#!/usr/bin/python2 # -*- coding: latin1 -*- #this is a library with modules for reading, writing and transforming CIF files # Written by Jerome Kieffer Email: jerome.kieffer at terre-adelie.org or jerome.kieffer at terre-adelie.org # # Needs a functionnal version of platon, convert (imageMagic) and mozilla to generate reports #!/usr/nekoware/bin/python #!/disk1/cambridge/c_sgiv6/bin/python2.2 import os.path, sys, re,time, os,string #at the moment, the symmetries are not yet complete. please send me the modifications by Email Symmetries={"x,y,z": ['Triclinic', 'P 1'], "x,y,z;-x,-y,-z": ['Triclinic', 'P -1'], "x,y,z;-x,y+1/2,-z": ['Monoclinic', 'P 21'], "x,y,z;-x,y+1/2,-z+1/2;-x,-y,-z;x,-y+1/2,z+1/2": ['Monoclinic', 'P 21/c'], "x,y,z;-x,y+1/2,-z+1/2;-x,-y,-z;x,-y-1/2,z-1/2": ['Monoclinic', 'P 21/c'], "x,y,z;-x+1/2,y+1/2,-z+1/2;-x,-y,-z;x-1/2,-y-1/2,z-1/2": ['Monoclinic', 'P 21/n'], "x,y,z;x+1/2,-y+1/2,z+1/2;-x,-y,-z;-x-1/2,y-1/2,-z-1/2": ['Monoclinic', 'P 21/n'], "x,y,z;-x+1/2,y+1/2,-z;-x,-y,-z;x-1/2,-y-1/2,z": ['Monoclinic', 'P 21/a'], "x,y,z;-x,y,-z+1/2;x+1/2,y+1/2,z;-x+1/2,y+1/2,-z+1/2;-x,-y,-z;x,-y,z+1/2;-x+1/2,-y+1/2,-z;x+1/2,-y+1/2,z+1/2": ['Monoclinic', 'C 2/c'], "x,y,z;-x,y,-z+1/2;x+1/2,y+1/2,z;-x+1/2,y+1/2,-z+1/2;-x,-y,-z;x,-y,z-1/2;-x+1/2,-y+1/2,-z;x+1/2,-y+1/2,z-1/2": ['Monoclinic', 'C 2/c'], "x,y,z;-x,y,-z;x+1/2,y+1/2,z;-x+1/2,y+1/2,-z": ['Monoclinic', 'C 2'], "x,y,z;x,-y,z+1/2": ['Monoclinic', 'P c'], "x,y,z;-x,y,-z;x+1/2,y+1/2,z+1/2;-x+1/2,y+1/2,-z+1/2": ['Monoclinic', 'I 2'], "x,y,z;-x+1/2,-y,z+1/2;-x,y+1/2,-z+1/2;x+1/2,-y+1/2,-z": ['Orthorhombic', 'P 21 21 21'], "x,y,z;-x+1/2,-y,z+1/2;x+1/2,-y+1/2,-z;-x,y+1/2,-z+1/2": ['Orthorhombic', 'P 21 21 21'], "x,y,z;-x,-y,z;-x+1/2,y+1/2,-z;x+1/2,-y+1/2,-z": ['Orthorhombic', 'P 21 21 21'], "x,y,z;x+1/2,-y+1/2,-z;-x,y+1/2,-z+1/2;-x+1/2,-y,z+1/2":['Orthorhombic', 'P 21 21 21'], "x,y,z;-x,-y,z+1/2;-x+1/2,y+1/2,z+1/2;x+1/2,-y+1/2,z": ['Orthorhombic', 'P n a 21'], "x,y,z;-x,-y,z+1/2;x+1/2,-y+1/2,z;-x+1/2,y+1/2,z+1/2": ['Orthorhombic', 'P n a 21'], "x,y,z;-x,-y,z+1/2;x+1/2,-y,z;-x+1/2,y,z+1/2": ['Orthorhombic', 'P c a 21'], "x,y,z;x+1/2,-y,-z;x,-y+1/2,z+1/2;x+1/2,y+1/2,-z+1/2": ['Orthorhombic', 'P 21 c n'], "x,y,z;x+1/2,-y,-z;x,y+1/2,-z+1/2;x+1/2,-y+1/2,z+1/2": ['Orthorhombic', 'P 21 n b'], "x,y,z;-x+1/2,-y,z+1/2;-x,y+1/2,-z+1/2;x+1/2,-y+1/2,-z;-x,-y,-z;x+1/2,y,-z+1/2;x,-y+1/2,z+1/2;-x+1/2,y+1/2,z": ['Orthorhombic', 'P b c a'], "x,y,z;-x+1/2,-y,z+1/2;-x,y+1/2,-z+1/2;x+1/2,-y+1/2,-z;-x,-y,-z;x-1/2,y,-z-1/2;x,-y-1/2,z-1/2;-x-1/2,y-1/2,z": ['Orthorhombic', 'P b c a'], "x,y,z;x,-y,-z;x,-y+1/2,z+1/2;x,y+1/2,-z+1/2;x+1/2,y+1/2,z;x+1/2,-y+1/2,-z;x+1/2,-y,z+1/2;x+1/2,y,-z+1/2": ['Orthorhombic', 'C 2 c b'], "x,y,z;-y,x-y,z+1/3;-x+y,-x,z+2/3": ['Trigonal', 'P 31'], "x,y,z;-x,-y,z+1/2;-y,x,z+1/4;y,-x,z+3/4": ['Tetragonal', 'P 43'], "x,y,z;-x+1/2,-y,z+1/2;-y+3/4,x+1/4,z+1/4;y+3/4,-x+3/4,z+3/4;x+1/2,y+1/2,z+1/2;-x+1,-y+1/2,z+1;-y+5/4,x+3/4,z+3/4;y+5/4,-x+5/4,z+5/4;-x,-y,-z;x-1/2,y,-z-1/2;y-3/4,-x-1/4,-z-1/4;-y-3/4,x-3/4,-z-3/4;-x+1/2,-y+1/2,-z+1/2;x,y+1/2,-z;y-1/4,-x+1/4,-z+1/4;-y-1/4,x-1/4,-z-1/4": ['Tetragonal', 'I 41/a'], } #Atomic moleculat weight taken from the MPQC program : http://www.mpqc.org AtomicWeight={ 'Ac':227.03, 'Ag':107.87, 'Al':26.98, 'Am':243.00, 'Ar':39.96, 'As':74.92, 'At':210.00, 'Au':196.97, 'B':11.01, 'Ba':137.33, 'Be':9.01, 'Bi':208.98, 'Bk':247.00, 'Br':79.90, 'C':12.01, 'Ca':39.96, 'Cd':112.41, 'Ce':140.12, 'Cf':251.00, 'Cl':35.45, 'Cm':247.00, 'Co':58.93, 'Cr':51.94, 'Cs':132.91, 'Cu':63.55, 'Dy':162.50, 'Er':167.26, 'Es':254.00, 'Eu':151.96, 'F':19.00, 'Fe':55.85, 'Fm':257.00, 'Fr':223.00, 'Ga':68.93, 'Gd':157.25, 'Ge':73.92, 'H':1.01, 'Ha':260.00, 'He':4.00, 'Hf':178.49, 'Hg':200.59, 'Ho':164.93, 'I':126.90, 'In':114.82, 'Ir':192.22, 'K':39.10, 'Kr':83.91, 'La':138.91, 'Li':6.94, 'Lr':260.00, 'Lu':174.97, 'Md':258.00, 'Mg':23.99, 'Mn':54.94, 'Mo':95.94, 'N':14.01, 'Na':22.99, 'Nb':92.91, 'Nd':144.24, 'Ne':19.99, 'Ni':58.70, 'No':259.00, 'Np':237.05, 'O':16.00, 'Os':190.20, 'P':30.97, 'Pa':231.04, 'Pb':207.20, 'Pd':106.40, 'Pm':145.00, 'Po':209.00, 'Pr':140.91, 'Pt':195.09, 'Pu':244.00, 'Ra':226.03, 'Rb':85.47, 'Re':186.21, 'Rf':260.00, 'Rh':102.91, 'Rn':222.00, 'Ru':101.07, 'S':32.06, 'Sb':121.75, 'Sc':44.96, 'Se':79.92, 'Si':27.98, 'Sm':150.40, 'Sn':118.69, 'Sr':87.62, 'Ta':180.95, 'Tb':158.93, 'Tc':98.00, 'Te':127.60, 'Th':232.04, 'Ti':47.95, 'Tl':204.37, 'Tm':168.93, 'U':238.03, 'Un':266.00, 'V':50.94, 'W':183.85, 'Xe':131.30, 'Y':88.91, 'Yb':173.04, 'Zn':65.35, 'Zr':91.22 } NeededForRST={"_chemical_name_common":"Name of the molecule", "_symmetry_cell_setting":"Cell setting", "_symmetry_space_group_name_H-M":"Space group", "_cell_length_a":"Length a (Å)", "_cell_length_b":"Length b (Å)", "_cell_length_c":"Length c (Å)", "_cell_angle_alpha":"Angle alpha (°)", "_cell_angle_beta":"Angle beta (°)", "_cell_angle_gamma":"Angle gamma (°)", "_chemical_formula_moiety":"Chemical formula", "_chemical_formula_weight":"Molecular weight", "_diffrn_ambient_temperature":"Temperature (K)", "_diffrn_radiation_wavelength":"Wavelength (Å)", "_diffrn_radiation_type":"X-Ray source", "_diffrn_radiation_monochromator":"Monochromator", "_cell_formula_units_Z":"Molecule per cell (Z)", "_exptl_crystal_density_diffrn":"Density (Mg/m³)", "_diffrn_reflns_number":"Total number of reflexions" , "_reflns_number_total": "Total number of UNIC reflexions", # "_refine_ls_R_factor_gt":"R factor", # "_computing_data_collection":"Data collection", "_diffrn_measurement_device_type":"Diffractometer", "_exptl_special_details" : "Experimental details", "_cell_volume": "Cell volume (ų)", "_exptl_crystal_F_000": "F(000) (effective number of electrons)", "_diffrn_reflns_theta_min": "Theta min (°)", "_diffrn_reflns_theta_max": "Theta max (°)", "_diffrn_reflns_limit_h_min":"Minimal h indice", "_diffrn_reflns_limit_h_max":"Maximal h indice", "_diffrn_reflns_limit_k_min":"Minimal k indice", "_diffrn_reflns_limit_k_max":"Maximal k indice", "_diffrn_reflns_limit_l_min":"Minimal l indice", "_diffrn_reflns_limit_l_max":"Maximal l indice", "_diffrn_reflns_av_R_equivalents":"Average Residual for each reflection class", "_diffrn_measured_fraction_theta_max":"Completeness to theta_max", "_refine_ls_number_reflns":"Number of reflexions", "_refine_ls_number_parameters":"Number of paramaters", "_refine_ls_number_restraints":"Number of restraints", "_refine_ls_goodness_of_fit_ref":"Goodness of fit", "_refine_ls_R_factor_gt":"R factor on intense reflections", "_refine_ls_R_factor_all":"R factor on all reflections", "_refine_ls_wR_factor_ref":"Weighted R factor on all reflections", "_refine_ls_wR_factor_gt":"Weighted R factor on intense reflections", "_refine_ls_abs_structure_Flack":"Absolute Structure parameter", # "_refine_ls_extinction_coef":"Extinction coefficient.", "_refine_diff_density_max":"Largest electron density peak (e/ų)", "_refine_diff_density_min":"Deepest electron density hole (e/ų)", "_exptl_absorpt_coefficient_mu":"Absorption coefficient", } NeededForCSD={#"_database_code_CSD":"Database Code", #by another way "_publ_author_name":"Author", "_symmetry_cell_setting":"Cell setting", "_symmetry_space_group_name_H-M":"Space group", "_cell_length_a":"Length a (Å)", "_cell_length_b":"Length b (Å)", "_cell_length_c":"Length c (Å)", "_cell_angle_alpha":"Angle alpha (°)", "_cell_angle_beta":"Angle beta (°)", "_cell_angle_gamma":"Angle gamma (°)", "_chemical_formula_moiety":"Chemical formula", "_chemical_formula_weight":"Molecular weight", "_diffrn_radiation_type":"X-Ray source", "_cell_formula_units_Z":"Molecule per cell (Z)", "_cell_volume": "Cell volume (ų)", "_exptl_crystal_density_diffrn":"Density (Mg/m³)", "_refine_ls_R_factor_gt":"R factor on intense reflections", "_chemical_name_systematic":"Chemical name", "_chemical_name_common":"Chemical name (synonym)", "_publ_section_comment":"Other