
string	`dot2virg(text)` Substitute the english dots with french virgules
	`encode(s, encoding)`
	`encode_entity(text, pattern)`
	`escape_attrib(s, encoding, replace)`
	`escape_cdata(s, encoding, replace)`
boolean	`exists(cif, key)` Check if the key exists in the CIF.
float	`floatp(txt)` Removes the () from the text and convert to a float
	`formula2chem(txt)` return a HTML representatin of the chemical formula
	`Html2table(html, BL, X, Y)` This function appends a table element to the html file with the X and Y headers
dictionnary	`LoadCIF(filename)` Load the CIF file and returns the dictionnary
	`MainreportEN(html, cif)` This function generates the report in ENGLISH and add it to the HTML file
	`MainreportFR(html, cif)` this function generates the report in FRENCH to the HTML file
dictionnary	`mergeplaton(cif, acc)` Merge cif and acc and returns a completed CIF-object.
dictionnary	`MergeSg(name, kcd, sg)` Merge 2 cif objects : add from sg the missing values in kcd
	`MolForm(cif, zp)` count the atoms and returns the molecular formula.
	`MolWeight(formula)` calculate the molecular weight of a compound using its formula
tupple	`oneloop(fields, start)` Processes one loop in the data extraction of the CIF file
dictionnary	`parsecif(text)` -Parses the text of a CIF file
dictionnary	`platon(filename)` process the data throught PLATON
string	`readcif(filename)` -Check if the filename exists
	`renamefile(infile, namelist)` The CSD database has only room for 8 char to define the reference of the molecule.
	`SaveCIF(cif, filename)` transforms the CIF object in string and write it into the given file
list	`splitcif(text)` Separate the text in fields as defined in the CIF
string	`stringmulti(text, value)` Convert a string to a real, multiplies by the value and returns a string
	`structureImage(basename, structure)` lauch PLATON and let the user chose the structural (or the ortep or powder) representation of the molecule
string	`symop(cif)` Lists all the symetricaly equivalent positions @param cif: CIF object of the Xtal structure
	`WriteReport(filename, cif, Lang)` This function writes out an X-Ray structure report as an HTML file in the given language with the data taken from the CIF dictionnary
	`XraySummary(html, cif)` This function appends a table summarizing the Xray analysis, usually in Annexe as table 1
	`Zprime(cif)` Calculate Z' = Z/nop if the latice is primitive zp=2*Z/nop if the latice is centered ...

Function Details

AbsStructEN(html, cif)

Adds some text to the English report about the absolute configuration of the molecule

Parameters:: html - HTML object where the text will be added to.
(type=XMLWrite object.); cif - The CIF-object of the structure
(type=CIF-like Dictionnary)

Returns:: None, le test is simply added to the HTML file

AsymetricCellContents(cif)

tries to find the contents of the asymetric cell

AtomicCoord(html, table)

This function appends a table with label, y, y, z and U to the html file

AtomPositions(cif)

Extract the atome name, position and U(eq) fropm the CIF. Each table contents the atome label + x, y and z coordinate and the U(eq)

Parameters:: cif - The CIF-object of the Xtal structure
(type=dictionnary)

Returns:: tupple of 2 tables, the first with the heavy atoms, the second with the hydrogens
(type=tupple)

BondAngle(cif)

Returns a dictionnary with all the bond/valence angles between heavy atoms Datas have to be already in the CIF

Parameters:: cif - The CIF-object of the Xtal structure
(type=dictionnary)

Returns:: dictionnary with all the "A1 - A2 - A3":"Angle"
(type=dictionnary)

BondLength(cif)

Returns a dictionnary with all the bond lengths between heavy atoms. Datas have to be already in the CIF

Parameters:: cif - The CIF-object of the Xtal structure
(type=dictionnary)

Returns:: a dictionnary with all the "A1 - A2": "distance"
(type=dictionnary)

CellVol(cif)

calculate the cell volume and return it as a real (in Å³)

ChechForCSD(cif, name='None')

check in the CIF data if all the data needed to generate a RST report are present. If not it will ask many anoying questions

ChechForRST(cif)

check in the CIF data if all the data needed to generate a RST report are present. If not it will ask many anoying questions

CheckSym(cif, fix=False)

Checks the symetry of a CIF file based on the symmetry operations

Parameters:: cif - the CIF dictionnary of a Xtal structure; fix - True if you want a corrected version of the CIF to be returned

Returns:: the warning if the symmetry is not coherent inside the CIF data
(type=string)

cif2str(cif)

converts a cif dictionnary to a string according to the CIF syntax

Parameters:: cif - the CIF dictionnary correspondinf to a Xtal structure @return : a sting that corresponds to the content of the CIF-file.

Density(cif)

calculate the density in Mg/m³, for information : 10^30/Na/10^6=1.66054018667

dot2virg(text)

Substitute the english dots with french virgules

Parameters:: text - input test
(type=string)

Returns:: modified text
(type=string)

exists(cif, key)

Check if the key exists in the CIF.