comments" } UpperKey=['_atom_site_B_iso_or_equiv','_symmetry_space_group_name_Hall', '_atom_site_Cartn_x','_atom_site_Cartn_y','_atom_site_Cartn_z','_atom_site_U_iso_or_equiv', '_atom_site_Wyckoff_symbol','_atom_site_aniso_B_11','_atom_site_aniso_B_12','_atom_site_aniso_B_13', '_atom_site_aniso_B_22','_atom_site_aniso_B_23','_atom_site_aniso_B_33','_atom_site_aniso_U_11', '_atom_site_aniso_U_12','_atom_site_aniso_U_13','_atom_site_aniso_U_22','_atom_site_aniso_U_23', '_atom_site_aniso_U_33','_atom_sites_Cartn_tran_matrix_11','_atom_sites_Cartn_tran_matrix_12','_atom_sites_Cartn_tran_matrix_13', '_atom_sites_Cartn_tran_matrix_21','_atom_sites_Cartn_tran_matrix_22','_atom_sites_Cartn_tran_matrix_23','_atom_sites_Cartn_tran_matrix_31', '_atom_sites_Cartn_tran_matrix_32','_atom_sites_Cartn_tran_matrix_33','_atom_sites_Cartn_transform_axes','_atom_type_scat_Cromer_Mann_a1', '_atom_type_scat_Cromer_Mann_a2','_atom_type_scat_Cromer_Mann_a3','_atom_type_scat_Cromer_Mann_a4','_atom_type_scat_Cromer_Mann_b1', '_atom_type_scat_Cromer_Mann_b2','_atom_type_scat_Cromer_Mann_b3','_atom_type_scat_Cromer_Mann_b4','_atom_type_scat_Cromer_Mann_c', '_cell_formula_units_Z','_chemical_conn_atom_NCA','_chemical_conn_atom_NH','_database_code_CAS', '_database_code_CSD','_database_code_ICSD','_database_code_MDF','_database_code_NBS', '_database_code_PDF','_database_journal_ASTM','_database_journal_CSD','_diffrn_orient_matrix_UB_11', '_diffrn_orient_matrix_UB_12','_diffrn_orient_matrix_UB_13','_diffrn_orient_matrix_UB_21','_diffrn_orient_matrix_UB_22', '_diffrn_orient_matrix_UB_23','_diffrn_orient_matrix_UB_31','_diffrn_orient_matrix_UB_32','_diffrn_orient_matrix_UB_33', '_diffrn_reflns_av_R_equivalents','_diffrn_reflns_av_sigmaI/netI','_exptl_absorpt_correction_T_max','_exptl_absorpt_correction_T_min', '_exptl_crystal_F_000','_geom_hbond_angle_DHA','_geom_hbond_atom_site_label_A','_geom_hbond_atom_site_label_D', '_geom_hbond_atom_site_label_H','_geom_hbond_distance_DA','_geom_hbond_distance_DH','_geom_hbond_distance_HA', '_geom_hbond_site_symmetry_A','_geom_hbond_site_symmetry_D','_geom_hbond_site_symmetry_H','_journal_coden_ASTM', '_journal_coden_Cambridge','_refine_ls_R_factor_all','_refine_ls_R_factor_gt','_refine_ls_R_factor_obs', '_refine_ls_abs_structure_Flack','_refine_ls_abs_structure_Rogers','_refine_ls_restrained_S_all','_refine_ls_restrained_S_obs', '_refine_ls_wR_factor_all','_refine_ls_wR_factor_gt','_refine_ls_wR_factor_obs','_refine_ls_wR_factor_ref', '_refln_A_calc','_refln_A_meas','_refln_B_calc','_refln_B_meas', '_refln_F-squared_meas','_refln_F_calc','_refln_F_meas','_refln_F_sigma', '_refln_F_squared_calc','_refln_F_squared_sigma','_reflns_scale_meas_F','_reflns_scale_meas_F_squared', '',','',','_space_group_IT_number','_space_group_name_H-M', '_space_group_name_H-M_alt','_space_group_name_Hall','_symmetry_Int_Tables_number','_symmetry_space_group_name_H-M', ] DefaultAuthor="J. Kieffer" Version=[" Generated by libcif.py : June 2005"," Written by Jerome Kieffer : Jerome.Kieffer@terre-adelie.org "," X-Ray Crystallography "," (France)"] #check for the existance of Booleans : this is only if your python is too old try: True except: True=(1==1) False=(1==0) EOL=["\r","\n","\r\n","\n\r"] Blank=[" "," "]+EOL StartComment=["\"","\'"] for i in EOL: StartComment.append((i+";")) EndComment=[] for i in EOL: EndComment.append(i+";") for i in ["\"","\'"]: for j in Blank: EndComment.append(i+j) def LoadCIF(filename): """Load the CIF file and returns the dictionnary @param filename: the name of the file to open @type filename: string @return: the CIF object corresponding to the Xtal structure @rtype: dictionnary""" cif=parsecif(readcif(filename)) #this corrects a bug that has existed for a long time about the case of the cif-keys: we just transform all the lowercase field in conventionnal writing keys={} for i in UpperKey: keys[i.lower()]=i cif2={} for i in cif: j=i.lower() if j in keys.keys(): cif2[keys[j]]=cif[i] else: cif2[j.lower()]=cif[i] return cif2 def readcif(filename): """-Check if the filename exists -read the cif file -removes the comments @param filename: the name of the CIF file @type filename: string @return: a string containing the raw data @rtype: string""" if not os.path.isfile(filename): raise("I cannot find the file %s"%filename) sys.exit(1) f=open(filename,"r").readlines() text="" for ligne in f: pos=ligne.find("#") if pos >=0: text+=ligne[:pos]+"\n" if pos>80 : print "Warning, this line is too long and could cause problems in PreQuest\n",ligne else : text+=ligne if len(ligne.strip())>80 : print "Warning, this line is too long and could cause problems in PreQuest\n",ligne return text def oneloop(fields,start): """Processes one loop in the data extraction of the CIF file @param fields: list of all the words contained in the cif file @type fields: list @param start: the starting index corresponding to the "loop_" key @type start: integer @return: the list of loop dictionnaries, the length of the data extracted from the fields and the list of all the keys of the loop. @rtype: tupple """ # in earch loop we first search the length of the loop curloop={} loop=[] keys=[] i=start+1 fini=False while not fini: if fields[i][0]=="_": keys.append(fields[i])#.lower()) i+=1 else: fini=True data=[] while True: if i>=len(fields): break elif len(fields[i])==0: break elif fields[i][0]=="_": break elif fields[i] in ["loop_","stop_","global_","data_","save_"]: break else: data.append(fields[i]) i+=1 # print len(keys), len(data) k=0 if len(data)0: for i in loopidx: loopone,length,keys=oneloop(fields,i) loop.append([keys,loopone]) looplen.append(length) for i in range(len(loopidx)-1,-1,-1): f1=fields[:loopidx[i]]+fields[loopidx[i]+looplen[i]:] fields=f1 cif["loop_"]=loop for i in range(len(fields)-1): if fields[i][0]=="_" and fields[i+1][0]!="_": cif[fields[i]]=fields[i+1] return cif def splitcif(text): """Separate the text in fields as defined in the CIF @param text: the content of the CIF-file @type text: string @return: list of all the fields of the CIF @rtype: list """ fields=[] while True: if len(text)==0: break elif text[0]=="'": idx=0 fini=False while not fini: idx+=1+text[idx+1:].find("'") ##########debuging in case we arrive at the end of the text if idx>=len(text)-1: # print text,idx,len(text) fields.append(text[1:-1].strip()) text="" fini=True break if text[idx+1] in Blank: fields.append(text[1:idx].strip()) text1=text[idx+1:] text=text1.strip() fini=True elif text[0]=='"': idx=0 fini=False while not fini: idx+=1+text[idx+1:].find('"') ##########debuging in case we arrive at the end of the text if idx>=len(text)-1: # print text,idx,len(text) fields.append(text[1:-1].strip()) text="" fini=True break if text[idx+1] in Blank: fields.append(text[1:idx].strip()) text1=text[idx+1:] text=text1.strip() fini=True elif text[0]==';': idx=0 fini=False while not fini: idx+=1+text[idx+1:].find(';') if text[idx-1] in EOL: fields.append(text[1:idx-1].strip()) text1=text[idx+1:] text=text1.strip() fini=True else: f=text.split(None,1)[0] fields.append(f) text1=text[len(f):].strip() text=text1 return fields ############################################################################################# ######## everything needed to write a cif file ######################################### ############################################################################################# def SaveCIF(cif,filename="test.cif"): """transforms the CIF object in string and write it into the given file""" txt=cif2str(cif) try: f=open(filename,"w") f.write(txt) f.close() except: raise("Error during the writing of this file : %s"%filename) def cif2str(cif): """converts a cif dictionnary to a string according to the CIF syntax @param cif: the CIF dictionnary correspondinf to a Xtal structure @return : a sting that corresponds to the content of the CIF-file. """ txt="" for i in Version: txt+="#"+i+"\n" if exists(cif,"_chemical_name_common"): t=cif["_chemical_name_common"].split()[0] else: t="" txt+="data_%s\n"%t #first of all get all the keys : keys=cif.keys() keys.sort() for i in keys: if i=="loop_":continue value=cif[i] if value.find("\n")>-1: #should add value between ;; ligne="%s \n;\n %s \n;\n"%(i,value) elif len(value.split())>1: #should add value between '' ligne="%s '%s' \n"%(i,value) if len(ligne)>80: ligne="%s\n '%s' \n"%(i,value) else: ligne="%s %s \n"%(i,value) if len(ligne)>80: ligne="%s\n %s \n"%(i,value) txt+=ligne if cif.has_key("loop_"): for loop in cif["loop_"]: txt+="loop_ \n" keys=loop[0] data=loop[1] for i in keys: txt+=" %s \n"%i for i in data: ligne="" for key in keys: rawvalue=i[key] if rawvalue.find("\n")>-1: #should add value between ;; ligne+="\n; %s \n;\n"%(rawvalue) txt+=ligne ligne="" else: if len(rawvalue.split())>1: #should add value between '' value="'%s'"%(rawvalue) else: value=rawvalue if len(ligne)+len(value) > 78: txt+=ligne+" \n" ligne=" "+value else: ligne+=" "+value txt+=ligne+" \n" txt+="\n" return txt ################################################################################################ ######### few calculation on the structure ###### ################################################################################################ def CheckSym(cif,fix=False): """ Checks the symetry of a CIF file based on the symmetry operations @param cif: the CIF dictionnary of a Xtal structure @param fix: True if you want a corrected version of the CIF to be returned @return: the warning if the symmetry is not coherent inside the CIF data @rtype: string """ warning="" so=symop(cif) if len(so)==0 : warning+="Warning : no symmetry operation detected\n" elif not Symmetries.has_key(so): warning+="Warning : the symmetry exists but is not defined in the program, please check the data and the programm\n%s\n"%so else: [cell,sg]=Symmetries[so] if cif.has_key("_symmetry_cell_setting"): if cell.lower()!=cif["_symmetry_cell_setting"].lower(): warning+="Warning : I found a %s cell wheras it is set to %s. \n"%(cell,cif["_symmetry_cell_setting"]) cif["_symmetry_cell_setting"]=cell else: warning+="Warning : The symmetry of the cell is not set but I think it is %s.\n"%(cell) cif["_symmetry_cell_setting"]=cell if cif.has_key("_symmetry_space_group_name_H-M"): if sg.lower()!=cif["_symmetry_space_group_name_H-M"].lower(): warning+="Warning : I found a %s space group wheras it is set to %s. \n"%(sg,cif["_symmetry_space_group_name_H-M"]) cif["_symmetry_space_group_name_H-M"]=sg else: warning+="Warning : The Space Group is not set but I think it is %s.\n"%(sg) cif["_symmetry_space_group_name_H-M"]=sg if fix: return warning,cif else: return warning def symop(cif): """Lists all the symetricaly equivalent positions\ @param cif: CIF object of the Xtal structure @type cif: dictionnary @return: ";" separated list of xyz equivalent positions @rtype: string """ txt="" for loop in cif["loop_"]: for key in loop[0]: if key=="_symmetry_equiv_pos_as_xyz": for i in loop[1]: txt+=(i["_symmetry_equiv_pos_as_xyz"]+";") txt2,count=re.subn(" ","",txt[:-1]) txt3,count=re.subn(";+",";",txt2.lower()) txt,count=re.subn(",+",",",txt3) newtxt="" for i in txt.split(";"): for j in i.split(","): # print "txt=", j pos=0 for k in ["x","y","z"]: if j.find(k)!=-1: pos=j.find(k) break if pos==0: sig="+" else: sig=j[pos-1] res="" if pos in [0,1]: if pos0 : if res[0] not in ["+","-"]: res="+"+res #print j+"="+sig,j[pos],res if sig=="-": t="-"+j[pos]+res else: t=j[pos]+res # if t!=j:print j+"="+t newtxt+=t+"," newtxt=newtxt[:-1]+";" return newtxt[:-1] def exists(cif,key): """ Check if the key exists in the CIF. @param key: CIF kay @type key: string @param cif: CIF dictionnary @return: True if the key exists in the CIF dictionnary and is non empty @rtype: boolean """ bool=False if cif.has_key(key): if len(cif[key])>=1: if cif[key][0]!="?" : bool=True return bool def CellVol(cif): """calculate the cell volume and return it as a real (in ų)""" needed=["_cell_length_a","_cell_length_b","_cell_length_c","_cell_angle_alpha", "_cell_angle_beta","_cell_angle_gamma"] for i in needed: if not exists(cif,i): return 0 import math a=floatp(cif["_cell_length_a"]) b=floatp(cif["_cell_length_b"]) c=floatp(cif["_cell_length_c"]) ca=math.cos(math.pi/180*floatp(cif["_cell_angle_alpha"])) cb=math.cos(math.pi/180*floatp(cif["_cell_angle_beta"])) cc=math.cos(math.pi/180*floatp(cif["_cell_angle_gamma"])) return a*b*c*math.sqrt(1-ca*ca-cb*cb-cc*cc+2*ca*cb*cc) def Zprime(cif): """Calculate Z' = Z/nop if the latice is primitive zp=2*Z/nop if the latice is centered ...""" zp=float(cif["_cell_formula_units_Z"])/len(symop(cif).split(";")) return str(int(zp)) #cif["_cell_formula_units_Z"]=str(zp*len(symop(cif).split(";"))) def MolForm(cif,zp): """count the atoms and returns the molecular formula. Zp is the number of molecule per asymetric cell""" form={} for loop in cif["loop_"]: for key in loop[0]: if key=="_atom_site_type_symbol": for i in loop[1]: atom=i["_atom_site_type_symbol"] try: occ=i["_atom_site_occupancy"] except: occ="1" if atom in form.keys(): form[atom]+=floatp(occ) else: form[atom]=floatp(occ) keys=form.keys() keys.sort() try: keys.remove("H") keys=["H"]+keys except: pass try: keys.remove("C") keys=["C"]+keys except: pass txt="" for i in keys: if abs(form[i]/zp-1)<1E-3: txt+="%s "%(i) else: txt+="%s%i "%(i,form[i]/zp) return txt.strip() def MolWeight(formula): """calculate the molecular weight of a compound using its formula""" MW=0 for sub in formula.split(): j=sub.strip() atom="" count="" for i in j: figures= [ str(x) for x in range(10)] if i in figures: count+=i else: atom+=i if AtomicWeight.has_key(atom): if len(count)==0: x=1 else: x=floatp(count) MW+=AtomicWeight[atom]*x else: print "WARNING !!! the program is lacking the molecular weight of "+atom return MW def Density(cif): """calculate the density in Mg/m³, for information : 10^30/Na/10^6=1.66054018667""" MW=floatp(cif["_chemical_formula_weight"]) cell=floatp(cif["_cell_volume"]) Z=int(cif["_cell_formula_units_Z"]) return 1.66054018667*MW*Z/cell def AsymetricCellContents(cif): """tries to find the contents of the asymetric cell """ txt="" if exists(cif,"_chemical_formula_moiety"): txt=cif["_chemical_formula_moiety"] return txt.split(",") def CheckForRST(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""" if exists(cif,"_computing_data_collection") and not exists(cif,"_diffrn_measurement_device_type"): cif["_diffrn_measurement_device_type"]=cif["_computing_data_collection"] table=NeededForRST.keys() table.sort() modified=False for key in table: if not exists(cif,key): modified=True txt=raw_input(" %s ? (%s) -->"%(NeededForRST[key],key)) if len(txt)==0:txt="?" cif[key]=txt return cif,modified def CheckForCSD(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""" if name[-4:].lower()==".cif":name=name[:-4] modified=False if not exists(cif,"_diffrn_ambient_temperature") and exists(cif,"_cell_measurement_temperature"): modified=True cif["_diffrn_ambient_temperature"]=cif["_cell_measurement_temperature"] if not exists(cif,"_cell_volume"): vol=CellVol(cif) if vol>1: modified=True cif["_cell_volume"]="%8.2f"%vol if not exists(cif,"_cell_formula_units_Z"): modified=True txt=raw_input(" Number of molecules per asymmetric cell ? (Z') -->") try: zp=int(txt) except: zp=1 cif["_cell_formula_units_Z"]=str(zp*len(symop(cif).split(";"))) if not exists(cif,"_chemical_formula_sum"): cif["_chemical_formula_sum"]=MolForm(cif,int(cif["_cell_formula_units_Z"])/len(symop(cif).split(";"))) if not exists(cif,"_chemical_formula_moiety"): modified=True txt=raw_input(" Chemical formula ? (_chemical_formula_moiety) [%s] -->"%cif["_chemical_formula_sum"]) if txt=="": cif["_chemical_formula_moiety"]=cif["_chemical_formula_sum"] else: cif["_chemical_formula_moiety"]=txt.upper().strip() if cif["_chemical_formula_moiety"]=="C6 H12 O6": modified=True txt=raw_input(" Chemical formula ? (_chemical_formula_moiety) [%s] -->"%cif["_chemical_formula_sum"]) if txt=="": cif["_chemical_formula_moiety"]=cif["_chemical_formula_sum"] else: cif["_chemical_formula_moiety"]=txt.upper().strip() if not exists(cif,"_chemical_formula_weight") and exists(cif,"_chemical_formula_sum"): cif["_chemical_formula_weight"]="%7.2f"%MolWeight(cif["_chemical_formula_sum"]) if not exists(cif,"_exptl_crystal_density_diffrn") and exists(cif,"_cell_volume") and exists(cif,"_cell_formula_units_Z") and exists(cif, "_chemical_formula_weight"): cif["_exptl_crystal_density_diffrn"]="%5.3f"%Density(cif) if not exists(cif,"_refine_ls_R_factor_gt") and exists(cif,"_refine_ls_R_factor_obs"): cif["_refine_ls_R_factor_gt"]=cif["_refine_ls_R_factor_obs"] if not exists(cif,"_publ_author_name"): modified=True txt=raw_input(" Author ? (_publ_author_name) [%s] -->"%DefaultAuthor) if txt=="": cif["_publ_author_name"]=DefaultAuthor else: cif["_publ_author_name"]=txt if not exists(cif,"_journal_coden_Cambridge"): cif["_journal_coden_Cambridge"]="1078" # CAD "private communication" if not exists(cif,"_journal_year"): cif["_journal_year"]=str(time.localtime()[0]) # Publication year needed if not exists(cif,"_chemical_name_systematic"): modified=True txt=raw_input(" Chemical name ? (_chemical_name_systematic) [%s] -->"%name) if txt=="": cif["_chemical_name_systematic"]=name else: cif["_chemical_name_systematic"]=txt if not exists(cif,"_chemical_name_common") and exists(cif,"_chemical_name_systematic"): modified=True txt=raw_input(" Chemical name (synonym) ? (_chemical_name_common) [%s] -->"%cif["_chemical_name_systematic"]) if txt=="": cif["_chemical_name_common"]=cif["_chemical_name_systematic"] else: cif["_chemical_name_common"]=txt table=NeededForCSD.keys() table.sort() for key in table: if not exists(cif,key): modified=True txt=raw_input(" %s ? (%s) -->"%(NeededForCSD[key],key)) if len(txt)==0:txt="?" cif[key]=txt return cif,modified ###################################################################### ###### Some P.L.A.T.O.N. related stuff #################### ###################################################################### def platon(filename): """process the data throught PLATON @param filename: name of the