Parameters:: cif - CIF dictionnary; key - CIF kay
(type=string)

Returns:: True if the key exists in the CIF dictionnary and is non empty
(type=boolean)

floatp(txt)

Removes the () from the text and convert to a float

Parameters:: txt - the input test
(type=string)

Returns:: the value of the txt
(type=float)

formula2chem(txt)

return a HTML representatin of the chemical formula

Html2table(html, BL, X, Y)

This function appends a table element to the html file with the X and Y headers

LoadCIF(filename)

Load the CIF file and returns the dictionnary

Parameters:: filename - the name of the file to open
(type=string)

Returns:: the CIF object corresponding to the Xtal structure
(type=dictionnary)

MainreportEN(html, cif)

This function generates the report in ENGLISH and add it to the HTML file

Parameters:: html - HTML file represented as an XML object
(type=XML object); cif - The CIF-object of the Xtal structure
(type=dictionnary)

Returns:: None

MainreportFR(html, cif)

this function generates the report in FRENCH to the HTML file

mergeplaton(cif, acc)

Merge cif and acc and returns a completed CIF-object. Special care is taken to select the most usefull data generated by platon

Parameters:: cif - the initial CIF-object
(type=dictionnary); acc - the CIF-object generated by platon
(type=dictionnary)

Returns:: merged CIF-object
(type=dictionnary)

MergeSg(name, kcd, sg)

Merge 2 cif objects : add from sg the missing values in kcd

Parameters:: name - the name of the molecule, used only if the value exist in kcd
(type=string); kcd - The CIF-object of the Xtal structure
(type=dictionnary); sg - The CIF-object of the Xtal structure
(type=dictionnary)

Returns:: a new cif-object
(type=dictionnary)

MolForm(cif, zp)

count the atoms and returns the molecular formula. Zp is the number of molecule per asymetric cell

MolWeight(formula)

calculate the molecular weight of a compound using its formula

oneloop(fields, start)

Processes one loop in the data extraction of the CIF file

Parameters:: fields - list of all the words contained in the cif file
(type=list); start - the starting index corresponding to the "loop_" key
(type=integer)

Returns:: the list of loop dictionnaries, the length of the data extracted from the fields and the list of all the keys of the loop.
(type=tupple)

parsecif(text)

-Parses the text of a CIF file

-Cut it in fields

-Find all the loops and process

-Find all the keys and values

Parameters:: text - the content of the CIF-file
(type=string)

Returns:: An CIF dictionnary
(type=dictionnary)

platon(filename)

process the data throught PLATON

Parameters:: filename - name of the CIF (or .res ....) file
(type=string)

Returns:: the CIF data generated by PLATON
(type=dictionnary)

readcif(filename)

-Check if the filename exists

-read the cif file

-removes the comments

Parameters:: filename - the name of the CIF file
(type=string)

Returns:: a string containing the raw data
(type=string)

renamefile(infile, namelist)

The CSD database has only room for 8 char to define the reference of the molecule. This function just tries to find a coherent name for the molecule in the database : it uses the 6 first numbers of the molecule name then "-" or a letter depending if the Xtal is a base or a salt (the letter corresponding to the number of the salt) The 8th position is for the polymorph or the data-acquisition.

Afterwars it asks the user for the name, provinding a suggestion.

Parameters:: infile - name of the CIF file
(type=string); namelist - list of all the files that already exists
(type=list)

Returns:: the name of the reference suggested by the program @rtype:string

SaveCIF(cif, filename='test.cif')

transforms the CIF object in string and write it into the given file

splitcif(text)

Separate the text in fields as defined in the CIF

Parameters:: text - the content of the CIF-file
(type=string)

Returns:: list of all the fields of the CIF
(type=list)

stringmulti(text, value)

Convert a string to a real, multiplies by the value and returns a string

Parameters:: text - input text
(type=string); value
(type=float or integer)

Returns:: txt*value
(type=string)

structureImage(basename, structure='structure')

lauch PLATON and let the user chose the structural (or the ortep or powder) representation of the molecule

Parameters:: basename - the name of the CIF-file without the extention
(type=string); structure - can be "powder" and "ortep", if not a simple structure is chosen @return None
(type=string)

symop(cif)

Lists all the symetricaly equivalent positions @param cif: CIF object of the Xtal structure

Parameters:: cif
(type=dictionnary)

Returns:: ";" separated list of xyz equivalent positions
(type=string)

WriteReport(filename, cif, Lang='En')

This function writes out an X-Ray structure report as an HTML file in the given language with the data taken from the CIF dictionnary

Parameters:: filename - Name of the file (usually .cif or .html)
(type=string); cif - The CIF-object of the Xtal structure
(type=dictionnary); Lang - The language in which the repport has to be written, the default is English
(type=string)

XraySummary(html, cif)

This function appends a table summarizing the Xray analysis, usually in Annexe as table 1

Parameters:: html - HTML file represented as an XML-object
(type=XML object); cif - The CIF-object of the Xtal structure
(type=dictionnary)

Returns:: None

Zprime(cif)

Calculate Z' = Z/nop if the latice is primitive zp=2*Z/nop if the latice is centered ...

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