CIF (or .res ....) file @type filename: string @return: the CIF data generated by PLATON @rtype: dictionnary """ chiral=[] if not os.path.isfile(filename): raise "error in the platon procedure : %s filename does not exist"%filename i,o=os.popen2("platon -o %s"%filename) i.write("TABL CIF\n") i.flush() for l in o.readlines(): print l.strip() if l.find("Chiral:")>-1: m=l.split() c={} c["_atom_site_asymmetry_label"]=m[1] c["_atom_site_asymmetry_type"]=m[9] chiral.append(c) o.close() i.close() cif=LoadCIF(os.path.splitext(filename)[0]+".acc") #here we remove the empty loops loops=cif["loop_"][:] #it is unwisy to modify a list used as loop iterator for loop in loops: if len(loop[1])==1: empty=True for i in loop[0]: if exists(loop[1][0],i):empty=False if empty: cif["loop_"].remove(loop) #here we append the information about chirality if len(chiral)>0: if exists(cif,"loop_"): cif["loop_"].append([["_atom_site_asymmetry_label","_atom_site_asymmetry_type"],chiral]) else: cif["loop_"]=[[chiral[0].keys(),chiral]] return cif def 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 @param cif: the initial CIF-object @type cif: dictionnary @param acc: the CIF-object generated by platon @type acc: dictionnary @return: merged CIF-object @rtype: dictionnary """ cif1=cif cif2=acc #first of all removes the sugar ;) if exists(cif,"_chemical_formula_moiety") and cif["_chemical_formula_moiety"]=="C6 H12 O6": cif["_chemical_formula_moiety"]="?" PassKey=["_publ_contact_letter","_publ_requested_journal","_publ_contact_letter","_loop","_publ_section_references","_publ_section_figure_captions"] for i in cif2: if i in PassKey: continue if ( not exists(cif,i)) and exists(cif2,i): cif[i]=cif2[i] loop1=[] for loop in cif["loop_"]: loop1.append(loop[0]) for loop in cif2["loop_"]: exist=False curkeys=loop[0] for l1 in loop1: c=0 for i in l1: if i in curkeys: c+=1 # if c>0 : print curkeys,c,len(l1),len(curkeys) if c==len(l1) or c>round(0.8*len(curkeys)): #here we accept if at least 80% is good. exist=True continue if not exist: cif["loop_"].append(loop) return cif ######################################################################################### ######################################################################### ###### Everything to write automaticalyy a report ####################### ######################################################################### def Html2table(html,BL,X,Y): """ This function appends a table element to the html file with the X and Y headers""" html.start("p") html.start("table cellspacing=10") html.start("tr") html.element("th",X) html.element("th",Y) keys=BL.keys() keys.sort() for i in keys: html.end("tr") html.start("tr") html.element("td", i) html.element("td", BL[i]) html.end("tr") html.end("table cellspacing=10") html.end("p") def AtomicCoord(html,table): """ This function appends a table with label, y, y, z and U to the html file""" html.start("p") html.start("table cellspacing=10") html.start("tr") html.element("th","Label") html.element("th","x") html.element("th","y") html.element("th","z") html.element("th","U(eq)") for i in table: html.end("tr") html.start("tr") html.element("td", i[0]) html.element("td", i[1]) html.element("td", i[2]) html.element("td", i[3]) html.element("td", i[4]) html.end("tr") html.end("table cellspacing=10") html.end("p") def XraySummary(html,cif): """ This function appends a table summarizing the Xray analysis, usually in Annexe as table 1 @param html: HTML file represented as an XML-object @type html: XML object @param cif: The CIF-object of the Xtal structure @type cif: dictionnary @return: None """ html.start("p") html.start("table cellspacing=15") html.start("tr") html.element("td","Identification code") html.element("td",cif["_chemical_name_common"]) html.end("tr") html.start("tr") html.element("td","Chemical formula") html.element("td",cif["_chemical_formula_sum"]) html.end("tr") html.start("tr") html.element("td","Molecular weight") html.element("td",cif["_chemical_formula_weight"]) html.end("tr") html.start("tr") html.element("td","Temperature") html.element("td",cif["_diffrn_ambient_temperature"]) html.end("tr") html.start("tr") html.element("td","Wavelength") html.element("td",cif["_diffrn_radiation_wavelength"]) html.end("tr") html.start("tr") html.element("td","Crystal system ; space group") html.element("td","%s ; %s"%(cif["_symmetry_cell_setting"],cif["_symmetry_space_group_name_H-M"])) html.end("tr") html.start("tr") html.element("td","Unit cell dimentions") html.start("td") html.rawdata(""%(cif["_cell_length_a"],cif["_cell_angle_alpha"])) html.rawdata(""%(cif["_cell_length_b"],cif["_cell_angle_beta"])) html.rawdata("
a = %s Å ; α = %s °
b = %s Å ; β = %s °
c = %s Å ; γ = %s °
"%(cif["_cell_length_c"],cif["_cell_angle_gamma"])) html.end("td") html.end("tr") html.start("tr") html.element("td","Volume") html.rawdata(" %s ų "%(cif["_cell_volume"])) html.end("tr") html.start("tr") html.element("td","Z, Calculated density") html.element("td","%s, %s Mg/m³"%(cif["_cell_formula_units_Z"],cif["_exptl_crystal_density_diffrn"])) html.end("tr") html.start("tr") html.element("td","Absorption coefficient") html.element("td","%s 1/mm"%(cif["_exptl_absorpt_coefficient_mu"])) html.end("tr") html.start("tr") html.element("td","F(000)") html.element("td",cif["_exptl_crystal_F_000"]) html.end("tr") html.start("tr") html.element("td","Theta range for data collection") html.element("td","%s° to %s°"%(cif["_diffrn_reflns_theta_min"],cif["_diffrn_reflns_theta_max"])) html.end("tr") html.start("tr") html.element("td","Limiting indices") html.element("td","%s <= h <= %s ; %s <= k <= %s ; %s <= l <= %s"%(cif["_diffrn_reflns_limit_h_min"],cif["_diffrn_reflns_limit_h_max"],cif["_diffrn_reflns_limit_k_min"],cif["_diffrn_reflns_limit_k_max"],cif["_diffrn_reflns_limit_l_min"],cif["_diffrn_reflns_limit_l_max"])) html.end("tr") html.start("tr") html.element("td","Reflexion collected / unique") html.element("td","%s / %s [R(int) = %s]"%(cif["_diffrn_reflns_number"],cif["_reflns_number_total"],cif["_diffrn_reflns_av_R_equivalents"])) html.end("tr") html.start("tr") html.element("td","Completness to theta max") try: r=float(cif["_diffrn_measured_fraction_theta_max"])*100 except: r=100 html.element("td","%s %%"%r) html.end("tr") html.start("tr") html.element("td","Refinement method") html.element("td","Full-matrix least-square on F²") html.end("tr") html.start("tr") html.element("td","Data / restraints / parameters") html.element("td","%s / %s / %s"%(cif["_refine_ls_number_reflns"],cif["_refine_ls_number_restraints"],cif["_refine_ls_number_parameters"])) html.end("tr") html.start("tr") html.element("td","Goodness of fit on F²") html.element("td",cif["_refine_ls_goodness_of_fit_ref"]) html.end("tr") html.start("tr") html.element("td","Final R indices [I>2sigma(I)]") html.element("td","R1 = %s ; wR2 = %s"%(cif["_refine_ls_R_factor_gt"],cif["_refine_ls_wR_factor_gt"])) html.end("tr") html.start("tr") html.element("td","Final R indices [all data]") html.element("td","R1 = %s ; wR2 = %s"%(cif["_refine_ls_R_factor_all"],cif["_refine_ls_wR_factor_ref"])) html.end("tr") html.start("tr") html.element("td","Absolute structure parameter") html.element("td",cif["_refine_ls_abs_structure_Flack"]) html.end("tr") # html.start("tr") # html.element("td","Extinction coefficient") # html.element("td",cif["_refine_ls_extinction_coef"]) # html.end("tr") html.start("tr") html.element("td","Largest diff peak and hole") html.rawdata(" %s and %s e/ų"%(cif["_refine_diff_density_max"],cif["_refine_diff_density_min"])) html.end("tr") #λ = %s Å html.end("table cellspacing=15") html.end("p") def 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 @param filename: Name of the file (usually .cif or .html) @type filename: string @param cif: The CIF-object of the Xtal structure @type cif: dictionnary @param Lang: The language in which the repport has to be written, the default is English @type Lang: string """ if filename[-4:].lower()in [".cif",".htm",".htl",".lis"]:basename=filename[:-4] if filename[-5:].lower()==".html":basename=filename[:-5] if not os.path.isdir(basename): os.mkdir(basename) basename=os.path.join(basename,basename) SaveCIF(cif,basename+".cif") while not os.path.isfile("%s-%s.png"%(basename,"structure")): structureImage(basename,structure="structure") while not os.path.isfile("%s-%s.png"%(basename,"ADP")): structureImage(basename,structure="ADP") while not os.path.isfile("%s-%s.png"%(basename,"powder")): structureImage(basename,structure="powder") f=open(basename+".html","w") w = XMLWriter(f) html=w.start("html") w.start("head") if Lang.lower()=="fr": w.element("title","Rapport de diffraction X du %s \n"%cif["_chemical_name_common"]) elif Lang.lower()in["en","us"]: w.element("title","Report of X-Ray diffraction of %s \n"%cif["_chemical_name_common"]) for i in Version: w.element("meta", name="generator", value=i) w.end("head") w.start("body") if Lang.lower()=="fr": MainreportFR(w,cif) elif Lang.lower()in["en","us"]: MainreportEN(w,cif) w.start("center") w.element("h2","Appendix\n") w.element("hr"," ") w.element("h3","Figure 1 : Structural representation of the molecule with atoms labels." ) w.rawdata(''% os.path.dirname(basename)) w.element("hr"," ") w.element("h3","Figure 2 : Ortep representation of the molecule with thermal ellipsoids at 50%." ) w.rawdata(''% os.path.dirname(basename)) w.element("hr"," ") w.element("h3","Figure 3 : Simulated powder diffraction pattern from the crystal structure." ) w.rawdata(''% os.path.dirname(basename)) w.element("hr"," ") w.element("h3","Table 1: Crystal data and structure refinement.\n") XraySummary(w,cif) w.element("hr"," ") w.start("h3") w.rawdata("""Table 2: Atomic coordinates (x 104) and equivalent isotropic displacements parameters (Å2 x 103).
U(eq) is defined as one third of the trace of the orthogonalized Uij tensor.""") w.end("h3") heavy,hydro=AtomPositions(cif) AtomicCoord(w,heavy) w.element("hr"," ") w.start("h3") w.rawdata("""Table 3: Bond lengths (Ångstrom).""") w.end("h3") Html2table(w,BondLength(cif),"Bond","Length (Å)") w.element("hr"," ") w.start("h3") w.rawdata("""Table 4: Bond angles (°).""") w.end("h3") Html2table(w,BondAngle(cif),"Atoms","Angle (°)") w.element("hr"," ") w.start("h3") w.rawdata("""Table 5: Hydrogen coordinates (x 104) and isotropic displacements parameters (Å2 x 103).""") w.end("h3") AtomicCoord(w,hydro) w.element("hr"," ") ##################### w.start("h3") w.rawdata("""Table 6: Hydrogen bonds with bond lengths (Ångstrom) and angles (degrees °).""") w.end("h3") w.start("p") w.start("table cellspacing=10") w.start("tr") w.element("th","D ---- H ...... A") w.element("th","Distance (D-H)") w.element("th","Distance (H..A)") w.element("th","Distance (D...A)") w.element("th","Angle (D-H..A)") for loop in cif["loop_"]: if loop[0][0].find("_geom_hbond")==0: for i in loop[1]: w.end("tr") w.start("tr") w.element("td", "%s - %s ... %s"%(i["_geom_hbond_atom_site_label_D"],i["_geom_hbond_atom_site_label_H"],i["_geom_hbond_atom_site_label_A"])) w.element("td",i["_geom_hbond_distance_DH"]) w.element("td",i["_geom_hbond_distance_HA"]) w.element("td",i["_geom_hbond_distance_DA"]) w.element("td",i["_geom_hbond_angle_DHA"]) w.end("tr") w.end("table cellspacing=10") w.end("p") w.element("hr"," ") w.end("center") w.end("body") w.close(html) f.close() print "Lauching Mozilla to view the report" os.system("mozilla file://%s &"%os.path.abspath("./"+basename+".html")) def MainreportEN(html,cif): """ This function generates the report in ENGLISH and add it to the HTML file @param html: HTML file represented as an XML object @type html: XML object @param cif: The CIF-object of the Xtal structure @type cif: dictionnary @return: None """ html.start("center") html.element("h1","Determination of the crystal structure of %s by single crystal X-ray diffraction"%cif["_chemical_name_common"]) html.end("center") html.start("ol") html.start("h2") html.element("li","Introduction") html.end("h2") html.element("p","\n The aim of this study was to determine the crystalline structure of %s, to establish its solid state molecular geometry and to generate a simulated X-ray powder diffraction pattern corresponding to the structure, which could be compared with experimental patterns."%cif["_chemical_name_common"]) #to prepare a list of major non-covalent bonds that are responsible for the cohesion of the crystalline structure html.start("h2") html.element("li","X-ray experimental parameters") html.end("h2") if exists(cif,"_exptl_special_details"): html.element("p","Slow evaporation from %s affords crystals suitable for X-rays diffraction studies. "%cif["_exptl_special_details"] ) html.start("p") html.data("\nA single crystal selected by observation under a binocular microscope was mounted on the goniometric head of a %s diffractometer. "%(cif["_diffrn_measurement_device_type"])) html.data("\n Intensities were collected at") try: T=float(re.sub("\(.\)","",cif["_diffrn_ambient_temperature"])) except: T=293 if T<280: html.data(" low temperature (T=%i K), "%T) else: html.data(" room temperature (T=%i K), "%T) html.data("with the use of a %s monochromated "%cif["_diffrn_radiation_monochromator"]) if cif["_diffrn_radiation_type"].find("Mo")==0: html.rawdata("Mo Kα radiation ") if cif["_diffrn_radiation_type"].find("Cu")==0: html.rawdata("Cu Kα radiation ") if cif["_diffrn_radiation_type"].lower().find("syn")==0: html.data("synchrotron radiation ") html.rawdata("( λ = %s Å ).\n"%(cif["_diffrn_radiation_wavelength"])) if cif["_symmetry_space_group_name_H-M"].upper()[0]=="I": tmptxt="body centered" elif cif["_symmetry_space_group_name_H-M"].upper()[0]=="C": tmptxt="centered" else: tmptxt="primitive" html.data(" Systematic investigation of the diffraction nodes indicate that the crystal belong to the %s system, with a %s Bravais lattice. The unit cell parameters are:\n"%(cif["_symmetry_cell_setting"].lower(),tmptxt)) html.end("p") html.start("center") html.rawdata("a (Å) = %5.2f ; b (Å) = %5.2f ; c (Å) = %5.2f ; α (°) = %5.2f ; β (°) = %5.2f ; γ (°) = %5.2f"%(floatp(cif["_cell_length_a"]),floatp(cif["_cell_length_b"]),floatp(cif["_cell_length_c"]),floatp(cif["_cell_angle_alpha"]),floatp(cif["_cell_angle_beta"]),floatp(cif["_cell_angle_gamma"]))) html.end("center") html.start("p") html.data("\nIn view of the number of atoms in the %s molecule and of the unit cell volume, it is concluded that this unit cell must contain %s molecules having the formula \n "%(cif["_chemical_name_common"],cif["_cell_formula_units_Z"])) html.rawdata(formula2chem(cif["_chemical_formula_sum"])) html.data("\n which is equivalent to a calculated density of %s. The number of reflections collected was %s, of which %s were unique.\n"%(cif["_exptl_crystal_density_diffrn"],cif["_diffrn_reflns_number"],cif["_reflns_number_total"] )) html.end("p") if cif["_symmetry_space_group_name_H-M"].upper() in ["P 21","P21"]: html.element("p","\nDetermination of the space group was achieved unequivocally due to the presence of an unique systematic extinction along the monoclinic axis.\n") elif cif["_symmetry_space_group_name_H-M"].upper() in ["P C","PC"]: html.element("p","\nDetermination of the space group was achieved unequivocally due to the presence of an unique zonal extinction orthogonal to the monoclinic axis.\n") elif cif["_symmetry_space_group_name_H-M"].upper()[0]=="C": html.element("p","\nDetermination of the space group was achieved unequivocally due to the presence of an integral extinction.\n") elif cif["_symmetry_space_group_name_H-M"].upper() in ["P 21 21 21","P212121"]: html.element("p","\nDetermination of the space group was achieved unequivocally due to the presence of three systematic extinctions along the main crystal directions.\n") elif cif["_symmetry_space_group_name_H-M"].upper() in ["P 21/C","P21/C","P21/A","P 21/A","P21/N","P 21/N","C 2/C","C2/C"]: html.element("p","\nDetermination of the space group was achieved unequivocally due to the presence of a systematic extinction along the monoclinic axis together with a systematic zonal extinction othogonal to this axis.\n") elif cif["_symmetry_space_group_name_H-M"].upper() in ["P -1","P -1"]: html.element("p","Based on the statistical distribution of the intensities, a centrosymetric structure is deduced.") elif cif["_symmetry_space_group_name_H-M"].upper() in ["P1","P 1"]: html.element("p","Based on the statistical distribution of the intensities, a non centrosymetric structure is deduced.") else : html.element("p","Raconter ici des conneries sur la symetrie de ce bordel") html.start("h2") html.element("li","Structure Refinements") html.end("h2") html.element("p","\nThe structure was solved by a direct methods using the SIR software [1]; and refined on F² by full least squares methods with SHELXTL [2]. All non hydrogen atoms were refined with anisotropic displacement parameters, a riding model was used for hydrogen atoms. Final agreement values are R1 = %s (observed reflections) and wR2 = %s (all data) for %s reflections and %s parameters, with a goodness of fit of %s.\n"%(cif["_refine_ls_R_factor_gt"],cif["_refine_ls_wR_factor_ref"],cif["_refine_ls_number_reflns"],cif["_refine_ls_number_parameters"],cif["_refine_ls_goodness_of_fit_ref"])) html.start("h2") html.element("li","\nDescription of the structure \n") html.end("h2") html.start("p") html.data("\n The compound (figure 1 and 2) crystallize in the space group %s, the asymmetric unit of the crystal is made up of %s molecule of "%(cif["_symmetry_space_group_name_H-M"],Zprime(cif))) html.rawdata(cif["_chemical_name_common"]) html.data(", thus %s formula are present in the unit cell. \n "%(cif["_cell_formula_units_Z"])) if len(cif["_chemical_formula_moiety"].split(","))==1: html.data("No additional molecule like organic or water is found.\n") else: html.data("The asymetric cell contains : ") html.rawdata(formula2chem(cif["_chemical_formula_moiety"])) html.data(".") html.data(" Examination of the molecular structure confirms that all bond angles and lengths stand in the standard range values.") html.end("p") html.element("p","""\n Crystal data, X-rays experimental parameters and structure refinements are given in Table 1. Table 2 lists the positional parameters for all independent non-hydrogen atoms together with their equivalent isotropic displacement parameters. Bond lengths and angles are listed Table 3 and 4. Hydrogen positions are reported Table 5. Table 6 lists all the hydrogen bonds. The figures were generated with the PLATON program [3].""") if exists(cif,"_refine_ls_abs_structure_Flack"): if cif["_refine_ls_abs_structure_Flack"]!=".": AbsStructEN(html,cif) html.start("h2") html.element("li","\nSimulated X-ray diffraction pattern.\n") html.end("h2") html.element("p","A simulated diffraction pattern (Figure 3) was produced from the experimentally determined crystalline structure. An experimental powder diffraction pattern can be compared to this theoretical pattern to demonstrate the nature of the crystalline structure. Minor differences (if any) can be explained by preferential orientations in the powder.") html.start("h2") html.element("li","\nConclusion\n") html.end("h2") html.element("p","The crystalline structure of %s was determined by X-ray diffraction on a single crystal, allowing the generation of a reference powder pattern."%cif["_chemical_name_common"]) html.start("h2") html.element("li","\nReferences\n") html.end("h2") html.start("p") html.rawdata("[1] Altomare, A.; Cascarano, G.; Giacovazzo, C.; Guagliardi, A.; Burla, M. C.; Polidori, G.; Cavalli, A. J. Appl. Crystallogr. 1994, 27, p 435-436.
") html.rawdata("[2] Sheldrick, G. M. SHELXTL-Plus, Rel. 5.03; Siemens Analytical X-ray Instruments Inc.: Madison, WI, 1995.
") html.rawdata("[3] Spek, A.L. J. Appl. Cryst. 2003 36, p 7-13.
") html.end("p") html.end("ol") html.element("hr"," ") def MainreportFR(html,cif): """this function generates the report in FRENCH to the HTML file""" html.start("center") html.element("h1","Détermination de la structure cristalline du composé %s par diffraction des rayons X sur monocristal"%cif["_chemical_name_common"]) html.end("center") html.start("ol") html.start("h2") html.element("li","Introduction") html.end("h2") html.element("p","\n Le but de ce travail est d'établir la structure cristalline du composé %s, de décrire sa géométrie moléculaire à l'état solide, d'inventorier les principales liaisons non covalentes responsables de la cohésion de l'édifice cristallin, et de générer le diagramme de diffraction X sur poudres simulé correspondant à la structure qui sera comparé aux enregistrements expérimentaux."%cif["_chemical_name_common"]) html.start("h2") html.element("li","Paramètres Expérimentaux") html.end("h2") if exists(cif,"_exptl_special_details"): html.element("p","Provenance des cristaux : %s. "%cif["_exptl_special_details"] ) html.start("p") html.data("\nUn monocristal sélectionné optiquement sous microscope binoculaire a été placé sur la tête goniométrique d'un diffractomètre %s"%(cif["_diffrn_measurement_device_type"])) try: T=floatp(cif["_diffrn_ambient_temperature"]) except: T=293 if T<280: html.data(" à basse température (T=%i K), "%T) else: html.data(" à température ambiante (T=%i K), "%T) if cif["_diffrn_radiation_type"].find("MoK")==0: html.data("et exposé aux rayons X produits par un tube à filament de molybdène ") if cif["_diffrn_radiation_type"].find("CuK")==0: html.data("et exposé aux rayons X produits par un tube à filament de cuivre ") if cif["_diffrn_radiation_type"].find("CoK")==0: html.data("et exposé aux rayons X produits par un tube à filament de cobalt ") html.rawdata("( λ = %s Å )\n"%(cif["_diffrn_radiation_wavelength"])) html.data(" après monochromatisation sur cristal de %s."%cif["_diffrn_radiation_monochromator"]) html.data(" Une recherche systématique de noeuds de diffraction indique que le cristal appartient au système %sque avec les paramètres de maille suivants :\n"%cif["_symmetry_cell_setting"].lower()[:-1]) html.end("p") html.start("center") html.rawdata(dot2virg("a = %5.2f Å ; b = %5.2f Å ; c = %5.2f Å ; α = %5.2f° ; β = %5.2f° ; γ = %5.2f°"%(floatp(cif["_cell_length_a"]),floatp(cif["_cell_length_b"]),floatp(cif["_cell_length_c"]),float(cif["_cell_angle_alpha"]),floatp(cif["_cell_angle_beta"]),floatp(cif["_cell_angle_gamma"])))) html.end("center") if cif["_symmetry_space_group_name_H-M"].upper() in ["P 21","P21"]: html.element("p","\nLa détermination du groupe spatial s'est déroulée sans ambiguïté en raison de l'unique extinction systématique axiale mise en évidence le long de l'axe monoclinique.\n") elif cif["_symmetry_space_group_name_H-M"].upper() in ["P C","PC"]: html.element("p","\nLa détermination du groupe spatial s'est déroulée sans ambiguïté en raison de l'unique extinction systématique zonale mise en évidence perpendiculairement à l'axe monoclinique.\n") elif cif["_symmetry_space_group_name_H-M"].upper()=="C": html.element("p","\nLa détermination du groupe spatial s'est déroulée sans ambiguïté en raison de l'unique extinction systématique intégrale mise en évidence.\n") elif cif["_symmetry_space_group_name_H-M"].upper() in ["P 21 21 21","P212121"]: html.element("p","\nLa détermination du groupe spatial s'est déroulée sans ambiguïté en raison de la présence de trois extinctions systématiques détectées le long des axes principaux du cristal.\n") elif cif["_symmetry_space_group_name_H-M"].upper() in ["P 21/C","P21/C"]: html.element("p","\nLa détermination du groupe spatial s'est déroulée sans ambiguïté en raison de la présence d'une extinction systématique axiale le long de l'axe monoclinique associée à une extinction systématique zonale perpendiculaire à cet axe.\n") html.start("p") html.data("\nCompte tenu du nombre d'atomes appartenant à la molécule de %s et des paramètres de la maille élémentaire, il est déduit que cette maille doit contenir %s molécules de formule\n "%(cif["_chemical_name_common"],cif["_cell_formula_units_Z"])) html.rawdata(formula2chem(cif["_chemical_formula_moiety"])) html.data("\n ce qui correspond à une densité calculée de %s. Le nombre de réflexions collectées est de %s, parmi lesquelles %s ont été trouvées uniques.\n"%(cif["_exptl_crystal_density_diffrn"],cif["_diffrn_reflns_number"],cif["_reflns_number_total"] )) html.end("p") # et [[] ont été] considérées comme observées, une [bonne faible médiocre] équivalence par symétrie ayant été constaté [en raison de la taille réduite de l'échantillon]. html.start("h2") html.element("li","Affinement de la structure") html.end("h2") try: Ra=float(cif["_refine_ls_R_factor_all"])*100 Ri=float(cif["_refine_ls_R_factor_gt"])*100 wRa=float(cif["_refine_ls_wR_factor_ref"])*100 wRi=float(cif["_refine_ls_wR_factor_gt"])*100 R=min(Ra,Ri,wRa,wRi) except: R=100 if R<5.5: txt="haute" elif R<7: txt="bonne" elif R<11: txt="moyenne" else : txt="mediocre" html.element("p","\nLa structure à été résolue par méthode directe à l'aide du programme SIR, les affinements par moindres carrés effectués grâce au programme SHELX ont permis d'aboutir à une structure de %s résolution, l'indice d'accord de référence atteignant la valeur %s %%. Les positions des atomes d'hydrogène ont été placées selon leurs coordonnées idéalisées et introduites, ainsi qu'une composante isotropique fonction de l'atome porteur, dans les calculs finaux des facteurs de structure.\n"%(txt,R)) html.start("h2") html.element("li","\nDescription de la structure\n") html.end("h2") html.element("p","\nLe schéma 1, en annexe, présente la numérotation atomique, alors que les tables jointes en annexe consignent les paramètres expérimentaux et d'affinements, ainsi que les valeurs des distances et angles de liaisons.\n") html.end("ol") html.element("hr"," ") def AbsStructEN(html,cif): """Adds some text to the English report about the absolute configuration of the molecule @param html: HTML object where the text will be added to. @type html: XMLWrite object. @param cif: The CIF-object of the structure @type cif: CIF-like Dictionnary @return: None, le test is simply added to the HTML file """ html.start("h2") html.element("li","\nAbsolute configuration\n") html.end("h2") html.start("p") if cif["_chemical_formula_sum"].find("S")>-1: txt="sulfur" elif cif["_chemical_formula_sum"].find("Cl")>-1: txt="chlorine" elif cif["_chemical_formula_sum"].find("Br")>-1: txt="bromine" else: txt="heavy" html.data("The %s molecule contains a %s atom that allows the absolute configuration to be determined, \ making used of a high resolution data collection"%(cif["_chemical_name_common"],txt)) if floatp(cif["_cell_measurement_temperature"])<280 : html.data(" (performed at low temperature).") else: html.data(".") txt="" chiral=[] if exists(cif,"loop_"): for i in cif["loop_"]: if i[0][0].find("_atom_site_asymmetry_label")==0: chiral=i[1] for i in chiral: txt+=" %s: %s ;"%(i["_atom_site_asymmetry_label"],i["_atom_site_asymmetry_type"]) if len(txt)>0: txt=txt[:-2] html.data(" The Flack x parameter is calculated based on the anomalous scattering method. \ It gives the absolute structure, providing a sufficient estimate standard deviation is reached. \ According to the theory, the expected values of the Flack x parameter are 0 for correct (within 3 esd.s) \ and +1 for inverted absolute structure. The results considering the configuration %s is %s, \ which unambiguously proved this absolute configuration for %s."%(txt,cif["_refine_ls_abs_structure_Flack"],cif["_chemical_name_common"])) #html.data(txt) html.end("p") def structureImage(basename,structure="structure"): """lauch PLATON and let the user chose the structural (or the ADP or powder) representation of the molecule @param basename: the name of the CIF-file without the extention @type basename: string @type structure: string @param structure: can be "powder" and "ADP", if not a simple structure is chosen @return None """ if structure.lower()=="powder": txt=raw_input("I will now lauch PLATON and let you chose the simulated powder pattern of the molecule\nOnce you have selected a nice view, please click on «EPS» to export the drawing and quit.") while not os.path.isfile(basename+".ps"): i=os.popen("platon %s.cif"%(basename)) for l in i.readlines(): print l.strip() i.close() else: txt=raw_input("I will now lauch PLATON and let you chose the %s representation of the molecule\nOnce you have selected a nice view, please click on «EPS» to export the drawing and quit."%structure) while not os.path.isfile(basename+".ps"): i,o=os.popen2("platon -o %s.cif"%(basename)) if structure.lower()=="adp": i.write("plot adp\n") else: i.write("pluton\n") i.flush() i.write("menu on\n") i.flush() for l in o.readlines(): print l.strip() i.close() os.rename(basename+".ps","%s-%s.ps"%(basename,structure)) print "Converting PostScript to PNG ... can take a while" inp=os.popen("convert -rotate 90 -quality 90 -geometry 2400x1800 %s-%s.ps %s-%s.png"%(basename,structure,basename,structure)) for l in inp.readlines(): print l.strip() inp.close() if (not os.path.isfile("%s-%s.png"%(basename,structure)) and os.path.isfile("%s-%s.png.0"%(basename,structure))): workdir=os.path.dirname(basename) name=os.path.basename(basename) if len(workdir)==0:workdir="." dir1=os.listdir(workdir) dir2=[] for i in dir1: if i.find("%s-%s.png."%(name,structure))==0 : dir2.append(i) dir2.sort() os.rename(os.path.join(workdir,dir2[-1]),"%s-%s.png"%(basename,structure)) print "Done !\n"+70*"_" def BondLength(cif): """Returns a dictionnary with all the bond lengths between heavy atoms. Datas have to be already in the CIF @param cif: The CIF-object of the Xtal structure @type cif: dictionnary @return: a dictionnary with all the "A1 - A2": "distance" @rtype: dictionnary """ BL={} for loop in cif["loop_"]: for key in loop[0]: if key=="_geom_bond_distance": for i in loop[1]: BL[" %s - %s "%(i["_geom_bond_atom_site_label_1"],i["_geom_bond_atom_site_label_2"])]=i["_geom_bond_distance"] return BL def BondAngle(cif): """Returns a dictionnary with all the bond/valence angles between heavy atoms Datas have to be already in the CIF @param cif: The CIF-object of the Xtal structure @type cif: dictionnary @return: dictionnary with all the "A1 - A2 - A3":"Angle" @rtype: dictionnary """ BA={} for loop in cif["loop_"]: for key in loop[0]: if key=="_geom_angle": for i in loop[1]: BA[" %s - %s - %s "%(i["_geom_angle_atom_site_label_1"],i["_geom_angle_atom_site_label_2"],i["_geom_angle_atom_site_label_3"])]=i["_geom_angle"] return BA def 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) @param cif: The CIF-object of the Xtal structure @type cif: dictionnary @return: tupple of 2 tables, the first with the heavy atoms, the second with the hydrogens @rtype: tupple """ heavy=[] hydro=[] for loop in cif["loop_"]: for key in loop[0]: if key=="_atom_site_U_iso_or_equiv": for i in loop[1]: atom=[] atom.append(i["_atom_site_label"]) x=stringmulti(i["_atom_site_fract_x"],10000) y=stringmulti(i["_atom_site_fract_y"],10000) z=stringmulti(i["_atom_site_fract_z"],10000) U=stringmulti(i["_atom_site_U_iso_or_equiv"],1000) atom.append(x) atom.append(y) atom.append(z) atom.append(U) if i["_atom_site_type_symbol"]=="H": hydro.append(atom) else: heavy.append(atom) heavy.sort() hydro.sort() return heavy,hydro def dot2virg(text): """ Substitute the english dots with french virgules @param text: input test @type text: string @return: modified text @rtype: string """ return re.sub("\.",",",text) def floatp(txt): """Removes the () from the text and convert to a float @param txt: the input test @type txt: string @return: the value of the txt @rtype: float """ #float(re.sub("\(","",re.sub("\)","",txt))) return float(txt.strip().split("(")[0]) def stringmulti(text,value): """Convert a string to a real, multiplies by the value and returns a string @param text: input text @type text: string @type value: float or integer @return: txt*value @rtype: string """ if "(" not in text: return str(float(text.strip().split("(")[0])*value) valuetxt,esdtxt=text.strip().split("(",1) l1=list(valuetxt) l1.reverse() l2=list(esdtxt.split(")",1)[0]) l2.reverse() chiffres=[str(i) for i in range(10)] for i in range(len(l1)): if l1[i] in chiffres: if i2 and len(esd2)>2: if valuef[-2:]==".0" and esd2[-2:]==".0": valuef=valuef[:-2] esd2=esd2[:-2] return "%s(%s)"%(valuef,esd2) def formula2chem(txt): """return a HTML representatin of the chemical formula""" out="" figu=[ str(x) for x in range(10)] for i in txt: if i in figu: out+="%s"%i # elif i==" ": # continue else: out+=i return out # # SimpleXMLWriter # $Id: SimpleXMLWriter.py 1862 2004-06-18 07:31:02Z Fredrik $ # # a simple XML writer # # history: # 2001-12-28 fl created # 2002-11-25 fl fixed attribute encoding # 2002-12-02 fl minor fixes for 1.5.2 # 2004-06-17 fl added pythondoc markup # # Copyright (c) 2001-2004 by Fredrik Lundh # # fredrik@pythonware.com # http://www.pythonware.com # # -------------------------------------------------------------------- # The SimpleXMLWriter module is # # Copyright (c) 2001-2004 by Fredrik Lundh # # By obtaining, using, and/or copying this software and/or its # associated documentation, you agree that you have read, understood, # and will comply with the following terms and conditions: # # Permission to use, copy, modify, and distribute this software and # its associated documentation for any purpose and without fee is # hereby granted, provided that the above copyright notice appears in # all copies, and that both that copyright notice and this permission # notice appear in supporting documentation, and that the name of # Secret Labs AB or the author not be used in advertising or publicity # pertaining to distribution of the software without specific, written # prior permission. # # SECRET LABS AB AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD # TO THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANT- # ABILITY AND FITNESS. IN NO EVENT SHALL SECRET LABS AB OR THE AUTHOR # BE LIABLE FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY # DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, # WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS # ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE # OF THIS SOFTWARE. # -------------------------------------------------------------------- ## # Tools to write XML files, without having to deal with encoding # issues, well-formedness, etc. #

# The current version does not provide built-in support for # namespaces. To create files using namespaces, you have to provide # "xmlns" attributes and explicitly add prefixes to tags and # attributes. # #

Patterns

# # The following example generates a small XHTML document. # 
#
# from elementtree.SimpleXMLWriter import XMLWriter
# import sys
#
# w = XMLWriter(sys.stdout)
#
# html = w.start("html")
#
# w.start("head")
# w.element("title", "my document")
# w.element("meta", name="generator", value="my application 1.0")
# w.end()
#
# w.start("body")
# w.element("h1", "this is a heading")
# w.element("p", "this is a paragraph")
#
# w.start("p")
# w.data("this is ")
# w.element("b", "bold")
# w.data(" and ")
# w.element("i", "italic")
# w.data(".")
# w.end("p")
#
# w.close(html)
#
## try: unicode("") except NameError: def encode(s, encoding): # 1.5.2: application must use the right encoding return s _escape = re.compile(r"[&<>\"\x80-\xff]+") # 1.5.2 else: def encode(s, encoding): return s.encode(encoding) _escape = re.compile(eval(r'u"[&<>\"\u0080-\uffff]+"')) def encode_entity(text, pattern=_escape): # map reserved and non-ascii characters to numerical entities def escape_entities(m): out = [] for char in m.group(): out.append("&#%d;" % ord(char)) return string.join(out, "") return encode(pattern.sub(escape_entities, text), "ascii") del _escape def escape_cdata(s, encoding=None, replace=string.replace): s = replace(s, "&", "&") s = replace(s, "<", "<") s = replace(s, ">", ">") if encoding: try: return encode(s, encoding) except UnicodeError: return encode_entity(s) return s def escape_attrib(s, encoding=None, replace=string.replace): s = replace(s, "&", "&") s = replace(s, "'", "'") s = replace(s, "\"", """) s = replace(s, "<", "<") s = replace(s, ">", ">") if encoding: try: return encode(s, encoding) except UnicodeError: return encode_entity(s) return s ## # XML writer class. # # @param file A file or file-like object. This object must implement # a write method that takes an 8-bit string. # @param encoding Optional encoding. class XMLWriter: def __init__(self, file, encoding="us-ascii"): self.__write = file.write self.__open = 0 # true if start tag is open self.__tags = [] self.__data = [] self.__encoding = encoding def __flush(self): if self.__open: self.__write(">") self.__open = 0 if self.__data: data = string.join(self.__data, "") self.__write(escape_cdata(data, self.__encoding)) self.__data = [] ## # Opens a new element. Attributes can be given as keyword # arguments, or as a string/string dictionary. You can pass in # 8-bit strings or Unicode strings; the former are assumed to use # the encoding passed to the constructor. The method returns an # opaque identifier that can be passed to the close method, # to close all open elements up to and including this one. # # @param tag Element tag. # @param attrib Attribute dictionary. Alternatively, attributes # can be given as keyword arguments. # @return An element identifier. def start(self, tag, attrib={}, **extra): self.__flush() tag = escape_cdata(tag, self.__encoding) self.__data = [] self.__tags.append(tag) self.__write("<%s" % tag) if attrib or extra: attrib = attrib.copy() attrib.update(extra) attrib = attrib.items() attrib.sort() for k, v in attrib: k = escape_cdata(k, self.__encoding) v = escape_attrib(v, self.__encoding) self.__write(" %s=\"%s\"" % (k, v)) self.__open = 1 return len(self.__tags)-1 ## # Adds a comment to the output stream. # # @param comment Comment text, as an 8-bit string or Unicode string. def comment(self, comment): self.__flush() self.__write("\n" % escape_cdata(comment, self.__encoding)) def rawdata(self, comment): """insert raw HTML data to the XML-file """ self.__flush() self.__write("%s" %(comment)) ## # Adds character data to the output stream. # # @param text Character data, as an 8-bit string or Unicode string. def data(self, text): """insert text data to the XML-file""" self.__data.append(text) ## # Closes the current element (opened by the most recent call to # start). # # @param tag Element tag. If given, the tag must match the start # tag. If omitted, the current element is closed. def end(self, tag=None): if tag: assert self.__tags, "unbalanced end(%s)" % tag assert escape_cdata(tag, self.__encoding) == self.__tags[-1],\ "expected end(%s), got %s" % (self.__tags[-1], tag) else: assert self.__tags, "unbalanced end()" tag = self.__tags.pop() if self.__data: self.__flush() elif self.__open: self.__open = 0 self.__write(" />") return self.__write("" % tag) ## # Closes open elements, up to (and including) the element identified # by the given identifier. # # @param id Element identifier, as returned by the start method. def close(self, id): while len(self.__tags) > id: self.end() ## # Adds an entire element. This is the same as calling start, # data, and end in sequence. The text argument # can be omitted. def element(self, tag, text=None, attrib={}, **extra): apply(self.start, (tag, attrib), extra) if text: self.data(text) self.end() def 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. @param infile: name of the CIF file @type infile: string @param namelist: list of all the files that already exists @type namelist: list @return: the name of the reference suggested by the program @rtype:string """ figures=[str(x) for x in range(10)] letters=[chr(x) for x in range(65,91)] ref="" sel="" if infile[:2].upper().find("SR")==0: for i in infile[2:9].upper(): if i in figures: if len(ref)>=6: continue ref+=i if i in letters: sel+=i break if i in[".","-","_"]: break elif infile[:3].upper().find("SSR")==0: for i in infile[3:10].upper(): if i in figures: if len(ref)>=6: continue ref+=i if i in letters: sel+=i break if i in[".","-","_"]: break elif infile[:2].upper().find("SL")==0: if len(infile)>12: try: if float(infile[10:12])>0:sel="A" except: sel="" for i in infile[2:9].upper(): if i in figures: if len(ref)>=6: continue ref+=i if i in letters: sel+=i break elif (infile[7] in figures) and (infile[6].upper() in letters+["-"]): a=0 for i in infile[:6].upper(): if i in figures : a+=1 if a>5: return infile else: ref=infile[:6] sel="" while len(ref)<6: ref="0"+ref if sel=="":sel="-" name=ref+sel count=1 for i in namelist: if i.find(name)==0:count+=1 name+=str(count) print "I suggest using %s as reference for the database for file %s"%(name,infile) while True: txt=raw_input(" Database reference (<= 8 characters) [%s]-->"%name) if len(txt)==0: break if len(txt)<=8: name=txt break if name[-1]=="?": count=1 name=name[:-1] for i in namelist: if i.find(name)==0:count+=1 name+=str(count) print "using "+name return name+".cif" def MergeSg(name,kcd,sg): """ Merge 2 cif objects : add from sg the missing values in kcd @param name: the name of the molecule, used only if the value exist in kcd @type name: string @param kcd: The CIF-object of the Xtal structure @type kcd: dictionnary @param sg: The CIF-object of the Xtal structure @type sg: dictionnary @return: a new cif-object @rtype: dictionnary """ DoNotMerge=["loop_","_chemical_formula_weight","_chemical_formula_moiety","_chemical_formula_sum"] if not exists(kcd,"_chemical_name_common"): kcd["_chemical_name_common"]=name for i in sg: if i in DoNotMerge: continue if not exists(kcd,i): kcd[i]=sg[i] w,cif=CheckSym(kcd,True) if len(w)==0: w="OK" print "Checking for symmetry : \n%s"%w return cif if __name__=='__main__': if sys.argv[0].lower().split("/")[-1]=="cif2csd": if len(sys.argv)==2: filename=sys.argv[1] outfile=filename[:-4]+"-process.cif" elif len(sys.argv)==3: filename=sys.argv[1] outfile=sys.argv[2] else: raise "Please enter the name of CIF file to process" sys.exit(1) cif=LoadCIF(filename) w,cif2=CheckSym(cif,True) if len(w)==0: w="OK" print "Checking for symmetry : \n%s"%w print "Checking for the data needed to enter them to the Database" cif,mod=CheckForCSD(cif2,name=filename) if not mod: print "OK" if mod or len(w)>0: outfile=raw_input("Please enter the name of the file where to save the CIF data -->") if len(outfile)>0: if outfile[-4:].lower()!=".cif":outfile+=".cif" SaveCIF(cif,outfile) elif sys.argv[0].lower().split("/")[-1]=="checkall2csd": infiles=[] table={} for i in os.listdir("."): if i[-4:].lower()==".cif":infiles.append(i) infiles.sort() if os.path.isfile("ConversionTable"): print "Loading the Conversion Table" f=open("ConversionTable","r") ct=f.readlines() f.close() for i in ct: j=i.split(None,1) table[j[0].strip()]=j[1].strip() print "Processing all the files : ",infiles if not os.path.isdir("process"): os.mkdir("process") for filename in infiles: print "Processing file : ",filename if table.has_key(filename): outfile=table[filename] else : outfile=renamefile(filename,table.values()) table[filename]=outfile if os.path.isfile(os.path.join("./process",outfile)): print "The destination file exists",os.path.join("./process",outfile) print "###########################################################" continue cif=LoadCIF(filename) w,cif2=CheckSym(cif,True) if len(w)==0: w="OK" print "Checking for symmetry : \n%s"%w cif2["_database_code_CSD"]=outfile[:-4] # print "Checking for the data needed to enter them to the Database" cif,mod=CheckForCSD(cif2,name=filename) if not mod: print "OK" print "Saving the Conversion Table" f=open("ConversionTable","w") for i in table: f.write("%s %s\n"%(i,table[i])) f.close() print "###########################################################" if outfile[-4:].lower()!=".cif":outfile+=".cif" SaveCIF(cif,"process/"+outfile) elif sys.argv[0].lower().split("/")[-1]=="report": if len(sys.argv)==2: filename=sys.argv[1] outfile=filename[:-4]+"-process.cif" elif len(sys.argv)==3: filename=sys.argv[1] outfile=sys.argv[2] else: raise "Please enter the name of CIF file to process" sys.exit(1) cif=LoadCIF(filename) w,cif2=CheckSym(cif,True) if len(w)==0: w="OK" print "Checking for symmetry : \n%s"%w print "Completing the CIF file with the data generated by PLATON" cif3=mergeplaton(cif2,platon(filename)) print "Checking for the data needed to generate a report" cif,mod=CheckForRST(cif3) if not mod: print "OK" WriteReport(filename,cif,Lang="En") elif sys.argv[0].lower().split("/")[-1]=="fixallsym": print "Doing a trivial rewrite with symmetry check" infiles=[] for i in os.listdir("."): if i[-4:].lower()==".cif":infiles.append(i) infiles.sort() print "Processing all the files : ",infiles for filename in infiles: print "Processing file : ",filename cif=LoadCIF(filename) w,cif2=CheckSym(cif,True) SaveCIF(cif,filename) elif sys.argv[0].lower().split("/")[-1]=="checksym": if len(sys.argv)==2: filename=sys.argv[1] outfile=filename[:-4]+"-process.cif" elif len(sys.argv)==3: filename=sys.argv[1] outfile=sys.argv[2] else: raise "Please enter the name of CIF file to process" sys.exit(1) # print "Doing a trivial rewrite with symmetry check on file : %s to %s"%(filename,outfile) # cif=LoadCIF(filename) cif=LoadCIF(filename) w,cif2=CheckSym(cif,True) if len(w)==0: w="OK" print "Checking for symmetry : %s ... %s -> %s"%(w,filename,outfile) SaveCIF(cif,outfile) else: print "What do you want me to do ?" # print "Done"